doc_id sent_index relation_id relation trigger trigger_offset arg_num arg_base_np arg_protein arg_domain arg_site arg_sugar PSource SiteSource NProtein NID SiteName sent_text 28381551 2 11 gly glycoproteins 321:333 arg1 well-defined glycoproteins well-defined glycoproteins Fterm glycoproteins However, access to well-defined glycoproteins is always important for both basic research and therapeutic purposes. 25614628 7 33 part_of protein 1059:1065 arg1 the N terminus protein the N terminus Fterm Site protein terminus Structural comparison with PNGase F revealed a relatively larger glycan-binding groove in the catalytic domain and an additional bowl-like domain with unknown function at the N terminus of the candidate protein. 25748215 4 37 gly glycosylated 854:865 arg1 glycosylated and deglycosylated proteins glycosylated and deglycosylated proteins Fterm proteins In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. 25748215 4 51 gly deglycosylated 871:884 arg1 glycosylated and deglycosylated proteins glycosylated and deglycosylated proteins Fterm proteins In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. 25437919 7 29 gly glycoproteins 1083:1095 arg1 membrane glycoproteins membrane glycoproteins Fterm glycoproteins Our data illustrate that the majority of membrane glycoproteins with bisecting glycosylation are common to both serous and endometrioid histological subtypes of ovarian cancer, and several have been reported to participate in signaling pathways such as Notch, Wnt, and TGFβ. 25437919 7 47 gly glycosylation 1112:1124 arg1 membrane glycoproteins membrane glycoproteins Fterm glycoproteins Our data illustrate that the majority of membrane glycoproteins with bisecting glycosylation are common to both serous and endometrioid histological subtypes of ovarian cancer, and several have been reported to participate in signaling pathways such as Notch, Wnt, and TGFβ. 25528754 4 60 part_of has 313:315 arg1 Its core protein AND five domains Its core protein five domains Fterm Site protein domains Its core protein has five domains (DI-DV) with disparate structures and DII is highly homologous to the ligand-binding portion of LDL receptor (LDLR). 25202310 2 6 gly glycoproteins 375:387 arg1 glycoproteins glycoproteins Fterm glycoproteins Herein, we document and mechanistically explain the formation of subcellular-specific N-glycosylation determinants on glycoproteins trafficking through the shared biosynthetic machinery of human cells. 28711789 3 29 gly N-glycoproteins 389:403 arg1 N-glycoproteins N-glycoproteins Fterm N-glycoproteins To understand the involvement of N-glycoproteins in the mechanism of drought response in leaves of common bean, a proteomic approach using lectin affinity chromatography, SDS-PAGE and LC-MS/MS was applied. 27851982 5 57 gly O-glycosylation 1202:1216 arg1 the linker region region region Electrostatics calculations identified these differences to result from charge neutralization by protonation and together with ion mobility pointed at higher electrostatic repulsion between CDH domains at neutral pH. In addition, we uncovered extensive O-glycosylation in the linker region and identified the long-unknown exact cleavage point in papain-mediated domain separation. 28988842 5 0 gly glycoproteins 938:950 arg1 glycoproteins glycoproteins Fterm glycoproteins In hemagglutination inhibition assay, the purified lectin was only inhibited by glycoproteins containing mucin-type O-glycans and reacted weakly with Galβ(1,3)GalNAc. 28988842 5 44 gly containing 952:961 arg1 glycoproteins AND mucin-type O-glycans glycoproteins mucin-type O-glycans Fterm glycoproteins In hemagglutination inhibition assay, the purified lectin was only inhibited by glycoproteins containing mucin-type O-glycans and reacted weakly with Galβ(1,3)GalNAc. 25452312 13 30 gly glycoproteins 1539:1551 arg1 37 glycoproteins 37 glycoproteins Fterm glycoproteins In total 126 N-glycopeptides from 51 N-glycosylation sites belonging to 37 glycoproteins were found in our results. 25452312 13 35 gly N-glycosylation 1501:1515 arg2 51 N-glycosylation sites 51 N-glycosylation sites sites In total 126 N-glycopeptides from 51 N-glycosylation sites belonging to 37 glycoproteins were found in our results. 25452312 13 93 gly N-glycopeptides 1477:1491 arg1 51 N-glycosylation sites 51 N-glycosylation sites sites In total 126 N-glycopeptides from 51 N-glycosylation sites belonging to 37 glycoproteins were found in our results. 25452312 13 93 gly N-glycopeptides 1477:1491 arg2 126 N-glycopeptides 126 N-glycopeptides N-glycopeptides In total 126 N-glycopeptides from 51 N-glycosylation sites belonging to 37 glycoproteins were found in our results. 28717478 4 51 gly glycopeptides 819:831 arg2 glycopeptides glycopeptides glycopeptides High-yielding enzymatic glycosylation afforded glycopeptides bearing defined homogeneous high-mannose N-glycan structures. 26571101 3 4 gly glycosites 740:749 arg2 individual glycosites individual glycosites glycosites Here, we describe a chemoenzymatic method called solid phase extraction of N-linked glycans and glycosite-containing peptides (NGAG) for the comprehensive characterization of glycoproteins that is able to determine glycan heterogeneity for individual glycosites in addition to providing information about the total N-linked glycan, glycosite-containing peptide and glycoprotein content of complex samples. 26571101 3 17 gly glycoprotein 854:865 arg1 glycoprotein content glycoprotein content Fterm glycoprotein Here, we describe a chemoenzymatic method called solid phase extraction of N-linked glycans and glycosite-containing peptides (NGAG) for the comprehensive characterization of glycoproteins that is able to determine glycan heterogeneity for individual glycosites in addition to providing information about the total N-linked glycan, glycosite-containing peptide and glycoprotein content of complex samples. 26571101 3 40 gly glycoproteins 664:676 arg1 glycoproteins glycoproteins Fterm glycoproteins Here, we describe a chemoenzymatic method called solid phase extraction of N-linked glycans and glycosite-containing peptides (NGAG) for the comprehensive characterization of glycoproteins that is able to determine glycan heterogeneity for individual glycosites in addition to providing information about the total N-linked glycan, glycosite-containing peptide and glycoprotein content of complex samples. 24234447 7 7 gly glycoproteins 1167:1179 arg1 35 glycoproteins 35 glycoproteins Fterm glycoproteins Among these are 35 glycoproteins, 502 structures and 60 publications previously not included in GlycoSuiteDB. 25499076 8 0 gly fucosylated 1507:1517 arg1 fucosylated (90.5%) glycans fucosylated (90.5%) glycans Among the main differences found in the pituitary sample were an extremely low presence of sialylated (1.7%) and a high percentage of sulfated (74.0%) and of fucosylated (90.5%) glycans. 25499076 8 0 gly fucosylated 1507:1517 arg1 90.5% 90.5% Among the main differences found in the pituitary sample were an extremely low presence of sialylated (1.7%) and a high percentage of sulfated (74.0%) and of fucosylated (90.5%) glycans. 25623399 0 86 part_of LLT1 93:96 arg1 soluble and stable ectodomain LLT1 soluble and stable ectodomain PUBTATOR Site LLT1 29121 ectodomain Expression and purification of soluble and stable ectodomain of natural killer cell receptor LLT1 through high-density transfection of suspension adapted HEK293S GnTI(-) cells. 25164811 10 73 gly sites 1382:1386 arg1 a single N-acetylglucosamine sites a single N-acetylglucosamine sites In H. jecorina-produced HjCel3A, a single N-acetylglucosamine is present at both sites, whereas in Pp-HjCel3A, the P. pastoris-produced HjCel3A enzyme, the glycan chains consist of 8 or 4 saccharides. 25164811 10 60 gly present 1366:1372 arg1 both sites AND a single N-acetylglucosamine HjCel3A sites a single N-acetylglucosamine Cterm HjCel3A sites In H. jecorina-produced HjCel3A, a single N-acetylglucosamine is present at both sites, whereas in Pp-HjCel3A, the P. pastoris-produced HjCel3A enzyme, the glycan chains consist of 8 or 4 saccharides. 25164811 10 80 gly present 1366:1372 arg1 both sites AND a single N-acetylglucosamine HjCel3A sites a single N-acetylglucosamine Cterm HjCel3A sites In H. jecorina-produced HjCel3A, a single N-acetylglucosamine is present at both sites, whereas in Pp-HjCel3A, the P. pastoris-produced HjCel3A enzyme, the glycan chains consist of 8 or 4 saccharides. 25164811 10 80 gly present 1366:1372 arg1 H. jecorina-produced HjCel3A AND a single N-acetylglucosamine HjCel3A sites a single N-acetylglucosamine Cterm HjCel3A sites In H. jecorina-produced HjCel3A, a single N-acetylglucosamine is present at both sites, whereas in Pp-HjCel3A, the P. pastoris-produced HjCel3A enzyme, the glycan chains consist of 8 or 4 saccharides. 25164811 10 80 gly present 1366:1372 arg1 both sites AND a single N-acetylglucosamine sites a single N-acetylglucosamine sites In H. jecorina-produced HjCel3A, a single N-acetylglucosamine is present at both sites, whereas in Pp-HjCel3A, the P. pastoris-produced HjCel3A enzyme, the glycan chains consist of 8 or 4 saccharides. 25164811 10 80 gly present 1366:1372 arg1 both sites AND a single N-acetylglucosamine HjCel3A sites a single N-acetylglucosamine Cterm HjCel3A sites In H. jecorina-produced HjCel3A, a single N-acetylglucosamine is present at both sites, whereas in Pp-HjCel3A, the P. pastoris-produced HjCel3A enzyme, the glycan chains consist of 8 or 4 saccharides. 28289219 1 24 gly N-glycosylation 94:108 arg2 a conserved N-glycosylation site a conserved N-glycosylation site site IgG antibodies contain a conserved N-glycosylation site on the Fc domain to which a complex, biantennary glycan is attached. 28289219 1 64 gly attached 174:181 arg2 the Fc domain AND a complex, biantennary glycan the Fc domain a complex, biantennary glycan domain IgG antibodies contain a conserved N-glycosylation site on the Fc domain to which a complex, biantennary glycan is attached. 25824821 7 21 part_of IgE 914:916 arg1 the constant domain 3 IgE the constant domain 3 PUBTATOR Site IgE P01854 domain The obligatory glycan was mapped to a single N-linked oligomannose structure in the constant domain 3 (Cε3) of IgE, at asparagine-394 (N394) in human IgE and N384 in mouse. 28887379 11 29 gly glycosylation 1751:1763 arg1 simple glycoproteins simple glycoproteins Fterm glycoproteins GlycoPAT is used to catalogue site-specific glycosylation on simple glycoproteins, standard protein mixtures and human plasma cryoprecipitate samples in three common MS/MS fragmentation modes: CID, HCD and ETD. 28887379 11 108 gly glycoproteins 1775:1787 arg1 simple glycoproteins simple glycoproteins Fterm glycoproteins GlycoPAT is used to catalogue site-specific glycosylation on simple glycoproteins, standard protein mixtures and human plasma cryoprecipitate samples in three common MS/MS fragmentation modes: CID, HCD and ETD. 28818784 1 44 gly glycoprotein 83:94 arg1 A novel glycoprotein imprinting strategy A novel glycoprotein imprinting strategy Fterm glycoprotein A novel glycoprotein imprinting strategy was proposed and was applied to the detection of the carbohydrate antigen 19-9. 26059692 0 61 gly glycosylation 42:54 arg1 the neuropilin-1 c/MAM-domain the neuropilin-1 c/MAM-domain c/MAM-domain Detailed characterization of the O-linked glycosylation of the neuropilin-1 c/MAM-domain. 28446609 3 51 part_of sites 564:568 arg1 Env Env sites PUBTATOR Site Env 30816 sites Previous attempts to alter glycosylation sites in Env typically involved mutating the glycosylated asparagine residues to structurally similar glutamines or alanines. 24702330 2 32 gly glycosylation 278:290 arg1 aldehyde-tagged proteins aldehyde-tagged proteins One approach toward constructing such molecules involves chemical glycosylation of aldehyde-tagged proteins. 28921966 6 66 gly glycosylation 982:994 arg2 glycosylation site glycosylation site site Remarkably, the glycan patterns, glycosylation site, and their occupancy by N-glycans are all detected and identified in a single experimental procedure. 29212317 3 59 part_of HDL 488:490 arg1 HDL particle composition HDL HDL particle composition OGER Site HDL Q9UNE0 position Great attention has been directed toward HDL particle composition because the relative abundances of HDL constituents determine HDL's functional properties. 27793989 5 15 gly glycosylated 1458:1469 arg1 an N25Q mutant form form of PECAM-1 position PUBTATOR form of PECAM-1 5175 position To verify the contribution of the Asn-25 glycan to endothelial barrier function, we generated an N25Q mutant form of PECAM-1 that is not glycosylated at this position and examined its ability to contribute to vascular integrity in endothelial cell-like REN cells. 27769287 8 42 gly glycoproteins 1668:1680 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins CONCLUSIONS: Overexpression of RHO1 in 'humanized' glycoprotein producing yeasts could significantly facilitate its future industrial applications for the production of therapeutic glycoproteins. 27769287 8 50 gly glycoprotein 1538:1549 arg1 'humanized' glycoprotein producing yeasts 'humanized' glycoprotein producing yeasts Fterm glycoprotein CONCLUSIONS: Overexpression of RHO1 in 'humanized' glycoprotein producing yeasts could significantly facilitate its future industrial applications for the production of therapeutic glycoproteins. 25016576 0 63 gly epitope 70:76 arg1 the V1/V2 domain the V1/V2 domain the V1/V2 domain Site domain Characterization of a monoclonal antibody to a novel glycan-dependent epitope in the V1/V2 domain of the HIV-1 envelope protein, gp120. 28649731 7 39 gly glycoproteins 1028:1040 arg1 glycoproteins glycoproteins Fterm glycoproteins However, for the samples containing glycoproteins, the signal intensity of 1 H15 N-HSQC recovered upon addition of lactose. 28277614 9 81 part_of I 1892:1892 arg1 the catalytic domain cellobiohydrolase I the catalytic domain Cterm Site cellobiohydrolase I domain Using glycopeptide analysis, this novel O-glycan composition was found to be present on the catalytic domain of cellobiohydrolase I, the most abundant secreted protein by T. reesei. 26388028 3 3 gly glycosylated 448:459 arg1 the HIV-1 Env viral spike protein the HIV-1 Env viral spike protein Fterm protein Thus, crystal structures of heavily glycosylated proteins such as the HIV-1 Env viral spike protein have been determined by removing the majority of glycans. 26388028 3 3 gly glycosylated 448:459 arg1 heavily glycosylated proteins heavily glycosylated proteins Fterm proteins Thus, crystal structures of heavily glycosylated proteins such as the HIV-1 Env viral spike protein have been determined by removing the majority of glycans. 26618856 5 5 gly glycosylated 904:915 arg1 human islet amyloid polypeptide human islet amyloid polypeptide polypeptide In this work, we particularly address the structural effects of O-linked glycosylation by investigating glycosylated and unglycosylated forms of two different IDPs, tau174-183 and human islet amyloid polypeptide (hIAPP), by all-atom explicit solvent simulations. 26618856 5 7 gly unglycosylated 921:934 arg1 human islet amyloid polypeptide human islet amyloid polypeptide polypeptide In this work, we particularly address the structural effects of O-linked glycosylation by investigating glycosylated and unglycosylated forms of two different IDPs, tau174-183 and human islet amyloid polypeptide (hIAPP), by all-atom explicit solvent simulations. 26791533 9 17 gly sialylated 1206:1215 arg1 the glycoproteins the glycoproteins Fterm glycoproteins Most of the glycoproteins were either sialylated, fucosylated, or both. 26791533 9 19 gly glycoproteins 1180:1192 arg1 the glycoproteins the glycoproteins Fterm glycoproteins Most of the glycoproteins were either sialylated, fucosylated, or both. 26791533 9 59 gly fucosylated 1218:1228 arg1 the glycoproteins the glycoproteins Fterm glycoproteins Most of the glycoproteins were either sialylated, fucosylated, or both. 29190644 1 0 gly glycoprotein 185:196 arg1 a glycoprotein a glycoprotein Fterm glycoprotein Human butyrylcholinesterase (BChE) is a glycoprotein capable of bioscavenging toxic compounds such as organophosphorus (OP) nerve agents. 27933952 5 36 gly heterogeneity 800:812 arg1 polysaccharides polysaccharides The end-site-specific conjugation is important for polysaccharide drug development because of the heterogeneity of polysaccharides. 24509848 0 50 gly Glycosylation 0:12 arg2 Asn211 Asn211 Asn211 Glycosylation at Asn211 regulates the activation state of the discoidin domain receptor 1 (DDR1). 29031045 4 46 gly glycosylated 583:594 arg2 N297 N297 N297 All IgG subclasses are glycosylated at N297, which is required for Fcγ receptor and C1q complement binding as well as maintaining optimal Fc conformation. 24279413 0 92 gly glycopeptides 53:65 arg2 intact glycopeptides intact glycopeptides glycopeptides Computational framework for identification of intact glycopeptides in complex samples. 28272765 0 40 gly 1,1'-Glycosylation 81:98 arg1 1,1'-Disaccharides 1,1'-Disaccharides Unusually Stable Picoloyl-Protected Trimethylsilyl Glycosides for Nonsymmetrical 1,1'-Glycosylation and Synthesis of 1,1'-Disaccharides with Diverse Configurations. 27884519 10 2 gly glycosylated 1185:1196 arg1 N-terminal modified proteins N-terminal modified proteins Fterm proteins N-terminal modified proteins were well glycosylated and produced. 27868361 3 32 part_of PGN 680:682 arg1 various PGN fragments PGN various PGN fragments OGER Site PGN Q9UQ90 fragments Namely, a 4'-O-Fmoc-protected disaccharide was utilized as the key intermediate in this efficient synthetic pathway for preparing various PGN fragments. 27869200 8 32 gly glycopeptides 1409:1421 arg2 N-linked glycopeptides N-linked glycopeptides glycopeptides The results showed that pre-classification of tandem spectra based on their glycosylation type improved the identification of N-linked glycopeptides. 27223297 3 11 part_of positions 535:543 arg1 The Rift Valley fever virus (RVFV) glycoproteins glycoproteins positions Fterm Site glycoproteins positions The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 26170448 3 0 gly glycoprotein 433:444 arg1 the S-layer glycoprotein the S-layer glycoprotein Fterm glycoprotein hispanica S-layer protein has been reported glycosylated, the S-layer glycoprotein and its glycosylation have not been investigated yet. 26170448 3 12 gly glycosylated 407:418 arg1 the S-layer glycoprotein the S-layer glycoprotein Fterm glycoprotein hispanica S-layer protein has been reported glycosylated, the S-layer glycoprotein and its glycosylation have not been investigated yet. 26773038 5 44 part_of VWF 848:850 arg1 the VWF A2 domain VWF the VWF A2 domain PUBTATOR Site VWF 7450 domain We show by differential scanning fluorimetry that the N-linked glycans thermodynamically stabilize the VWF A2 domain. 24509848 5 63 gly N-glycosylation 648:662 arg1 the Asn(211) residue Asn(211) residue Asn(211) residue Here, we report that N-glycosylation at the Asn(211) residue plays a unique role in the control of DDR1 dimerization and autophosphorylation. 28378791 3 5 part_of GluN2B 343:348 arg1 GluN2B ligand binding domains GluN2B GluN2B ligand binding domains PUBTATOR Site GluN2B 2904 domains In this work, we use extensive molecular dynamics simulations of GluN1 and GluN2B ligand binding domains (LBDs) of NMDARs to investigate these effects. 28378791 3 9 part_of GluN1 333:337 arg1 GluN2B ligand binding domains GluN1 GluN2B ligand binding domains PUBTATOR Site GluN1 2902 domains In this work, we use extensive molecular dynamics simulations of GluN1 and GluN2B ligand binding domains (LBDs) of NMDARs to investigate these effects. 26306636 5 43 gly glycopeptides 1039:1051 arg2 glycopeptides glycopeptides glycopeptides We compiled a method pipeline that combined hydrophilic interaction liquid chromatography enrichment of glycopeptides, high accuracy mass spectrometry and automated interpretation of the mass spectra with in-house developed "MassAI" software, which proved efficient in glycan site microheterogeneity analysis. 27873218 10 7 gly glycopeptides 1987:1999 arg2 sulfated glycopeptides sulfated glycopeptides glycopeptides Also, the combined use of protonated and sodiated precursors for positive mode HCD fragmentation analysis will likely become useful for additional classes of sulfated glycopeptides. 24965454 3 54 part_of supersite 658:666 arg1 gp120 gp120 supersite PUBTATOR Site gp120 3700 supersite Several glycans in and around the 2G12 epitope have been shown to interact with other potent, broadly neutralizing antibodies; therefore, this region constitutes a supersite of vulnerability on gp120. 27585995 14 160 gly glycoprotein 3118:3129 arg1 glycoprotein O-glycans glycoprotein O-glycans The novel strategy introduced here provides a simple and versatile analytical method for the precise quantitation of glycoprotein O-glycans by mass spectrometry, enabling rapid evaluation of the differences or changes of O-glycans in expression level. 27320861 4 26 gly glycoproteins 560:572 arg1 glycoproteins glycoproteins Fterm glycoproteins In a previous study, we showed that the main type of N-glycan transition is from the paucimannosidic to complex type before and after germination in Oryza sativa, suggesting that transitions of N-glycan, including those of glycoproteins and glycosyltransferases, are closely associated with plant growth. 25849464 6 49 part_of sites 1000:1004 arg1 the enzyme enzyme sites Fterm Site enzyme sites Endo H-deglycosylated nLcc4 (dLcc4), with only one GlcNAc residue remaining at each of the three N-glycosylation sites in the enzyme, exhibited similar kinetic efficiency and thermal stability to that of nLcc4. 26239923 1 45 gly glycoprotein 121:132 arg1 a major glycoprotein a major glycoprotein Fterm glycoprotein Immunoglobulin G (IgG) is a major glycoprotein in ruminant colostrum. 26307003 7 92 gly subdomains 1703:1712 arg1 monosaccharides subdomains monosaccharides subdomains Overall, the present study reveals how family 1 CBM structures are affected by covalent attachment of monosaccharides, which are likely important post-translational modifications of these common subdomains of fungal plant cell wall degrading enzymes. 26301455 1 42 part_of has 195:197 arg1 Cellobiohydrolase I AND four potential N-glycosylation sites Cellobiohydrolase I four potential N-glycosylation sites Cterm Site Cellobiohydrolase I sites Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 25598335 1 9 gly glycoproteins 181:193 arg1 recombinant therapeutic glycoproteins recombinant therapeutic glycoproteins Fterm glycoproteins Yeast has advanced as an alternative for mammalian cell culture for the production of recombinant therapeutic glycoproteins. 26926155 1 20 gly Attachment 184:193 arg2 proteins AND oligosaccharides proteins oligosaccharides Fterm proteins Attachment of oligosaccharides to proteins is a major post-translational modification. 26800543 5 28 gly glycopeptides 744:756 arg2 N-linked glycopeptides N-linked glycopeptides glycopeptides In our research, we mathematically formulated the glycan de novo sequencing problem and proposed a heuristic algorithm for glycan de novo sequencing from HCD MS/MS spectra of N-linked glycopeptides. 27151270 9 3 gly glycoproteins 1329:1341 arg1 plant vacuolar glycoproteins plant vacuolar glycoproteins Fterm glycoproteins Although complex and hybrid glycans were identified, the majority of glycans were paucimannosidic, characteristic of plant vacuolar glycoproteins. 27722599 8 30 gly fucosylated 1145:1155 arg1 several tri- and tetra-antennary fucosylated N-glycans several tri- and tetra-antennary fucosylated N-glycans Interestingly, abundances of several tri- and tetra-antennary fucosylated N-glycans were increased in gastric cancer patients. 24799124 4 24 gly core-fucosylated 821:836 arg1 four core-fucosylated sites sites sites This procedure simplified the structures for further analysis by mass spectrometry, where four core-fucosylated sites (sites 138, 358, 397, and 762) were detected in ceruloplasmin. 26272370 1 91 gly glycoproteins 149:161 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins The market of therapeutic glycoproteins (including coagulation factors, antibodies, cytokines and hormones) is one of the profitable, fast-growing and challenging sectors of the biopharmaceutical industry. 26272370 1 91 gly glycoproteins 149:161 arg1 coagulation factors coagulation factors Fterm factors The market of therapeutic glycoproteins (including coagulation factors, antibodies, cytokines and hormones) is one of the profitable, fast-growing and challenging sectors of the biopharmaceutical industry. 24308717 1 2 gly glycosylated 205:216 arg1 a highly glycosylated therapeutic Fc-fusion protein a highly glycosylated therapeutic Fc-fusion protein Fterm protein Etanercept is a highly glycosylated therapeutic Fc-fusion protein that contains multiple N- and O-glycosylation sites. 24308717 1 28 gly O-glycosylation 278:292 arg2 multiple N- and O-glycosylation sites multiple N- and O-glycosylation sites sites Etanercept is a highly glycosylated therapeutic Fc-fusion protein that contains multiple N- and O-glycosylation sites. 26208004 8 84 gly glycan 1309:1314 arg1 the carbohydrate recognition domain the carbohydrate recognition domain the carbohydrate recognition domain Furthermore, a complex between a glycan on DENV and the carbohydrate recognition domain (CRD) of DC-SIGN was mimicked with computational docking experiments. 26492619 5 4 part_of PLAG1/2 734:740 arg1 PLAG1/2 domain PLAG1 PLAG1/2 domain PUBTATOR Site PLAG1 5324 domain Herein, we developed and characterized a novel anti-PDPN monoclonal antibody, LpMab-10, which targets PLAG1/2 domain. 28672164 7 37 gly core-fucosylated 1036:1051 arg1 Several carbohydrate chains Several carbohydrate chains Several carbohydrate chains in β-HlH are core-fucosylated without Xyl and also possess a high degree of methylation. 26082214 4 30 gly glycoproteins 464:476 arg1 glycoproteins glycoproteins Fterm glycoproteins We describe a method to produce glycoproteins carrying N-linked N-acetylglucosamine (GlcNAc) through glyco-engineered E. coli cells and enzymatic treatment. 26082214 4 9 gly carrying 478:485 arg1 glycoproteins AND N-linked N-acetylglucosamine glycoproteins N-linked N-acetylglucosamine Fterm glycoproteins We describe a method to produce glycoproteins carrying N-linked N-acetylglucosamine (GlcNAc) through glyco-engineered E. coli cells and enzymatic treatment. 26082214 4 9 gly carrying 478:485 arg1 glycoproteins AND GlcNAc glycoproteins GlcNAc Fterm glycoproteins We describe a method to produce glycoproteins carrying N-linked N-acetylglucosamine (GlcNAc) through glyco-engineered E. coli cells and enzymatic treatment. 26855252 0 6 part_of Bean 105:108 arg1 Coffee Bean Regions Coffee Bean Coffee Bean Regions OGER Coffee Bean Q3B7T3 Nonenzymatic Transglycosylation Reactions Induced by Roasting: New Insights from Models Mimicking Coffee Bean Regions with Distinct Polysaccharide Composition. 26855252 0 8 part_of Coffee 98:103 arg1 Coffee Bean Regions Coffee Bean Coffee Bean Regions OGER Coffee Bean Q3B7T3 Nonenzymatic Transglycosylation Reactions Induced by Roasting: New Insights from Models Mimicking Coffee Bean Regions with Distinct Polysaccharide Composition. 28921955 7 25 gly glycosylation 1191:1203 arg2 Six glycosylation sites Six glycosylation sites sites Six glycosylation sites fitting the sequon N-X-S/T were successfully confirmed, and the glycan heterogeneity as well as the ratios of glycoforms were determined at each site. 28230186 5 5 part_of hFCMR 609:613 arg1 the Cμ4 domain hFCMR the Cμ4 domain PUBTATOR Site hFCMR 9214 domain In this study, we identify the Cμ4 domain of IgM as the target of hFCMR, and show that binding and internalization of IgM by hFCMR is glycan-independent. 28230186 5 35 part_of IgM 588:590 arg1 the Cμ4 domain IgM the Cμ4 domain PUBTATOR Site IgM P01871 domain In this study, we identify the Cμ4 domain of IgM as the target of hFCMR, and show that binding and internalization of IgM by hFCMR is glycan-independent. 29146600 1 1 gly glycoproteins 159:171 arg1 circulating glycoproteins circulating glycoproteins Fterm glycoproteins OBJECTIVE Poorer glycemic control in type 1 diabetes may alter N-glycosylation patterns on circulating glycoproteins, and these alterations may be linked with diabetic kidney disease (DKD). 28445724 2 20 part_of CD4 357:359 arg1 the CD4 supersite CD4 the CD4 supersite PUBTATOR Site CD4 920 supersite Here, we use targeted deglycosylation to measure the impact of the glycan shield on elicitation of antibodies against the CD4 supersite. 27525954 5 20 part_of contained 587:595 arg1 a signal peptide AND seven tandem putative Type-II functional chitin-binding domains a signal peptide seven tandem putative Type-II functional chitin-binding domains domains Bioinformatic analysis showed that a signal peptide composed of 17 amino acids located at the N-terminal of SeCBP66 contained seven tandem putative Type-II functional chitin-binding domains and five potential N-glycosylation sites, but no O-linked glycosylation sites. 27525954 5 20 part_of contained 587:595 arg1 a signal peptide AND O-linked glycosylation sites sites sites Bioinformatic analysis showed that a signal peptide composed of 17 amino acids located at the N-terminal of SeCBP66 contained seven tandem putative Type-II functional chitin-binding domains and five potential N-glycosylation sites, but no O-linked glycosylation sites. 26339047 4 13 gly utilized 876:883 arg2 The introduced T116N and G130N sites The introduced T116N and G130N sites sites The introduced T116N and G130N sites were utilized as glycosylation anchors resulting in the formation of hyperglycosylated VLPs. 26160412 4 45 gly glycopeptides 676:688 arg1 CSF proteins proteins glycopeptides Fterm proteins glycopeptides Tryptic glycopeptides from CSF proteins were also enriched by hydrophilic interaction, and the resulting extracts divided into two equal aliquots. 26482295 0 8 gly N-glycosylation 80:94 arg2 unique N-glycosylation site preferences unique N-glycosylation site preferences site Substitute sweeteners: diverse bacterial oligosaccharyltransferases with unique N-glycosylation site preferences. 24473128 6 17 gly glycosylation 712:724 arg2 these 15 glycosylation sites these 15 glycosylation sites sites The loss of these 15 glycosylation sites significantly enhanced pseudovirion transduction in Vero cells, which correlated with an increase in protease sensitivity. 26082214 3 13 gly glycoproteins 417:429 arg1 homogeneous glycoproteins homogeneous glycoproteins Fterm glycoproteins Several approaches have been developed to produce homogeneous glycoproteins. 26171609 4 73 part_of epitopes 720:727 arg1 HAI-2 polypeptide epitopes HAI-2 polypeptide polypeptide The two different types of N-glycan differentially mask two epitopes on HAI-2 polypeptide, recognized by two different HAI-2 mAbs. 26171609 4 90 part_of HAI-2 732:736 arg1 HAI-2 polypeptide HAI-2 HAI-2 polypeptide PUBTATOR Site HAI-2 10653 polypeptide The two different types of N-glycan differentially mask two epitopes on HAI-2 polypeptide, recognized by two different HAI-2 mAbs. 25501957 10 20 gly N-glycosylation 1726:1740 arg1 enzyme thermal stability enzyme thermal stability Fterm enzyme Moreover, 10 of 13 putative N-glycosylation sites were glycosylated on N.BfrA, and N-glycosylation was essential for enzyme thermal stability and optima activity. 25501957 10 83 gly N-glycosylation 1671:1685 arg2 10 of 13 putative N-glycosylation sites 10 of 13 putative N-glycosylation sites sites Moreover, 10 of 13 putative N-glycosylation sites were glycosylated on N.BfrA, and N-glycosylation was essential for enzyme thermal stability and optima activity. 25501957 10 38 gly glycosylated 1698:1709 arg1 10 of 13 putative N-glycosylation sites sites sites Moreover, 10 of 13 putative N-glycosylation sites were glycosylated on N.BfrA, and N-glycosylation was essential for enzyme thermal stability and optima activity. 26618856 3 58 gly glycosylated 608:619 arg1 Intrinsically disordered proteins proteins regions Fterm proteins regions Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) of large proteins are also frequently glycosylated, yet how glycosylation affects their function remains to be elucidated. 25628020 0 55 gly N-glycosylation 25:39 arg2 novel N-glycosylation sites novel N-glycosylation sites sites The acquisition of novel N-glycosylation sites in conserved proteins during human evolution. 24927272 1 54 part_of protein 319:325 arg1 the linker sequence protein the linker sequence Fterm Site protein sequence A xylose-based glycosaminoglycan (GAG) core was recently identified at a Ser residue in the linker sequence of a recombinant Fc fusion protein. 26983412 0 31 gly homogeneity 30:40 arg1 a human-type N-glycan structure a human-type N-glycan structure A dual approach for improving homogeneity of a human-type N-glycan structure in Saccharomyces cerevisiae. 26203194 0 9 part_of Region 58:63 arg1 Human Glypican-1 Human Glypican-1 Region PUBTATOR Human Glypican-1 2817 Structural Aspects of N-Glycosylations and the C-terminal Region in Human Glypican-1. 25193875 2 7 gly presence 296:303 arg2 glycoproteins AND paucimannosidic-type N-glycan glycoproteins paucimannosidic-type N-glycan Fterm glycoproteins However, the presence of paucimannosidic-type N-glycan in glycoproteins restricts their clinical use. 25193875 2 19 gly glycoproteins 341:353 arg1 glycoproteins glycoproteins Fterm glycoproteins However, the presence of paucimannosidic-type N-glycan in glycoproteins restricts their clinical use. 27928741 7 85 gly glycopeptides 1204:1216 arg1 the haemagglutinin-neuraminidase protein protein glycopeptides Fterm protein glycopeptides Reverse-phase liquid chromatography tandem mass spectrometry strategies including collision induced dissociation, higher-energy collision dissociation and electron-transfer dissociation were implemented to characterise glycopeptides from the haemagglutinin-neuraminidase protein. 25361541 9 4 gly O-mannosylated 1627:1640 arg1 O-mannosylated glycans O-mannosylated glycans Since O-mannosylated glycans on phosphacan/RPTPβ could also present human natural killer-1, another glycan epitope specifically expressed in the nervous system, our results revealed the importance of O-mannosylated glycan chains in the presentation of functional glycan epitopes in the brain. 25361541 9 72 gly O-mannosylated 1821:1834 arg1 O-mannosylated glycan chains O-mannosylated glycan chains Since O-mannosylated glycans on phosphacan/RPTPβ could also present human natural killer-1, another glycan epitope specifically expressed in the nervous system, our results revealed the importance of O-mannosylated glycan chains in the presentation of functional glycan epitopes in the brain. 26598643 5 3 gly O-glycans 1059:1067 arg1 human blood plasma proteins proteins O-glycans Fterm proteins To this end pooled human blood plasma of healthy donors was proteolytically digested using a broad-specific enzyme (Proteinase K), followed by a precipitation step, as well as a glycopeptide enrichment and fractionation step via hydrophilic interaction liquid chromatography, the latter being optimized for intact O-glycopeptides carrying short mucin-type core-1 and -2 O-glycans, which represent the vast majority of O-glycans on human blood plasma proteins. 26598643 5 19 gly O-glycopeptides 955:969 arg2 intact O-glycopeptides intact O-glycopeptides O-glycopeptides To this end pooled human blood plasma of healthy donors was proteolytically digested using a broad-specific enzyme (Proteinase K), followed by a precipitation step, as well as a glycopeptide enrichment and fractionation step via hydrophilic interaction liquid chromatography, the latter being optimized for intact O-glycopeptides carrying short mucin-type core-1 and -2 O-glycans, which represent the vast majority of O-glycans on human blood plasma proteins. 26598643 5 115 gly glycopeptide 819:830 arg2 a glycopeptide enrichment a glycopeptide enrichment glycopeptide To this end pooled human blood plasma of healthy donors was proteolytically digested using a broad-specific enzyme (Proteinase K), followed by a precipitation step, as well as a glycopeptide enrichment and fractionation step via hydrophilic interaction liquid chromatography, the latter being optimized for intact O-glycopeptides carrying short mucin-type core-1 and -2 O-glycans, which represent the vast majority of O-glycans on human blood plasma proteins. 26598643 5 20 gly carrying 971:978 arg1 intact O-glycopeptides AND -2 O-glycans intact O-glycopeptides -2 O-glycans O-glycopeptides To this end pooled human blood plasma of healthy donors was proteolytically digested using a broad-specific enzyme (Proteinase K), followed by a precipitation step, as well as a glycopeptide enrichment and fractionation step via hydrophilic interaction liquid chromatography, the latter being optimized for intact O-glycopeptides carrying short mucin-type core-1 and -2 O-glycans, which represent the vast majority of O-glycans on human blood plasma proteins. 29233759 9 62 part_of -3 1364:1365 arg1 the -3 and -1 subsites -3 and -1 the -3 and -1 subsites OGER Site -3 and -1 O75717 subsites Molecular docking studies with chitohexaose showed that the side chains of Trp residues mediate stacking interactions with sugar residues from the -3 and -1 subsites, indicating the importance of these residues in the enzymatic activity of StmChiA. 29233759 9 80 part_of -1 1371:1372 arg1 the -3 and -1 subsites -3 and -1 the -3 and -1 subsites OGER Site -3 and -1 O75717 subsites Molecular docking studies with chitohexaose showed that the side chains of Trp residues mediate stacking interactions with sugar residues from the -3 and -1 subsites, indicating the importance of these residues in the enzymatic activity of StmChiA. 27769287 0 35 gly glycoproteins 65:77 arg1 recombinant glycoproteins recombinant glycoproteins Fterm glycoproteins Effects of Rho1, a small GTPase on the production of recombinant glycoproteins in Saccharomyces cerevisiae. 28749929 5 66 gly site 1265:1268 arg1 diverse natural and non-natural glycan structures site diverse natural and non-natural glycan structures site Compared with in vivo glycoengineering technologies and the glycosyltransferase-enabled in vitro engineering method, the current approach is robust and features quantitative yield, homogeneous glycoforms of produced antibodies and ADCs, compatibility with diverse natural and non-natural glycan structures, convenient exploitation of native IgG as the starting material, and a well-defined conjugation site for antibody modifications. 28749929 5 92 gly robust 1004:1009 arg1 a well-defined conjugation site a well-defined conjugation site site Compared with in vivo glycoengineering technologies and the glycosyltransferase-enabled in vitro engineering method, the current approach is robust and features quantitative yield, homogeneous glycoforms of produced antibodies and ADCs, compatibility with diverse natural and non-natural glycan structures, convenient exploitation of native IgG as the starting material, and a well-defined conjugation site for antibody modifications. 28717478 1 55 gly glycopeptides 316:328 arg2 glycopeptides glycopeptides glycopeptides The combination of solid phase peptide synthesis and endo-β-N-acetylglucosaminidase (ENGase) catalysed glycosylation is a powerful convergent synthetic method allowing access to glycopeptides bearing full-length N-glycan structures. 28711789 5 5 gly glycoproteins 680:692 arg1 Thirty five glycoproteins Thirty five glycoproteins Fterm glycoproteins Thirty five glycoproteins were changed in abundance in leaves of common bean under drought. 25498018 4 72 gly glycosylation 1004:1016 arg2 the glycosylation sites the glycosylation sites sites The off-line coupling of nano-LC with a MALDI-QIT-TOF mass spectrometer was demonstrated to be capable of sensitive and direct elucidation of the glycosylation difference between HMW and LMW CLEC-2, simultaneously providing information about their oligosaccharide structures and the glycosylation sites. 26563299 9 10 gly sialylated 1414:1423 arg1 core 1 core 1 IL-15 contained no O-glycans, whereas sIL-15Rα was heavily O-glycosylated with partially sialylated core 1 and 2-type mono- to hexasaccharides on Thr2, Thr81, Thr86, Thr156, Ser158, and Ser160. 25568322 10 60 gly N-glycosylated 1508:1521 arg1 N-glycosylated sites N-glycosylated sites sites In the crystal structure, N-glycosylated sites and a potential heparin-binding site face opposite sides. 26784534 1 26 gly occupancy 205:213 arg2 the 10 putative O-glycosylation sites the 10 putative O-glycosylation sites sites BACKGROUND: O-glycosylation of von Willebrand factor (VWF) affects many of its functions; however, there is currently no information on the occupancy of the 10 putative O-glycosylation sites. 26784534 1 76 gly O-glycosylation 234:248 arg2 the 10 putative O-glycosylation sites the 10 putative O-glycosylation sites sites BACKGROUND: O-glycosylation of von Willebrand factor (VWF) affects many of its functions; however, there is currently no information on the occupancy of the 10 putative O-glycosylation sites. 27808502 7 54 gly N-glycopeptides 1509:1523 arg2 609 N-glycopeptides 609 N-glycopeptides N-glycopeptides In this study, simultaneous analysis of the combined oligomannosylated N-glycopeptidome and the native glycopeptidome leads to the identification of 609 N-glycopeptides from the secretome and lysates of Huh7 cells. 26599081 7 23 gly glycosylated 1124:1135 arg1 The lipoproteins The lipoproteins Fterm lipoproteins The lipoproteins of Mycoplasma pneumoniae also are glycosylated. 29233911 7 68 gly O-glycosylation 997:1011 arg2 five known O-glycosylation sites five known O-glycosylation sites sites Five novel and five known O-glycosylation sites were identified, carrying mainly core1-type O-glycans. 24664808 10 57 gly residue 1719:1725 arg1 intact glycan moiety Asn residue intact glycan moiety Asn residue When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36](-), was abundantly formed. 24664808 10 59 gly glycosylated 1634:1645 arg1 a glycosylated Asn a glycosylated Asn Asn When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36](-), was abundantly formed. 24664808 10 105 gly Asn 1715:1717 arg1 [glycan Asn residue [glycan Asn residue When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36](-), was abundantly formed. 24664808 10 108 gly having 1705:1710 arg1 an interesting fragment AND [glycan an interesting fragment an interesting fragment [glycan fragment When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36](-), was abundantly formed. 24685714 12 74 part_of PAC 1834:1836 arg1 its PAC domain PAC its PAC domain OGER Site PAC Q9H813 domain Finally, AGP31 was able to interact with itself in vitro through its PAC domain. 27581986 3 25 part_of CD4 644:646 arg1 the CD4 binding site CD4 the CD4 binding site PUBTATOR Site CD4 920 site We previously described an HIV-1 clade C-infected donor, CAP257, who developed broadly neutralizing plasma antibodies targeting an N276 glycan-dependent epitope in the CD4 binding site. 25763881 3 10 gly N-glycosylation 371:385 arg1 patatin proteins patatin proteins Fterm proteins In this work, N-glycosylation profiles of patatin proteins isolated from tubers of different potato species were investigated and compared. 24855066 7 70 gly sialylated 1424:1433 arg1 α 2-6 sialylated N-glycans α 2-6 sialylated N-glycans We identified characteristic glycan features that were unique to the ovarian cancer membrane proteins, namely the "bisecting N-acetyl-glucosamine" type N-glycans, increased levels of α 2-6 sialylated N-glycans and "N,N'-diacetyl-lactosamine" type N-glycans. 28199092 8 91 gly glycopeptide 1951:1962 arg2 the glycopeptide the glycopeptide glycopeptide Furthermore, no significant impact from the glycoform on the ionization properties of the glycopeptide is observed. 28717478 6 65 gly glycopeptides 1224:1236 arg2 glycopeptides glycopeptides glycopeptides Binding assays showed increased binding of glycopeptides to APCs compared to the non-glycosylated control. 26478188 7 7 gly N-glycosylation 1234:1248 arg1 its fibrinogen-like domain domain domain We also revealed that these effects of dimeric CMP-Ang1 were affected by specified N-glycosylation in its fibrinogen-like domain. 27506355 9 43 gly glycopeptide 962:973 arg2 possible glycopeptide sequences possible glycopeptide sequences glycopeptide sequences Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. 25482815 4 31 gly glycan 867:872 arg1 K1 flagellin flagellin glycan Fterm flagellin A deglycosylated K1 flagellin induced immune responses in the same manner as N1141 flagellin, suggesting that the glycan in K1 flagellin prevent epitope recognition in rice. 25482815 4 49 gly deglycosylated 755:768 arg1 A deglycosylated K1 flagellin A deglycosylated K1 flagellin Fterm flagellin A deglycosylated K1 flagellin induced immune responses in the same manner as N1141 flagellin, suggesting that the glycan in K1 flagellin prevent epitope recognition in rice. 27500750 5 48 gly glycopeptide 913:924 arg2 glycopeptide enrichment glycopeptide enrichment glycopeptide The optimized dipeptide-based homopolymers display excellent performance (e.g., selectivity up to ∼70% for real biosamples and strong anti-interference capacity capable of resisting 1000-fold bovine serum albumin interference) in glycopeptide enrichment. 27501865 6 2 gly sialylated 1195:1204 arg1 sialylated tetraantennary and FA3G3S[3,3,3]3 structures sialylated tetraantennary and FA3G3S[3,3,3]3 structures Most changes occurred 24 hours after surgery with the decrease of most core-fucosylated biantennary structures, as well as the increase in sialylated tetraantennary and FA3G3S[3,3,3]3 structures. 27501865 6 15 gly core-fucosylated 1127:1142 arg1 most core-fucosylated biantennary structures most core-fucosylated biantennary structures Most changes occurred 24 hours after surgery with the decrease of most core-fucosylated biantennary structures, as well as the increase in sialylated tetraantennary and FA3G3S[3,3,3]3 structures. 25451932 4 37 gly sites 467:471 arg1 N-glycans sites N-glycans sites It remains unknown, however, how N-glycans at different sites may regulate corin biosynthesis and processing. 25318901 1 6 gly glycosylations 228:241 arg1 suitably functionalized monosaccharide intermediates suitably functionalized monosaccharide intermediates The tetrasaccharide repeating unit of the O-antigen of Escherichia coli O174 strain was synthesized applying sequential glycosylations of suitably functionalized monosaccharide intermediates. 25358049 0 30 gly glycopeptides 106:118 arg2 glycopeptides glycopeptides glycopeptides Assignment of saccharide identities through analysis of oxonium ion fragmentation profiles in LC-MS/MS of glycopeptides. 24234447 6 25 gly glycosylation 1039:1051 arg2 Further, 598 protein glycosylation sites Further, 598 protein glycosylation sites sites Further, 598 protein glycosylation sites have been annotated with experimentally confirmed glycan structures from the literature. 27573070 4 32 gly N-glycopeptide 950:963 arg2 N-glycopeptide backbones N-glycopeptide backbones N-glycopeptide These merged spectra expedite the identification of both glycans and N-glycopeptide backbones in tandem MS data using the glycan database and a proteomic search tool (e.g., Mascot). 26059692 0 67 part_of neuropilin-1 63:74 arg1 the neuropilin-1 c/MAM-domain neuropilin-1 the neuropilin-1 c/MAM-domain OGER Site neuropilin-1 O14786 c/MAM-domain Detailed characterization of the O-linked glycosylation of the neuropilin-1 c/MAM-domain. 29016103 1 44 gly glycoproteins 280:292 arg1 glycoproteins glycoproteins Fterm glycoproteins Heterogeneity of protein glycosylation poses great challenges for analysis that is key to understand structure and function of glycoproteins. 24941220 8 25 gly glycopeptides 1348:1360 arg2 460 unique glycopeptides 460 unique glycopeptides glycopeptides For the recombinant gp120, this "copy-paste" spectral pattern of glycopeptides facilitated identification of 2224 spectra using only 18 spectral templates, and after precursor mass correction, 1268 (57%) spectra were assigned to 460 unique glycopeptides accommodating 19 N-linked and one O-linked glycosylation sites (glycosites). 24941220 8 41 gly glycopeptides 1173:1185 arg2 glycopeptides glycopeptides glycopeptides For the recombinant gp120, this "copy-paste" spectral pattern of glycopeptides facilitated identification of 2224 spectra using only 18 spectral templates, and after precursor mass correction, 1268 (57%) spectra were assigned to 460 unique glycopeptides accommodating 19 N-linked and one O-linked glycosylation sites (glycosites). 24941220 8 49 gly glycosites 1426:1435 arg2 glycosites glycosites glycosites For the recombinant gp120, this "copy-paste" spectral pattern of glycopeptides facilitated identification of 2224 spectra using only 18 spectral templates, and after precursor mass correction, 1268 (57%) spectra were assigned to 460 unique glycopeptides accommodating 19 N-linked and one O-linked glycosylation sites (glycosites). 24941220 8 49 gly glycosites 1426:1435 arg2 one O-linked glycosylation sites one O-linked glycosylation sites sites For the recombinant gp120, this "copy-paste" spectral pattern of glycopeptides facilitated identification of 2224 spectra using only 18 spectral templates, and after precursor mass correction, 1268 (57%) spectra were assigned to 460 unique glycopeptides accommodating 19 N-linked and one O-linked glycosylation sites (glycosites). 24941220 8 94 gly glycosylation 1405:1417 arg2 glycosites glycosites glycosites For the recombinant gp120, this "copy-paste" spectral pattern of glycopeptides facilitated identification of 2224 spectra using only 18 spectral templates, and after precursor mass correction, 1268 (57%) spectra were assigned to 460 unique glycopeptides accommodating 19 N-linked and one O-linked glycosylation sites (glycosites). 24941220 8 94 gly glycosylation 1405:1417 arg2 one O-linked glycosylation sites one O-linked glycosylation sites sites For the recombinant gp120, this "copy-paste" spectral pattern of glycopeptides facilitated identification of 2224 spectra using only 18 spectral templates, and after precursor mass correction, 1268 (57%) spectra were assigned to 460 unique glycopeptides accommodating 19 N-linked and one O-linked glycosylation sites (glycosites). 27558752 4 19 gly glycoproteins 723:735 arg1 Arabidopsis glycoproteins Arabidopsis glycoproteins Fterm glycoproteins In-house databases of Arabidopsis glycoproteins and glycopeptides containing Asn-X-Ser/Thr/Cys motifs were constructed by reducing 20% and 90% of the public database size, respectively, to enable a rapid analysis of large datasets for comprehensive identification and quantification of glycoproteins and heterogeneous N-glycans in a complex mixture. 27558752 4 26 gly glycoproteins 975:987 arg1 glycoproteins glycoproteins Fterm glycoproteins In-house databases of Arabidopsis glycoproteins and glycopeptides containing Asn-X-Ser/Thr/Cys motifs were constructed by reducing 20% and 90% of the public database size, respectively, to enable a rapid analysis of large datasets for comprehensive identification and quantification of glycoproteins and heterogeneous N-glycans in a complex mixture. 27558752 4 29 gly glycopeptides 741:753 arg2 glycopeptides glycopeptides glycopeptides In-house databases of Arabidopsis glycoproteins and glycopeptides containing Asn-X-Ser/Thr/Cys motifs were constructed by reducing 20% and 90% of the public database size, respectively, to enable a rapid analysis of large datasets for comprehensive identification and quantification of glycoproteins and heterogeneous N-glycans in a complex mixture. 24130173 5 65 gly tri-sialylated 1053:1066 arg1 tri-sialylated structures tri-sialylated structures Attempts to increase that sialylation content of rBChE by the over-expression of an additional glycosylation enzyme that generates branched N-glycans (i.e. β1,4-N-acetylglucosaminyl-transferase IV), allowed the production of rBChE decorated with tri-sialylated structures (up to 70%). 28486782 8 34 part_of EGFR 1070:1073 arg1 the monomeric EGFR extracellular domain EGFR the monomeric EGFR extracellular domain PUBTATOR Site EGFR 1956 domain Here, atomistic MD simulations show that N-glycosylation of the EGFR extracellular domain plays critical roles in the binding of growth factors, monoclonal antibodies, and the dimeric partners to the monomeric EGFR extracellular domain. 28486782 8 38 part_of EGFR 924:927 arg1 the EGFR extracellular domain EGFR the EGFR extracellular domain PUBTATOR Site EGFR 1956 domain Here, atomistic MD simulations show that N-glycosylation of the EGFR extracellular domain plays critical roles in the binding of growth factors, monoclonal antibodies, and the dimeric partners to the monomeric EGFR extracellular domain. 26439794 2 50 gly glycopeptides 343:355 arg2 glycopeptides glycopeptides glycopeptides However, one has trouble in mass spectrometric glycoproteomics of membrane fraction because of lower intensity of glycopeptides in the existence of surfactants. 25458834 5 48 part_of CLEC-2 711:716 arg1 the noncanonical "side" face CLEC-2 the noncanonical "side" face PUBTATOR Site CLEC-2 51266 face Both podoplanin and rhodocytin bind to the noncanonical "side" face of CLEC-2. 25016576 8 23 gly glycopeptide 1402:1413 arg2 glycopeptide glycopeptide glycopeptide fragments Epitope mapping using glycopeptide fragments and in vitro mutagenesis showed that binding of this antibody depends on N-linked glycosylation at asparagine N130 (HXB2 numbering) in the gp120 V1/V2 domain. 25016576 8 91 gly glycosylation 1507:1519 arg1 the gp120 V1/V2 domain domain domain Epitope mapping using glycopeptide fragments and in vitro mutagenesis showed that binding of this antibody depends on N-linked glycosylation at asparagine N130 (HXB2 numbering) in the gp120 V1/V2 domain. 25016576 8 91 gly glycosylation 1507:1519 arg2 asparagine N130 asparagine N130 asparagine N130 Epitope mapping using glycopeptide fragments and in vitro mutagenesis showed that binding of this antibody depends on N-linked glycosylation at asparagine N130 (HXB2 numbering) in the gp120 V1/V2 domain. 26307003 4 22 gly Ser14 888:892 arg1 monosaccharides Ser3 and Ser14 monosaccharides Ser3 and Ser14 The structures clearly reveal that monosaccharides at both Ser3 and Ser14 on family 1 CBMs present additional cellulose binding platforms, similar to well-characterized aromatic residues at the binding interface, which align to the cellulose surface. 26307003 4 50 gly Ser3 879:882 arg1 monosaccharides Ser3 and Ser14 monosaccharides Ser3 and Ser14 The structures clearly reveal that monosaccharides at both Ser3 and Ser14 on family 1 CBMs present additional cellulose binding platforms, similar to well-characterized aromatic residues at the binding interface, which align to the cellulose surface. 25113421 8 95 gly glycosylation 990:1002 arg2 the glycosylation site information the glycosylation site information site The latter approach has the advantage of retaining the glycosylation site information. 24797265 0 100 gly O-Glycosylation 0:14 arg1 the N-terminal region the N-terminal region region O-Glycosylation of the N-terminal region of the serine-rich adhesin Srr1 of Streptococcus agalactiae explored by mass spectrometry. 24794851 1 19 gly glycoproteins 173:185 arg1 pharmaceutical glycoproteins pharmaceutical glycoproteins Fterm glycoproteins Production of pharmaceutical glycoproteins, such as therapeutic antibodies and cytokines, in plants has many advantages in safety and reduced costs. 27111718 5 34 gly glycopeptide 1097:1108 arg2 glycopeptide glycopeptide glycopeptide In this paper, we present GlycoSeq, an open-source software tool that implements a heuristic iterated glycan sequencing algorithm coupled with prior knowledge for automated elucidation of the glycan structure within a glycopeptide from its collision-induced dissociation tandem mass spectrum. 24616211 1 21 gly glycoproteins 105:117 arg1 Several N-linked glycoproteins Several N-linked glycoproteins Fterm glycoproteins Several N-linked glycoproteins have been identified in archaea and there is growing evidence that the N-glycan is involved in survival and functioning of archaea in extreme conditions. 25188817 4 0 gly glycosylation 604:616 arg2 the glycosylation site the glycosylation site site These simulations suggest that the effects of glycosylation may be quite sensitive to steric crowding by the side chain immediately following the glycosylation site but less sensitive to stacking interactions with the aromatic Trp residue. 25205566 6 17 gly glycoproteins 859:871 arg1 glycoproteins glycoproteins Fterm glycoproteins Proteins are first immobilized to a solid support and unconjugated molecules are washed away; glycans, while still linked to glycoproteins on the solid support, can be treated enzymatically or chemically on solid phase for glycan derivatization. 28493134 6 21 gly glycoproteins 1156:1168 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins Herein we describe and discuss the analytical approaches for glycosylation analysis of therapeutic glycoproteins produced in CHO (Chinese Hamster Ovary) cells. 28493134 6 31 gly glycosylation 1118:1130 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins Herein we describe and discuss the analytical approaches for glycosylation analysis of therapeutic glycoproteins produced in CHO (Chinese Hamster Ovary) cells. 28199092 2 3 gly present 407:413 arg1 a particular site AND the individual glycan species a particular site the individual glycan species site Therefore, for proteins containing multiple glycosylation sites, the individual glycan species present at a particular site cannot be differentiated from those species present at the other glycosylation sites on the molecule. 28199092 2 61 gly glycosylation 356:368 arg2 multiple glycosylation sites multiple glycosylation sites sites Therefore, for proteins containing multiple glycosylation sites, the individual glycan species present at a particular site cannot be differentiated from those species present at the other glycosylation sites on the molecule. 28199092 2 113 gly glycosylation 501:513 arg2 the other glycosylation sites the other glycosylation sites sites Therefore, for proteins containing multiple glycosylation sites, the individual glycan species present at a particular site cannot be differentiated from those species present at the other glycosylation sites on the molecule. 28277614 4 58 gly glycopeptides 744:756 arg2 glycopeptides glycopeptides glycopeptides O-Glycans were analysed in negative ion mode by electrospray ionisation linear ion trap mass spectrometry and glycopeptides in positive ion mode by electrospray ionisation hybrid quadrupole-orbitrap mass spectrometry. 26083631 0 25 part_of C2 26:27 arg1 the C2 Domain C2 the C2 Domain Cterm C2 A Conserved Glycan in the C2 Domain of HIV-1 Envelope Acts as a Molecular Switch to Control X4 Utilization by Clonal Variants with Identical V3 Loops. 26507102 10 131 gly disialylated 1466:1477 arg1 disialylated Core 1 O-glycan disialylated Core 1 O-glycan Additionally, synovial fluid from normal joints (26.7 ± 6.7%) showed higher amounts of disialylated Core 1 O-glycan than from joints with osteochondral fragments (21.2 ± 4.9%, P = 0.03). 29187599 12 60 gly glycosylation 1794:1806 arg2 all four glycosylation sites all four glycosylation sites sites These functional results are reflected in the high evolutionary conservation of all four glycosylation sites. 28888681 6 2 gly glycopeptides 893:905 arg2 glycopeptides glycopeptides glycopeptides The presence of sialic acids prolonged the retention of glycopeptides in both chromatographic modes. 24509848 10 68 part_of motif 1531:1535 arg1 N-glycosylation t N-glycosylation motif PUBTATOR Site t N-glycosylation 780 motif Taken together, these data suggest that N-glycosylation at the highly conserved (211)NDS motif evolved to act as a negative repressor of DDR1 phosphorylation in the absence of ligand. 24519758 5 40 gly glycoproteins 803:815 arg1 human and bovine milk glycoproteins human and bovine milk glycoproteins Fterm glycoproteins After the protein was isolated from milk by affinity chromatography, N-glycans were enzymatically released and a complete characterization of glycan composition was carried out by advanced MS. The glycosylation of goat milk lactoferrin was compared with that of human and bovine milk glycoproteins. 26211613 3 34 gly aglycosylated 522:534 arg1 the aglycosylated Fc variant the aglycosylated Fc variant Fterm Fc variant However, the conformation of the C'E loop, which contains N297, was significantly perturbed in the aglycosylated Fc variant. 24085030 3 73 gly glycoproteins 482:494 arg1 salivary glycoproteins salivary glycoproteins Fterm glycoproteins This work is focused on glycan structures altered in salivary glycoproteins of alcoholics, indicating the most efficient carriers of such marker glycoepitopes. 26272370 5 12 gly glycoproteins 938:950 arg1 two model glycoproteins two model glycoproteins Fterm glycoproteins Since the initial analysis of cell membrane proteins showed a promising glycosylation of TE671 cells for biotechnological purposes, we focused on the recombinant expression of two model glycoproteins of therapeutical relevance. 24806200 8 26 gly glycoprotein 1754:1765 arg1 human glycoprotein hormone human glycoprotein hormone Fterm glycoprotein The final assembly of the individual glycopeptide fragments involved a stepwise native chemical ligation strategy to provide the longest and most complex human glycoprotein hormone (β-hCG) as well as its closely related homologue (β-hLH) as discrete glycoforms. 24806200 8 100 gly glycopeptide 1631:1642 arg2 glycopeptide glycopeptide glycopeptide fragments The final assembly of the individual glycopeptide fragments involved a stepwise native chemical ligation strategy to provide the longest and most complex human glycoprotein hormone (β-hCG) as well as its closely related homologue (β-hLH) as discrete glycoforms. 28437635 0 35 part_of SLC52A1 27:33 arg1 Three cysteine residues SLC52A1 Three cysteine residues PUBTATOR AminoAcid SLC52A1 55065 cysteine residues Three cysteine residues of SLC52A1, a receptor for the porcine endogenous retrovirus-A (PERV-A), play a critical role in cell surface expression and infectivity. 28375048 8 63 gly glycoproteins 1869:1881 arg1 mammalian expressed glycoproteins mammalian expressed glycoproteins Fterm glycoproteins Protein arabinosylation represents an expansion of the N-glycan code in mammalian expressed glycoproteins. 25533529 0 63 gly N-glycosylation 18:32 arg2 single N-glycosylation site knockout single N-glycosylation site knockout site Effects of single N-glycosylation site knockout on folding and defibrinogenating activities of acutobin recombinants from HEK293T. 24981920 3 56 gly glycopeptides 657:669 arg2 glycopeptides glycopeptides two glycan chains glycopeptides With the large size and tremendous structural complexity of these molecules, multiple unexpected obstacles were encountered during the synthesis, including high sensitivity to base treatment and the instability of glycopeptides with two glycan chains towards catalytic hydrogenation conditions. 25646460 4 32 gly Nonsialylated 634:646 arg1 Nonsialylated glycan structures Nonsialylated glycan structures Nonsialylated glycan structures have a negative impact on disease-homing activity, highlighting the importance of glycosylation control and characterization during process development. 28693729 8 69 gly proteins 1953:1960 arg1 clinical glycan biomarker discovery proteins clinical glycan biomarker discovery Fterm proteins Herein, SSAP derivatization combined with MALDI-TOF MS exhibits unique advantages for glycomic analysis and shows potential in glycosylation profiling of therapeutic proteins and clinical glycan biomarker discovery. 26603318 5 41 gly deglycosylated 1271:1284 arg1 the deglycosylated recombinant lectin the deglycosylated recombinant lectin Fterm lectin In thermal and guanidine hydrochloride (GdnCl)-induced unfolding, the wild-type and high-mannose lectins possess higher stability compared with the deglycosylated recombinant lectin and both mutants, as measured by a higher Tm of denaturation or a greater free energy change, respectively. 25916169 7 67 gly N-glycosylation 1005:1019 arg2 The individual N-glycosylation sites The individual N-glycosylation sites sites The individual N-glycosylation sites had different effects on ST3Gal-II enzymatic activity. 24475074 2 19 gly glycoproteins 216:228 arg1 glycoproteins glycoproteins Fterm glycoproteins In animals, glycoproteins transit through the Golgi where the N-glycans are trimmed and rebuilt with sequences that bind lectins, an innovation that greatly increases structural diversity and redundancy of glycoprotein-lectin interaction at the cell surface. 26038399 1 4 gly glycoproteins 163:175 arg1 viral glycoproteins viral glycoproteins Fterm glycoproteins BACKGROUND: N-linked glycosylation is a common posttranslational modification found on viral glycoproteins (GPs) and involved in promoting expression, cellular attachment, protection from proteases, and antibody evasion. 28902916 1 64 gly glycoproteins 209:221 arg1 the HIV envelope glycoproteins the HIV envelope glycoproteins Fterm glycoproteins 155971 Extensive shielding by N-glycans on the surface of the HIV envelope glycoproteins (Env) restricts B cell recognition of conserved neutralizing determinants. 28193332 8 63 gly N-glycosylation 1490:1504 arg2 A fourth N-glycosylation site A fourth N-glycosylation site site A fourth N-glycosylation site of AmPDH1 could be confirmed by mass spectrometry at N319, which appeared to be conserved in related fungal pyranose dehydrogenases but not in other members of the glucose-methanol-choline oxidoreductase structural family. 26339047 11 3 gly N-glycosylation 2351:2365 arg2 additional N-glycosylation sites additional N-glycosylation sites sites We have generated virus-like particles (VLPs) composed of hepatitis B virus envelope proteins (HBsAgS) with additional N-glycosylation sites. 25462875 7 41 gly fucosylation 1346:1357 arg1 hybrid structures hybrid structures The results demonstrated a correlation between the levels of intracellular B4GALT1 activity and terminally galactosylated N-glycans, N-glycan branching, the appearance of hybrid structures, and reduced core fucosylation. 26328495 2 56 gly N-glycosylation 325:339 arg2 no potential N-glycosylation sites no potential N-glycosylation sites sites POMGNT1 is not modified by N-glycans because there are no potential N-glycosylation sites; however, it is not clear whether POMGNT1 is modified by O-glycans. 24440233 7 39 gly glycopeptides 1303:1315 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides We evaluated the HCD approach with alternating NCE parameters for confident characterization of intact N- and O-linked glycopeptides in a single liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. 27500750 2 11 gly glycopeptides 316:328 arg2 low-abundance glycopeptides low-abundance glycopeptides glycopeptides However, these studies are restricted by the bottleneck to enrich low-abundance glycopeptides from complex biosamples and the difficulties in analyzing glycan structures by mass spectrometry. 26189796 5 6 gly modification 939:950 arg1 this specific asparagine site this specific asparagine site this specific asparagine site AminoAcid asparagine site This aberrant glycan modification on this specific asparagine site of E-cadherin was demonstrated to affect its critical functions in gastric cancer cells by affecting E-cadherin cellular localization, cis-dimer formation, molecular assembly and stability of the adherens junctions and cell-cell aggregation, which was further observed in human gastric carcinomas. 24981920 0 47 gly glycopeptides 33:45 arg2 syndecan-3 glycopeptides syndecan-3 glycopeptides glycopeptides Chemical synthesis of syndecan-3 glycopeptides bearing two heparan sulfate glycan chains. 25551295 11 86 gly glycoprotein 2168:2179 arg1 glycoprotein studies glycoprotein studies Fterm glycoprotein Gnt1 and Gnt2 catalyze fundamental reactions in the synthesis of every glycoprotein with a complex-type N-glycan; thus, the strategies presented herein can be applied to a broad range of glycoprotein studies. 25551295 11 38 gly glycoprotein 2052:2063 arg1 a complex-type N-glycan glycoprotein a complex-type N-glycan Fterm glycoprotein Gnt1 and Gnt2 catalyze fundamental reactions in the synthesis of every glycoprotein with a complex-type N-glycan; thus, the strategies presented herein can be applied to a broad range of glycoprotein studies. 24797265 9 41 gly modified 1203:1210 arg1 the same protein residue AND different glycan combinations the same protein residue different glycan combinations residue Our data unambiguously indicate that the same protein residue can be modified with different glycan combinations including N-acetylhexosamine, hexose, and a novel modification that was identified as O-acetylated-N-acetylhexosamine. 24797265 9 41 gly modified 1203:1210 arg3 the same protein residue AND hexose the same protein residue hexose residue Our data unambiguously indicate that the same protein residue can be modified with different glycan combinations including N-acetylhexosamine, hexose, and a novel modification that was identified as O-acetylated-N-acetylhexosamine. 26170448 0 51 gly glycoproteins 30:42 arg1 the S-layer glycoproteins glycoproteins their covalently linked glycans Fterm glycoproteins Identification of the S-layer glycoproteins and their covalently linked glycans in the halophilic archaeon Haloarcula hispanica. 24108499 8 0 gly glucoamylase 1287:1298 arg1 polysaccharides glucoamylase polysaccharides Fterm glucoamylase Taken together, two carbohydrate binding sites in RoSBD cooperate to reinforce binding mode of glucoamylase with polysaccharides as well as the starch. 26270612 3 28 part_of galectin-8 535:544 arg1 the N-terminal domain galectin-8 the N-terminal domain PUBTATOR Site galectin-8 O00214 domain Cell binding by using glycosylation mutants reveals binding of the N-terminal domain of chicken galectin-8 (CG-8N) to α-2,3-sialylated and galactose-terminated glycan chains. 28888681 0 49 gly glycopeptides 117:129 arg2 hemopexin glycopeptides hemopexin glycopeptides glycopeptides Nano reversed phase versus nano hydrophilic interaction liquid chromatography on a chip in the analysis of hemopexin glycopeptides. 27956708 1 13 part_of Antibodies 289:298 arg1 the Fab-domain Antibodies (ACPA the Fab-domain PUBTATOR Site Antibodies (ACPA 5657 Fab-domain Recently, we showed the unexpectedly high abundance of N-linked glycans on the Fab-domain of Anti-Citrullinated Protein Antibodies (ACPA). 26507102 13 91 part_of lubricin 2021:2028 arg1 an identical proteolytic cleavage site lubricin an identical proteolytic cleavage site OGER Site lubricin Q92954 site We demonstrate an identical proteolytic cleavage site of lubricin both in vitro and in vivo. 25450502 3 14 gly O-glycopeptides 666:680 arg2 O-glycopeptides O-glycopeptides O-glycopeptides In this work, we profiled the overall glycan pattern of human recombinant OPN using a lectin array and completed detailed structural analysis of O-glycopeptides by mass spectrometry (MS). 26563299 5 78 gly glycopeptides 806:818 arg2 glycopeptides glycopeptides glycopeptides Intact IL-15 and sIL-15Rα and derived glycans and glycopeptides were separately profiled using multiple LC-MS/MS strategies. 27714557 0 35 gly transglycosylation 17:34 arg1 sialo-complex-type oligosaccharide sialo-complex-type oligosaccharide Highly efficient transglycosylation of sialo-complex-type oligosaccharide using Coprinopsis cinerea endoglycosidase and sugar oxazoline. 24511137 6 60 gly attached 1305:1312 arg2 the hinge region AND O-linked glycans the hinge region O-linked glycans region Collectively, our data suggest a critical role of O-linked glycans attached to the hinge region in the development of IgA nephropathy-like GN induced by 6-19 IgA rheumatoid factor in mice. 26066491 9 47 gly sialylated 1225:1234 arg1 sialylated core 5 sialylated core 5 Intestinal mucins carried only cores 1, 2, and 5, Neu5Ac was the only sialic acid present, and sialylated core 5 was the most dominant structure. 26512079 9 0 gly glycans 1861:1867 arg1 the HIV-1 envelope protein protein glycans Fterm protein IMPORTANCE: N-linked glycans on the HIV-1 envelope protein have been postulated to contribute to viral escape from host immune responses. 27574189 13 37 gly found 1304:1308 arg1 the disintegrin domain AND one additional O-fucosylation site the disintegrin domain one additional O-fucosylation site domain Unexpectedly, one additional O-fucosylation site was found in the disintegrin domain. 28244757 5 5 gly glycopeptide 789:800 arg2 a new high-fidelity pattern-searching and glycopeptide validation algorithm a new high-fidelity pattern-searching and glycopeptide validation algorithm glycopeptide The effort was enabled by a new high-fidelity pattern-searching and glycopeptide validation algorithm termed IsoStamp v2.0, as well as by novel stable isotope probes. 28328971 4 50 part_of proteins 607:614 arg1 242 glycosites proteins 242 glycosites Fterm Site proteins glycosites A total of 242 glycosites from 191 unique proteins was discovered. 24417605 3 69 gly glycopeptides 404:416 arg2 glycopeptides glycopeptides glycopeptides N-Glycans, glycopeptides, and gangliosides were extracted and purified followed by analysis with nano-HPLC Chip quadrupole time of flight mass spectrometry and MS/MS. 25551295 2 79 gly glycoprotein 503:514 arg1 the glycoprotein the glycoprotein Fterm glycoprotein Attempts to characterize the structure-activity relationship of each N-glycan are hindered by inherent properties of the glycoprotein, including glycan conformational and compositional heterogeneity. 24234447 5 51 gly glycoproteins 985:997 arg1 400 glycoproteins 400 glycoproteins Fterm glycoproteins For the first release over 890 references, 3740 glycan structure entries and 400 glycoproteins have been curated. 24393138 1 2 gly glycopeptides 227:239 arg2 proteolytic glycopeptides proteolytic glycopeptides glycopeptides Glycans are important modulators of the biological function of proteins and are normally characterized from proteolytic glycopeptides or from (N-)glycans released enzymatically by glycosidase treatment or chemically by hydrazinolysis. 28258464 9 97 gly glycopeptides 1427:1439 arg2 4514 intact glycopeptides 4514 intact glycopeptides glycopeptides We identified 4514 intact glycopeptides coming from 947 glycosites and 1011 unique peptide sequences from HepG2 cells. 28258464 9 106 gly glycosites 1457:1466 arg2 947 glycosites 947 glycosites glycosites We identified 4514 intact glycopeptides coming from 947 glycosites and 1011 unique peptide sequences from HepG2 cells. 26921321 3 9 gly glycoprotein 605:616 arg1 glycoprotein trimerization glycoprotein trimerization Fterm glycoprotein It is then followed by a repetitive collagen-like neck bearing a globular head (C-terminal domain) that promotes glycoprotein trimerization. 27569415 6 48 gly glycosylation 1231:1243 arg1 a previously uncharacterized non-mAb protein therapeutic a previously uncharacterized non-mAb protein therapeutic Fterm protein This methodology was used to comprehensively identify and quantify glycosylation, degradation, unexpected post-translational modifications, and three types of sequence variants in a previously uncharacterized non-mAb protein therapeutic expressed in approximately 100 clones from three host cell lines. 27569415 6 48 gly glycosylation 1231:1243 arg1 sequence variants sequence variants Fterm variants This methodology was used to comprehensively identify and quantify glycosylation, degradation, unexpected post-translational modifications, and three types of sequence variants in a previously uncharacterized non-mAb protein therapeutic expressed in approximately 100 clones from three host cell lines. 28905229 7 27 gly sialylation 1755:1765 arg1 plasma protein N-glycans plasma protein N-glycans RESULTS Individuals with increased risk for diabetes type 2 development (AcuteInflammation and AcuteInflammation Replication populations), incident cases of type 2 diabetes collected at baseline (FinRisk population) and individuals with elevated HbA1c (ORCADES and SABRE populations) all presented with increased branching, galactosylation and sialylation of plasma protein N-glycans and these changes were of similar magnitude. 28737213 5 34 gly N-glycoproteins 785:799 arg1 the identified N-glycoproteins the identified N-glycoproteins Fterm N-glycoproteins Furthermore, insights into the role of N-glycosylation in B. braunii were gained from functional annotation of the identified N-glycoproteins. 26156869 1 14 gly glycoproteins 187:199 arg1 glycoproteins glycoproteins Fterm glycoproteins Enzymes that affect glycoproteins of the human immune system, and thereby modulate defense responses, are abundant among bacterial pathogens. 29125207 2 25 gly asparagine-linked 401:417 arg1 an asparagine-linked glycoprotein glycan asparagine an asparagine-linked glycoprotein glycan asparagine These derivatives correspond to the core structure of an asparagine-linked glycoprotein glycan with a β-mannose unit of a non-natural-type monosaccharide, including β-glucose, β-galactose, and β-talose in place of the β-mannose moiety. 29125207 2 31 gly glycoprotein 419:430 arg1 an asparagine-linked glycoprotein glycan an asparagine-linked glycoprotein glycan These derivatives correspond to the core structure of an asparagine-linked glycoprotein glycan with a β-mannose unit of a non-natural-type monosaccharide, including β-glucose, β-galactose, and β-talose in place of the β-mannose moiety. 25658763 4 52 gly less-glycosylated 822:838 arg1 highly- and less-glycosylated proteins highly- and less-glycosylated proteins Fterm proteins After the purification of highly- and less-glycosylated proteins respectively, the impacts of different glycosylation forms on the pro-inflammatory effects of EMMPRIN were examined in various aspects, such as cell adhesion to endothelial cells, cell migrations, cytokine expression, and activation of inflammatory signalling pathway. 24854630 11 53 gly glycoprotein 1849:1860 arg1 prostate cancer specific glycoprotein biomarkers prostate cancer specific glycoprotein biomarkers Fterm glycoprotein Alterations of O-linked glycosylation could be important in prostate cancer biology and could provide a new avenue for development of prostate cancer specific glycoprotein biomarkers. 27151270 6 51 gly observed 946:953 arg1 each site AND Glycan microheterogeneity each site Glycan microheterogeneity site Glycan microheterogeneity was observed at each site. 25449758 7 16 gly glycosylation 1096:1108 arg2 an engineered glycosylation motif an engineered glycosylation motif motif Finally, glycopeptide mass spectrometry confirmed the transfer of the assembled glycan moiety onto an engineered glycosylation motif of recombinant maltose binding protein. 25449758 7 31 gly glycopeptide 992:1003 arg2 glycopeptide mass spectrometry glycopeptide mass spectrometry glycopeptide Finally, glycopeptide mass spectrometry confirmed the transfer of the assembled glycan moiety onto an engineered glycosylation motif of recombinant maltose binding protein. 25113421 7 27 gly glycopeptides 920:932 arg2 intact glycopeptides intact glycopeptides glycopeptides The other approach produces spectra directly from intact glycopeptides. 28328971 0 60 gly glycosites 21:30 arg2 the N-linked glycosites the N-linked glycosites glycosites Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos. 25824821 7 11 gly structure 870:878 arg1 the constant domain 3 the constant domain 3 the constant domain 3 Site domain The obligatory glycan was mapped to a single N-linked oligomannose structure in the constant domain 3 (Cε3) of IgE, at asparagine-394 (N394) in human IgE and N384 in mouse. 28960760 4 13 gly Bos 778:780 arg1 the divalent cation cofactor cofactor Bos Fterm cofactor We report native ternary complexes of the retaining glycosyltransferase α-1,3-galactosyltransferase (α3GalT) from Bos taurus, which contains such a nucleophile in the active site, in a productive mode for catalysis in the presence of its sugar donor UDP-Gal, the acceptor substrate lactose, and the divalent cation cofactor. 27223297 7 63 gly N-glycosylated 1042:1055 arg1 Gc N794 N794, N1035, and N1077 N794, N1035, and N1077 Results showed that Gc N794, N1035, and N1077 were N-glycosylated but N829 was not. 27223297 7 63 gly N-glycosylated 1042:1055 arg1 N1035 N794, N1035, and N1077 N794, N1035, and N1077 Results showed that Gc N794, N1035, and N1077 were N-glycosylated but N829 was not. 27223297 7 63 gly N-glycosylated 1042:1055 arg1 N1035 N794, N1035, and N1077 N794, N1035, and N1077 Results showed that Gc N794, N1035, and N1077 were N-glycosylated but N829 was not. 29145098 4 57 gly used 1069:1072 arg2 The sialylglycopeptide The sialylglycopeptide sialylglycopeptide The sialylglycopeptide (SGP) of the complex type was used to demonstrate that QMERSIL facilitates the relative quantitation over a linear dynamic range (up to d0/d8=0.02:20) of 3 orders of magnitude. 29145098 4 44 gly sialylglycopeptide 1020:1037 arg2 The sialylglycopeptide sialylglycopeptide the complex type sialylglycopeptide The sialylglycopeptide (SGP) of the complex type was used to demonstrate that QMERSIL facilitates the relative quantitation over a linear dynamic range (up to d0/d8=0.02:20) of 3 orders of magnitude. 28445724 6 19 gly deglycosylated 1164:1177 arg1 site-selective deglycosylated trimers site-selective deglycosylated trimers Fterm trimers 100616444 Based on these high titers and exponential relationship, we propose site-selective deglycosylated trimers as priming immunogens to increase the frequency of site-targeting antibodies. 26232512 4 43 gly α1,2-fucosylation 774:790 arg1 cell-surface glycans cell-surface glycans In conclusion, our data are the first to identify HIF-1α as a suppressor of FUT1/2 expression, thereby regulating α1,2-fucosylation of cell-surface glycans. 29085933 2 12 part_of proteins 305:312 arg1 asparagine residues proteins asparagine residues Fterm AminoAcid proteins asparagine residues N-Glycans, which are attached to asparagine residues of proteins, are studied most often due to their compatibility with enzymatic release. 26663535 4 25 gly glycopeptide 656:667 arg2 glycopeptide glycopeptide glycopeptide Such patterns could be used to distinguish between glycopeptide structural isomers. 25016576 2 10 part_of gp120 472:476 arg1 the first and second variable (V1/V2) domain gp120 the first and second variable (V1/V2) domain PUBTATOR Site gp120 Q14624 domain These were recovered from HIV-1 infected subjects, and several (e.g., PG9, PG16, CH01, CH03) target glycans in the first and second variable (V1/V2) domain of gp120. 26156869 2 53 gly immunoglobulin 460:473 arg1 N-linked glycans immunoglobulin G N-linked glycans Fterm immunoglobulin G Two endoglycosidases from the human pathogen Streptococcus pyogenes, EndoS and EndoS2, have recently been shown to hydrolyze N-linked glycans of human immunoglobulin G. However, detailed characterization and comparison of the hydrolyzing activities have not been performed. 26248080 4 5 gly glycoprotein 549:560 arg1 glycoprotein galectin-3 binding protein glycoprotein galectin-3 binding protein Fterm glycoprotein The glycoprotein galectin-3 binding protein (LGALS3BP) was strongly enriched in EVs and it contained sialylated complex N-glycans. 26248080 4 56 gly sialylated 646:655 arg1 sialylated complex N-glycans sialylated complex N-glycans The glycoprotein galectin-3 binding protein (LGALS3BP) was strongly enriched in EVs and it contained sialylated complex N-glycans. 24621270 0 19 gly heterogeneity 69:81 arg1 plant cell-wall matrix glycans plant cell-wall matrix glycans Epitope detection chromatography: a method to dissect the structural heterogeneity and inter-connections of plant cell-wall matrix glycans. 27938679 7 10 gly glycosylated 1078:1089 arg1 the asparagine residues N256 and N271 asparagine residues N256 and N271 asparagine residues N256 and N271 The increase of electrophoretic mobility of EnvA256 and EnvA271 derived SU showed that the asparagine residues N256 and N271 were also glycosylated. 27938679 7 10 gly glycosylated 1078:1089 arg1 N271 asparagine residues N256 and N271 asparagine residues N256 and N271 The increase of electrophoretic mobility of EnvA256 and EnvA271 derived SU showed that the asparagine residues N256 and N271 were also glycosylated. 27938679 7 10 gly glycosylated 1078:1089 arg1 N271 asparagine residues N256 and N271 asparagine residues N256 and N271 The increase of electrophoretic mobility of EnvA256 and EnvA271 derived SU showed that the asparagine residues N256 and N271 were also glycosylated. 25552259 9 3 gly heterogeneity 1241:1253 arg1 the GPC N-glycans the GPC N-glycans The results obtained indicate structural heterogeneity of the GPC N-glycans and show the existence of structural elements not found in glycophorin A N-glycans. 26565680 2 51 gly microheterogeneity 467:484 arg1 glycans glycans Several research groups have demonstrated that mass spectrometry is an efficient technique for glycopeptide identification; however, this problem is still challenging because of the enormous diversity of glycan structures and the microheterogeneity of glycans. 26565680 2 51 gly microheterogeneity 467:484 arg1 glycan structures glycan structures Several research groups have demonstrated that mass spectrometry is an efficient technique for glycopeptide identification; however, this problem is still challenging because of the enormous diversity of glycan structures and the microheterogeneity of glycans. 26565680 2 57 gly glycopeptide 332:343 arg2 glycopeptide identification glycopeptide identification glycopeptide Several research groups have demonstrated that mass spectrometry is an efficient technique for glycopeptide identification; however, this problem is still challenging because of the enormous diversity of glycan structures and the microheterogeneity of glycans. 27791356 0 38 gly Glycosylation 24:36 arg1 Mucus Glycoproteins Mucus Glycoproteins Fterm Glycoproteins Secondary Structure and Glycosylation of Mucus Glycoproteins by Raman Spectroscopies. 27864768 4 2 gly N-glycosylation 656:670 arg2 numerous potential N-glycosylation sites numerous potential N-glycosylation sites sites In this respect, plant hormone receptors are an interesting group of proteins as several of these proteins are present at distinct sites in the secretory pathway or at the plasma membrane and have numerous potential N-glycosylation sites. 27259834 1 8 gly glycoproteins 233:245 arg1 disease-related glycoproteins disease-related glycoproteins Fterm glycoproteins BACKGROUND Production of various mucin-like glycoproteins could be useful for development of antibodies specific to disease-related glycoproteins as well as for the biosynthesis of clinically useful glycoproteins. 27259834 1 63 gly glycoproteins 145:157 arg1 various mucin-like glycoproteins various mucin-like glycoproteins Fterm glycoproteins BACKGROUND Production of various mucin-like glycoproteins could be useful for development of antibodies specific to disease-related glycoproteins as well as for the biosynthesis of clinically useful glycoproteins. 27259834 1 65 gly glycoproteins 300:312 arg1 clinically useful glycoproteins clinically useful glycoproteins Fterm glycoproteins BACKGROUND Production of various mucin-like glycoproteins could be useful for development of antibodies specific to disease-related glycoproteins as well as for the biosynthesis of clinically useful glycoproteins. 28188786 7 49 gly glycosylation 1173:1185 arg2 the glycosylation sequon the glycosylation sequon sequon Moreover, in the condition of inserting the glycosylation sequon in the loop of FN3 (the acceptor sequon with local structural conformation), the glycosylation efficiency was increased from 35% to 80% by our optimized auto-induction procedures. 28188786 7 80 gly FN3 1209:1211 arg1 the acceptor sequon the acceptor sequon sequon Moreover, in the condition of inserting the glycosylation sequon in the loop of FN3 (the acceptor sequon with local structural conformation), the glycosylation efficiency was increased from 35% to 80% by our optimized auto-induction procedures. 26791533 7 4 gly glycopeptides 971:983 arg2 243 glycopeptides 243 glycopeptides glycopeptides We have elucidated glycan compositions and proposed structures for 243 glycopeptides belonging to 73 N-glycosylation sites on 50 glycoproteins. 26791533 7 32 gly N-glycosylation 1001:1015 arg2 73 N-glycosylation sites 73 N-glycosylation sites sites We have elucidated glycan compositions and proposed structures for 243 glycopeptides belonging to 73 N-glycosylation sites on 50 glycoproteins. 26791533 7 56 gly glycoproteins 1029:1041 arg1 50 glycoproteins 50 glycoproteins Fterm glycoproteins We have elucidated glycan compositions and proposed structures for 243 glycopeptides belonging to 73 N-glycosylation sites on 50 glycoproteins. 24702330 1 9 gly glycosylation 100:112 arg2 chemically defined glycosylation sites chemically defined glycosylation sites sites Glycoproteins with chemically defined glycosylation sites and structures are important biopharmaceutical targets and critical tools for glycobiology. 27412689 7 96 part_of proteins 1358:1365 arg1 these tissue regions proteins these tissue regions Fterm Site proteins regions The N-linked glycan repertoires carried by the proteins in these tissue regions were structurally characterized for the first time in FFPE ovarian cancer tissue regions, using enzymatic peptide-N-glycosidase F (PNGase F) release of N-glycans. 25251695 1 9 gly glycoproteins 262:274 arg1 newly synthesized glycoproteins newly synthesized glycoproteins Fterm glycoproteins 6400 N-glycosylation of proteins plays an important role in the determination of the fate of newly synthesized glycoproteins in the endoplasmic reticulum (ER). 25251695 1 35 gly N-glycosylation 156:170 arg1 proteins proteins Fterm proteins 6400 N-glycosylation of proteins plays an important role in the determination of the fate of newly synthesized glycoproteins in the endoplasmic reticulum (ER). 26578555 8 38 gly lectin-glycoprotein 1060:1078 arg1 a glycan-mediated protein-protein interaction lectin-glycoprotein a glycan-mediated protein-protein interaction Fterm lectin-glycoprotein Thus, a glycan-lectin binding pair of SugarBindDB can lead to the identification of a glycan-mediated protein-protein interaction, that is, a lectin-glycoprotein interaction, via substructure search and the knowledge of site-specific glycosylation stored in UniCarbKB. 25978763 5 28 gly glycopeptides 1052:1064 arg2 N-linked glycopeptides N-linked glycopeptides glycopeptides However, the carbamidomethylation of Met residues leads to sulfonium ether formation, and the resulting fixed positive charge triggers a characteristic fragmentation, that eliminates the normal Y1 fragment from the HCD spectra of N-linked glycopeptides, producing an abundant Y1-48 Da ion instead (the nominal mass difference is given relative to the unmodified amino acid sequence), that easily can be mistaken for the side chain loss from Met sulfoxide. 26863921 3 11 gly glycoprotein 620:631 arg1 the seven putative S-layer glycoprotein N-glycosylation sites the seven putative S-layer glycoprotein N-glycosylation sites Fterm glycoprotein In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 19 gly N-glycosylation 633:647 arg2 the seven putative S-layer glycoprotein N-glycosylation sites the seven putative S-layer glycoprotein N-glycosylation sites sites In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 25 gly attached 564:571 arg2 the seven putative S-layer glycoprotein N-glycosylation sites AND this glycan the seven putative S-layer glycoprotein N-glycosylation sites this glycan sites In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 19 gly N-glycosylation 633:647 arg2 Asn-83 Asn-13, Asn-83, Asn-274 and Asn-279 Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 19 gly N-glycosylation 633:647 arg2 Asn-274 Asn-13, Asn-83, Asn-274 and Asn-279 Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 19 gly N-glycosylation 633:647 arg2 Asn-13 Asn-13, Asn-83, Asn-274 and Asn-279 Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 19 gly N-glycosylation 633:647 arg2 Asn-274 Asn-13, Asn-83, Asn-274 and Asn-279 Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 19 gly N-glycosylation 633:647 arg2 Asn-13 Asn-13, Asn-83, Asn-274 and Asn-279 Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 19 gly N-glycosylation 633:647 arg2 Asn-13 Asn-13, Asn-83, Asn-274 and Asn-279 Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 25 gly attached 564:571 arg2 Asn-279 AND this glycan Asn-13, Asn-83, Asn-274 and Asn-279 this glycan Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 25 gly attached 564:571 arg2 Asn-83 AND this glycan Asn-13, Asn-83, Asn-274 and Asn-279 this glycan Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 25 gly attached 564:571 arg1 Asn-274 AND this glycan Asn-13, Asn-83, Asn-274 and Asn-279 this glycan Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 25 gly attached 564:571 arg2 Asn-83 AND this glycan Asn-13, Asn-83, Asn-274 and Asn-279 this glycan Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 25 gly attached 564:571 arg1 Asn-274 AND this glycan Asn-13, Asn-83, Asn-274 and Asn-279 this glycan Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 25 gly attached 564:571 arg1 Asn-274 AND this glycan Asn-13, Asn-83, Asn-274 and Asn-279 this glycan Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26599081 9 51 gly glycoproteins 1254:1266 arg1 N-linked glycoproteins N-linked glycoproteins Fterm glycoproteins As far as we are aware, N-linked glycoproteins have not been previously described in Gram-positive bacteria, the organisms to which the mycoplasmas are phylogenetically related. 28486782 2 51 gly glycosylated 223:234 arg1 The extracellular domain EGFR domain PUBTATOR EGFR 1956 domain The extracellular domain of EGFR is known to be heavily glycosylated. 25753710 4 15 part_of sites 552:556 arg1 proteins proteins sites Fterm Site proteins sites It centers on a glycan structure database and accumulates information such as glycan preferences of lectins, glycosylation sites in proteins, and genes related to glycan syntheses from glycoscience and related fields. 25759508 3 42 part_of IgG3 425:428 arg1 the IgG3 hinge region IgG3 the IgG3 hinge region PUBTATOR Site IgG3 P01860 region This study reports partial O-glycosylation of the IgG3 hinge region, observed with nanoLC-ESI-IT-MS(/MS) analysis after proteolytic digestion. 24975648 9 48 part_of β-mannosidase 1434:1446 arg1 The T. harzianum β-mannosidase 2A nucleotide sequence β-mannosidase The T. harzianum β-mannosidase 2A nucleotide sequence Fterm Site β-mannosidase sequence The T. harzianum β-mannosidase 2A nucleotide sequence has GenBank accession number BankIt1712036 GeneMark.hmm KJ624918. 24975648 9 64 part_of 2A 1448:1449 arg1 The T. harzianum β-mannosidase 2A nucleotide sequence 2A The T. harzianum β-mannosidase 2A nucleotide sequence Cterm Site 2A sequence The T. harzianum β-mannosidase 2A nucleotide sequence has GenBank accession number BankIt1712036 GeneMark.hmm KJ624918. 24702330 4 34 gly N-glycosylation 499:513 arg2 the natural Fc N-glycosylation sequon the natural Fc N-glycosylation sequon sequon We replaced the natural Fc N-glycosylation sequon with a five amino-acid sequence that was efficiently converted by recombinant formylglycine generating enzyme in vitro, thereby introducing aldehyde groups for subsequent chemical elaboration. 28199092 4 31 gly glycosylation 1096:1108 arg2 two distinct N-linked glycosylation sites two distinct N-linked glycosylation sites sites In this paper we describe the application of an MAM based method for site specific quantification of N-linked glycan heterogeneity present on an IgG1 mAb molecule containing two distinct N-linked glycosylation sites: one present on the heavy chain (HC) variable region (Fab) and the other present on the conserved HC constant region (Fc). 28199092 4 24 gly describe 917:924 arg1 one present on the heavy chain (HC) variable region region region In this paper we describe the application of an MAM based method for site specific quantification of N-linked glycan heterogeneity present on an IgG1 mAb molecule containing two distinct N-linked glycosylation sites: one present on the heavy chain (HC) variable region (Fab) and the other present on the conserved HC constant region (Fc). 26791533 10 76 gly glycoproteins 1365:1377 arg1 multiple seminal plasma glycoproteins multiple seminal plasma glycoproteins Fterm glycoproteins Many Lewis x/a and y/b epitopes bearing glycans were found, suggesting immune-modulating epitopes on multiple seminal plasma glycoproteins. 25230686 6 4 part_of GnTI 996:999 arg1 the stem region GnTI the stem region OGER Site GnTI P26572 region By contrast, the stem region of GnTI contributes predominately to homomeric and heteromeric protein complex formation. 24682362 4 73 gly glycosylation 1175:1187 arg1 asparagine 85 asparagine 85 asparagine 85 The structures of three unliganded forms of S25-26 have a labile complementary-determining region H3 adjacent to significant glycosylation of the variable heavy chain on asparagine 85 in Framework Region 3. 28729420 8 44 gly fucosylation 1653:1664 arg1 N-glycans N-glycans This study represents the first report of in vitro FUT8-catalyzed core fucosylation of N-glycans lacking the α1,3-arm GlcNAc moiety. 27956708 5 22 gly glycopeptide 921:932 arg2 the glycopeptide level the glycopeptide level glycopeptide The Fc-glycosylation of ACPA-IgG and IgG was analyzed at the glycopeptide level using LC-MS. 27020775 0 42 gly glycosylation 30:42 arg1 donkey milk lactoferrin lactoferrin sites PUBTATOR lactoferrin P02788 sites Sequence characterization and glycosylation sites identification of donkey milk lactoferrin by multiple enzyme digestions and mass spectrometry. 28199092 6 37 gly glycopeptides 1386:1398 arg2 the glycopeptides the glycopeptides glycopeptides The ionization properties of the glycopeptides with different classes of glycan structural variants, including high mannose, sialylated, and terminal galactosylated species were studied in detail. 26075384 12 46 gly spectrometry 2004:2015 arg1 average compositions average compositions positions To visualize the differences between serous and mucinous ovarian tumors based on the O-glycosylation, a hierarchical cluster analysis was performed using mass spectrometry average compositions (MSAC). 29268168 4 23 part_of found 727:731 arg2 mFcγRIV AND the N162 glycosylation site mFcγRIV the N162 glycosylation site PUBTATOR Site FcγRIV 246256 site Here we report that the N162 glycosylation site is also found in the orthologous mouse FcγR, mFcγRIV. 28221766 6 60 gly glycans 1222:1228 arg1 the N-terminal region the N-terminal region the N-terminal region Site region Our study provides a detailed specification, validation, and quantification of 15 co-occurring C9 proteoforms and the first direct experimental evidence of O-linked glycans in the N-terminal region. 24747898 2 64 gly glycans 370:376 arg1 cellobiohydrolase I cellobiohydrolase I glycans Fterm cellobiohydrolase I We investigated the significance of the three N-linked glycans on the catalytic domain of cellobiohydrolase I (CBH1) from the filamentous fungus Trichoderma reesei in its secretion and activity. 24747898 2 64 gly glycans 370:376 arg1 the catalytic domain the catalytic domain the catalytic domain Site domain We investigated the significance of the three N-linked glycans on the catalytic domain of cellobiohydrolase I (CBH1) from the filamentous fungus Trichoderma reesei in its secretion and activity. 29274340 8 48 gly glycosylation 1736:1748 arg2 three M6P glycosylation sites three M6P glycosylation sites sites The glycopeptides obtained from protease-digested rhGAA were analyzed using nano-LC-ESI-HCD-MS/MS, and the extracted-ion chromatograms of M6P-derived oxonium ions confirmed three M6P glycosylation sites comprising Asn 140, Asn 233 (newly found), and Asn 470 attached heterogeneously to nine M6P glycans (two types), eight M6P glycans (four types), and seven M6P glycans (two types), respectively. 29274340 8 71 gly glycopeptides 1557:1569 arg2 The glycopeptides The glycopeptides glycopeptides The glycopeptides obtained from protease-digested rhGAA were analyzed using nano-LC-ESI-HCD-MS/MS, and the extracted-ion chromatograms of M6P-derived oxonium ions confirmed three M6P glycosylation sites comprising Asn 140, Asn 233 (newly found), and Asn 470 attached heterogeneously to nine M6P glycans (two types), eight M6P glycans (four types), and seven M6P glycans (two types), respectively. 28696719 11 22 gly N-glycosites 1278:1289 arg2 previously unreported N-glycosites previously unreported N-glycosites N-glycosites Noteworthy, previously unreported N-glycosites within domain D'(TIL'-E') showed glycosylation. 28489325 0 16 part_of EGF-Like 100:107 arg1 the Lectin and EGF-Like Domains EGF the Lectin and EGF-Like Domains OGER EGF P01133 Reducing Macro- and Microheterogeneity of N-Glycans Enables the Crystal Structure of the Lectin and EGF-Like Domains of Human L-Selectin To Be Solved at 1.9 Å Resolution. 28489325 0 42 part_of L-Selectin 126:135 arg1 the Lectin and EGF-Like Domains Human L-Selectin the Lectin and EGF-Like Domains PUBTATOR Human L-Selectin 6402 Reducing Macro- and Microheterogeneity of N-Glycans Enables the Crystal Structure of the Lectin and EGF-Like Domains of Human L-Selectin To Be Solved at 1.9 Å Resolution. 24308717 9 73 gly O-glycopeptides 1468:1482 arg2 the O-glycopeptides the O-glycopeptides O-glycopeptides α2→3,6,8,9 sialidase was used to remove the sialic acid residues on the O-glycans allowing the use of an automated LC/MS(E) protocol to identify the O-glycopeptides. 25927005 0 28 gly proteins 74:81 arg1 insect and Mammalian cells proteins insect and Mammalian cells Fterm proteins The role of HCV e2 protein glycosylation in functioning of virus envelope proteins in insect and Mammalian cells. 25927005 0 151 gly glycosylation 27:39 arg1 virus envelope proteins virus envelope proteins Fterm proteins The role of HCV e2 protein glycosylation in functioning of virus envelope proteins in insect and Mammalian cells. 26797772 3 55 part_of has 487:489 arg1 TNSALP AND five potential N-glycosylation sites TNSALP five potential N-glycosylation sites PUBTATOR Site TNSALP 249 sites TNSALP has five potential N-glycosylation sites at N140, N230, N271, N303 and N430 by standard nomenclature. 27111718 4 74 gly glycopeptides 753:765 arg2 intact glycopeptides intact glycopeptides glycopeptides Complete characterization of protein glycosylation requires the identification of intact glycopeptides in samples, including identification of the modification site as well as the structure of the attached glycans. 26791533 2 26 gly glycoproteins 346:358 arg1 seminal plasma glycoproteins seminal plasma glycoproteins Fterm glycoproteins Epitopes such as Lewis x and y are known to be present on seminal plasma glycoproteins, which can modulate the maternal immune response. 26791533 2 31 gly present 320:326 arg2 seminal plasma glycoproteins AND Lewis x glycoproteins Lewis x Fterm glycoproteins Epitopes such as Lewis x and y are known to be present on seminal plasma glycoproteins, which can modulate the maternal immune response. 29285644 5 9 gly glycopeptides 1041:1053 arg2 site-specific glycopeptides site-specific glycopeptides glycopeptides Serum haptoglobin enriched by immunoaffinity chromatography was subjected to multispecific proteolysis to generate site-specific glycopeptides and to investigate the macroheterogeneity and microheterogeneity. 25660649 10 0 gly asparagine 1432:1441 arg1 high mannose-type structures asparagine 67 high mannose-type structures asparagine 67 Predominant glycoforms at asparagine 67 are high mannose-type structures while mainly complex- and hybrid-type structures are detected at asparagine 153. 25660649 10 24 gly detected 1532:1539 arg2 asparagine 153 AND complex- and hybrid-type structures asparagine 153 complex- and hybrid-type structures asparagine 153 Predominant glycoforms at asparagine 67 are high mannose-type structures while mainly complex- and hybrid-type structures are detected at asparagine 153. 25660649 10 96 gly glycoforms 1418:1427 arg2 asparagine 67 asparagine 67 asparagine 67 Predominant glycoforms at asparagine 67 are high mannose-type structures while mainly complex- and hybrid-type structures are detected at asparagine 153. 27573070 2 49 gly glycopeptides 488:500 arg2 glycopeptides glycopeptides glycopeptides The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to the development of proteome informatics tools that facilitate the MS analysis of glycans and glycopeptides. 27573070 2 61 gly glycosylation 284:296 arg2 glycosylation sites glycosylation sites sites The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to the development of proteome informatics tools that facilitate the MS analysis of glycans and glycopeptides. 27573070 2 65 gly glycoprotein 267:278 arg1 glycoprotein glycoprotein Fterm glycoprotein The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to the development of proteome informatics tools that facilitate the MS analysis of glycans and glycopeptides. 26916835 4 66 gly protein 588:594 arg1 glucosamine protein glucosamine Fterm protein RESULTS GC-SPI contained glucosamine of 13.6 g kg-1 protein, but less reactable &bond;NH2 than SPI (0.42 vs. 0.50 mol kg-1 protein). 28177314 5 41 gly glycoproteins 1052:1064 arg1 glycoproteins glycoproteins Fterm glycoproteins With structural glycoscience finally gaining popularity and steadily increasing the deposition rate of three-dimensional structures of glycoproteins, the need for a clear way of depicting these interactions is more pressing than ever. 25614628 1 23 gly glycoproteins 281:293 arg1 glycoproteins glycoproteins Fterm glycoproteins Peptide:N-glycosidase (PNGase) F, the first PNGase identified in prokaryotic cells, catalyzes the removal of intact asparagine-linked oligosaccharide chains from glycoproteins and/or glycopeptides. 25614628 1 37 gly glycopeptides 302:314 arg2 glycopeptides glycopeptides glycopeptides Peptide:N-glycosidase (PNGase) F, the first PNGase identified in prokaryotic cells, catalyzes the removal of intact asparagine-linked oligosaccharide chains from glycoproteins and/or glycopeptides. 25614628 1 62 gly asparagine-linked 235:251 arg1 intact asparagine-linked oligosaccharide chains asparagine intact asparagine-linked oligosaccharide chains asparagine Peptide:N-glycosidase (PNGase) F, the first PNGase identified in prokaryotic cells, catalyzes the removal of intact asparagine-linked oligosaccharide chains from glycoproteins and/or glycopeptides. 26630650 5 101 part_of enzyme 571:576 arg1 The amino acid sequence enzyme The amino acid sequence Fterm Site enzyme sequence The amino acid sequence of the enzyme was determined by cDNA analysis of the venom gland transcriptome and confirmed by protein analysis. 29212317 6 32 gly glycoproteins 959:971 arg1 glycoproteins glycoproteins Fterm glycoproteins Apolipoprotein CIII, fetuin A, and alpha 1 antitrypsin are glycoproteins associated with lipoproteins and are implicated in many cardiovascular and other disease conditions. 24997456 1 2 gly glycoprotein 169:180 arg1 Proteoglycan 4 glycoprotein Proteoglycan 4 Fterm glycoprotein Proteoglycan 4 (PRG4, or lubricin) is a lubricating mucin-like glycoprotein recently discovered at the ocular surface, where it functions as a boundary lubricant and appears to play a protective role. 24798328 0 81 gly O-glycosylated 53:66 arg1 Low density lipoprotein receptor class A repeats regions Low density lipoprotein receptor class A repeats regions Low density lipoprotein receptor class A repeats are O-glycosylated in linker regions. 28928219 8 85 part_of protein 1714:1720 arg1 a disordered region protein a disordered region Fterm Site protein region These results offer an unprecedented view of how a glycan modification influences a disordered region of a full-length protein. 25124036 2 97 part_of proteins 312:319 arg1 The trefoil factor peptides proteins The trefoil factor peptides Fterm Site proteins peptides The trefoil factor peptides are a family of small highly conserved proteins that are claimed to play essential roles in cytoprotection and epithelial repair within the gastrointestinal tract. 28696719 12 69 gly sialylated 1349:1358 arg1 sialylated core 1 and core 2 O-glycans sialylated core 1 and core 2 O-glycans Moreover, sialylated core 1 and core 2 O-glycans were detected on 2298T. 28752594 5 25 gly glycoproteins 767:779 arg1 serum glycoproteins serum glycoproteins Fterm glycoproteins Only 2 μL of serum from individual patients was used in this assay where the N-glycome of serum glycoproteins was profiled by DNA sequencer-assisted fluorophore-assisted capillary electrophoresis (DSA-FACE) technology. 24685714 2 50 part_of domain 519:524 arg1 the Pro-rich domain domain the Pro-rich domain domain AGP31 displays different O-glycosylation patterns with arabinogalactans on the AGP domain and Hyp-O-Gal/Ara-rich motifs on the Pro-rich domain. 27254475 2 29 gly glycoproteins 363:375 arg1 glycoproteins glycoproteins Fterm glycoproteins Media components and cell culture conditions have been shown to significantly affect N-linked glycosylation during the production of glycoproteins using mammalian cell fed-batch cultures. 27161092 6 64 gly α1,2-fucosylated 1074:1089 arg1 α1,2-fucosylated structures α1,2-fucosylated structures Our results demonstrated that the FUT2 determines the O-glycosylation pattern of Muc5ac, with Fut2 knock-out leading to a marked decrease in α1,2-fucosylated structures and increased expression of the terminal type 1 glycan structure Lewis-a. 26082235 2 70 gly presence 256:263 arg1 the Fc domain AND the conserved N-glycans the Fc domain the conserved N-glycans domain Compelling data have shown that the presence and fine structures of the conserved N-glycans at the Fc domain can profoundly affect the effector functions of antibodies. 25016576 8 52 part_of gp120 1564:1568 arg1 the gp120 V1/V2 domain gp120 the gp120 V1/V2 domain PUBTATOR Site gp120 Q14624 domain Epitope mapping using glycopeptide fragments and in vitro mutagenesis showed that binding of this antibody depends on N-linked glycosylation at asparagine N130 (HXB2 numbering) in the gp120 V1/V2 domain. 25036289 6 77 part_of Fc 1010:1011 arg1 each Fc CH2 domain Fc each Fc CH2 domain Cterm Site Fc domain In particular, the anti-inflammatory activity of intravenous IgG is ascribed to a small population of IgGs in which the Asn297-linked complex N-glycans attached to each Fc CH2 domain include terminal α2,6-linked sialic acids. 25253346 14 146 gly glycoproteins 2247:2259 arg1 envelope surface glycoproteins envelope surface glycoproteins Fterm glycoproteins IMPORTANCE: Major obstacles to developing an effective HIV-1 vaccine include the variability of the envelope surface glycoproteins and its high-density glycan shield, generated by incorporation of host (human) glycosylation. 25212784 3 48 gly hypersialylated 1025:1039 arg1 biantennary hypersialylated structures biantennary hypersialylated structures We found that the majority of glycans on bovine FF are based on biantennary hypersialylated structures, where the glycans are sialylated on both the galactose and N-acetylglucosamine terminal sugars. 25212784 3 81 gly sialylated 1075:1084 arg1 the glycans the glycans We found that the majority of glycans on bovine FF are based on biantennary hypersialylated structures, where the glycans are sialylated on both the galactose and N-acetylglucosamine terminal sugars. 24473128 2 5 gly glycosylated 249:260 arg1 two heavily glycosylated domains two heavily glycosylated domains domains The GP1 subunit contains two heavily glycosylated domains, the glycan cap and the mucin-like domain (MLD). 28860626 1 38 part_of site 351:354 arg1 neuraminidase neuraminidase site Fterm Site neuraminidase site The outbreak of a pandemic influenza H1N1 in 2009 required the rapid generation of high-yielding vaccines against the A/California/7/2009 virus, which were achieved by either addition or deletion of a glycosylation site in the influenza proteins hemagglutinin and neuraminidase. 28860626 1 38 part_of site 351:354 arg1 the influenza proteins hemagglutinin hemagglutinin site Fterm Site hemagglutinin site The outbreak of a pandemic influenza H1N1 in 2009 required the rapid generation of high-yielding vaccines against the A/California/7/2009 virus, which were achieved by either addition or deletion of a glycosylation site in the influenza proteins hemagglutinin and neuraminidase. 26983412 3 66 gly N-glycans 593:601 arg1 a recently developed S. cerevisiae strain strain N-glycans Fterm strain In this work, we present further improvements in the humanization of the N-glycans in a recently developed S. cerevisiae strain. 28096352 5 42 gly glycoprotein 1163:1174 arg1 glycoprotein degradation glycoprotein degradation Fterm glycoprotein This insight builds upon the paradigm of how peptidases recognize substrates and provides a molecular understanding of glycoprotein degradation. 29085933 6 56 gly sialylated 1565:1574 arg1 sialylated glycans sialylated glycans Of the derivatization strategies examined, RFMS provided the highest MS signal enhancement for neutral glycans, while permethylation significantly enhanced the MS intensity and structural stability of sialylated glycans. 29197583 0 56 gly glycopeptide 147:158 arg2 glycopeptide glycopeptide glycopeptide Evaluation of ion mobility for the separation of glycoconjugate isomers due to different types of sialic acid linkage, at the intact glycoprotein, glycopeptide and glycan level. 29197583 0 78 gly glycoprotein 133:144 arg1 the intact glycoprotein the intact glycoprotein Fterm glycoprotein Evaluation of ion mobility for the separation of glycoconjugate isomers due to different types of sialic acid linkage, at the intact glycoprotein, glycopeptide and glycan level. 26515403 6 6 part_of Typhimurium 962:972 arg1 the Burkholderia cenocepacia and Salmonella enterica serovar Typhimurium ArnT C-terminal domain Typhimurium ArnT the Burkholderia cenocepacia and Salmonella enterica serovar Typhimurium ArnT C-terminal domain OGER Site Typhimurium ArnT P27540 domain We also demonstrate that the Burkholderia cenocepacia and Salmonella enterica serovar Typhimurium ArnT C-terminal domain is required for polymyxin B resistance in vivo. 26515403 6 50 part_of ArnT 974:977 arg1 the Burkholderia cenocepacia and Salmonella enterica serovar Typhimurium ArnT C-terminal domain Typhimurium ArnT the Burkholderia cenocepacia and Salmonella enterica serovar Typhimurium ArnT C-terminal domain OGER Site Typhimurium ArnT P27540 domain We also demonstrate that the Burkholderia cenocepacia and Salmonella enterica serovar Typhimurium ArnT C-terminal domain is required for polymyxin B resistance in vivo. 25638265 2 42 gly released 565:572 arg1 glycoproteins AND labeled N-glycans glycoproteins labeled N-glycans Fterm glycoproteins Porous graphitized carbon (PGC) as stationary phase in capillary scale HPLC coupled to electrospray mass spectrometry with time of flight analyzer was applied for the determination of labeled N-glycans released from glycoproteins. 25638265 2 75 gly glycoproteins 579:591 arg1 glycoproteins glycoproteins Fterm glycoproteins Porous graphitized carbon (PGC) as stationary phase in capillary scale HPLC coupled to electrospray mass spectrometry with time of flight analyzer was applied for the determination of labeled N-glycans released from glycoproteins. 27249581 9 71 gly N-glycoprotein 1585:1598 arg1 N-glycoprotein N-glycoprotein Fterm N-glycoprotein Peracetylation of the monosaccharides substantially increases the strength of the sugar-aromatic interaction in the context of our N-glycoprotein host. 29016103 5 83 gly glycopeptides 730:742 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides Here, we studied three different enrichment methods for enrichment of N- and O-linked glycopeptides. 25230686 5 13 part_of GnTI 895:898 arg1 the transmembrane domain GnTI the transmembrane domain OGER Site GnTI P26572 domain Using co-localization analysis and N-glycan profiling, we show that the transmembrane domain of GnTI is the major determinant for its cis/medial-Golgi localization. 26831718 7 1 gly sialylation 1047:1057 arg1 core-fucosylation core-fucosylation RESULTS We have found that colorectal cancer associates with decrease in IgG galactosylation, IgG sialylation and increase in core-fucosylation of neutral glycans with concurrent decrease of core-fucosylation of sialylated glycans. 26831718 7 17 gly core-fucosylation 1140:1156 arg1 sialylated glycans sialylated glycans RESULTS We have found that colorectal cancer associates with decrease in IgG galactosylation, IgG sialylation and increase in core-fucosylation of neutral glycans with concurrent decrease of core-fucosylation of sialylated glycans. 26831718 7 28 gly sialylated 1161:1170 arg1 sialylated glycans sialylated glycans RESULTS We have found that colorectal cancer associates with decrease in IgG galactosylation, IgG sialylation and increase in core-fucosylation of neutral glycans with concurrent decrease of core-fucosylation of sialylated glycans. 26831718 7 87 gly core-fucosylation 1075:1091 arg1 neutral glycans neutral glycans RESULTS We have found that colorectal cancer associates with decrease in IgG galactosylation, IgG sialylation and increase in core-fucosylation of neutral glycans with concurrent decrease of core-fucosylation of sialylated glycans. 24798328 5 58 gly O-glycosylation 702:716 arg2 O-glycosylation sites O-glycosylation sites sites Herein, we have systematically characterized O-glycosylation sites on recombinant LDLR shed from HEK293 SimpleCells and CHO wild-type cells. 26082214 1 27 part_of glycoproteins 148:160 arg1 asparagine (N) residues glycoproteins asparagine (N) residues Fterm Site glycoproteins residues Glycans linked to asparagine (N) residues of eukaryotic glycoproteins are typically heterogeneous. 25849464 8 115 gly glycosylation 1451:1463 arg2 single glycosylation site single glycosylation site site Recombinant wild-type Lcc4 and mutant enzymes N75D, N238D and N458D were expressed in Pichia pastoris cells to evaluate the effect on enzyme activity by single glycosylation site deficiency. 28104755 1 34 gly glycoprotein 260:271 arg1 a secreted N-linked glycoprotein a secreted N-linked glycoprotein Fterm glycoprotein Sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a recently identified phosphodiesterase, which is a secreted N-linked glycoprotein. 28104755 1 34 gly glycoprotein 260:271 arg1 a recently identified phosphodiesterase a recently identified phosphodiesterase Fterm phosphodiesterase Sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a recently identified phosphodiesterase, which is a secreted N-linked glycoprotein. 26850169 5 45 gly regions 809:815 arg1 afucosylated glycans regions afucosylated glycans regions For example, Fc regions with afucosylated glycans bind more tightly to FcγRIIIa than fucosylated Fc, and afucosylated Fcs exhibit enhanced ADCC activity in vivo and in vitro. 26850169 5 54 gly afucosylated 822:833 arg1 afucosylated glycans afucosylated glycans For example, Fc regions with afucosylated glycans bind more tightly to FcγRIIIa than fucosylated Fc, and afucosylated Fcs exhibit enhanced ADCC activity in vivo and in vitro. 28849661 2 8 gly serine 233:238 arg1 the octasaccharide serine cassette serine the octasaccharide serine cassette serine The sequence of glycosylation to form the octasaccharide serine cassette was critical. 26599081 5 63 gly glycoproteins 776:788 arg1 O-linked glycoproteins O-linked glycoproteins Fterm glycoproteins In the current study, O-linked glycoproteins were similarly found in M. pulmonis and both species of mycoplasma were found to also possess N-linked glycans at residues of asparagine and glutamine. 24326352 4 8 part_of residues 764:771 arg1 dimers dimers residues Fterm AminoAcid dimers residues in In contrast, lectin binding assays, which enable the total amounts of specific sugar residues to be detected, showed that both galactose and fucose residues in dimers and large aggregates were reduced to 70-80% of the amount in monomers. 28880909 5 30 gly glycosylation 953:965 arg1 asparagine (Asn) 52 α-subunit Asn) 52 Fterm α-subunit Asn) 52 The focus of this analysis was the site-specific glycosylation at asparagine (Asn) 52 of the α-subunit of FSH, owing to the pivotal role of Asn52 glycosylation in FSH receptor (FSHR) activation/signalling. 28880909 5 30 gly glycosylation 953:965 arg2 asparagine (Asn) 52 α-subunit Asn) 52 Fterm α-subunit Asn) 52 The focus of this analysis was the site-specific glycosylation at asparagine (Asn) 52 of the α-subunit of FSH, owing to the pivotal role of Asn52 glycosylation in FSH receptor (FSHR) activation/signalling. 28880909 5 30 gly glycosylation 953:965 arg2 asparagine (Asn) 52 Asn) 52 Asn) 52 The focus of this analysis was the site-specific glycosylation at asparagine (Asn) 52 of the α-subunit of FSH, owing to the pivotal role of Asn52 glycosylation in FSH receptor (FSHR) activation/signalling. 28370937 6 48 gly asialylated 681:691 arg1 asialylated or monosialylated biantennary and triantennary N-glycans asialylated or monosialylated biantennary and triantennary N-glycans In contrast, complex-type N-glycans such as asialylated or monosialylated biantennary and triantennary N-glycans were dominant in HLCs, and fully galactosylated structures were significantly more abundant than in undifferentiated hESCs. 28370937 6 60 gly monosialylated 696:709 arg1 asialylated or monosialylated biantennary and triantennary N-glycans asialylated or monosialylated biantennary and triantennary N-glycans In contrast, complex-type N-glycans such as asialylated or monosialylated biantennary and triantennary N-glycans were dominant in HLCs, and fully galactosylated structures were significantly more abundant than in undifferentiated hESCs. 27928741 1 3 gly glycoproteins 230:242 arg1 haemagglutinin-neuraminidase glycoproteins haemagglutinin-neuraminidase glycoproteins Fterm glycoproteins Members of the Avulavirus, Respirovirus and Rubulavirus genera of the Paramyxoviridae family of viruses utilise haemagglutinin-neuraminidase glycoproteins as their attachment proteins. 27928741 1 3 gly glycoproteins 230:242 arg1 their attachment proteins their attachment proteins Fterm proteins Members of the Avulavirus, Respirovirus and Rubulavirus genera of the Paramyxoviridae family of viruses utilise haemagglutinin-neuraminidase glycoproteins as their attachment proteins. 29016103 3 27 gly glycopeptides 540:552 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides To this end, hydrophilic interaction chromatography (HILIC) has been commonly used to enrich intact N- and O-linked glycopeptides. 24511137 3 24 part_of CH1 649:651 arg1 the CH1 domain CH1 the CH1 domain OGER Site CH1 Q8C341 domain Because the levels of O-linked glycosylation in the hinge region and the structures of N-linked glycans in the CH1 domain differ in 6-19 IgA and 46-42 IgA, we determined the respective contributions of O- and N-linked glycans to the nephritogenic potential of the 6-19 IgA rheumatoid factor in mice. 29062024 1 42 part_of IIIa 273:276 arg1 the Fc region Fcγ receptor IIIa the Fc region PUBTATOR Site Fcγ receptor IIIa 2214 region Antibody-dependent cellular cytotoxicity (ADCC) is promoted through interaction between the Fc region of immunoglobulin G1 (IgG1) and Fcγ receptor IIIa (FcγRIIIa), depending on N-glycosylation of these glycoproteins. 29062024 1 78 part_of G1 246:247 arg1 the Fc region G1 (IgG1 the Fc region OGER Site G1 (IgG1 P01857 region Antibody-dependent cellular cytotoxicity (ADCC) is promoted through interaction between the Fc region of immunoglobulin G1 (IgG1) and Fcγ receptor IIIa (FcγRIIIa), depending on N-glycosylation of these glycoproteins. 28696719 4 23 gly occupancy 524:532 arg2 all canonical N-glycosites all canonical N-glycosites N-glycosites Thus, the intention of this exploration was to estimate the occupancy of all canonical N-glycosites besides simultaneous characterization of N- and O-glycoforms. 28696719 4 76 gly N-glycosites 551:562 arg2 all canonical N-glycosites all canonical N-glycosites N-glycosites Thus, the intention of this exploration was to estimate the occupancy of all canonical N-glycosites besides simultaneous characterization of N- and O-glycoforms. 28576848 6 41 gly receptors 1380:1388 arg1 the glycan profiles receptors the glycan profiles Fterm receptors The glycan profiles of CHO expressed FcγRI and FcγRIIIaPhe158/Val158 were compared with the glycan profiles of the receptors expressed in NS0 and HEK293 cells and we show that the glycan type and abundance differs significantly between the receptors and that these glycan differences lead to the observed differences in the respective FcγR binding patterns with rituximab. 29062024 0 3 gly region 76:81 arg1 N-glycan core fucosylation region N-glycan core fucosylation region Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa. 29062024 0 66 gly fucosylation 40:51 arg1 immunoglobulin G Fc region immunoglobulin G Fc region region Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa. 25793890 10 101 gly glycosylation 2113:2125 arg2 glycosylation sites glycosylation sites sites This strategy might improve the efficacy of the vaccines used in the partially successful RV144 HIV vaccine trial, where the two CRF01_AE immunogens (derived from the A244 and TH023 isolates) both possessed glycosylation sites at N136 and N149. 25458834 0 23 gly nonglycosylated 91:105 arg1 nonglycosylated rhodocytin nonglycosylated rhodocytin Fterm rhodocytin A platform of C-type lectin-like receptor CLEC-2 for binding O-glycosylated podoplanin and nonglycosylated rhodocytin. 27722599 9 70 gly fucosylated 1276:1286 arg1 the fucosylated complex type N-glycans the fucosylated complex type N-glycans Additionally, structural analysis via LC/MS/MS indicated that the fucosylated complex type N-glycans were primarily decorated with antenna fucose, which can be categorized as sialyl-Lea or sialyl-Lex type structures. 27629418 2 41 gly core-fucosylated 460:475 arg1 core-fucosylated N-glycans core-fucosylated N-glycans Although Endo-M has been known to act on various N-glycans, it does not act on core-fucosylated N-glycans, which exist widely in mammalian glycoproteins, thus limiting its application. 27629418 2 84 gly glycoproteins 520:532 arg1 mammalian glycoproteins mammalian glycoproteins Fterm glycoproteins Although Endo-M has been known to act on various N-glycans, it does not act on core-fucosylated N-glycans, which exist widely in mammalian glycoproteins, thus limiting its application. 28654715 5 20 part_of -Y-a 1002:1005 arg1 the consensus motifs X-β1,4-[Fucα1,3]-Y and X-β1,3-[Fucα1,4]-Y-a secondary structure Fucα1,4]-Y the consensus motifs X-β1,4-[Fucα1,3]-Y and X-β1,3-[Fucα1,4]-Y-a secondary structure PUBTATOR Site Fucα1,4]-Y 2517 motifs The set of trisaccharide motifs can be summarized with the consensus motifs X-β1,4-[Fucα1,3]-Y and X-β1,3-[Fucα1,4]-Y-a secondary structure we name [3,4]F-branch. 26729457 1 31 gly glycoproteins 265:277 arg1 glycoproteins glycoproteins Fterm glycoproteins In-depth site-specific investigations of protein glycosylation are the basis for understanding the biological function of glycoproteins. 27938679 1 23 gly glycoproteins 283:295 arg1 the mature surface (SU) and transmembrane (TM) glycoproteins the mature surface (SU) and transmembrane (TM) glycoproteins Fterm glycoproteins The bovine leukaemia virus (BLV) envelope protein (Env) is synthesized as a polyprotein precursor (gp72) proteolytically cleaved into the mature surface (SU) and transmembrane (TM) glycoproteins. 25210040 1 38 gly glycoproteins 283:295 arg1 extracellular matrix glycoproteins extracellular matrix glycoproteins Fterm glycoproteins The disaccharide N,N'-di-N-acetyllactose diamine (LacdiNAc, GalNAcβ1-4GlcNAcβ) is found in a limited number of extracellular matrix glycoproteins and neuropeptide hormones indicating a protein-specific transfer of GalNAc by the glycosyltransferases β4GalNAc-T3/T4. 28525772 13 62 gly glycans 1895:1901 arg1 output WURCS sequences output WURCS sequences output WURCS sequences Site sequences Moreover, the new GlycanBuilder can now easily output WURCS sequences from glycans drawn on the canvas. 28336547 4 28 gly glycosylation 705:717 arg1 sequon N50 N50 N50 Here, we show that for the murine protein the inhibition of glycosylation at sequon N50 by substituting N50 with glutamine, lysine, or cysteine or by replacing S52 with alanine equally altered PEPT1 transport kinetics in oocytes. 26077366 3 78 gly glycosylation 453:465 arg1 protein stability protein stability Fterm protein In this study, we have examined the effect of glycosylation on protein stability using molecular dynamics simulation of legume lectin soybean agglutinin (SBA). 26863921 2 12 gly modified 322:329 arg3 the S-layer glycoprotein AND an N-linked pentasaccharide the S-layer glycoprotein an N-linked pentasaccharide Fterm glycoprotein In the halophilic archaea Haloferax volcanii, glycoproteins such as the S-layer glycoprotein are modified by an N-linked pentasaccharide assembled by a series of Agl (archaeal glycosylation) proteins. 26863921 2 12 gly modified 322:329 arg3 glycoproteins AND an N-linked pentasaccharide glycoproteins an N-linked pentasaccharide Fterm glycoproteins In the halophilic archaea Haloferax volcanii, glycoproteins such as the S-layer glycoprotein are modified by an N-linked pentasaccharide assembled by a series of Agl (archaeal glycosylation) proteins. 26863921 2 14 gly glycoprotein 305:316 arg1 the S-layer glycoprotein the S-layer glycoprotein Fterm glycoprotein In the halophilic archaea Haloferax volcanii, glycoproteins such as the S-layer glycoprotein are modified by an N-linked pentasaccharide assembled by a series of Agl (archaeal glycosylation) proteins. 26863921 2 37 gly glycoproteins 271:283 arg1 the S-layer glycoprotein the S-layer glycoprotein Fterm glycoprotein In the halophilic archaea Haloferax volcanii, glycoproteins such as the S-layer glycoprotein are modified by an N-linked pentasaccharide assembled by a series of Agl (archaeal glycosylation) proteins. 26863921 2 37 gly glycoproteins 271:283 arg1 glycoproteins glycoproteins Fterm glycoproteins In the halophilic archaea Haloferax volcanii, glycoproteins such as the S-layer glycoprotein are modified by an N-linked pentasaccharide assembled by a series of Agl (archaeal glycosylation) proteins. 26869352 4 69 gly has 980:982 arg1 Asn184 Asn184 Asn184, Asn207, Asn211, Asn241 To ascertain if characteristic fucosylation is observed in each cancer type, we undertook site-specific analyses of N-glycans on haptoglobin in the sera of patients with five types of operable gastroenterological cancer (esophageal, gastric, colon, gallbladder, pancreatic), a non-gastroenterological cancer (prostate cancer) and normal controls using ODS column LC-ESI MS. Haptoglobin has four potential glycosylation sites (Asn184, Asn207, Asn211, Asn241). 26869352 4 91 gly glycosylation 999:1011 arg2 four potential glycosylation sites four potential glycosylation sites sites To ascertain if characteristic fucosylation is observed in each cancer type, we undertook site-specific analyses of N-glycans on haptoglobin in the sera of patients with five types of operable gastroenterological cancer (esophageal, gastric, colon, gallbladder, pancreatic), a non-gastroenterological cancer (prostate cancer) and normal controls using ODS column LC-ESI MS. Haptoglobin has four potential glycosylation sites (Asn184, Asn207, Asn211, Asn241). 26869352 4 59 gly Asn184 1020:1025 arg1 Asn211 Asn184, Asn207, Asn211, Asn241 Asn184, Asn207, Asn211, Asn241 To ascertain if characteristic fucosylation is observed in each cancer type, we undertook site-specific analyses of N-glycans on haptoglobin in the sera of patients with five types of operable gastroenterological cancer (esophageal, gastric, colon, gallbladder, pancreatic), a non-gastroenterological cancer (prostate cancer) and normal controls using ODS column LC-ESI MS. Haptoglobin has four potential glycosylation sites (Asn184, Asn207, Asn211, Asn241). 25793407 2 87 gly glycoproteins 378:390 arg1 glycoproteins glycoproteins Fterm glycoproteins Many important biological roles of glycoproteins are modulated by N-linked oligosaccharides. 25029371 1 13 gly glycosylation 111:123 arg1 efficient protein folding efficient protein folding Fterm protein Asparagine (N)-linked glycosylation is essential for efficient protein folding in the endoplasmic reticulum (ER) and anterograde trafficking through the secretory pathway. 29273683 3 59 gly N-glycosylation 287:301 arg2 N-glycosylation sites N-glycosylation sites sites Glycosylation of human CBG influences its steroid-binding activity, and there are N-glycosylation sites in the reactive center loops (RCLs) of human and rat CBGs. 28486471 1 66 gly glycosylated 151:162 arg1 glycosylated recombinant proteins glycosylated recombinant proteins Fterm proteins The Chinese hamster ovary (CHO) cell is the gold standard for manufacturing of glycosylated recombinant proteins for production of biotherapeutics. 26160412 8 7 gly N-glycosites 1310:1321 arg2 55 N-glycosites 55 N-glycosites N-glycosites Under these conditions, 124 N-glycopeptides representing 55 N-glycosites from 36 glycoproteins were tentatively identified. 26160412 8 50 gly N-glycopeptides 1278:1292 arg2 124 N-glycopeptides 124 N-glycopeptides N-glycopeptides Under these conditions, 124 N-glycopeptides representing 55 N-glycosites from 36 glycoproteins were tentatively identified. 26160412 8 57 gly glycoproteins 1331:1343 arg1 36 glycoproteins 36 glycoproteins Fterm glycoproteins Under these conditions, 124 N-glycopeptides representing 55 N-glycosites from 36 glycoproteins were tentatively identified. 26646445 3 35 gly bifucosylated 441:453 arg1 bifucosylated N-glycan bifucosylated N-glycan A unique structural pattern of bifucosylated N-glycan, with both core and antennary fucosylation, was identified in breast cancer patients. 24702330 1 37 part_of Glycoproteins 62:74 arg1 chemically defined glycosylation sites Glycoproteins chemically defined glycosylation sites Fterm Site Glycoproteins sites Glycoproteins with chemically defined glycosylation sites and structures are important biopharmaceutical targets and critical tools for glycobiology. 28860626 3 60 gly neuraminidase 938:950 arg1 the glycan structures neuraminidase the glycan structures Fterm neuraminidase Proteomic data analyses of the full-length protein sequences determined 9 N-glycosylation sites of hemagglutinin, and defined 6 N-glycosylation sites and the glycan structures of low abundance neuraminidase, which were occupied by high-mannose, hybrid and complex-type N-glycans. 28860626 3 18 gly N-glycosylation 873:887 arg2 6 N-glycosylation sites neuraminidase sites Fterm neuraminidase sites Proteomic data analyses of the full-length protein sequences determined 9 N-glycosylation sites of hemagglutinin, and defined 6 N-glycosylation sites and the glycan structures of low abundance neuraminidase, which were occupied by high-mannose, hybrid and complex-type N-glycans. 28860626 3 31 gly N-glycosylation 819:833 arg2 9 N-glycosylation sites hemagglutinin sites Fterm hemagglutinin sites Proteomic data analyses of the full-length protein sequences determined 9 N-glycosylation sites of hemagglutinin, and defined 6 N-glycosylation sites and the glycan structures of low abundance neuraminidase, which were occupied by high-mannose, hybrid and complex-type N-glycans. 24794851 2 2 gly glycoproteins 313:325 arg1 plant-made glycoproteins plant-made glycoproteins Fterm glycoproteins However, plant-made glycoproteins have N-glycans with plant-specific sugar residues (core β-1,2-xylose and α-1,3-fucose) and a Lewis a (Le(a)) epitope, Galβ(1-3)[Fucα(1-4)]GlcNAc. 24794851 2 68 gly epitope 436:442 arg1 α-1,3-fucose α-1,3-fucose However, plant-made glycoproteins have N-glycans with plant-specific sugar residues (core β-1,2-xylose and α-1,3-fucose) and a Lewis a (Le(a)) epitope, Galβ(1-3)[Fucα(1-4)]GlcNAc. 24794851 2 68 gly epitope 436:442 arg1 plant-specific sugar residues plant-specific sugar residues However, plant-made glycoproteins have N-glycans with plant-specific sugar residues (core β-1,2-xylose and α-1,3-fucose) and a Lewis a (Le(a)) epitope, Galβ(1-3)[Fucα(1-4)]GlcNAc. 24794851 2 68 gly epitope 436:442 arg1 core β-1,2-xylose core β-1,2-xylose However, plant-made glycoproteins have N-glycans with plant-specific sugar residues (core β-1,2-xylose and α-1,3-fucose) and a Lewis a (Le(a)) epitope, Galβ(1-3)[Fucα(1-4)]GlcNAc. 24794851 2 41 gly have 327:330 arg1 plant-made glycoproteins AND N-glycans plant-made glycoproteins N-glycans Fterm glycoproteins However, plant-made glycoproteins have N-glycans with plant-specific sugar residues (core β-1,2-xylose and α-1,3-fucose) and a Lewis a (Le(a)) epitope, Galβ(1-3)[Fucα(1-4)]GlcNAc. 24794851 2 41 gly have 327:330 arg1 plant-made glycoproteins AND Galβ(1-3)[Fucα(1-4)]GlcNAc plant-made glycoproteins Galβ(1-3)[Fucα(1-4)]GlcNAc Fterm glycoproteins However, plant-made glycoproteins have N-glycans with plant-specific sugar residues (core β-1,2-xylose and α-1,3-fucose) and a Lewis a (Le(a)) epitope, Galβ(1-3)[Fucα(1-4)]GlcNAc. 24794851 2 41 gly have 327:330 arg1 plant-made glycoproteins AND a Lewis a (Le(a)) epitope plant-made glycoproteins a Lewis a (Le(a)) epitope Fterm glycoproteins However, plant-made glycoproteins have N-glycans with plant-specific sugar residues (core β-1,2-xylose and α-1,3-fucose) and a Lewis a (Le(a)) epitope, Galβ(1-3)[Fucα(1-4)]GlcNAc. 24903886 1 15 gly glycoproteins 154:166 arg1 glycoproteins glycoproteins Fterm glycoproteins Glycosylation engineering is used to generate glycoproteins, glycolipids, or proteoglycans with a more defined complement of glycans on their glycoconjugates. 25182382 10 80 gly glycopeptides 1755:1767 arg2 Intact glycopeptides Intact glycopeptides glycopeptides Intact glycopeptides and their deglycosylated forms were identified respectively and combined according to the commonality of molecular weights of peptide backbones. 25234305 8 13 gly core-fucosylated 1531:1546 arg1 core-fucosylated tetraantennary N-glycans core-fucosylated tetraantennary N-glycans For the first time, we could demonstrate that not only antennary fucosylation was of relevance in tetraantennary structures but also core-fucosylated tetraantennary N-glycans were statistically increased in EOC patients. 28277614 5 48 gly glycopeptides 903:915 arg2 glycopeptides glycopeptides glycopeptides Tandem mass spectrometry was used on O-glycans and glycopeptides including ion trap higher energy collision-induced dissociation (tHCD) to detect glycan fragments not detectable with standard ion trap fragmentation. 26618856 2 43 gly glycosylation 255:267 arg1 globular proteins globular proteins Fterm proteins Previous work on glycosylation of globular proteins has revealed remarkable effects of glycosylation on protein function, altering the folding stability and structure and/or altering the protein surface which affects their binding characteristics. 26618856 2 71 gly glycosylation 325:337 arg1 protein function protein function Fterm protein Previous work on glycosylation of globular proteins has revealed remarkable effects of glycosylation on protein function, altering the folding stability and structure and/or altering the protein surface which affects their binding characteristics. 28424265 4 42 part_of GNE 539:541 arg1 both GNE domains GNE both GNE domains PUBTATOR Site GNE 10020 domains Mutations to both GNE domains are linked to GNE myopathy. 25182382 1 14 part_of sites 232:236 arg1 proteins proteins sites Fterm Site proteins sites The detailed characterization of site-specific glycosylation requires the identification of glycan composition and specific attachment sites on proteins, which need the identification of intact glycopeptides by mass spectrometry. 24766575 3 4 gly N-glycopeptide 649:662 arg2 N-glycopeptide spectra N-glycopeptide spectra N-glycopeptide We performed an extensive validation and a high-throughput N-glycosylation study on serum and identified thousands of N-glycopeptide spectra with high confidence. 29157724 7 53 gly sialylated 913:922 arg1 sialylated N-glycans sialylated N-glycans We show that high mannose type N-glycans are upregulated, while sialylated N-glycans are downregulated in our FFPE lung adenocarcinoma samples, compared to the control samples. 24497634 8 25 gly contactin 1084:1092 arg1 the oligomannose type sugars contactin the oligomannose type sugars Fterm contactin Strikingly, the oligomannose type sugars of contactin are required for association with its glial partner NF155 (2). 28585084 2 15 gly glycoproteins 384:396 arg1 glycoproteins glycoproteins Fterm glycoproteins This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. 26088564 1 1 gly glycoprotein 175:186 arg1 an abundant human plasma glycoprotein glycoprotein Fterm glycoprotein Human α1-acid glycoprotein (AGP) is an abundant human plasma glycoprotein that may be N-glycosylated at five positions. 26088564 1 20 gly N-glycosylated 200:213 arg1 Human α1-acid glycoprotein glycoprotein positions Fterm glycoprotein positions Human α1-acid glycoprotein (AGP) is an abundant human plasma glycoprotein that may be N-glycosylated at five positions. 26088564 1 20 gly N-glycosylated 200:213 arg1 an abundant human plasma glycoprotein glycoprotein positions Fterm glycoprotein positions Human α1-acid glycoprotein (AGP) is an abundant human plasma glycoprotein that may be N-glycosylated at five positions. 26088564 1 20 gly N-glycosylated 200:213 arg1 an abundant human plasma glycoprotein glycoprotein Fterm glycoprotein Human α1-acid glycoprotein (AGP) is an abundant human plasma glycoprotein that may be N-glycosylated at five positions. 26088564 1 42 gly glycoprotein 128:139 arg1 an abundant human plasma glycoprotein glycoprotein Fterm glycoprotein Human α1-acid glycoprotein (AGP) is an abundant human plasma glycoprotein that may be N-glycosylated at five positions. 28581490 4 24 gly glycoprotein 729:740 arg1 an endogenous tumor-associated glycoprotein MUC1 an endogenous tumor-associated glycoprotein MUC1 Fterm glycoprotein Here we demonstrate a possible method for differential glycoform analysis of an endogenous tumor-associated glycoprotein MUC1 by an antibody-overlay lectin microarray. 26255982 7 52 gly glycoproteins 1094:1106 arg1 glycoproteins glycoproteins Fterm glycoproteins In addition, there were significant correlations between the abundance of the O-glycans and glycoproteins (MUC1, CEA) in the serum of GC. 25190359 7 47 gly over-sialylation/fucosylation 1391:1419 arg1 complex/hybrid N-glycans complex/hybrid N-glycans Comparative N-glycome analysis between inter-patient group revealed that lung infection/colonization, in general, extensively enriches the CF sputum N-glycosylation phenotype with paucimannose with simultaneous over-sialylation/fucosylation and under-bisecting GlcNAcylation of complex/hybrid N-glycans. 28452462 8 38 gly glycoproteins 1869:1881 arg1 complex glycoproteins complex glycoproteins This study represents the first example of site-selective chemoenzymatic glycan engineering of complex glycoproteins carrying multiple N-glycans. 29048990 5 84 gly glycosylation 926:938 arg2 potential glycosylation sites potential glycosylation sites sites Nonetheless, this sequence-based approach can only predict potential glycosylation sites. 28816453 1 11 gly glycoproteins 108:120 arg1 glycoproteins glycoproteins Fterm glycoproteins In spite of the abundance of glycoproteins in biological processes, relatively little three-dimensional structural data is available for glycan structures. 25725350 1 27 gly glycan 121:126 arg1 the Fc domain the Fc domain the Fc domain Site domain We recently revealed a unique glycan on the Fc domain of IgG antibodies in ALS patients that mediates antibody-dependent cell cytotoxicity (ADCC). 28797655 2 51 gly N-glycosylation 266:280 arg2 N-glycosylation sites N-glycosylation sites sites In this study, the distribution and evolution of N-glycosylation sites in the hemagglutinin (HA) and neuraminidase (NA) of H9N2 virus were explored using phylogenetic analysis. 25995273 3 9 gly proteins 579:586 arg1 The N-glycan structures proteins The N-glycan structures Fterm proteins The N-glycan structures of predicted lysosomal, endoplasmic reticulum (ER), secreted and transmembrane proteins were compared. 27808502 3 13 gly glycosylation 758:770 arg2 glycosylation site glycosylation site site Oligomannosylated glycopeptidome produced by NGlycoReduction can be mixed with the intact N-glycopeptidome and analyzed by HPLC-ESI-MS together to enable the identification of peptide sequence, glycosylation site and the structure of intact glycopeptides. 27808502 3 59 gly glycopeptides 805:817 arg2 intact glycopeptides intact glycopeptides glycopeptides Oligomannosylated glycopeptidome produced by NGlycoReduction can be mixed with the intact N-glycopeptidome and analyzed by HPLC-ESI-MS together to enable the identification of peptide sequence, glycosylation site and the structure of intact glycopeptides. 27808502 3 13 gly glycosylation 758:770 arg1 intact glycopeptides glycopeptides glycopeptides Oligomannosylated glycopeptidome produced by NGlycoReduction can be mixed with the intact N-glycopeptidome and analyzed by HPLC-ESI-MS together to enable the identification of peptide sequence, glycosylation site and the structure of intact glycopeptides. 26537504 3 31 gly N-glycosylation 664:678 arg2 an N-glycosylation site an N-glycosylation site site Deglycosylation with PNGase F in the presence of a buffer prepared with 40% H2 (18)O allowed the assignment of an N-glycosylation site. 26991339 1 9 gly glycoforms 162:171 arg1 the basic salivary proline-rich protein 3M the basic salivary proline-rich protein 3M Fterm protein In the present study, we show that the heterogeneous mixture of glycoforms of the basic salivary proline-rich protein 3M, encoded by PRB3-M locus, is a major component of the acidic soluble fraction of human whole saliva in the first years of life. 26479949 7 92 gly glycopeptides 1254:1266 arg2 glycopeptides peroxidase glycopeptides Fterm peroxidase glycopeptides The hydrophilic Fe3O4-DA-Maltose NPs were applied in isolation and enrichment of glycopeptides from horseradish peroxidase (HRP), immunoglobulin (IgG) digests. 26059044 8 5 gly N-glycosylation 1162:1176 arg2 this position position position The combination of site-directed mutagenesis of Asn54 and in vivo deglycosylation with PNGase F also revealed that N-glycosylation at this position is not required for proper protein folding. 26059044 8 5 gly N-glycosylation 1162:1176 arg1 proper protein folding protein position Fterm protein position The combination of site-directed mutagenesis of Asn54 and in vivo deglycosylation with PNGase F also revealed that N-glycosylation at this position is not required for proper protein folding. 26059044 8 5 gly N-glycosylation 1162:1176 arg1 proper protein folding protein position Fterm protein position The combination of site-directed mutagenesis of Asn54 and in vivo deglycosylation with PNGase F also revealed that N-glycosylation at this position is not required for proper protein folding. 27558752 1 56 gly glycoprotein 173:184 arg1 glycoprotein structure glycoprotein structure Fterm glycoprotein N-glycosylation has a great impact on glycoprotein structure, conformation, stability, solubility, immunogenicity and enzyme activity. 24308486 3 10 gly N-glycosylation 723:737 arg2 all seven potential N-glycosylation sites all seven potential N-glycosylation sites sites The heavy chains were isolated and digested with either trypsin, proteinase K, or chymotrypsin, which permitted coverage of all seven potential N-glycosylation sites. 26483525 6 110 gly glycoform 776:784 arg1 a heretofore unrecognized tetrasaccharide glycoform a heretofore unrecognized tetrasaccharide glycoform glycolytica, a heretofore unrecognized tetrasaccharide glycoform consisting of di-N-acetylbacillosamine-glucose-di-N-acetyl hexuronic acid-N-acetylhexosamine (diNAcBac-Glc-diNAcHexA-HexNAc) was identified. 28255882 3 9 part_of proteins 477:484 arg1 α/β TCR constant domains proteins α/β TCR constant domains Fterm Site proteins domains Here we present a mass spectrometry based protocol with a "bottom up" approach to characterize glycosylation in recombinant fusion proteins with α/β TCR constant domains expressed in mammalian cells. 28255882 3 33 part_of α/β 491:493 arg1 α/β TCR constant domains /β TCR α/β TCR constant domains PUBTATOR Site /β TCR 351 domains Here we present a mass spectrometry based protocol with a "bottom up" approach to characterize glycosylation in recombinant fusion proteins with α/β TCR constant domains expressed in mammalian cells. 28255882 3 36 part_of TCR 495:497 arg1 α/β TCR constant domains /β TCR α/β TCR constant domains PUBTATOR Site /β TCR 351 domains Here we present a mass spectrometry based protocol with a "bottom up" approach to characterize glycosylation in recombinant fusion proteins with α/β TCR constant domains expressed in mammalian cells. 26192331 1 40 gly polysialylation 169:183 arg1 surface-localized glycoproteins surface-localized glycoproteins Fterm glycoproteins Sialyltransferases of the mammalian ST8Sia family catalyze oligo- and polysialylation of surface-localized glycoproteins and glycolipids through transfer of sialic acids from CMP-sialic acid to the nonreducing ends of sialic acid acceptors. 26192331 1 43 gly glycoproteins 206:218 arg1 surface-localized glycoproteins glycoproteins oligo- Fterm glycoproteins Sialyltransferases of the mammalian ST8Sia family catalyze oligo- and polysialylation of surface-localized glycoproteins and glycolipids through transfer of sialic acids from CMP-sialic acid to the nonreducing ends of sialic acid acceptors. 26192331 1 43 gly glycoproteins 206:218 arg1 surface-localized glycoproteins glycoproteins polysialylation Fterm glycoproteins Sialyltransferases of the mammalian ST8Sia family catalyze oligo- and polysialylation of surface-localized glycoproteins and glycolipids through transfer of sialic acids from CMP-sialic acid to the nonreducing ends of sialic acid acceptors. 27718394 3 86 gly glycosylation 510:522 arg1 individual proteins individual proteins Fterm proteins Furthermore, alterations in the glycosylation pattern of individual proteins, exhibiting larger variability in disease states, have been suggested as biomarkers for different types of cancer, as well as inflammatory and neurodegenerative diseases. 26416237 6 47 part_of agglutinin 773:782 arg1 The amino acid sequence agglutinin The amino acid sequence Fterm Site agglutinin sequence The amino acid sequence of this agglutinin was determined by Edman degradation and tertiary as well as quaternary structure by X-ray crystallography. 25422509 6 59 gly sialylated 879:888 arg1 sialylated N-linked glycans sialylated N-linked glycans In this study, to our knowledge, we show for the first time that sialylated N-linked glycans induce the internalization of IgM by T cells, which in turn causes severe inhibition of T cell responses. 25036289 6 56 gly Asn297-linked 961:973 arg1 the Asn297-linked complex N-glycans Asn297 the Asn297-linked complex N-glycans Asn297 In particular, the anti-inflammatory activity of intravenous IgG is ascribed to a small population of IgGs in which the Asn297-linked complex N-glycans attached to each Fc CH2 domain include terminal α2,6-linked sialic acids. 25036289 6 66 gly attached 993:1000 arg1 each Fc CH2 domain AND the Asn297-linked complex N-glycans each Fc CH2 domain the Asn297-linked complex N-glycans domain In particular, the anti-inflammatory activity of intravenous IgG is ascribed to a small population of IgGs in which the Asn297-linked complex N-glycans attached to each Fc CH2 domain include terminal α2,6-linked sialic acids. 28334934 4 96 gly glycoproteins 832:844 arg1 the bacterium's abundant S-layer glycoproteins the bacterium's abundant S-layer glycoproteins Fterm glycoproteins This study aims to shed light on the transfer of either nonulosonic acid derivative on a proximal N-acetylmannosaminuronic acid residue within the O-glycan structure, exemplified with the bacterium's abundant S-layer glycoproteins. 24637934 5 39 gly region 1031:1036 arg1 N-linked glycan structures region N-linked glycan structures region NSDs are the co-substrates of the glycosylation process in the Golgi apparatus and their simulated dynamic intracellular concentration profiles were linked to an existing model describing the distribution of N-linked glycan structures of the antibody constant region. 25793890 7 86 gly glycosylation 1386:1398 arg2 this glycosylation site this glycosylation site site Although N136 has previously been implicated in the binding of broadly neutralizing monoclonal antibodies, this glycosylation site appears to inhibit the binding of neutralizing antibodies in plasma from HIV-1 infected subjects. 26075384 5 35 gly O-glycosylation 727:741 arg1 acidic glycoproteins acidic glycoproteins Fterm glycoproteins METHODS In this study, we analyzed the expression of the MUC5AC and the O-glycosylation of acidic glycoproteins secreted into ovarian cyst fluids. 26075384 5 119 gly glycoproteins 753:765 arg1 acidic glycoproteins acidic glycoproteins Fterm glycoproteins METHODS In this study, we analyzed the expression of the MUC5AC and the O-glycosylation of acidic glycoproteins secreted into ovarian cyst fluids. 25850302 5 72 part_of region 813:818 arg1 additional allowed region region additional allowed region region Quality assessment by Ramachandran plot showed that 91% amino acids lie in most favourable region and 9% in additional allowed region. 25182382 3 3 gly glycopeptides 570:582 arg2 intact glycopeptides intact glycopeptides glycopeptides N-glycopeptides were identified using the spectra acquired for intact glycopeptides as well as de-glycopeptides. 25182382 3 22 gly de-glycopeptides 595:610 arg2 de-glycopeptides de-glycopeptides de-glycopeptides N-glycopeptides were identified using the spectra acquired for intact glycopeptides as well as de-glycopeptides. 25182382 3 91 gly N-glycopeptides 500:514 arg2 N-glycopeptides N-glycopeptides N-glycopeptides N-glycopeptides were identified using the spectra acquired for intact glycopeptides as well as de-glycopeptides. 26160412 10 70 gly carry 1636:1640 arg1 only a few proteins AND such particular glycan motifs only a few proteins such particular glycan motifs Fterm proteins Using our workflow, only a few proteins were shown to carry such particular glycan motifs. 26306636 0 16 gly sialidase 61:69 arg1 Automated N-glycan profiling sialidase Automated N-glycan profiling Fterm sialidase Automated N-glycan profiling of a mutant Trypanosoma rangeli sialidase expressed in Pichia pastoris, using tandem mass spectrometry and bioinformatics. 26869352 2 36 gly fucosylated 353:363 arg1 fucosylated N-glycans fucosylated N-glycans Previously, we reported that fucosylated N-glycans on haptoglobin in the sera of patients with pancreatic cancer were increased by lectin-ELISA and mass spectrometry analyses. 28921955 3 14 gly glycosylation 533:545 arg1 Influenza hemagglutinin Influenza hemagglutinin Fterm hemagglutinin In our study, we used glycoproteomic analysis based on multienzyme digestion followed by LC tandem MS analysis to determine the glycosylation of Influenza hemagglutinin (H1/A/California/04/2009) using the following steps: PNGaseF treatment combined with trypsin or pepsin digestion was used to determine the glycosites and glycan occupancy. 28921955 3 64 gly glycosites 713:722 arg2 the glycosites the glycosites glycosites In our study, we used glycoproteomic analysis based on multienzyme digestion followed by LC tandem MS analysis to determine the glycosylation of Influenza hemagglutinin (H1/A/California/04/2009) using the following steps: PNGaseF treatment combined with trypsin or pepsin digestion was used to determine the glycosites and glycan occupancy. 27938679 3 21 gly N-glycosylation 561:575 arg2 eight asparagine (N) residues eight asparagine (N) residues residues The SU contains eight asparagine (N) residues that are putative N-glycosylation sites. 27938679 3 21 gly N-glycosylation 561:575 arg2 putative N-glycosylation sites putative N-glycosylation sites sites The SU contains eight asparagine (N) residues that are putative N-glycosylation sites. 25575808 9 68 part_of endocan 1006:1012 arg1 endocan polypeptide endocan endocan polypeptide PUBTATOR Site endocan 11082 polypeptide In vitro, endocan polypeptide did not affect HT-29 cell proliferation, nor cell viability. 29197583 6 59 gly glycopeptides 1200:1212 arg2 the glycopeptides the glycopeptides glycopeptides Straightforward separation of isomers was achieved with the analysis of released glycans, as opposed to the glycopeptides which showed a more complex pattern. 28079948 1 0 gly attachment 174:183 arg1 Thr AND α-mannopyranose Thr α-mannopyranose Thr residues Mammalian protein O-mannosylation, initiated by attachment of α-mannopyranose to Ser or Thr residues, comprise a group of post-translational modifications (PTMs) involved in muscle and brain development. 28079948 1 0 gly attachment 174:183 arg1 Ser AND α-mannopyranose Ser α-mannopyranose Ser Mammalian protein O-mannosylation, initiated by attachment of α-mannopyranose to Ser or Thr residues, comprise a group of post-translational modifications (PTMs) involved in muscle and brain development. 26156869 6 20 part_of Fc 1535:1536 arg1 the Fc fragments Fc the Fc fragments Cterm Site Fc fragments We utilized this difference in glycoform selectivity, in combination with the IdeS protease, and developed a LC separation method to quantify high mannose content in the Fc fragments of the selected mAbs. 26156869 6 76 part_of mAbs 1564:1567 arg1 the Fc fragments mAbs the Fc fragments PUBTATOR Site mAbs 72935 fragments We utilized this difference in glycoform selectivity, in combination with the IdeS protease, and developed a LC separation method to quantify high mannose content in the Fc fragments of the selected mAbs. 24692304 2 18 gly heterogeneity 287:299 arg1 the oligosaccharide (glycan) moiety the oligosaccharide (glycan) moiety Glycoproteins can be hard to crystallize because of the heterogeneity of the oligosaccharide (glycan) moiety. 29016103 7 40 gly glycopeptides 1172:1184 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides We also compared the enrichment of intact N- and O-linked glycopeptides using other chromatography methods and found that using cartridges containing materials for strong anion exchange (SAX) chromatography increased yield and identification of N- and O-linked glycopeptides. 29016103 7 80 gly glycopeptides 969:981 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides We also compared the enrichment of intact N- and O-linked glycopeptides using other chromatography methods and found that using cartridges containing materials for strong anion exchange (SAX) chromatography increased yield and identification of N- and O-linked glycopeptides. 26646445 5 67 gly glycoproteins 721:733 arg1 Permethylated N-glycans glycoproteins Permethylated N-glycans Fterm glycoproteins Permethylated N-glycans of the glycoproteins extracted from 91 breast cancer patients and 43 healthy controls were detected using linear ion-trap quadrupole-electrospray ionization mass spectrometry, which appeared to be a highly sensitive and useful approach in the detection and identification of N-glycans. 25837443 2 10 gly glycoprotein 160:171 arg1 Each glycoprotein Each glycoprotein Fterm glycoprotein Each glycoprotein can be glycosylated at multiple glycosites, and each glycosites can be modified by different glycans. 25837443 2 28 gly glycosites 226:235 arg2 each glycosites each glycosites glycosites Each glycoprotein can be glycosylated at multiple glycosites, and each glycosites can be modified by different glycans. 25837443 2 37 gly modified 244:251 arg3 each glycosites AND different glycans each glycosites different glycans glycosites Each glycoprotein can be glycosylated at multiple glycosites, and each glycosites can be modified by different glycans. 25837443 2 42 gly glycosites 205:214 arg2 multiple glycosites multiple glycosites glycosites Each glycoprotein can be glycosylated at multiple glycosites, and each glycosites can be modified by different glycans. 25837443 2 9 gly glycosylated 180:191 arg2 multiple glycosites glycoprotein glycosites Fterm glycoprotein glycosites Each glycoprotein can be glycosylated at multiple glycosites, and each glycosites can be modified by different glycans. 24085030 0 40 gly glycoproteins 38:50 arg1 the salivary glycoproteins the salivary glycoproteins Fterm glycoproteins Glycosylation changes in the salivary glycoproteins of alcohol-dependent patients: a pilot study. 29273683 9 80 gly presence 1298:1305 arg2 this conserved position AND an N-glycan this conserved position an N-glycan position Thus, the presence and composition of an N-glycan in this conserved position both appear to influence the steroid binding of CBG. 24295789 4 33 gly subunits 1013:1020 arg1 complete N-glycan structures subunits complete N-glycan structures Fterm subunits De novo sequencing provided new insights into the disulfide linkage organization, intersection of subunits and complete N-glycan structures along with site specificities. 26328495 5 53 gly sialylated 772:781 arg1 a sialylated core-1 O-glycan a sialylated core-1 O-glycan These results suggest that POMGNT1 is modified by a sialylated core-1 O-glycan. 28400175 6 19 gly glycosites 889:898 arg2 adjacent glycosites adjacent glycosites glycosites Computational modelling suggests that spatial position (or orientation) of glycans can impair processing or site occupancy on adjacent glycosites. 26797772 1 46 gly glycoprotein 220:231 arg1 a membrane glycoprotein a membrane glycoprotein Fterm glycoprotein Tissue-nonspecific alkaline phosphatase (TNSALP) is a membrane glycoprotein with a proposed role in bone mineralization. 27705835 4 63 gly glycoproteins 848:860 arg1 glycoproteins glycoproteins Fterm glycoproteins In this study, we have found that three water plants, Elodea nuttallii, Egeria densa, and Ceratophyllum demersum, produce glycoproteins bearing Lewis a units. 24085030 9 99 gly glycoproteins 1405:1417 arg1 the salivary glycoproteins the salivary glycoproteins Fterm glycoproteins CONCLUSION Alterations in the glycosylation profiles in the salivary glycoproteins of alcohol-dependent people were found. 25205566 0 11 gly released 29:36 arg2 glycoproteins AND glycans glycoproteins glycans Fterm glycoproteins Glycomic analysis of glycans released from glycoproteins using chemical immobilization and mass spectrometry. 25205566 0 50 gly glycoproteins 43:55 arg1 glycoproteins glycoproteins Fterm glycoproteins Glycomic analysis of glycans released from glycoproteins using chemical immobilization and mass spectrometry. 26993603 2 4 gly glycosylation 303:315 arg2 glycosylation sites glycosylation sites sites In this study, we used mass spectrometry to identify glycosylation sites and the glycan structure, high-throughput lectin microarray to provide rapid and sensitive profiling of glycoconjugates, and site-directed mutagenesis to clarify the impact of glycans on target glycoproteins in vivo. 26993603 2 24 gly glycoproteins 517:529 arg1 target glycoproteins target glycoproteins Fterm glycoproteins In this study, we used mass spectrometry to identify glycosylation sites and the glycan structure, high-throughput lectin microarray to provide rapid and sensitive profiling of glycoconjugates, and site-directed mutagenesis to clarify the impact of glycans on target glycoproteins in vivo. 26479949 1 58 gly glycopeptides 227:239 arg2 low-abundance glycopeptides low-abundance glycopeptides glycopeptides The development of methods to isolate and enrich low-abundance glycopeptides from biological samples is crucial to glycoproteomics. 27694851 4 46 gly HS 671:672 arg1 attachment sites attachment sites sites Here we present a glycoproteomic approach that identifies and differentiates between HS and CS attachment sites and provides identity to the core proteins. 27932460 7 26 gly O-mannosylated 1426:1439 arg1 O-mannosylated sites O-mannosylated sites sites These findings begin to define the selectivity of POMGNT2 and suggest that this enzyme functions as a gatekeeper enzyme to prevent the vast majority of O-mannosylated sites on proteins from becoming modified with glycan structures functional for binding laminin globular domain-containing proteins. 27791356 8 9 part_of region 1708:1713 arg1 the mucin mucin region PUBTATOR Site mucin 281333 region Interestingly, the molecule was found to contain a large amount of α-helix/unordered structures and many signatures of glycosylation, pointing to a highly O-glycosylated region on the mucin. 27653286 3 40 gly glycosylated 396:407 arg1 a glycosylated protein a glycosylated protein Fterm protein However, the fact that Robo1 is a glycosylated protein prevents employment of commonly used bacterial hosts for expression of properly glycosylated forms with the uniform 15N, 13C, and 2H labeling needed for NMR studies. 24806200 7 15 part_of β-hCG 1364:1368 arg1 the N-terminal fragment hCG the N-terminal fragment PUBTATOR Site hCG 93659 fragment Key steps in these syntheses include a successful double Lansbury glycosylation en route to the N-terminal fragment of β-hCG and the sequential installation of four O-linked glycosyl-amino acid cassettes into closely spaced O-glycosylation sites in a single, high-yielding solid-supported synthesis to access the C-terminal portion of the molecule. 24806200 7 72 part_of N-terminal 1341:1350 arg1 the N-terminal fragment N-terminal the N-terminal fragment Cterm Site N-terminal fragment Key steps in these syntheses include a successful double Lansbury glycosylation en route to the N-terminal fragment of β-hCG and the sequential installation of four O-linked glycosyl-amino acid cassettes into closely spaced O-glycosylation sites in a single, high-yielding solid-supported synthesis to access the C-terminal portion of the molecule. 25029371 5 52 gly hypoglycosylation 1055:1071 arg1 NXS sites NXS sites sites Post-translational modification of the cotranslationally skipped sites by STT3B was similarly hindered by the middle X residue, resulting in hypoglycosylation of NXS sites containing large hydrophobic and negatively charged side chains. 24806200 1 30 gly glycoprotein 200:211 arg1 human glycoprotein hormones human glycoprotein hormones Fterm glycoprotein Human luteinizing hormone (hLH) and human chorionic gonadotropin (hCG) are human glycoprotein hormones each consisting of two subunits, an identical α-subunit and a unique β-subunit, that form noncovalent heterodimers. 26082214 2 4 gly glycoproteins 328:340 arg1 glycoproteins glycoproteins Fterm glycoproteins This diversity complicates the study of biological functions associated with particular glycan structures and impairs the application of glycoproteins in medicine. 28958711 1 7 gly glycosylated 85:96 arg1 an abundant non-collagenous phosphoprotein an abundant non-collagenous phosphoprotein Fterm phosphoprotein The highly glycosylated bone sialoprotein (BSP) is an abundant non-collagenous phosphoprotein in bone which enhances osteoblast differentiation and new bone deposition in vitro and in vivo. 28958711 1 7 gly glycosylated 85:96 arg1 The highly glycosylated bone sialoprotein The highly glycosylated bone sialoprotein Fterm sialoprotein The highly glycosylated bone sialoprotein (BSP) is an abundant non-collagenous phosphoprotein in bone which enhances osteoblast differentiation and new bone deposition in vitro and in vivo. 26082214 0 19 gly Asparagine-Linked 33:49 arg1 Asparagine-Linked N-Acetylglucosamine Asparagine Asparagine-Linked N-Acetylglucosamine Asparagine Production of Glycoproteins with Asparagine-Linked N-Acetylglucosamine in Escherichia coli. 25188817 7 47 gly glycosylation 1079:1091 arg2 glycosylation sites glycosylation sites sites Moreover, our analysis highlights the significance of left-handed conformations for compact β-hairpins at glycosylation sites. 26990841 1 50 gly glycopeptides 188:200 arg2 glycopeptides glycopeptides glycopeptides This work presents a detailed analysis of glycopeptides produced in the tryptic digestion of an IgG1 reference material. 28077298 4 44 gly fucosylated 900:910 arg1 sulphated, glucuronylated, core difucosylated and Lewis-like antennal fucosylated structures sulphated, glucuronylated, core difucosylated and Lewis-like antennal fucosylated structures RESULTS We detected not only sulphated, glucuronylated, core difucosylated and Lewis-like antennal fucosylated structures, but also the zwitterion phosphorylcholine on antennal GlcNAc residues, a modification otherwise familiar from nematodes; in L. dispar, N-glycans with glycolipid-like antennae containing α-linked N-acetylgalactosamine were also revealed. 28077298 4 69 gly difucosylated 862:874 arg1 sulphated, glucuronylated, core difucosylated and Lewis-like antennal fucosylated structures sulphated, glucuronylated, core difucosylated and Lewis-like antennal fucosylated structures RESULTS We detected not only sulphated, glucuronylated, core difucosylated and Lewis-like antennal fucosylated structures, but also the zwitterion phosphorylcholine on antennal GlcNAc residues, a modification otherwise familiar from nematodes; in L. dispar, N-glycans with glycolipid-like antennae containing α-linked N-acetylgalactosamine were also revealed. 26316330 0 33 gly glycoproteins 12:24 arg1 Recombinant glycoproteins Recombinant glycoproteins Fterm glycoproteins Recombinant glycoproteins: The impact of cell lines and culture conditions on the generation of protein species. 26240146 7 8 part_of subunit 1193:1199 arg1 the epitope subunit the epitope Fterm Site subunit epitope Hydrogen/deuterium exchange-MS reveals that the peptide β65-83 of the hCG β subunit is the epitope for MCA1024. 26990841 3 7 gly glycopeptides 582:594 arg2 the glycopeptides the glycopeptides glycopeptides An extended version of NIST-developed software for analysis of "shotgun" proteomics served to identify the glycopeptides from their precursor masses and product ions for peptides with up to three missed cleavages. 29106908 10 16 gly Asn563 1349:1354 arg1 predominantly complex type structures Asn402 and Asn563 predominantly complex type structures Asn402 and Asn563 We present the first detailed glycan analysis of IgM produced in CHO cells with predominantly complex type structures at Asn171, Asn332 and Asn395 and oligomannosidic structures at Asn402 and Asn563 similar to human serum-IgM. 29106908 10 25 gly Asn332 1286:1291 arg1 predominantly complex type structures Asn171, Asn332 and Asn395 predominantly complex type structures Asn171, Asn332 and Asn395 We present the first detailed glycan analysis of IgM produced in CHO cells with predominantly complex type structures at Asn171, Asn332 and Asn395 and oligomannosidic structures at Asn402 and Asn563 similar to human serum-IgM. 29106908 10 31 gly Asn395 1297:1302 arg1 predominantly complex type structures Asn171, Asn332 and Asn395 predominantly complex type structures Asn171, Asn332 and Asn395 We present the first detailed glycan analysis of IgM produced in CHO cells with predominantly complex type structures at Asn171, Asn332 and Asn395 and oligomannosidic structures at Asn402 and Asn563 similar to human serum-IgM. 29106908 10 43 gly Asn402 1338:1343 arg1 predominantly complex type structures Asn402 and Asn563 predominantly complex type structures Asn402 and Asn563 We present the first detailed glycan analysis of IgM produced in CHO cells with predominantly complex type structures at Asn171, Asn332 and Asn395 and oligomannosidic structures at Asn402 and Asn563 similar to human serum-IgM. 29106908 10 66 gly Asn171 1278:1283 arg1 predominantly complex type structures Asn171, Asn332 and Asn395 predominantly complex type structures Asn171, Asn332 and Asn395 We present the first detailed glycan analysis of IgM produced in CHO cells with predominantly complex type structures at Asn171, Asn332 and Asn395 and oligomannosidic structures at Asn402 and Asn563 similar to human serum-IgM. 25902405 2 2 gly glycosylated 328:339 arg1 glycosylated Asn glycosylated Asn Asn However, by current strategies for N-glycoproteome profiling, peptides with glycosylated Asn at N-terminus (PGANs), generated by protease digestion, could hardly be identified, due to the poor deglycosylation capacity by enzymes. 25151378 7 19 gly glycopeptides 1542:1554 arg2 glycopeptides glycopeptides glycopeptides Mapping of site occupancy without addressing the full range of occupying glycans by direct sequencing of glycopeptides is essentially inadequate for any glycobiology driven venture. 27932460 4 43 gly O-mannosylated 795:808 arg1 O-mannosylated peptides O-mannosylated peptides peptides Here, we demonstrate that POMGNT1 is promiscuous for O-mannosylated peptides, whereas POMGNT2 displays significant primary amino acid selectivity near the site of O-mannosylation. 28692416 5 3 gly N-glycopeptide 911:924 arg2 Fourteen IgG subclass-specific Fc N-glycopeptide structures Fourteen IgG subclass-specific Fc N-glycopeptide structures N-glycopeptide Fourteen IgG subclass-specific Fc N-glycopeptide structures, along with one derived glycosylation trait in subclasses IgG2/3 and IgG4, were found to correlate with systolic blood pressure and/or diastolic blood pressure. 24028868 6 91 gly Glycans 758:764 arg1 peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) Site peptides Glycans on peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) were quantified, and their abundances were normalized to total IgGn glycoform abundance. 27758867 2 90 gly glycopeptides 434:446 arg2 putative glycopeptides putative glycopeptides glycopeptides In this study, we describe the structural characterization of novel flagellar glycans from a number of hypervirulent strains of C. difficile We used mass spectrometry (nano-LC-MS and MS/MS analysis) to identify a number of putative glycopeptides that carried a variety of glycoform substitutions, each of which was linked through an initial N-acetylhexosamine residue to Ser or Thr. 27515086 1 41 gly glycoprotein 310:321 arg1 glycoprotein analysis glycoprotein analysis Fterm glycoprotein In recent years, the study of glycans is progressing remarkably by the development of glycan analysis systems using mass spectrometry, glycan profiling systems using lectin microarrays, and glycoprotein analysis by the isotope-coded glycosylation site-specific tagging method. 29255015 4 39 gly glycosylation 647:659 arg2 the glycosylation sites the glycosylation sites sites The crystallographic data identified most of the monosaccharides located close to the protein backbone, but failed to detect those further from the glycosylation sites. 27023912 1 15 gly glycoprotein 242:253 arg1 a peripheral membrane-associated glycoprotein a peripheral membrane-associated glycoprotein Fterm glycoprotein Gaucher disease, an autosomal recessive disorder, is caused by a deficiency of glucocerebrosidase (GCase) enzyme, a peripheral membrane-associated glycoprotein that hydrolyses glucosylceramide in lysosomes. 27023912 1 15 gly glycoprotein 242:253 arg1 glucocerebrosidase (GCase) enzyme glucocerebrosidase (GCase) enzyme Fterm enzyme Gaucher disease, an autosomal recessive disorder, is caused by a deficiency of glucocerebrosidase (GCase) enzyme, a peripheral membrane-associated glycoprotein that hydrolyses glucosylceramide in lysosomes. 27851982 5 85 part_of CDH 1139:1141 arg1 CDH domains CDH CDH domains PUBTATOR Site CDH 55349 domains Electrostatics calculations identified these differences to result from charge neutralization by protonation and together with ion mobility pointed at higher electrostatic repulsion between CDH domains at neutral pH. In addition, we uncovered extensive O-glycosylation in the linker region and identified the long-unknown exact cleavage point in papain-mediated domain separation. 24797265 14 10 gly glycosylation 2267:2279 arg2 six glycosylation sites six glycosylation sites sites In summary, our data obtained by a combination of fragmentation mass spectrometry techniques associated to a new software tool, demonstrate glycosylation heterogeneity of Srr1, characterize a new protein modification, and identify six glycosylation sites located in the N-terminal region of the protein. 26154505 8 13 gly glycoproteins 1804:1816 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins In this way, coordinated overexpression of these three glycosyltransferases for the first time in model CHO-K1 cell lines provides a mean for enhancing both N-glycan branching complexity and sialylation with opportunities to generate tailored complex N-glycan structures on therapeutic glycoproteins in the future. 26154505 8 29 gly structures 1778:1787 arg1 therapeutic glycoproteins glycoproteins structures Fterm glycoproteins In this way, coordinated overexpression of these three glycosyltransferases for the first time in model CHO-K1 cell lines provides a mean for enhancing both N-glycan branching complexity and sialylation with opportunities to generate tailored complex N-glycan structures on therapeutic glycoproteins in the future. 24440233 5 73 gly glycopeptides 982:994 arg1 non-glycopeptides non-glycopeptides non-glycopeptides In addition, detection of the oxonium ions enabled unambiguous differentiation of glycopeptides from non-glycopeptides. 24440233 5 73 gly glycopeptides 982:994 arg2 glycopeptides glycopeptides glycopeptides In addition, detection of the oxonium ions enabled unambiguous differentiation of glycopeptides from non-glycopeptides. 24440233 5 75 gly non-glycopeptides 1001:1017 arg2 non-glycopeptides non-glycopeptides non-glycopeptides In addition, detection of the oxonium ions enabled unambiguous differentiation of glycopeptides from non-glycopeptides. 25833378 3 40 gly glycosylation 542:554 arg2 engineered glycosylation sites engineered glycosylation sites sites Polysaccharide antigens of pathogenic bacteria can be covalently coupled to immunogenic acceptor proteins bearing engineered glycosylation sites. 27629418 5 10 gly α1,6-fucosylated 960:975 arg1 a synthetic α1,6-fucosylated trimannosyl core structure a synthetic α1,6-fucosylated trimannosyl core structure Such mutant enzymes exhibited increased hydrolysis of a synthetic α1,6-fucosylated trimannosyl core structure, whereas their activity on the afucosylated form decreased. 27629418 5 18 gly afucosylated 1035:1046 arg1 the afucosylated form the afucosylated form Such mutant enzymes exhibited increased hydrolysis of a synthetic α1,6-fucosylated trimannosyl core structure, whereas their activity on the afucosylated form decreased. 28669180 6 22 gly mannoproteins 907:919 arg1 Mannose residues mannoproteins Mannose residues Fterm mannoproteins Mannose residues from mannoproteins were significantly predominant in those cultures where T. delbrueckii was present in the fermentation process in comparison with when pure cultures of S. cerevisiae were present in the fermenation process. 28493134 7 6 gly glycoprotein 1244:1255 arg1 glycoprotein purification glycoprotein purification Fterm glycoprotein This chapter will describe glycoprotein purification after separation from producing cell lines, N-glycan release and their variants fine structural characterization through mass spectrometry techniques. 24663386 5 7 gly sialylated 885:894 arg1 other sialylated glycans other sialylated glycans NeuAcα2-3Galβ1-3N-acetylgalactosamine (GalNAc) (61-64%), NeuAcα2-3Galβ1-3(NeuAcα2-6)GalNAc (15-26%) and Galβ1-3GalNAc (6-14%) were major components while other sialylated glycans, Galβ1-3(NeuAcα2-6)GalNAc, Galβ1-4GlcNAcβ1-6(NeuAcα2-3Galβ1-3)GalNAc and NeuAcα2-3Galβ1-4GlcNAcβ1-6(NeuAcα2-3Galβ1-3)GalNAc were relatively minor components, accounting for ∼1-2%. 26972002 4 5 gly glycosylation 602:614 arg1 a soluble, recombinant trimer a soluble, recombinant trimer Fterm trimer 155971 Our site-specific glycosylation analysis of a soluble, recombinant trimer (BG505 SOSIP.664) maps the extremes of simplicity and diversity of glycan processing at individual sites and reveals a mosaic of dense clusters of oligomannose glycans on the outer domain. 26972002 4 11 gly sites 757:761 arg1 glycan processing sites glycan processing sites Our site-specific glycosylation analysis of a soluble, recombinant trimer (BG505 SOSIP.664) maps the extremes of simplicity and diversity of glycan processing at individual sites and reveals a mosaic of dense clusters of oligomannose glycans on the outer domain. 26972002 4 36 gly glycans 818:824 arg1 the outer domain the outer domain the outer domain Site domain Our site-specific glycosylation analysis of a soluble, recombinant trimer (BG505 SOSIP.664) maps the extremes of simplicity and diversity of glycan processing at individual sites and reveals a mosaic of dense clusters of oligomannose glycans on the outer domain. 26138399 8 50 gly glycoprotein 1554:1565 arg1 glycoprotein substrates glycoprotein substrates Fterm glycoprotein EndoBI-1-released N-glycans were quantified by a phenol-sulphuric total carbohydrate assay and the resultant N-glycan structures monitored by nano-LC-Chip-Q-TOF MS. The kinetic parameters and structural characterization of glycans released suggest EndoBI-1 can facilitate large-scale release of complex, bioactive glycans from a variety of glycoprotein substrates. 27957769 9 91 gly glycopeptide 1941:1952 arg2 the branched core 2 glycopeptide epitopes the branched core 2 glycopeptide epitopes glycopeptide epitopes With the extended mucin core structures in hand, antibody cross-reactivity toward the branched core 2 glycopeptide epitopes is explored. 27810711 4 49 part_of syndecan-3 627:636 arg1 syndecan-3 glycopeptides syndecan-3 syndecan-3 glycopeptides OGER Site syndecan-3 O75056 glycopeptides For assembly of glycans, a convergent 3+2+3 approach was developed producing two different octasaccharide amino acid cassettes, which were utilized towards syndecan-3 glycopeptides. 28516782 9 84 part_of IgA 1488:1490 arg1 the CH2 domain IgA the CH2 domain PUBTATOR Site IgA P11912 domain Interestingly, a shift in unfolding of the CH2 domain of plant-produced IgA toward lower temperatures can be observed with differential scanning calorimetry, suggesting that distinct glycoforms affect the thermal stability of IgAs. 26984886 9 65 gly glycosylation 1336:1348 arg2 the glycosylation sites the glycosylation sites sites Underprocessed glycoforms predominated at the glycosylation sites found to be involved in viral evolution in response to selection pressures and interactions with innate immune-lectins. 24828077 1 55 gly position 234:241 arg1 the glycan position 332 the glycan position 332 Broadly neutralizing monoclonal antibodies (bnmAbs) that target the high-mannose patch centered around the glycan at position 332 on HIV Env are promising vaccine leads and therapeutic candidates because they effectively protect against mucosal SHIV challenge and strongly suppress SHIV viremia in established infection in macaque models. 26869352 6 9 gly difucosylated 1169:1181 arg1 difucosylated N-glycans difucosylated N-glycans Moreover, difucosylated N-glycans were detected at Asn 184, Asn207 and Asn241 only in cancer samples. 26869352 6 90 gly detected 1198:1205 arg2 Asn241 AND difucosylated N-glycans Asn 184, Asn207 and Asn241 difucosylated N-glycans Asn 184, Asn207 and Asn241 Moreover, difucosylated N-glycans were detected at Asn 184, Asn207 and Asn241 only in cancer samples. 26869352 6 90 gly detected 1198:1205 arg2 Asn 184 AND difucosylated N-glycans Asn 184, Asn207 and Asn241 difucosylated N-glycans Asn 184, Asn207 and Asn241 Moreover, difucosylated N-glycans were detected at Asn 184, Asn207 and Asn241 only in cancer samples. 26869352 6 90 gly detected 1198:1205 arg2 Asn 184 AND difucosylated N-glycans Asn 184, Asn207 and Asn241 difucosylated N-glycans Asn 184, Asn207 and Asn241 Moreover, difucosylated N-glycans were detected at Asn 184, Asn207 and Asn241 only in cancer samples. 26307003 5 56 gly Ser3 1164:1167 arg1 glycans Ser3 and Ser14 glycans Ser3 and Ser14 These results are in agreement with previous experimental work demonstrating that glycans at Ser3 and Ser14 impart significant improvements in binding affinity. 26307003 5 64 gly Ser14 1173:1177 arg1 glycans Ser3 and Ser14 glycans Ser3 and Ser14 These results are in agreement with previous experimental work demonstrating that glycans at Ser3 and Ser14 impart significant improvements in binding affinity. 28400175 4 11 gly glycosite 580:588 arg2 non-occupied at glycosite 6 non-occupied at glycosite 6 glycosite Mass spectrometric profiling revealed that plant IgE has a site occupancy rate that ranges from non-occupied at glycosite 6 (GS6) to 100% occupancy at GS1 and 2. 26765751 3 91 part_of domains 573:579 arg1 the human Notch transmembrane receptor receptor domains Fterm Site receptor domains To evaluate the structural and functional roles of various glycoforms at multiple EGF domains in the human Notch transmembrane receptor, we established a universal method for the construction of NOTCH1 EGF modules displaying the desired O-glycans at the designated glycosylation sites. 26765751 3 118 part_of EGF 569:571 arg1 multiple EGF domains EGF multiple EGF domains OGER Site EGF P01133 domains To evaluate the structural and functional roles of various glycoforms at multiple EGF domains in the human Notch transmembrane receptor, we established a universal method for the construction of NOTCH1 EGF modules displaying the desired O-glycans at the designated glycosylation sites. 25110774 7 83 gly glycopeptides 1291:1303 arg2 glycopeptides glycopeptides glycopeptides In the selectivity assessment, the non-glycopeptides causing ion suppression to the glycopeptides were effectively removed, the signal of glycopeptides were enhanced significantly by LCD-MOFs, and twenty glycopeptides were identified with 67 fmol of IgG digest. 25110774 7 91 gly glycopeptides 1357:1369 arg2 twenty glycopeptides twenty glycopeptides glycopeptides In the selectivity assessment, the non-glycopeptides causing ion suppression to the glycopeptides were effectively removed, the signal of glycopeptides were enhanced significantly by LCD-MOFs, and twenty glycopeptides were identified with 67 fmol of IgG digest. 25110774 7 93 gly non-glycopeptides 1188:1204 arg2 the non-glycopeptides the non-glycopeptides non-glycopeptides In the selectivity assessment, the non-glycopeptides causing ion suppression to the glycopeptides were effectively removed, the signal of glycopeptides were enhanced significantly by LCD-MOFs, and twenty glycopeptides were identified with 67 fmol of IgG digest. 25110774 7 94 gly glycopeptides 1237:1249 arg2 the glycopeptides the glycopeptides glycopeptides In the selectivity assessment, the non-glycopeptides causing ion suppression to the glycopeptides were effectively removed, the signal of glycopeptides were enhanced significantly by LCD-MOFs, and twenty glycopeptides were identified with 67 fmol of IgG digest. 27629418 0 71 gly Core-fucosylated 67:82 arg1 Core-fucosylated N-Glycans Core-fucosylated N-Glycans Generation of a Mutant Mucor hiemalis Endoglycosidase That Acts on Core-fucosylated N-Glycans. 26571101 2 0 gly glycoprotein 348:359 arg1 current glycoprotein analyses current glycoprotein analyses Fterm glycoprotein However, due to the complexity and heterogeneity of glycoprotein conformations, current glycoprotein analyses focus mainly on either the de-glycosylated glycosylation site (glycosite)-containing peptides or the released glycans. 26571101 2 16 gly glycoprotein 312:323 arg1 glycoprotein conformations glycoprotein conformations Fterm glycoprotein However, due to the complexity and heterogeneity of glycoprotein conformations, current glycoprotein analyses focus mainly on either the de-glycosylated glycosylation site (glycosite)-containing peptides or the released glycans. 26571101 2 35 gly glycosite 433:441 arg2 glycosite glycosite glycosite However, due to the complexity and heterogeneity of glycoprotein conformations, current glycoprotein analyses focus mainly on either the de-glycosylated glycosylation site (glycosite)-containing peptides or the released glycans. 26571101 2 39 gly glycosylation 413:425 arg2 the de-glycosylated glycosylation site the de-glycosylated glycosylation site site However, due to the complexity and heterogeneity of glycoprotein conformations, current glycoprotein analyses focus mainly on either the de-glycosylated glycosylation site (glycosite)-containing peptides or the released glycans. 26571101 2 47 gly de-glycosylated 397:411 arg1 the de-glycosylated glycosylation site the de-glycosylated glycosylation site site However, due to the complexity and heterogeneity of glycoprotein conformations, current glycoprotein analyses focus mainly on either the de-glycosylated glycosylation site (glycosite)-containing peptides or the released glycans. 26571101 2 53 gly -containing 443:453 arg1 the de-glycosylated glycosylation site the de-glycosylated glycosylation site site However, due to the complexity and heterogeneity of glycoprotein conformations, current glycoprotein analyses focus mainly on either the de-glycosylated glycosylation site (glycosite)-containing peptides or the released glycans. 28649731 9 66 gly glycoproteins 1341:1353 arg1 serum glycoproteins serum glycoproteins Fterm glycoproteins The quinary interaction between Gal-3 and serum glycoproteins, could help to co-localize Gal-3 at the cell surface, and may play a role in adhesion and signalling functions of this protein. 24575722 2 29 gly glycoproteins 392:404 arg1 glycoproteins glycoproteins Fterm glycoproteins To identify potential diagnostic candidate markers, we have developed a novel method for analysis of glycosylation changes of glycoproteins from crude serum samples using lectin-based glycoprotein capture followed by detection with biotin/HRP-conjugated antibodies. 24575722 2 71 gly glycoprotein 450:461 arg1 lectin-based glycoprotein capture lectin-based glycoprotein capture Fterm glycoprotein To identify potential diagnostic candidate markers, we have developed a novel method for analysis of glycosylation changes of glycoproteins from crude serum samples using lectin-based glycoprotein capture followed by detection with biotin/HRP-conjugated antibodies. 26963691 2 46 gly removal 295:301 arg3 terminal N-acetylglucosamine AND PG fragments PG fragments terminal N-acetylglucosamine fragments β-N-Acetylglucosaminidases (NagZ enzymes) are involved in the PG process and they catalyze the removal of terminal N-acetylglucosamine in PG fragments. 25231986 6 78 gly has 1009:1011 arg1 the reducing end region AND 5-7 unbranched α-6-linked-mannosyl residues the reducing end region 5-7 unbranched α-6-linked-mannosyl residues region Using an MSMEG_4241 mutant that lacks the α-(1,6)-mannosyltransferase used late in LM elongation, we showed that the reducing end region of the mannan that is attached to inositol has 5-7 unbranched α-6-linked-mannosyl residues followed by two or three α-6-linked mannosyl residues branched with single α-mannopyranose residues at O-2. 26984886 11 33 gly presence 1661:1668 arg2 a particular site AND immature, high-mannose type glycans a particular site immature, high-mannose type glycans site We observed that the presence of immature, high-mannose type glycans at a particular site correlated with reduced accessibility to glycan remodeling enzymes. 28534482 5 30 gly glycopeptides 933:945 arg2 N-linked glycopeptides N-linked glycopeptides glycopeptides In particular, we demonstrate that the Fbs1 GYR variant may be employed for substantially unbiased enrichment of N-linked glycopeptides from human serum. 28277614 3 117 gly proteins 535:542 arg1 METHODS proteins METHODS Fterm proteins METHODS O-Glycans and glycopeptides from secreted proteins were separated by porous graphitised carbon and C-18 liquid chromatography, respectively. 28277614 3 84 gly glycopeptides 507:519 arg2 glycopeptides proteins glycopeptides Fterm proteins glycopeptides METHODS O-Glycans and glycopeptides from secreted proteins were separated by porous graphitised carbon and C-18 liquid chromatography, respectively. 27038031 4 10 part_of GluC 683:686 arg1 HILIC-enriched tryptic and GluC glycopeptides GluC HILIC-enriched tryptic and GluC glycopeptides PUBTATOR Site GluC 57733 glycopeptides In this study, the N-glycosylation of recombinant pentameric and hexameric IgM produced by the same human cell type and culture conditions was site-specifically profiled by RP-LC-CID/ETD-MS/MS using HILIC-enriched tryptic and GluC glycopeptides. 27743372 5 64 gly glycoproteins 907:919 arg1 N-glycan profiling glycoproteins N-glycan profiling Fterm glycoproteins Therefore, there is a great demand for widely applicable, high-throughput sample preparation and analysis methods for N-glycan profiling of glycoproteins. 25282312 3 16 gly degree 918:923 arg1 the glycoform composition the glycoform composition position Intact protein analysis was carried out to quantify the glycosylation degree and profile the glycoform composition of all the prepared neo glycoconjugates, while pronase and chymotriptic digests were analyzed to map and rank the reactivity of protein residues. 26773038 4 16 gly domain 631:636 arg1 the N-linked glycans domain the N-linked glycans domain We investigated how the N-linked glycans of the VWF A2 domain affect thermostability and regulate both the exposure of the ADAMTS13 binding sites and the scissile bond. 25227423 2 58 gly glycosylation 416:428 arg2 surface residues surface residues residues One common assumption is that N-glycans physically shield surface residues that are near to glycosylation sites, thereby preventing antibodies from binding to them. 25227423 2 58 gly glycosylation 416:428 arg2 glycosylation sites glycosylation sites sites One common assumption is that N-glycans physically shield surface residues that are near to glycosylation sites, thereby preventing antibodies from binding to them. 28433761 12 91 part_of protein 2038:2044 arg1 site protein site Fterm Site protein site Therefore, characterization of type and site of glycosidic chains in this protein may help to understand these important properties. 28433761 12 104 part_of site 2004:2007 arg1 this protein protein site Fterm Site protein site Therefore, characterization of type and site of glycosidic chains in this protein may help to understand these important properties. 28199092 2 47 part_of containing 336:345 arg1 proteins AND multiple glycosylation sites proteins multiple glycosylation sites Fterm Site proteins sites Therefore, for proteins containing multiple glycosylation sites, the individual glycan species present at a particular site cannot be differentiated from those species present at the other glycosylation sites on the molecule. 29119347 4 99 gly lysosomal 1564:1572 arg1 lysosomal enzyme N-acetylglucosamine [GlcNAc]-1-phosphotransferase enzyme lysosomal enzyme N-acetylglucosamine [GlcNAc]-1-phosphotransferase Fterm enzyme Because recombinant lysosomal enzymes produced in plants require the addition of mannose-6-phosphate (M6P) in order to be suitable for lysosomal delivery in human cells, we characterized the two IDUA proteins for their amenability to downstream in vitro mannose phosphorylation mediated by a soluble form of the human phosphotransferase (UDP-GlcNAc: lysosomal enzyme N-acetylglucosamine [GlcNAc]-1-phosphotransferase). 28193043 5 66 part_of glycoprotein 813:824 arg1 regions glycoprotein regions Fterm Site glycoprotein regions HDX information can typically not be obtained from regions of the glycoprotein that contain the actual N-linked glycan as glycan heterogeneity combined with pepsin digestion yields a large diversity of peptic N-glycosylated peptides that can be difficult to detect. 25451932 5 51 gly N-glycosylation 597:611 arg2 the 19 predicted N-glycosylation sites the 19 predicted N-glycosylation sites sites In this study, we examined corin mutants, in which each of the 19 predicted N-glycosylation sites was mutated individually. 28754360 2 77 gly protein 281:287 arg1 the glycan structure protein the glycan structure Fterm protein Importantly, the glycan structure of a therapeutic protein influences its efficacy, pharmacokinetics, pharmacodynamics and immunogenicity. 26791533 6 68 gly glycoproteins 885:897 arg1 human seminal plasma total glycoproteins human seminal plasma total glycoproteins Fterm glycoproteins This strategy has been applied to human seminal plasma total glycoproteins. 25092234 6 82 gly glycosites 920:929 arg2 the three heavy-chain glycosites the three heavy-chain glycosites glycosites MS analyses of intact hFXI revealed full occupation of two of the three heavy-chain glycosites and almost full-site occupancy of the light chain. 26630650 7 23 part_of EGF-like 813:820 arg1 A C-terminal EGF-like domain EGF A C-terminal EGF-like domain OGER Site EGF P01133 domain A C-terminal EGF-like domain was identified in spider hyaluronidase using InterPro. 28331984 1 4 gly glycosylate 162:172 arg1 their proteins their proteins Fterm proteins Results from recent studies are breaking the paradigm that all viruses depend on their host machinery to glycosylate their proteins. 26330553 6 81 gly residue 1078:1084 arg1 an α-l-Rha-(1→3)-d-GlcNAc motif residue in an α-l-Rha-(1→3)-d-GlcNAc motif residue in Although O-antigen production is cryptic in Escherichia coli K-12, because of a mutation in the synthesis genes, it possesses a prophage glucosylation cluster, which modifies the GlcNAc residue in an α-l-Rha-(1→3)-d-GlcNAc motif found in the original O16 antigen. 25458834 6 42 part_of residues 781:788 arg1 CLEC-2 CLEC-2 residues PUBTATOR Site CLEC-2 51266 residues There is a common interaction mode between consecutive acidic residues on the ligands and the same arginine residues on CLEC-2. 25458834 6 51 part_of residues 827:834 arg1 CLEC-2 CLEC-2 residues PUBTATOR AminoAcid CLEC-2 51266 arginine residues There is a common interaction mode between consecutive acidic residues on the ligands and the same arginine residues on CLEC-2. 28939751 1 6 gly glycosylated 178:189 arg2 36 extracellular EGF domains domains domains The transmembrane signaling protein Notch, which is crucial for embryonic cell fate decisions, has 36 extracellular EGF domains that are glycosylated in variable and complex ways. 26488311 5 18 gly glycosylation 830:842 arg2 the different glycosylation sites the different glycosylation sites sites Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we have determined the differences in the glycoforms associated at each of the different glycosylation sites in plasma clusterin obtained from subjects of low hippocampal atrophy (n = 13) and high hippocampal atrophy (n = 14). 25753700 2 0 gly glycoproteins 297:309 arg1 glycoproteins glycoproteins Fterm glycoproteins Determining the structure and functional relationship of glycoproteins requires the comprehensive characterization of glycan structures by a range of analytical methods. 28717478 9 1 gly glycopeptides 1747:1759 arg2 the glycopeptides the glycopeptides glycopeptides We conclude that chemo-enzymatic synthesis of mannosylated glycopeptides enhances uptake by human APCs while preserving the immunogenicity of peptide epitopes within the glycopeptides, provided those epitopes are not themselves glycosylated. 28717478 9 22 gly glycopeptides 1636:1648 arg2 mannosylated glycopeptides mannosylated glycopeptides glycopeptides We conclude that chemo-enzymatic synthesis of mannosylated glycopeptides enhances uptake by human APCs while preserving the immunogenicity of peptide epitopes within the glycopeptides, provided those epitopes are not themselves glycosylated. 28717478 9 69 gly mannosylated 1623:1634 arg1 mannosylated glycopeptides mannosylated glycopeptides glycopeptides We conclude that chemo-enzymatic synthesis of mannosylated glycopeptides enhances uptake by human APCs while preserving the immunogenicity of peptide epitopes within the glycopeptides, provided those epitopes are not themselves glycosylated. 25552259 3 60 part_of glycophorin 566:576 arg1 Amino-acid sequence glycophorin Amino-acid sequence Fterm Site glycophorin sequence Adv Exp Med Biol, 491:155-169; Tomita M and Marchesi VT. 1975, Amino-acid sequence and oligosaccharide attachment sites of human erythrocyte glycophorin. 27928741 9 13 gly observed 1483:1490 arg2 site 481 AND paucimannose glycans site 481 paucimannose glycans site N-linked sites 433 and 481 were observed to contain high mannose glycans with paucimannose glycans also observed at site 481. 27928741 9 37 gly contain 1423:1429 arg1 N-linked sites AND high mannose glycans N-linked sites high mannose glycans sites N-linked sites 433 and 481 were observed to contain high mannose glycans with paucimannose glycans also observed at site 481. 28654715 5 64 gly motifs 912:917 arg1 trisaccharide motifs trisaccharide motifs The set of trisaccharide motifs can be summarized with the consensus motifs X-β1,4-[Fucα1,3]-Y and X-β1,3-[Fucα1,4]-Y-a secondary structure we name [3,4]F-branch. 24028868 6 40 part_of EEQFNSTFR 799:807 arg1 peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) EEQFNSTFR (IgG2 peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) OGER Site EEQFNSTFR (IgG2 P01859 peptides Glycans on peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) were quantified, and their abundances were normalized to total IgGn glycoform abundance. 24028868 6 52 part_of EEQYNSTYR 778:786 arg1 peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) EEQYNSTYR (IgG1 peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) OGER Site EEQYNSTYR (IgG1 P01857 peptides Glycans on peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) were quantified, and their abundances were normalized to total IgGn glycoform abundance. 28444691 6 95 gly mono-sialylated 1058:1072 arg1 mono-sialylated glycoform mono-sialylated glycoform When compared with age-matched controls, COG5-CDG showed a significant increase of apoC-III0a (aglycosylated glycoform), whereas apoC-III1 (mono-sialylated glycoform) decreased significantly. 28576848 8 8 gly sialylated 1831:1840 arg1 large and sialylated glycans large and sialylated glycans On FcγRI and FcγRIIIa large and sialylated glycans have a negative impact on rituximab binding, likely through destabilization of the interaction. 26190824 5 3 gly N-glycosylation 866:880 arg2 N-glycosylation sequons N-glycosylation sequons These results demonstrate that manipulating the sequence space surrounding N-glycosylation sequons is useful both for controlling glycosylation efficiency, thus enhancing glycan occupancy, and for influencing the N-glycan structures produced. 24279413 8 77 gly glycopeptides 1427:1439 arg2 103 highly confident N-linked glycopeptides 103 highly confident N-linked glycopeptides glycopeptides Using this framework, 103 highly confident N-linked glycopeptides from 53 sites across 33 glycoproteins were identified in complex human serum proteome samples using conventional proteomic platforms with standard depletion of the 7-most abundant proteins. 24279413 8 77 gly glycopeptides 1427:1439 arg1 53 sites 53 sites sites Using this framework, 103 highly confident N-linked glycopeptides from 53 sites across 33 glycoproteins were identified in complex human serum proteome samples using conventional proteomic platforms with standard depletion of the 7-most abundant proteins. 24279413 8 85 gly glycoproteins 1465:1477 arg1 33 glycoproteins 33 glycoproteins Fterm glycoproteins Using this framework, 103 highly confident N-linked glycopeptides from 53 sites across 33 glycoproteins were identified in complex human serum proteome samples using conventional proteomic platforms with standard depletion of the 7-most abundant proteins. 26993603 4 27 gly glycoforms 629:638 arg2 Asn144 Asn144 Asn144 We found five glycoforms on Asn144, including biantennary, triantennary and fucosylated glycans. 26993603 4 42 gly fucosylated 691:701 arg1 fucosylated glycans fucosylated glycans We found five glycoforms on Asn144, including biantennary, triantennary and fucosylated glycans. 27038031 9 2 gly peptide 1624:1630 arg1 global glycan or deglycosylated peptide profiling global glycan or deglycosylated peptide profiling This study highlights the information obtained by characterization of the site-heterogeneity of a highly glycosylated protein of high molecular mass with quaternary structure, revealing differences that would not be seen by global glycan or deglycosylated peptide profiling. 27038031 9 22 gly site-heterogeneity 1442:1459 arg1 a highly glycosylated protein a highly glycosylated protein Fterm protein This study highlights the information obtained by characterization of the site-heterogeneity of a highly glycosylated protein of high molecular mass with quaternary structure, revealing differences that would not be seen by global glycan or deglycosylated peptide profiling. 27038031 9 26 gly glycosylated 1473:1484 arg1 a highly glycosylated protein a highly glycosylated protein Fterm protein This study highlights the information obtained by characterization of the site-heterogeneity of a highly glycosylated protein of high molecular mass with quaternary structure, revealing differences that would not be seen by global glycan or deglycosylated peptide profiling. 27928741 13 114 gly glycosylation 2038:2050 arg2 N-linked glycosylation sites haemagglutinin-neuraminidase sites Fterm haemagglutinin-neuraminidase sites These finding will form the basis for future quantitative glycomic studies of the distribution of glycan structures across N-linked glycosylation sites of Newcastle disease virus haemagglutinin-neuraminidase and assessment of the functional significance of the O-linked glycan in the stalk domain of this protein. 27320861 2 42 gly linked 156:161 arg1 proteins AND N-glycans proteins N-glycans Fterm proteins In animals, N-glycans linked to proteins function in cell-cell recognition, sorting, transport, and other biological phenomena. 28630087 1 25 gly N-glycosylated 170:183 arg1 an important N-glycosylated serine protease an important N-glycosylated serine protease Fterm protease Human neutrophil elastase (HNE) is an important N-glycosylated serine protease in the innate immune system, but the structure and immune-modulating functions of HNE N-glycosylation remain undescribed. 28035807 6 4 gly glycopeptides 1140:1152 arg2 the glycopeptides the glycopeptides glycopeptides About 81% of the glycopeptides contained at least one sialic acid, which could reveal the microheterogeneity of O-GalNAc glycosylation. 28035807 6 33 gly microheterogeneity 1213:1230 arg1 O-GalNAc glycosylation O-GalNAc glycosylation About 81% of the glycopeptides contained at least one sialic acid, which could reveal the microheterogeneity of O-GalNAc glycosylation. 28035807 6 68 gly contained 1154:1162 arg1 the glycopeptides AND at least one sialic acid the glycopeptides at least one sialic acid glycopeptides About 81% of the glycopeptides contained at least one sialic acid, which could reveal the microheterogeneity of O-GalNAc glycosylation. 28039139 8 41 gly glycoprotein 1427:1438 arg1 S-layer glycoprotein susceptibility S-layer glycoprotein susceptibility Fterm glycoprotein Finally, an assessment of S-layer glycoprotein susceptibility to added proteases in the mutants revealed that in cells lacking AglD, which is involved in adding the final pentasaccharide sugar, a distinct S-layer glycoprotein conformation was assumed in which the N-terminal region was readily degraded. 28039139 8 95 gly glycoprotein 1606:1617 arg1 a distinct S-layer glycoprotein conformation a distinct S-layer glycoprotein conformation Fterm glycoprotein Finally, an assessment of S-layer glycoprotein susceptibility to added proteases in the mutants revealed that in cells lacking AglD, which is involved in adding the final pentasaccharide sugar, a distinct S-layer glycoprotein conformation was assumed in which the N-terminal region was readily degraded. 27073020 0 49 gly N-glycosylation 100:114 arg1 secreted glycoproteins secreted glycoproteins Fterm glycoproteins DNA hypomethylation upregulates expression of the MGAT3 gene in HepG2 cells and leads to changes in N-glycosylation of secreted glycoproteins. 27073020 0 61 gly glycoproteins 128:140 arg1 secreted glycoproteins secreted glycoproteins Fterm glycoproteins DNA hypomethylation upregulates expression of the MGAT3 gene in HepG2 cells and leads to changes in N-glycosylation of secreted glycoproteins. 25155433 4 69 gly isoenzymes 693:702 arg1 GalNAc-Ts isoenzymes GalNAc-Ts Fterm isoenzymes What determines O-glycan site occupancy is still poorly understood, although it is clear that the substrate specificities of individual isoenzymes and the repertoire of GalNAc-Ts in cells are key parameters. 26791533 10 65 part_of epitopes 1329:1336 arg1 multiple seminal plasma glycoproteins glycoproteins epitopes Fterm Site glycoproteins epitopes Many Lewis x/a and y/b epitopes bearing glycans were found, suggesting immune-modulating epitopes on multiple seminal plasma glycoproteins. 24855066 5 17 gly released 935:942 arg2 membrane glycoproteins AND N-glycans membrane glycoproteins N-glycans Fterm glycoproteins N-glycans were released from membrane glycoproteins by PNGase F and analyzed using nano-liquid chromatography on porous graphitized carbon and negative-ion electrospray ionization mass spectrometry (ESI-MS). 24855066 5 38 gly glycoproteins 958:970 arg1 membrane glycoproteins membrane glycoproteins Fterm glycoproteins N-glycans were released from membrane glycoproteins by PNGase F and analyzed using nano-liquid chromatography on porous graphitized carbon and negative-ion electrospray ionization mass spectrometry (ESI-MS). 25636227 9 80 gly glycopeptides 1371:1383 arg1 36 distinctive glycoproteins 36 distinctive glycoproteins Fterm glycoproteins Using only one drop of blood, a total of 49 O-GalNAc-linked glycopeptides from 36 distinctive glycoproteins in human plasma were identified unambiguously. 25636227 9 56 gly glycoproteins 1405:1417 arg1 49 O-GalNAc-linked glycopeptides glycoproteins 49 O-GalNAc-linked glycopeptides Fterm glycoproteins Using only one drop of blood, a total of 49 O-GalNAc-linked glycopeptides from 36 distinctive glycoproteins in human plasma were identified unambiguously. 25326312 2 54 gly glycoproteins 554:566 arg1 glycoproteins glycoproteins Fterm glycoproteins These four UDP-sugars are essential donors for driving the synthesis of glycoproteins and glycolipids, which heavily decorate cell surfaces and extracellular spaces. 26162743 2 15 gly glycosylation 415:427 arg1 a GlcNAc acceptor a GlcNAc acceptor The trisaccharide was prepared in a highly convergent synthesis (seven steps, longest linear sequence) and in a 38% overall yield using a strategy that involved the regioselective glycosylation of a GlcNAc acceptor with a galactose thioglycoside donor, followed by fucosylation of the remaining free GlcNAc hydroxyl as key steps. 26162743 2 34 gly fucosylation 500:511 arg1 the remaining free GlcNAc hydroxyl the remaining free GlcNAc hydroxyl The trisaccharide was prepared in a highly convergent synthesis (seven steps, longest linear sequence) and in a 38% overall yield using a strategy that involved the regioselective glycosylation of a GlcNAc acceptor with a galactose thioglycoside donor, followed by fucosylation of the remaining free GlcNAc hydroxyl as key steps. 28902916 9 25 gly glycosylated 1506:1517 arg1 fully glycosylated NFL fully glycosylated NFL We performed rabbit immunogenicity experiments using two approaches comparing glycan-deleted to fully glycosylated NFL trimers. 27054587 7 63 gly glycoforms 1201:1210 arg1 Lewis Y Lewis Y In the absence of β4Gal-T4, all Lewis X, sialyl-Lewis X, Lewis Y and Sda/Cad glycoforms were eliminated, in contrast to knockouts of the N-acetylglucosaminyltransferases, which did not affect the relative abundances of O-glycans expressing these epitopes. 27054587 7 63 gly glycoforms 1201:1210 arg1 Lewis X Lewis X In the absence of β4Gal-T4, all Lewis X, sialyl-Lewis X, Lewis Y and Sda/Cad glycoforms were eliminated, in contrast to knockouts of the N-acetylglucosaminyltransferases, which did not affect the relative abundances of O-glycans expressing these epitopes. 27054587 7 63 gly glycoforms 1201:1210 arg1 Sda/Cad Sda/Cad In the absence of β4Gal-T4, all Lewis X, sialyl-Lewis X, Lewis Y and Sda/Cad glycoforms were eliminated, in contrast to knockouts of the N-acetylglucosaminyltransferases, which did not affect the relative abundances of O-glycans expressing these epitopes. 27054587 7 63 gly glycoforms 1201:1210 arg1 sialyl-Lewis X sialyl-Lewis X In the absence of β4Gal-T4, all Lewis X, sialyl-Lewis X, Lewis Y and Sda/Cad glycoforms were eliminated, in contrast to knockouts of the N-acetylglucosaminyltransferases, which did not affect the relative abundances of O-glycans expressing these epitopes. 28193043 6 25 gly glycopeptides 1205:1217 arg2 labeled peptic N-linked glycopeptides labeled peptic N-linked glycopeptides glycopeptides Here, we present a novel HDX-MS workflow for analysis of the conformational dynamics of N-linked glycoproteins that utilizes the enzyme PNGase A for deglycosylation of labeled peptic N-linked glycopeptides at HDX quench conditions, i.e., acidic pH and low temperature. 28193043 6 49 gly glycoproteins 1110:1122 arg1 N-linked glycoproteins N-linked glycoproteins Fterm glycoproteins Here, we present a novel HDX-MS workflow for analysis of the conformational dynamics of N-linked glycoproteins that utilizes the enzyme PNGase A for deglycosylation of labeled peptic N-linked glycopeptides at HDX quench conditions, i.e., acidic pH and low temperature. 28193043 6 107 gly deglycosylation 1162:1176 arg1 labeled peptic N-linked glycopeptides labeled peptic N-linked glycopeptides glycopeptides Here, we present a novel HDX-MS workflow for analysis of the conformational dynamics of N-linked glycoproteins that utilizes the enzyme PNGase A for deglycosylation of labeled peptic N-linked glycopeptides at HDX quench conditions, i.e., acidic pH and low temperature. 25587188 0 80 part_of ACPA-IgG 27:34 arg1 ACPA-IgG variable domains ACPA ACPA-IgG variable domains PUBTATOR Site ACPA 5657 domains Extensive glycosylation of ACPA-IgG variable domains modulates binding to citrullinated antigens in rheumatoid arthritis. 26991339 0 56 gly glycosylation 16:28 arg2 N- and O-linked glycosylation site N- and O-linked glycosylation site site N- and O-linked glycosylation site profiling of the human basic salivary proline-rich protein 3M. 25094044 2 7 gly glycosylated 440:451 arg1 newly synthesized glycosylated polypeptides newly synthesized glycosylated polypeptides polypeptides UGGT1 acts as a folding sensor of newly synthesized glycosylated polypeptides in the endoplasmic reticulum, and the transferase itself is known to be glycosylated. 25094044 2 40 gly glycosylated 538:549 arg1 the transferase itself the transferase itself Fterm transferase UGGT1 acts as a folding sensor of newly synthesized glycosylated polypeptides in the endoplasmic reticulum, and the transferase itself is known to be glycosylated. 27649061 7 70 gly fucosylated 1363:1373 arg1 doubly fucosylated glycoforms doubly fucosylated glycoforms Under optimized conditions, we achieve label-free quantification of the majority of previously reported glycoforms of IgG (26 glycoforms of IgG1, 22 glycoforms of IgG 2/3, and 19 glycoforms of IgG4) directly in unfractionated samples of human plasma and we detect traces of previously unreported glycoforms of IgG1, including doubly fucosylated glycoforms. 24308717 2 34 gly N- 493:494 arg1 the occupied O-glycosylation sites the occupied O-glycosylation sites sites An in-depth characterization of the glycosylation of etanercept was carried out using liquid chromatography/mass spectrometry (LC/MS) methods in a systematic approach in which we analyzed the N- and O-linked glycans and located the occupied O-glycosylation sites. 24308717 2 76 gly O-glycosylation 542:556 arg2 the occupied O-glycosylation sites the occupied O-glycosylation sites sites An in-depth characterization of the glycosylation of etanercept was carried out using liquid chromatography/mass spectrometry (LC/MS) methods in a systematic approach in which we analyzed the N- and O-linked glycans and located the occupied O-glycosylation sites. 26699903 1 25 part_of motifs 376:381 arg1 multiple potential N-linked glycosylation sites motifs multiple potential N-linked glycosylation sites sites SCUBE1 (S1), a secreted and membrane-bound glycoprotein, has a modular protein structure composed of an N-terminal signal peptide sequence followed by nine epidermal growth factor (EGF)-like repeats, a spacer region and three cysteine-rich (CR) motifs with multiple potential N-linked glycosylation sites, and one CUB domain at the C-terminus. 26699903 1 36 part_of domain 449:454 arg1 multiple potential N-linked glycosylation sites domain multiple potential N-linked glycosylation sites sites SCUBE1 (S1), a secreted and membrane-bound glycoprotein, has a modular protein structure composed of an N-terminal signal peptide sequence followed by nine epidermal growth factor (EGF)-like repeats, a spacer region and three cysteine-rich (CR) motifs with multiple potential N-linked glycosylation sites, and one CUB domain at the C-terminus. 26699903 1 79 part_of region 340:345 arg1 multiple potential N-linked glycosylation sites region multiple potential N-linked glycosylation sites sites SCUBE1 (S1), a secreted and membrane-bound glycoprotein, has a modular protein structure composed of an N-terminal signal peptide sequence followed by nine epidermal growth factor (EGF)-like repeats, a spacer region and three cysteine-rich (CR) motifs with multiple potential N-linked glycosylation sites, and one CUB domain at the C-terminus. 28510654 3 79 gly glycoproteins 374:386 arg1 glycoproteins glycoproteins Fterm glycoproteins Here, we enriched glycoproteins from cultured P. calidifontis cells, by ConA lectin chromatography. 28924016 0 28 gly Epitope 38:44 arg1 Epitope Mapping Epitope Mapping A Synthetic Glycan Microarray Enables Epitope Mapping of Plant Cell Wall Glycan-Directed Antibodies. 26618856 3 17 part_of proteins 579:586 arg1 intrinsically disordered regions proteins intrinsically disordered regions Fterm Site proteins regions Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) of large proteins are also frequently glycosylated, yet how glycosylation affects their function remains to be elucidated. 28680094 5 38 gly domain 702:707 arg1 the headpiece and leg domain interface the headpiece and leg domain interface We found that the N-glycan site, β3-N320 at the headpiece and leg domain interface positively regulates αIIbβ3 but not αVβ3 activation. 26812091 8 49 gly N-glycopeptides 1235:1249 arg2 the N-glycopeptides the N-glycopeptides N-glycopeptides A high degree of heterogeneity was observed in the N-glycopeptides of both hFSHs. 26067753 1 67 part_of Fab 218:220 arg1 the Fab domain Fab the Fab domain PUBTATOR Site Fab 2187 domain We investigated N-glycan processing of immunoglobulin G1 using the monoclonal antibody cetuximab (CxMab), which has a glycosite in the Fab domain in addition to the conserved Fc glycosylation, as a reporter. 26067753 1 53 part_of has 195:197 arg1 CxMab AND a glycosite CxMab a glycosite Cterm Site (CxMab) glycosite We investigated N-glycan processing of immunoglobulin G1 using the monoclonal antibody cetuximab (CxMab), which has a glycosite in the Fab domain in addition to the conserved Fc glycosylation, as a reporter. 29062024 0 53 part_of immunoglobulin 56:69 arg1 immunoglobulin G Fc region immunoglobulin G immunoglobulin G Fc region Cterm Site immunoglobulin G region Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa. 27223297 3 11 gly positions 535:543 arg1 five putative N-glycan sequons positions five putative N-glycan sequons positions The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 N794 N794, N829, N1035, and N1077 N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 five putative N-glycan sequons N794, N829, N1035, and N1077 N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 The Rift Valley fever virus (RVFV) glycoproteins glycoproteins N794, N829, N1035, and N1077 Fterm glycoproteins N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 N829 N794, N829, N1035, and N1077 N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 N1077 N794, N829, N1035, and N1077 N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 five putative N-glycan sequons N794, N829, N1035, and N1077 N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 The Rift Valley fever virus (RVFV) glycoproteins glycoproteins N794, N829, N1035, and N1077 Fterm glycoproteins N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 N829 N794, N829, N1035, and N1077 N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 N1077 N794, N829, N1035, and N1077 N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 The Rift Valley fever virus (RVFV) glycoproteins glycoproteins Fterm glycoproteins The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 N829 N794, N829, N1035, and N1077 N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 N1077 N794, N829, N1035, and N1077 N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 N829 glycoproteins N794, N829, N1035, and N1077 Fterm glycoproteins N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 N1077 glycoproteins N794, N829, N1035, and N1077 Fterm glycoproteins N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 27223297 3 55 gly glycoproteins 411:423 arg1 N1077 N794, N829, N1035, and N1077 N794, N829, N1035, and N1077 The Rift Valley fever virus (RVFV) glycoproteins (Gn/Gc) encode five putative N-glycan sequons (asparagine (N)-any amino acid (X)-serine (S)/threonine (T)) at positions: N438 (Gn), and N794, N829, N1035, and N1077 (Gc). 26286102 11 98 gly proteins 1714:1721 arg1 aberrant N-glycan structures proteins aberrant N-glycan structures Fterm proteins In conclusion, the study first shows aberrant N-glycan structures of CSF proteins in LOTSD; unveils possible pathomechanisms of GM2-gangliosidosis; supports existing relationships between neuropsychiatric disorders and unproper protein glycosylation in the CNS. 28860626 0 36 gly N-glycosylation 12:26 arg1 influenza proteins influenza proteins Fterm proteins Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. 28860626 0 37 gly proteins 78:85 arg1 site-specific N-glycan sulfation proteins site-specific N-glycan sulfation Fterm proteins Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. 28539451 13 80 part_of gp120 2411:2415 arg1 the gp120 V3 region gp120 the gp120 V3 region OGER Site gp120 Q14624 region Here, we have inserted two glycans into the dominant site for tier-1 NAbs, the gp120 V3 region, to block the induction of off-target antibodies. 28539451 13 80 part_of gp120 2411:2415 arg1 the dominant site gp120 the dominant site OGER Site gp120 Q14624 site Here, we have inserted two glycans into the dominant site for tier-1 NAbs, the gp120 V3 region, to block the induction of off-target antibodies. 25628020 0 19 part_of sites 41:45 arg1 conserved proteins proteins sites Fterm Site proteins sites The acquisition of novel N-glycosylation sites in conserved proteins during human evolution. 25110774 2 27 gly glycopeptides 468:480 arg2 glycopeptides glycopeptides glycopeptides Hydrophilic interaction chromatography (HILIC)-based strategies have been proposed for selective isolation of glycopeptides via the interactions between the glycan of glycopeptides and the matrices. 25110774 2 89 gly glycopeptides 525:537 arg1 the glycan glycopeptides the glycan glycopeptides Hydrophilic interaction chromatography (HILIC)-based strategies have been proposed for selective isolation of glycopeptides via the interactions between the glycan of glycopeptides and the matrices. 26082228 5 32 gly glycoproteins 792:804 arg1 recombinant glycoproteins recombinant glycoproteins Fterm glycoproteins These protocols can be used to fine-tune the subcellular localization of glycosyltransferases and glycosidases in plants and consequently to increase the homogeneity of glycosylation on recombinant glycoproteins. 29233911 9 66 gly N-glycosylation 1217:1231 arg2 all known six N-glycosylation sites all known six N-glycosylation sites sites Likewise, all known six N-glycosylation sites were covered and confirmed by this site-specific glycosylation analysis. 25849117 1 12 gly glycosylation 162:174 arg1 cell surface proteins cell surface proteins Fterm proteins The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. 25092234 0 28 gly glycosite 96:104 arg2 a noncanonical NXC glycosite a noncanonical NXC glycosite glycosite Site-specific N-glycosylation analysis of human factor XI: Identification of a noncanonical NXC glycosite. 27663739 9 50 gly proteins 1217:1224 arg1 O-fucose proteins O-fucose Fterm proteins Host cells modify secreted proteins with O-fucose; here we describe the O-fucosylation pathway in the nucleocytosol of a eukaryote. 27869200 4 47 gly glycopeptides 802:814 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides Tandem spectra of glycopeptides from fetuin, glycophorin A, ovalbumin and gp120 tryptic digests were used to build a spectral database of N- and O-linked glycopeptides. 27869200 4 69 gly glycopeptides 666:678 arg2 glycopeptides glycopeptides glycopeptides Tandem spectra of glycopeptides from fetuin, glycophorin A, ovalbumin and gp120 tryptic digests were used to build a spectral database of N- and O-linked glycopeptides. 28717478 3 33 gly used 741:744 arg2 A peptide A peptide peptide A peptide from the human cytomegalovirus (CMV) tegument protein pp65 that incorporates a well-characterised T cell epitope, containing N-acetylglucosamine at specific Asn residues, was accessed by solid phase peptide synthesis, and used as an acceptor substrate. 28717478 3 25 gly containing 633:642 arg1 A peptide AND N-acetylglucosamine A peptide N-acetylglucosamine peptide A peptide from the human cytomegalovirus (CMV) tegument protein pp65 that incorporates a well-characterised T cell epitope, containing N-acetylglucosamine at specific Asn residues, was accessed by solid phase peptide synthesis, and used as an acceptor substrate. 24664808 5 24 gly fragment 995:1002 arg1 glycan-lost fragment ions glycan-lost fragment ions The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. 24664808 5 61 gly fragment 963:970 arg1 (i) glycan fragment ions (i) glycan fragment ions The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. 25759508 7 7 gly O-glycosylation 1035:1049 arg2 potential O-glycosylation sites potential O-glycosylation sites sites The O-glycosylation site was further confirmed by the recombinant production of mutant IgG3 in which potential O-glycosylation sites had been knocked out. 25759508 7 34 gly O-glycosylation 928:942 arg2 The O-glycosylation site The O-glycosylation site site The O-glycosylation site was further confirmed by the recombinant production of mutant IgG3 in which potential O-glycosylation sites had been knocked out. 24806200 5 97 gly glycoproteins 1025:1037 arg1 these glycoproteins these glycoproteins Fterm glycoproteins In clinical applications, these hormones are administered as mixtures of glycoforms due to limitations of biological methods in producing homogeneous samples of these glycoproteins. 25182382 5 46 gly glycopeptides 901:913 arg2 intact glycopeptides intact glycopeptides glycopeptides The peptide sequences of intact glycopeptides were identified by matching the molecular weight calculated from Y1 ion to that of deglycosylated peptides from the same HILIC enrichment and identified by a separated LC-MS/MS analysis. 25182382 5 77 gly deglycosylated 998:1011 arg1 deglycosylated peptides deglycosylated peptides peptides The peptide sequences of intact glycopeptides were identified by matching the molecular weight calculated from Y1 ion to that of deglycosylated peptides from the same HILIC enrichment and identified by a separated LC-MS/MS analysis. 26563299 6 33 gly α1-6-core-fucosylated 995:1015 arg1 mostly α1-6-core-fucosylated and β-GlcNAc-terminating complex-type structures mostly α1-6-core-fucosylated and β-GlcNAc-terminating complex-type structures IL-15 Asn79 and sIL-15Rα Asn107 carried the same repertoire of biosynthetically-related N-glycans covering mostly α1-6-core-fucosylated and β-GlcNAc-terminating complex-type structures. 26563299 6 21 gly carried 913:919 arg1 IL-15 Asn79 AND biosynthetically-related N-glycans IL-15 Asn79 biosynthetically-related N-glycans Asn79 IL-15 Asn79 and sIL-15Rα Asn107 carried the same repertoire of biosynthetically-related N-glycans covering mostly α1-6-core-fucosylated and β-GlcNAc-terminating complex-type structures. 26563299 6 21 gly carried 913:919 arg1 sIL-15Rα Asn107 AND biosynthetically-related N-glycans sIL-15Rα Asn107 biosynthetically-related N-glycans Asn107 IL-15 Asn79 and sIL-15Rα Asn107 carried the same repertoire of biosynthetically-related N-glycans covering mostly α1-6-core-fucosylated and β-GlcNAc-terminating complex-type structures. 25552259 7 74 part_of GPC 949:951 arg1 the GPC binding site GPC the GPC binding site PUBTATOR Site GPC 2995 site The elucidation of these structures seems essential for full characterization of the GPC binding site for the EBA-140 ligand. 29233911 6 2 gly O-glycosylated 937:950 arg1 an extensively O-glycosylated N-terminal region an extensively O-glycosylated N-terminal region region The analysis revealed an extensively O-glycosylated N-terminal region. 26160412 4 3 part_of proteins 699:706 arg1 Tryptic glycopeptides proteins Tryptic glycopeptides Fterm Site proteins glycopeptides Tryptic glycopeptides from CSF proteins were also enriched by hydrophilic interaction, and the resulting extracts divided into two equal aliquots. 28956227 7 88 gly non-glycosylated 1390:1405 arg1 the non-glycosylated NTPDase3/CD39L3 ecto-enzymatic domain the non-glycosylated NTPDase3/CD39L3 ecto-enzymatic domain domain Our functional data indicate that the non-glycosylated NTPDase3/CD39L3 ecto-enzymatic domain retains activity, but that N-glycan attachments, such as the GlcNAc-Asn, substantially upregulate specific NTPDase activity by 2-20 fold. 26059692 4 7 gly disialylated 665:676 arg1 disialylated core 1 and core 2 O-glycans disialylated core 1 and core 2 O-glycans We found that the c/MAM domain was heavily O-glycosylated with up to 24 monosaccharide units in the form of disialylated core 1 and core 2 O-glycans. 26059692 4 28 gly O-glycosylated 600:613 arg1 the c/MAM domain domain domain We found that the c/MAM domain was heavily O-glycosylated with up to 24 monosaccharide units in the form of disialylated core 1 and core 2 O-glycans. 27705835 5 34 gly glycoproteins 947:959 arg1 almost all glycoproteins almost all glycoproteins Fterm glycoproteins Structural analysis of the N-glycans revealed that almost all glycoproteins expressed in these three water plants predominantly carry plant complex type N-glycans including the Lewis a type, suggesting that these water plants are good sources for preparation of Lewis a type plant N-glycans in substantial amounts. 27705835 5 24 gly carry 1013:1017 arg1 almost all glycoproteins AND plant complex type N-glycans almost all glycoproteins plant complex type N-glycans Fterm glycoproteins Structural analysis of the N-glycans revealed that almost all glycoproteins expressed in these three water plants predominantly carry plant complex type N-glycans including the Lewis a type, suggesting that these water plants are good sources for preparation of Lewis a type plant N-glycans in substantial amounts. 25193875 6 62 gly glycoproteins 847:859 arg1 many glycoproteins many glycoproteins Fterm glycoproteins The fat body is the main tissue of recombinant protein expression by baculovirus, and many glycoproteins are secreted into the hemolymph. 27808502 4 23 gly oligomannosylated 985:1001 arg1 the oligomannosylated glycopeptides the oligomannosylated glycopeptides glycopeptides The glycan structure of intact glycopeptides can be identified from MS/MS spectra of their own and their peptide sequences were identified by the MS3 spectra of the oligomannosylated glycopeptides with the same Y1 ion. 27808502 4 27 gly glycopeptides 1003:1015 arg2 the oligomannosylated glycopeptides the oligomannosylated glycopeptides glycopeptides The glycan structure of intact glycopeptides can be identified from MS/MS spectra of their own and their peptide sequences were identified by the MS3 spectra of the oligomannosylated glycopeptides with the same Y1 ion. 27808502 4 69 gly glycopeptides 851:863 arg1 The glycan structure glycopeptides The glycan structure glycopeptides The glycan structure of intact glycopeptides can be identified from MS/MS spectra of their own and their peptide sequences were identified by the MS3 spectra of the oligomannosylated glycopeptides with the same Y1 ion. 28486471 12 77 gly glycoprotein 2360:2371 arg1 glycoprotein products glycoprotein products Fterm glycoprotein Quantitative models of CHO cell glycosylation have the potential for predicting how glycoengineering manipulations might affect glycoform distributions to improve the therapeutic performance of glycoprotein products. 25038691 1 13 gly glycoprotein 110:121 arg1 The bovine milk glycoprotein bovine lactoferrin The bovine milk glycoprotein bovine lactoferrin Fterm glycoprotein The bovine milk glycoprotein bovine lactoferrin (bLF) has a variety of biological activities related to its constituent glycans. 27489265 15 22 gly glycosylation 2461:2473 arg2 surgical glycosylation site modification surgical glycosylation site modification site This indicates that surgical glycosylation site modification may be an effective way of sculpting epitope presentation in Env-based vaccines. 25793890 6 7 gly glycosylation 1048:1060 arg2 N-linked glycosylation sites N-linked glycosylation sites sites All three mutations created N-linked glycosylation sites (two at N136 and one at N149) proximal to the hypervariable connecting peptide between the C-terminus of the A strand and the N-terminus of the B strand in the four-stranded V1/V2 domain β-sheet structure. 25793890 6 31 gly sites 1062:1066 arg1 N-linked glycosylation sites N-linked glycosylation sites sites All three mutations created N-linked glycosylation sites (two at N136 and one at N149) proximal to the hypervariable connecting peptide between the C-terminus of the A strand and the N-terminus of the B strand in the four-stranded V1/V2 domain β-sheet structure. 24575722 1 11 gly glycosylation 106:118 arg1 glycoproteins glycoproteins Fterm glycoproteins Altered glycosylation in glycoproteins is associated with carcinogenesis, and certain glycan structures and glycoproteins are well-known markers for tumor progression. 24575722 1 13 gly glycoproteins 123:135 arg1 glycoproteins glycoproteins Fterm glycoproteins Altered glycosylation in glycoproteins is associated with carcinogenesis, and certain glycan structures and glycoproteins are well-known markers for tumor progression. 24575722 1 52 gly glycoproteins 206:218 arg1 certain glycan structures glycoproteins certain glycan structures Fterm glycoproteins Altered glycosylation in glycoproteins is associated with carcinogenesis, and certain glycan structures and glycoproteins are well-known markers for tumor progression. 25748215 2 29 gly linked 307:312 arg1 proteins AND The N-glycans proteins The N-glycans Fterm proteins The N-glycans that are covalently linked to proteins are involved in numerous biological processes. 27216994 8 12 part_of sites 1521:1525 arg1 GluN2B GluN2B sites PUBTATOR Site GluN2B Q13224 sites Finally, using mutant recombinant GluN subunits expressed in HEK293 cells, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 27216994 8 12 part_of sites 1521:1525 arg1 GluN1 GluN1 sites PUBTATOR Site GluN1 2902 sites Finally, using mutant recombinant GluN subunits expressed in HEK293 cells, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 27216994 8 33 part_of sites 1567:1571 arg1 GluN2B GluN2B sites PUBTATOR Site GluN2B Q13224 sites Finally, using mutant recombinant GluN subunits expressed in HEK293 cells, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 27216994 8 33 part_of sites 1567:1571 arg1 GluN1 GluN1 sites PUBTATOR Site GluN1 2902 sites Finally, using mutant recombinant GluN subunits expressed in HEK293 cells, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 28797655 11 23 gly glycosylation 1553:1565 arg2 the glycosylation sites the glycosylation sites sites Alterations in the glycosylation sites for the evolution and role of IAVs have been widely described; however, little is known about the exact glycan structures for the same influenza strain from different hosts. 26348906 9 18 gly N-glycosylation 1557:1571 arg1 the sites the sites sites Substitution of Asn(171) and Asn(183) by aspartate individually caused no loss of BGT-1 activity, whereas the double mutant was inactive, suggesting that N-glycosylation of at least one of the sites is required for function. 26729457 3 78 gly glycopeptide 554:565 arg2 glycopeptide fragmentation regimes glycopeptide fragmentation regimes glycopeptide However, the depth of information is highly dependent on the applied analytical tools, including glycopeptide fragmentation regimes and automated data analysis. 26492619 4 19 gly glycosylation 561:573 arg1 Thr34 Thr34 Thr34 In contrast, the glycosylation of Thr34 of PLAG1 of human PDPN remains to be clarified. 24451549 4 60 gly O-glycosylated 831:844 arg1 previously only flagellin proteins previously only flagellin proteins Fterm proteins Significantly, the MOMP was shown to be O-glycosylated at Thr(268); previously only flagellin proteins were known to be O-glycosylated in C. jejuni. 24451549 4 20 gly O-glycosylated 751:764 arg2 Thr Thr(268) Thr(268) Significantly, the MOMP was shown to be O-glycosylated at Thr(268); previously only flagellin proteins were known to be O-glycosylated in C. jejuni. 27356208 4 22 gly N-glycosylation 739:753 arg2 a new N-glycosylation site a new N-glycosylation site site In this regard, selection of a suitable location on the surface of a protein for introduction of a new N-glycosylation site is a main concern. 26241388 2 27 gly glycoproteins 358:370 arg1 glycoproteins glycoproteins Fterm glycoproteins Accordingly, FDL function accounts, at least in part, for major differences in the N-glycosylation patterns of glycoproteins produced by insect and mammalian cells. 26241388 2 48 gly N-glycosylation 330:344 arg1 glycoproteins glycoproteins Fterm glycoproteins Accordingly, FDL function accounts, at least in part, for major differences in the N-glycosylation patterns of glycoproteins produced by insect and mammalian cells. 29212317 8 8 gly glycosylated 1345:1356 arg1 The proteins The proteins Fterm proteins The proteins found in the plasma are differentially glycosylated compared to those isolated in HDL. 25499076 6 6 gly glycosylation 1131:1143 arg2 the glycosylation site occupancy the glycosylation site occupancy site To obtain recombinant G-hPRL, genetically modified Chinese hamster ovary cells (CHO), adapted to growth in suspension, were treated with cycloheximide, thus increasing the glycosylation site occupancy from 5.5% to 38.3%, thereby facilitating G-hPRL purification. 26160412 8 15 part_of glycoproteins 1331:1343 arg1 55 N-glycosites glycoproteins 55 N-glycosites Fterm Site glycoproteins N-glycosites Under these conditions, 124 N-glycopeptides representing 55 N-glycosites from 36 glycoproteins were tentatively identified. 27574189 9 27 gly attached 987:994 arg2 one to Thr AND Five O-linked glycans one to Thr Five O-linked glycans Thr Five O-linked glycans were attached to a Ser and one to Thr. 27574189 9 27 gly attached 987:994 arg1 a Ser AND Five O-linked glycans a Ser Five O-linked glycans Ser Five O-linked glycans were attached to a Ser and one to Thr. 28443077 4 59 gly glycosylated 975:986 arg1 the glycosylated HA trimers the glycosylated HA trimers Fterm trimers Comparison of the equilibrated structures of the glycosylated HA trimers with and without the 3C.2a-specific mutations reveals that the mutations could induce a drastic reduction in the apical space for the ligand binding via glycan-shield rearrangement. 25113421 5 68 gly glycopeptides 726:738 arg2 glycopeptides glycopeptides glycopeptides Two experimental approaches exist to obtain MS/MS spectral data of glycopeptides. 25210040 0 96 part_of factor 8:13 arg1 Trefoil factor family domains factor Trefoil factor family domains Fterm Site factor domains Trefoil factor family domains represent highly efficient conformational determinants for N-linked N,N'-di-N-acetyllactosediamine (LacdiNAc) synthesis. 29187599 4 51 gly occupied 713:720 arg2 Asn-110 Asn-110 Asn-110 Here, we show that Asn-110 in native hDAO from amniotic fluid and Caco-2 cells, DAO from porcine kidneys, and rhDAO produced in two different HEK293 cell lines is also consistently occupied by oligomannosidic glycans. 29016103 2 59 gly glycopeptides 373:385 arg2 intact glycopeptides intact glycopeptides glycopeptides Resolving this conundrum requires efficient and specific enrichment of intact glycopeptides for identification and quantitation. 28729420 1 7 gly fucosylation 220:231 arg1 N-glycans N-glycans The mammalian α1,6-fucosyltransferase (FUT8) catalyzes the core fucosylation of N-glycans in the biosynthesis of glycoproteins. 28729420 1 33 gly glycoproteins 269:281 arg1 glycoproteins glycoproteins Fterm glycoproteins The mammalian α1,6-fucosyltransferase (FUT8) catalyzes the core fucosylation of N-glycans in the biosynthesis of glycoproteins. 25737449 7 68 part_of E2 1039:1040 arg1 its E2(412-423) epitope E2 its E2(412-423) epitope Cterm Site E2 epitope To understand how HC33.1 penetrates the glycan shield created by the glycosylation shift to Asn-415, we determined the structure of this broadly neutralizing mAb in complex with its E2(412-423) epitope to 2.0 Å resolution. 28960760 3 41 part_of containing 521:530 arg1 those enzymes AND a putative nucleophilic residue those enzymes a putative nucleophilic residue Fterm AminoAcid enzymes residue in To date, the catalytic mechanism of retaining GTs is a topic of great controversy, particularly for those enzymes containing a putative nucleophilic residue in the active site, for which the occurrence of a double-displacement mechanism has been suggested. 24941220 10 9 gly glycosites 1697:1706 arg2 an additional four N-linked glycosites an additional four N-linked glycosites glycosites We further revealed that except for Asn276 in the C2 region, glycans were processed to contain both high mannose and hybrid/complex glycans; an additional four N-linked glycosites were decorated with high mannose type. 27320861 10 67 gly glycoproteins 1529:1541 arg1 different glycoproteins different glycoproteins Fterm glycoproteins This result suggests that the shoot and root of O. sativa have different glycoproteins and distinct N-glycan synthetic systems. 25746926 2 6 gly lectin 403:408 arg1 predominant N-acetylglucosamine-binding specificity lectin predominant N-acetylglucosamine-binding specificity Fterm lectin Here, we report that the stinging nettle lectin (UDA), with predominant N-acetylglucosamine-binding specificity, interacts with glycosylated VSGs and kills parasites by provoking defects in endocytosis together with impaired cytokinesis. 27550041 5 0 gly fucosylated 1047:1057 arg1 two high mannose N-glycans two high mannose N-glycans In addition, two high mannose N-glycans, four sialylated fucosylated complex N-glycans and six sialylated non-fucosylated complex N-glycans, one of which containing N-glycolylneuraminic acid (Neu5Gc), were found. 27550041 5 0 gly fucosylated 1047:1057 arg1 four sialylated fucosylated complex N-glycans four sialylated fucosylated complex N-glycans In addition, two high mannose N-glycans, four sialylated fucosylated complex N-glycans and six sialylated non-fucosylated complex N-glycans, one of which containing N-glycolylneuraminic acid (Neu5Gc), were found. 27550041 5 18 gly sialylated 1085:1094 arg1 two high mannose N-glycans two high mannose N-glycans In addition, two high mannose N-glycans, four sialylated fucosylated complex N-glycans and six sialylated non-fucosylated complex N-glycans, one of which containing N-glycolylneuraminic acid (Neu5Gc), were found. 27550041 5 18 gly sialylated 1085:1094 arg1 six sialylated non-fucosylated complex N-glycans six sialylated non-fucosylated complex N-glycans In addition, two high mannose N-glycans, four sialylated fucosylated complex N-glycans and six sialylated non-fucosylated complex N-glycans, one of which containing N-glycolylneuraminic acid (Neu5Gc), were found. 27550041 5 19 gly non-fucosylated 1096:1110 arg1 two high mannose N-glycans two high mannose N-glycans In addition, two high mannose N-glycans, four sialylated fucosylated complex N-glycans and six sialylated non-fucosylated complex N-glycans, one of which containing N-glycolylneuraminic acid (Neu5Gc), were found. 27550041 5 19 gly non-fucosylated 1096:1110 arg1 six sialylated non-fucosylated complex N-glycans six sialylated non-fucosylated complex N-glycans In addition, two high mannose N-glycans, four sialylated fucosylated complex N-glycans and six sialylated non-fucosylated complex N-glycans, one of which containing N-glycolylneuraminic acid (Neu5Gc), were found. 27550041 5 20 gly sialylated 1036:1045 arg1 two high mannose N-glycans two high mannose N-glycans In addition, two high mannose N-glycans, four sialylated fucosylated complex N-glycans and six sialylated non-fucosylated complex N-glycans, one of which containing N-glycolylneuraminic acid (Neu5Gc), were found. 27550041 5 20 gly sialylated 1036:1045 arg1 four sialylated fucosylated complex N-glycans four sialylated fucosylated complex N-glycans In addition, two high mannose N-glycans, four sialylated fucosylated complex N-glycans and six sialylated non-fucosylated complex N-glycans, one of which containing N-glycolylneuraminic acid (Neu5Gc), were found. 24806200 3 59 gly glycoproteins 599:611 arg1 These glycoproteins These glycoproteins Fterm glycoproteins These glycoproteins play important roles in reproduction and are used clinically in the treatment of infertility. 24798333 3 13 gly non-N-glycosylated 485:502 arg1 wild-type and non-N-glycosylated F27C variants wild-type and non-N-glycosylated F27C variants Fterm variants This was shown by investigating the biosynthesis and trafficking of wild-type and non-N-glycosylated F27C variants in metabolic pulse-chase assays coupled with flow cytometry and cell surface biotinylation. 24417605 1 15 gly glycosylated 185:196 arg1 functional proteins functional proteins Fterm proteins Many of the functional proteins and lipids in high density lipoprotein (HDL) particles are potentially glycosylated, yet very little is known about the glycoconjugates of HDL. 25740940 4 45 gly trifucosylated 675:688 arg1 A dominant trifucosylated Hex3HexNAc2Fuc3 glycan A dominant trifucosylated Hex3HexNAc2Fuc3 glycan A dominant trifucosylated Hex3HexNAc2Fuc3 glycan was modified not only with α1,6-fucose but also with a proximal core α1,3-fucose and a galactosylated distal α1,3-fucose; thereby, only two of the hexose residues were mannose. 27694851 8 6 gly glycosylations 1452:1465 arg1 proteoglycans proteoglycans This analytical approach will become useful when addressing fundamental questions in basic biology specifically in elucidating the functional roles of site-specific glycosylations of proteoglycans. 25995273 5 11 gly glycopeptides 755:767 arg2 several mouse liver and mouse brain glycopeptides several mouse liver and mouse brain glycopeptides glycopeptides The glycosylation patterns of several mouse liver and mouse brain glycopeptides were compared. 25995273 5 14 gly glycosylation 693:705 arg1 several mouse liver and mouse brain glycopeptides several mouse liver and mouse brain glycopeptides glycopeptides The glycosylation patterns of several mouse liver and mouse brain glycopeptides were compared. 28620050 5 43 gly glycosylation 962:974 arg1 Asn-297 Asn-297 Asn-297 We report here that glycosylation at Asn-297 is critical for interactions with Fc receptors and complement and that glycosylation at Asn-563 is essential for controlling multimerization. 28620050 5 75 gly glycosylation 1058:1070 arg2 Asn-563 Asn-563 Asn-563 We report here that glycosylation at Asn-297 is critical for interactions with Fc receptors and complement and that glycosylation at Asn-563 is essential for controlling multimerization. 28167607 10 24 gly N-glycosylation 1296:1310 arg1 the β-propeller domain domain domain These findings indicate that N-glycosylation on the β-propeller domain functions as a molecular switch to control the dynamics of α5β1 on the cell surface that in turn is required for optimum adhesion for cell migration. 25883177 1 5 gly present 168:174 arg1 glycoproteins AND Glycans glycoproteins Glycans Fterm glycoproteins Glycans present on glycoproteins and glycolipids of the major human parasite Schistosoma mansoni induce innate as well as adaptive immune responses in the host. 25883177 1 64 gly glycoproteins 179:191 arg1 glycoproteins glycoproteins Fterm glycoproteins Glycans present on glycoproteins and glycolipids of the major human parasite Schistosoma mansoni induce innate as well as adaptive immune responses in the host. 26503433 3 14 gly fucosylated 393:403 arg1 The fucosylated glycans The fucosylated glycans The fucosylated glycans are then derivatized by Meladrazine, which significantly enhances the detection of the glycans in electrospray ionization. 28849661 1 13 gly glycopeptide 99:110 arg2 Syndecan-1 chondroitin sulfate glycopeptide Syndecan-1 chondroitin sulfate glycopeptide glycopeptide Syndecan-1 chondroitin sulfate glycopeptide was synthesized for the first time using the cassette approach. 25820733 0 43 gly glycopeptides 43:55 arg2 bacterial glycopeptides bacterial glycopeptides glycopeptides Enrichment and identification of bacterial glycopeptides by mass spectrometry. 26492619 1 38 part_of possesses 192:200 arg1 Podoplanin AND a platelet aggregation-stimulating (PLAG) domain Podoplanin a platelet aggregation-stimulating (PLAG) domain PUBTATOR Site Podoplanin 10630 domain Podoplanin (PDPN) is a type-I transmembrane sialoglycoprotein that possesses a platelet aggregation-stimulating (PLAG) domain in the N-terminus. 26492619 1 38 part_of possesses 192:200 arg1 a type-I transmembrane sialoglycoprotein AND a platelet aggregation-stimulating (PLAG) domain a type-I transmembrane sialoglycoprotein a platelet aggregation-stimulating (PLAG) domain Fterm Site sialoglycoprotein domain Podoplanin (PDPN) is a type-I transmembrane sialoglycoprotein that possesses a platelet aggregation-stimulating (PLAG) domain in the N-terminus. 28620050 4 70 part_of contains 800:807 arg1 Hexa-Fc AND two N-linked sites Hexa-Fc two N-linked sites PUBTATOR Site Hexa 3073 sites Hexa-Fc contains two N-linked sites at Asn-77 (equivalent to Asn-297 in the Fc of IgG1) and Asn-236 (equivalent to Asn-563 in the tail piece of IgM). 25182382 7 92 gly N-glycopeptides 1399:1413 arg2 2249 unique intact N-glycopeptides 2249 unique intact N-glycopeptides N-glycopeptides This platform was applied to detailed characterization of site-specific glycosylation in HEK 293T cells, which led to the identification of 2249 unique intact N-glycopeptides. 26192331 2 13 part_of polysialyltransferase-specific 539:568 arg1 polysialyltransferase-specific structural motifs polysialyltransferase polysialyltransferase-specific structural motifs Fterm Site polysialyltransferase motifs The crystal structure of human ST8SiaIII at 1.85-Å resolution presented here is, to our knowledge, the first solved structure of a polysialyltransferase from any species, and it reveals a cluster of polysialyltransferase-specific structural motifs that collectively provide an extended electropositive surface groove for binding of oligo-polysialic acid chain products. 26507102 11 52 part_of site 1600:1603 arg1 lubricin lubricin site OGER Site lubricin Q92954 site A C-terminal proteolytic cleavage site in lubricin was found in synovial fluid from normal and osteochondral fragment joints and in media from interleukin-1β stimulated and unstimulated articular cartilage explants. 25261856 6 57 gly monosialylated 1134:1147 arg1 A2G2S(6)1 A2G2S(6)1 As compared with controls the ALS group had a significant increase of a peak composed of the monosialylated diantennary glycans A2G2S(6)1 and FA2G2S(3)1 (P=0.0348). 25261856 6 57 gly monosialylated 1134:1147 arg1 FA2G2S(3)1 FA2G2S(3)1 As compared with controls the ALS group had a significant increase of a peak composed of the monosialylated diantennary glycans A2G2S(6)1 and FA2G2S(3)1 (P=0.0348). 25261856 6 57 gly monosialylated 1134:1147 arg1 the monosialylated diantennary glycans A2G2S(6)1 and FA2G2S(3)1 (P=0.0348) the monosialylated diantennary glycans A2G2S(6)1 and FA2G2S(3)1 (P=0.0348) As compared with controls the ALS group had a significant increase of a peak composed of the monosialylated diantennary glycans A2G2S(6)1 and FA2G2S(3)1 (P=0.0348). 26956389 10 32 gly released 1480:1487 arg1 the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 AND N-glycans the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 N-glycans Fterm glycoproteins Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. 26956389 10 42 gly glycoproteins 1517:1529 arg1 the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 Fterm glycoproteins Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. 26082218 2 37 gly glycoproteins 233:245 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins As a protein production platform, further development for therapeutic glycoproteins has been hindered by the high-mannose-type N-glycosylation common to yeast and fungi. 27216994 11 50 gly receptors 1960:1968 arg1 the N-glycan composition receptors the N-glycan composition Fterm receptors We examined the N-glycan composition of NMDA receptors (NMDARs) using deglycosylating enzymes, lectin-based biochemistry, and electrophysiology. 26339047 3 92 gly glycosylation 614:626 arg2 the wild-type (WT) HBsAgS N146 glycosylation site the wild-type (WT) HBsAgS N146 glycosylation site site For the generation of hypoglycosylated VLPs, the wild-type (WT) HBsAgS N146 glycosylation site was converted to N146Q; for constructing hyperglycosylated VLPs, potential glycosylation sites were introduced in the HBsAgS external loop region at positions T116 and G130 in addition to the WT site. 26339047 3 147 gly glycosylation 708:720 arg2 potential glycosylation sites potential glycosylation sites sites For the generation of hypoglycosylated VLPs, the wild-type (WT) HBsAgS N146 glycosylation site was converted to N146Q; for constructing hyperglycosylated VLPs, potential glycosylation sites were introduced in the HBsAgS external loop region at positions T116 and G130 in addition to the WT site. 26339047 3 40 gly positions 782:790 arg1 G130 positions positions For the generation of hypoglycosylated VLPs, the wild-type (WT) HBsAgS N146 glycosylation site was converted to N146Q; for constructing hyperglycosylated VLPs, potential glycosylation sites were introduced in the HBsAgS external loop region at positions T116 and G130 in addition to the WT site. 25186198 3 6 gly fucosylates 394:404 arg1 Epidermal Growth Factor-like (EGF) repeats Epidermal Growth Factor-like (EGF) repeats Notably, Protein O-fucosyltransferase 1 (Ofut1/Pofut1), a soluble, ER localized enzyme that fucosylates Epidermal Growth Factor-like (EGF) repeats, functions as a chaperone involved in the proper localization of the Notch receptor in certain contexts. 27501865 7 25 gly trisialylated 1484:1496 arg1 trisialylated triantennary glycans trisialylated triantennary glycans Moreover, we observed a progressive increase of sialylated triantennary and tetraantennary structures two days after surgery, with a concomitant decrease of the structures containing bisecting N-acetylglucosamine along with bi- and trisialylated triantennary glycans. 28956227 1 52 gly glycosylated 230:241 arg1 eight heavily glycosylated ecto-enzymes eight heavily glycosylated ecto-enzymes Fterm ecto-enzymes The GDA1/CD39 ecto-nucleoside triphosphate diphosphosphohydrolase (E-NTPDase) superfamily is a group of eight heavily glycosylated ecto-enzymes that hydrolyze extracellular nucleosides di- and tri-phosphates in the presence of divalent cations, to generate the monophosphate derivatives. 27751954 6 43 gly fucosylated 1021:1031 arg1 fucosylated glycans fucosylated glycans Seemingly, simple methylated paucimannosidic structures can be considered 'male', while methylation of fucosylated glycans was more pronounced in females. 27928741 10 58 gly contained 1542:1550 arg1 Asparagine residues 341, 433 and 481 AND complex or hybrid glycans Asparagine residues 341, 433 and 481 complex or hybrid glycans Asparagine residues 341, 433 and 481 Asparagine residues 341, 433 and 481 contained complex or hybrid glycans with many of the compositions containing variations of fucose and sulfate or phosphate. 28186137 7 71 gly glycoproteins 699:711 arg1 PNS myelin glycoproteins PNS myelin glycoproteins Fterm glycoproteins PNS myelin glycoproteins contain highly abundant sulfated N-glycans. 28186137 7 43 gly contain 713:719 arg1 PNS myelin glycoproteins AND highly abundant sulfated N-glycans PNS myelin glycoproteins highly abundant sulfated N-glycans Fterm glycoproteins PNS myelin glycoproteins contain highly abundant sulfated N-glycans. 25098670 2 10 gly thioglycosylation 202:218 arg1 6-iodinated sugars 6-iodinated sugars Key steps of the synthesis involved thioglycosylation of 6-iodinated sugars with α-glycosyl thiols under phase transfer conditions. 25763881 2 25 gly composition 322:332 arg1 Fuc position Fuc position Patatin is the most abundant glycoprotein in potato and has been described to have an oligosaccharide of composition Man3(Xyl)GlcNAc2(Fuc). 25763881 2 25 gly composition 322:332 arg1 composition Man3(Xyl)GlcNAc2 position composition Man3(Xyl)GlcNAc2 position Patatin is the most abundant glycoprotein in potato and has been described to have an oligosaccharide of composition Man3(Xyl)GlcNAc2(Fuc). 25763881 2 33 gly glycoprotein 246:257 arg1 the most abundant glycoprotein the most abundant glycoprotein Fterm glycoprotein Patatin is the most abundant glycoprotein in potato and has been described to have an oligosaccharide of composition Man3(Xyl)GlcNAc2(Fuc). 25763881 2 33 gly glycoprotein 246:257 arg1 Patatin Patatin Fterm Patatin Patatin is the most abundant glycoprotein in potato and has been described to have an oligosaccharide of composition Man3(Xyl)GlcNAc2(Fuc). 25763881 2 30 gly have 295:298 arg1 the most abundant glycoprotein AND an oligosaccharide the most abundant glycoprotein an oligosaccharide Fterm glycoprotein Patatin is the most abundant glycoprotein in potato and has been described to have an oligosaccharide of composition Man3(Xyl)GlcNAc2(Fuc). 25763881 2 30 gly have 295:298 arg1 Patatin AND an oligosaccharide Patatin an oligosaccharide Fterm Patatin Patatin is the most abundant glycoprotein in potato and has been described to have an oligosaccharide of composition Man3(Xyl)GlcNAc2(Fuc). 24912705 0 59 gly oligochitosan-glycosylated 42:67 arg1 an oligochitosan-glycosylated and crosslinked soybean protein an oligochitosan-glycosylated and crosslinked soybean protein Fterm protein Structure and property modification of an oligochitosan-glycosylated and crosslinked soybean protein generated by microbial transglutaminase. 28785176 2 5 gly O-glycosylated 300:313 arg1 O-glycosylated peptides O-glycosylated peptides peptides Reverse-phase (RP) chromatography is the most common chromatographic approach to analyze O-glycosylated peptides and their unmodified counterparts, even though this approach often does not provide adequate separation of these two species. 24440233 1 66 gly glycosylation 160:172 arg2 the glycosylation site the glycosylation site site Simultaneous elucidation of the glycan structure and the glycosylation site are needed to reveal the biological function of protein glycosylation. 28582506 9 7 gly sequence 1648:1655 arg1 an intuitive glycan sequence search tool an intuitive glycan sequence search tool Glycan Fragment Database in GlycanStructure.Org is also updated to provide an intuitive glycan sequence search tool for complex glycan structures with various chemical modifications in the PDB. 24644239 2 3 part_of having 324:329 arg1 a 73 amino acid protein AND one N-glycosylation site a 73 amino acid protein one N-glycosylation site Fterm Site protein site Originally, CCL1 was identified as a 73 amino acid protein having one N-glycosylation site, and a variant 74 residue non-glycosylated form, Ser-CCL1, has also been described. 24644239 2 3 part_of having 324:329 arg1 CCL1 AND one N-glycosylation site CCL1 one N-glycosylation site PUBTATOR Site Originally, CCL1 6346 site Originally, CCL1 was identified as a 73 amino acid protein having one N-glycosylation site, and a variant 74 residue non-glycosylated form, Ser-CCL1, has also been described. 27412689 7 12 gly tissue 1465:1470 arg1 regions regions regions The N-linked glycan repertoires carried by the proteins in these tissue regions were structurally characterized for the first time in FFPE ovarian cancer tissue regions, using enzymatic peptide-N-glycosidase F (PNGase F) release of N-glycans. 26657071 7 72 part_of enzymes 1199:1205 arg1 the active sites enzymes the active sites Fterm Site enzymes sites Comparison of the active sites of these un-liganded enzymes with the structures of hCES1-ligand complexes showed that side-chains of the catalytic triad were pre-disposed for substrate binding. 25978763 2 74 gly glycopeptides 474:486 arg2 glycopeptides glycopeptides glycopeptides Here, we report that both incomplete derivatization of Cys side chains and overalkylation of the peptides may lead to the misassignment of glycoforms when LC-MS/MS with electron-transfer dissociation (ETD) alone is used for the structural characterization of glycopeptides. 26248080 7 52 gly glycoproteins 1150:1162 arg1 several glycoproteins several glycoproteins Fterm glycoproteins The inhibition of N-glycosylation processing from high mannose to complex glycans using kifunensine caused changes in the composition of EVs and induced a decrease of several glycoproteins. 28947169 1 41 gly proteins 100:107 arg1 Glycan profiling proteins Glycan profiling Fterm proteins Glycan profiling of proteins was studied through their lectin binding activity by Surface Plasmon Resonance (SPR). 26286102 8 89 gly sialylated 1306:1315 arg1 sialylated biantennary and triantennary structures sialylated biantennary and triantennary structures We found definite changes of CSF N-glycans due to a dramatic decrease of sialylated biantennary and triantennary structures and an increase of asialo-core fucosylated bisected N-glycans. 26286102 8 102 gly fucosylated 1388:1398 arg1 asialo-core fucosylated bisected N-glycans asialo-core fucosylated bisected N-glycans We found definite changes of CSF N-glycans due to a dramatic decrease of sialylated biantennary and triantennary structures and an increase of asialo-core fucosylated bisected N-glycans. 27333379 2 39 gly glycosylated 345:356 arg1 aberrantly glycosylated O-glycans aberrantly glycosylated O-glycans The IgA1 in these immune complexes carries aberrantly glycosylated O-glycans. 26590834 1 58 gly sites 264:268 arg1 an N-linked tetrasaccharide sites an N-linked tetrasaccharide sites In Methanococcus maripaludis, the three archaellins which comprise the archaellum are modified at multiple sites with an N-linked tetrasaccharide with the structure of Sug-4-β-ManNAc3NAmA6Thr-4-β-GlcNAc3NAcA-3-β-GalNAc, where Sug is a unique sugar (5S)-2-acetamido-2,4-dideoxy-5-O-methyl-L-erythro-hexos-5-ulo-1,5-pyranose, so far found exclusively in this species. 27773703 1 20 gly glycoprotein 115:126 arg1 Megalin Megalin Fterm Megalin 14725 Megalin is a 600-kDa single-spanning transmembrane glycoprotein and functions as an endocytic receptor, distributed not only in the kidney but also in other tissues. 27773703 1 20 gly glycoprotein 115:126 arg1 a 600-kDa single-spanning transmembrane glycoprotein a 600-kDa single-spanning transmembrane glycoprotein Fterm glycoprotein Megalin is a 600-kDa single-spanning transmembrane glycoprotein and functions as an endocytic receptor, distributed not only in the kidney but also in other tissues. 25202310 5 62 gly glycoproteins 1213:1225 arg1 endoplasmic reticulum resident glycoproteins endoplasmic reticulum resident glycoproteins Fterm glycoproteins Subcellular proteomics and gene ontology revealed substantial presence of endoplasmic reticulum resident glycoproteins in the microsomes and confirmed significant enrichment of secreted and cell-surface glycoproteins in the respective subcellular fractions. 25202310 5 87 gly glycoproteins 1311:1323 arg1 secreted and cell-surface glycoproteins secreted and cell-surface glycoproteins Fterm glycoproteins Subcellular proteomics and gene ontology revealed substantial presence of endoplasmic reticulum resident glycoproteins in the microsomes and confirmed significant enrichment of secreted and cell-surface glycoproteins in the respective subcellular fractions. 27936757 5 66 gly fucosylated 965:975 arg1 fucosylated glycans fucosylated glycans The abundance of neutral glycans containing terminal galactose was highest in SMM, while agalactosylated glycans and fucosylated glycans were lowest in MM. 27038031 2 54 gly N-glycosylation 247:261 arg2 five potential N-glycosylation sites five potential N-glycosylation sites sites Polymeric IgM, the largest known antibody in humans, displays five potential N-glycosylation sites on each heavy chain monomer. 27997162 6 87 gly glycoproteins 1209:1221 arg1 N-azidoacetyl-neuraminic acid (NeuAz)-carrying glycoproteins N-azidoacetyl-neuraminic acid (NeuAz)-carrying glycoproteins Intravenous administration of CNH molecules in mice (C57BL/6J and BALB/cByJ) resulted in robust expression of N-azidoacetyl-neuraminic acid (NeuAz)-carrying glycoproteins in both brain and heart, while the nonhybrid molecule Ac4ManNAz showed NeuAz expression in heart but not in brain. 26182462 2 10 gly glycoproteins 327:339 arg1 glycoproteins glycoproteins Fterm glycoproteins The structural alterations of N-linked glycans in glycoproteins are always associated with many diseases, such as diabetes, heart failure and malignant tumors. 26850169 6 31 part_of Fc 1028:1029 arg1 Fc regions Fc Fc regions Cterm Site Fc regions Enhanced pro-inflammatory responses have also been seen for Fc regions with amino acid substitutions. 28109443 9 14 gly O-glycosylated 2021:2034 arg1 any other O-glycosylated proteins any other O-glycosylated proteins Fterm proteins The method could also be applied to the analysis of any other O-glycosylated proteins. 28754360 1 45 gly glycosylation 155:167 arg1 proteins proteins Fterm proteins N-linked glycosylation of proteins has both functional and structural significance. 26984886 4 80 gly glycosylation 614:626 arg2 HA glycosylation sites HA glycosylation sites sites Mutations leading to changes in the number of HA glycosylation sites are often reported. 25451932 7 24 part_of frizzled-1 949:958 arg1 the frizzled-1 domain frizzled-1 the frizzled-1 domain OGER Site frizzled-1 Q9UP38 domain Similarly, N-glycosylation at Asn-231 protected corin from autocleavage in the frizzled-1 domain. 26083095 1 11 gly O-glycosylation 111:125 arg1 polysaccharides polysaccharides Chemical O-glycosylation of polysaccharides is an almost unexplored reaction. 27412689 4 94 gly released 825:832 arg1 proteins AND profile N-glycan compositions proteins profile N-glycan compositions Fterm proteins A novel method for investigating tissue-specific N-linked glycans is using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) on formalin-fixed paraffin-embedded (FFPE) tissue sections that can spatially profile N-glycan compositions released from proteins in tissue-specific regions. 28433761 13 88 gly glycoprotein 2174:2185 arg1 S-layer glycoprotein S-layer glycoprotein Fterm glycoprotein Furthermore, this is the first description of N-glycosidic chains in S-layer glycoprotein from Lactobacillus spp. 24798328 7 18 gly glycosites 1079:1088 arg2 The glycosites The glycosites glycosites The glycosites in linker regions of LDLR class A repeats are conserved in LDLR from man to Xenopus and found in other homologous receptors. 24927272 0 41 gly O-glycosylation 0:14 arg1 recombinant Fc-fusion proteins recombinant Fc-fusion proteins Fterm proteins O-glycosylation of glycine-serine linkers in recombinant Fc-fusion proteins: attachment of glycosaminoglycans and other intermediates with phosphorylation at the xylose sugar subunit. 29016103 4 66 gly glycopeptides 613:625 arg2 isobarically labeled glycopeptides isobarically labeled glycopeptides glycopeptides However, its effectiveness to enrich isobarically labeled glycopeptides remains unclear. 25533529 1 35 part_of contains 196:203 arg1 Acutobin AND four N-glycosylation sites Acutobin four N-glycosylation sites Fterm Site Acutobin sites Acutobin, the α-fibrinogenase from Deinagkistrodon acutus venom, contains four N-glycosylation sites with disialylated complex-typed glycans. 25533529 1 35 part_of contains 196:203 arg1 the α-fibrinogenase AND four N-glycosylation sites the α-fibrinogenase four N-glycosylation sites Fterm Site α-fibrinogenase 2244 sites Acutobin, the α-fibrinogenase from Deinagkistrodon acutus venom, contains four N-glycosylation sites with disialylated complex-typed glycans. 26991339 2 44 gly N- 746:747 arg1 sites sites sites Reversed-phase high-performance liquid chromatography with high-resolution electrospray ionization mass spectrometry analysis of the intact proteoforms before and after N-deglycosylation with Peptide-N-Glycosidase F and tandem mass spectrometry sequencing of peptides obtained after Endoproteinase GluC digestion allowed the structural characterization of the peptide backbone and identification of N- and O-glycosylation sites. 27867116 0 76 gly glycopeptides 38:50 arg2 glycopeptides glycopeptides glycopeptides Automatic and rapid identification of glycopeptides by nano-UPLC-LTQ-FT-MS and proteomic search engine. 28895795 8 14 gly glycoprotein 1221:1232 arg1 this glycoprotein this glycoprotein Fterm glycoprotein For this glycoprotein, we confidently identified 35 N-linked glycans and all three major classes, high mannose, complex, and hybrid, were present. 25094044 0 30 part_of glycoprotein 62:73 arg1 site glycoprotein site Fterm Site glycoprotein site Glycan structure and site of glycosylation in the ER-resident glycoprotein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferases 1 from rat, porcine, bovine, and human. 25094044 0 42 part_of site 21:24 arg1 the ER-resident glycoprotein glycoprotein site Fterm Site glycoprotein site Glycan structure and site of glycosylation in the ER-resident glycoprotein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferases 1 from rat, porcine, bovine, and human. 26868756 7 15 gly N-glycosylation 1092:1106 arg2 the four occupied N-glycosylation sites the four occupied N-glycosylation sites sites The N-glycan structures that were presented on all of the four occupied N-glycosylation sites of recombinant GC in NbGNTI-RNAi plants (GC(gnt1) ) showed that the majority (ranging from 73.3% up to 85.5%) of the N-glycans had mannose-type structures lacking potential immunogenic β1,2-xylose and α1,3-fucose epitopes. 26701617 6 82 part_of sites 1087:1091 arg1 rhPDGF-BB rhPDGF sites OGER Site rhPDGF sites By site-directed mutagenesis and high-resolution LC/MS analysis, we, for the first time, identified two threonine residues at the C-terminus as the major O-glycosylation sites on rhPDGF-BB produced in P. pastoris. 26831718 6 95 part_of IgG 834:836 arg1 IgG glycome composition Furthermore, Ig IgG glycome composition Cterm Site Furthermore, Ig position Furthermore, IgG glycome composition was analyzed in 39 plasma samples collected before initial diagnosis of colorectal cancer. 26729242 6 46 part_of sites 1001:1005 arg1 20 proteins proteins sites Fterm Site proteins sites Altogether, 52 unique glycosylation sites in 20 proteins were identified in this study. 24685714 1 6 part_of PAC 399:401 arg1 a PAC (PRP-AGP containing Cys) domain PAC a PAC (PRP-AGP containing Cys) domain OGER Site PAC Q9H813 domain BACKGROUND AND AIMS Arabinogalactan protein 31 (AGP31) is a remarkable plant cell-wall protein displaying a multi-domain organization unique in Arabidopsis thaliana: it comprises a predicted signal peptide (SP), a short AGP domain of seven amino acids, a His-stretch, a Pro-rich domain and a PAC (PRP-AGP containing Cys) domain. 24685714 1 6 part_of PAC 399:401 arg1 PRP-AGP containing Cys PAC PRP-AGP containing Cys OGER AminoAcid PAC Q9H813 Cys BACKGROUND AND AIMS Arabinogalactan protein 31 (AGP31) is a remarkable plant cell-wall protein displaying a multi-domain organization unique in Arabidopsis thaliana: it comprises a predicted signal peptide (SP), a short AGP domain of seven amino acids, a His-stretch, a Pro-rich domain and a PAC (PRP-AGP containing Cys) domain. 24685714 1 6 part_of PAC 399:401 arg1 a predicted signal peptide PAC a predicted signal peptide OGER Site PAC Q9H813 peptide BACKGROUND AND AIMS Arabinogalactan protein 31 (AGP31) is a remarkable plant cell-wall protein displaying a multi-domain organization unique in Arabidopsis thaliana: it comprises a predicted signal peptide (SP), a short AGP domain of seven amino acids, a His-stretch, a Pro-rich domain and a PAC (PRP-AGP containing Cys) domain. 24685714 1 7 part_of PRP-AGP 404:410 arg1 a PAC (PRP-AGP containing Cys) domain PRP a PAC (PRP-AGP containing Cys) domain OGER Site PRP P32119 domain BACKGROUND AND AIMS Arabinogalactan protein 31 (AGP31) is a remarkable plant cell-wall protein displaying a multi-domain organization unique in Arabidopsis thaliana: it comprises a predicted signal peptide (SP), a short AGP domain of seven amino acids, a His-stretch, a Pro-rich domain and a PAC (PRP-AGP containing Cys) domain. 24685714 1 7 part_of PRP-AGP 404:410 arg1 PRP-AGP containing Cys PRP PRP-AGP containing Cys OGER AminoAcid PRP P32119 Cys BACKGROUND AND AIMS Arabinogalactan protein 31 (AGP31) is a remarkable plant cell-wall protein displaying a multi-domain organization unique in Arabidopsis thaliana: it comprises a predicted signal peptide (SP), a short AGP domain of seven amino acids, a His-stretch, a Pro-rich domain and a PAC (PRP-AGP containing Cys) domain. 24509848 6 32 gly N-glycosylation 899:913 arg2 other N-glycosylation sites other N-glycosylation sites sites Using site-directed mutagenesis, we found that mutations that disrupt the conserved (211)NDS N-glycosylation motif, but not other N-glycosylation sites (Asn(260), Asn(371), and Asn(394)), result in collagen I-independent constitutive phosphorylation. 24509848 6 64 gly sites 915:919 arg1 other N-glycosylation sites other N-glycosylation sites sites Using site-directed mutagenesis, we found that mutations that disrupt the conserved (211)NDS N-glycosylation motif, but not other N-glycosylation sites (Asn(260), Asn(371), and Asn(394)), result in collagen I-independent constitutive phosphorylation. 24509848 6 82 gly N-glycosylation 862:876 arg2 the conserved (211)NDS N-glycosylation motif the conserved (211)NDS N-glycosylation motif motif Using site-directed mutagenesis, we found that mutations that disrupt the conserved (211)NDS N-glycosylation motif, but not other N-glycosylation sites (Asn(260), Asn(371), and Asn(394)), result in collagen I-independent constitutive phosphorylation. 24509848 6 32 gly N-glycosylation 899:913 arg2 Asn(371) Asn(260), Asn(371), and Asn(394) Asn(260), Asn(371), and Asn(394) Using site-directed mutagenesis, we found that mutations that disrupt the conserved (211)NDS N-glycosylation motif, but not other N-glycosylation sites (Asn(260), Asn(371), and Asn(394)), result in collagen I-independent constitutive phosphorylation. 24509848 6 32 gly N-glycosylation 899:913 arg2 Asn(394) Asn(260), Asn(371), and Asn(394) Asn(260), Asn(371), and Asn(394) Using site-directed mutagenesis, we found that mutations that disrupt the conserved (211)NDS N-glycosylation motif, but not other N-glycosylation sites (Asn(260), Asn(371), and Asn(394)), result in collagen I-independent constitutive phosphorylation. 24509848 6 32 gly N-glycosylation 899:913 arg2 Asn(394) Asn(260), Asn(371), and Asn(394) Asn(260), Asn(371), and Asn(394) Using site-directed mutagenesis, we found that mutations that disrupt the conserved (211)NDS N-glycosylation motif, but not other N-glycosylation sites (Asn(260), Asn(371), and Asn(394)), result in collagen I-independent constitutive phosphorylation. 24509848 6 64 gly sites 915:919 arg1 Asn(371) Asn(260), Asn(371), and Asn(394) Asn(260), Asn(371), and Asn(394) Using site-directed mutagenesis, we found that mutations that disrupt the conserved (211)NDS N-glycosylation motif, but not other N-glycosylation sites (Asn(260), Asn(371), and Asn(394)), result in collagen I-independent constitutive phosphorylation. 24509848 6 64 gly sites 915:919 arg1 Asn(260) Asn(260), Asn(371), and Asn(394) Asn(260), Asn(371), and Asn(394) Using site-directed mutagenesis, we found that mutations that disrupt the conserved (211)NDS N-glycosylation motif, but not other N-glycosylation sites (Asn(260), Asn(371), and Asn(394)), result in collagen I-independent constitutive phosphorylation. 24509848 6 64 gly sites 915:919 arg1 Asn(260) Asn(260), Asn(371), and Asn(394) Asn(260), Asn(371), and Asn(394) Using site-directed mutagenesis, we found that mutations that disrupt the conserved (211)NDS N-glycosylation motif, but not other N-glycosylation sites (Asn(260), Asn(371), and Asn(394)), result in collagen I-independent constitutive phosphorylation. 28680094 7 2 gly removal 1002:1008 arg3 the β3-N371 N-glycan AND the I-EGF1 domain the I-EGF1 domain the β3-N371 N-glycan domain In contrast, removal of the β3-N371 N-glycan near the β3 hybrid and I-EGF3 interface, or the β3-N452 N-glycan at the I-EGF1 domain rendered β3 integrin more active than the wild type. 27073020 1 55 gly N-glycosylation 154:168 arg1 plasma proteins plasma proteins Fterm proteins Changes in N-glycosylation of plasma proteins are observed in many types of cancer, nevertheless, few studies suggest the exact mechanism involved in aberrant protein glycosylation. 28271226 4 85 gly composition 952:962 arg1 N-glycans position, N-glycans position, When subjected to liquid chromatography-ESI-MS in positive and negative modes, the glyco tune mix clearly demonstrated the futility of quantitation of N-glycans of different overall composition, different number of sialic acids, and strongly differing size without compensation for their very different molar responses. 25499076 2 26 gly N-glycosylation 349:363 arg2 a single, partially occupied N-glycosylation site a single, partially occupied N-glycosylation site site It has a single, partially occupied N-glycosylation site located at Asn-31, which makes it a particularly simple and interesting model for glycosylation studies. 27629418 3 83 gly core-α1,6-fucosylated 691:711 arg1 mammalian-type core-α1,6-fucosylated glycans mammalian-type core-α1,6-fucosylated glycans Therefore, we performed site-directed mutagenesis on Endo-M to isolate mutant enzymes that are able to act on mammalian-type core-α1,6-fucosylated glycans. 26488311 1 43 gly glycosylated 108:119 arg1 Specific glycosylated peptides Specific glycosylated peptides peptides Specific glycosylated peptides of clusterin are found associated with hippocampal atrophy. 25737449 3 61 gly glycoprotein 453:464 arg1 its E2 envelope glycoprotein its E2 envelope glycoprotein Fterm glycoprotein Glycan shielding is a mechanism by which HCV masks such epitopes on its E2 envelope glycoprotein. 26202417 1 46 gly glycoprotein 170:181 arg1 The influenza virus surface glycoprotein hemagglutinin The influenza virus surface glycoprotein hemagglutinin Fterm glycoprotein The influenza virus surface glycoprotein hemagglutinin (HA) is the major target of host neutralizing antibodies. 26869352 0 81 gly fucosylated 38:48 arg1 fucosylated N-glycans fucosylated N-glycans Site-specific and linkage analyses of fucosylated N-glycans on haptoglobin in sera of patients with various types of cancer: possible implication for the differential diagnosis of cancer. 26143917 0 4 part_of CHIT1 68:72 arg1 human chitotriosidase (CHIT1) catalytic domain CHIT1 human chitotriosidase (CHIT1) catalytic domain PUBTATOR Site CHIT1 1118 domain New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM. 25253346 0 36 part_of CD4 65:67 arg1 the CD4 binding site CD4 the CD4 binding site PUBTATOR Site CD4 920 site Hyperglycosylated stable core immunogens designed to present the CD4 binding site are preferentially recognized by broadly neutralizing antibodies. 29146600 7 78 gly sialylation 1230:1240 arg1 more complex structures more complex structures RESULTS Higher HbA1c was associated with a lower relative abundance of simple biantennary N-glycans and a higher relative abundance of more complex structures with more branching, galactosylation, and sialylation (GP12, 26, 31, 32, and 34, and IGP19 and 23; all P < 3.79 × 10-4). 27295180 8 27 gly α1,3fucosylated 1099:1113 arg1 α1,3fucosylated glycans α1,3fucosylated glycans Accordingly, the relative abundance of α1,3fucosylated glycans in AGP (FUCAGP) was found to be significantly high in cancer patients as compared with the healthy controls. 27748959 7 43 gly asialoglycoprotein 1273:1290 arg1 asialoglycoprotein receptor asialoglycoprotein receptor Fterm asialoglycoprotein RESULTS First, we detected that EtOH administration results in the loss of sialylated N-glycans on asialoglycoprotein receptor; however, the high-mannose-type N-glycans are increased. 27748959 7 83 gly sialylated 1249:1258 arg1 sialylated N-glycans sialylated N-glycans RESULTS First, we detected that EtOH administration results in the loss of sialylated N-glycans on asialoglycoprotein receptor; however, the high-mannose-type N-glycans are increased. 29164281 7 37 gly glycoprotein 954:965 arg1 any glycoprotein extraction any glycoprotein extraction Fterm glycoprotein N-Glycans were enzymatically released by PNGase F without any glycoprotein extraction. 25267679 2 41 gly glycosylated 323:334 arg1 The major structural flagellin proteins The major structural flagellin proteins Fterm proteins The major structural flagellin proteins have been shown to be glycosylated with the nonulosonate sugar, pseudaminic acid (Pse). 28489325 5 51 part_of EGF-like 1002:1009 arg1 EGF-like domain EGF EGF-like domain OGER Site EGF P01133 domain The orientation of the lectin and EGF-like domain was similar to the described "bent" conformation of E- and P-selectins. 25359784 9 51 part_of N-glycosylated 1117:1130 arg1 only N-glycosylated Asn residue N-glycosylated only N-glycosylated Asn residue Cterm AminoAcid N-glycosylated Asn residue Our results indicate that mutation of only N-glycosylated Asn residue may lead to incorrect conclusion for the evaluation of the function of N-glycan. 26083095 0 33 gly Fucosylation 9:20 arg1 a Polysaccharide a Polysaccharide Chemical Fucosylation of a Polysaccharide: A Semisynthetic Access to Fucosylated Chondroitin Sulfate. 27581986 15 22 part_of CD4 2799:2801 arg1 the CD4 binding site CD4 the CD4 binding site PUBTATOR Site CD4 920 site These data highlight how glycan holes can play a role in the elicitation of B-cell lineages targeting the CD4 binding site. 28729420 7 86 gly core-fucosylated 1494:1509 arg1 a mature bi-antennary complex-type N-glycan a mature bi-antennary complex-type N-glycan Interestingly, when placed in the V3 polypeptide context, a mature bi-antennary complex-type N-glycan also could be core-fucosylated by FUT8, albeit at much lower efficiency than the Man5GlcNAc2 peptide. 27493216 5 23 gly O-mannosylated 1244:1257 arg1 substrate O-mannosylated proteins substrate O-mannosylated proteins Fterm proteins Our crystal structures of POMGnT1 agreed with our previous results showing that the catalytic domain recognizes substrate O-mannosylated proteins via hydrophobic interactions with little sequence specificity. 29019687 0 42 part_of Ligand-Binding 33:46 arg1 Ligand-Binding Domain Ligand-Binding Ligand-Binding Domain Cterm Ligand-Binding Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core. 28935113 5 86 gly glycosylation 789:801 arg2 all glycosylation sites all glycosylation sites sites Although yeast, mammalian and Escherichia coli cells can be engineered to produce a homogenous glycoform at all glycosylation sites, there are just a few specific glycan structures that can readily be accessed in this manner. 24497634 6 1 part_of contactin 898:906 arg1 the Ig domains contactin the Ig domains Fterm Site contactin domains In three patients, immunoreactivity was directed against the Ig domains of contactin and was dependent on N-glycans. 25733616 1 7 gly glycoprotein 340:351 arg1 glycoprotein subunits glycoprotein subunits Fterm glycoprotein UNLABELLED Methanococcus maripaludis has two surface appendages, archaella and type IV pili, which are composed of glycoprotein subunits. 25737449 3 53 part_of epitopes 425:432 arg1 its E2 envelope glycoprotein glycoprotein epitopes Fterm Site glycoprotein epitopes Glycan shielding is a mechanism by which HCV masks such epitopes on its E2 envelope glycoprotein. 26963691 2 61 part_of PG 338:339 arg1 PG fragments PG PG fragments Cterm Site PG fragments β-N-Acetylglucosaminidases (NagZ enzymes) are involved in the PG process and they catalyze the removal of terminal N-acetylglucosamine in PG fragments. 28446609 4 85 gly glycosylation 741:753 arg2 multiple glycosylation sites multiple glycosylation sites sites Here, we confirmed that such mutations at multiple glycosylation sites greatly diminish viral infectivity and result in significantly reduced binding to both neutralizing and non-neutralizing antibodies. 29255015 6 24 gly glycoprotein 1005:1016 arg1 a glycoprotein a glycoprotein Fterm glycoprotein Thus, combining X-ray crystallography with carbohydrate molecular modeling resulted in determining the complete glycosylated structure of a glycoprotein. 26301455 0 39 gly glycosylation 9:21 arg1 recombinant cellobiohydrolase I recombinant cellobiohydrolase I Fterm cellobiohydrolase I N-linked glycosylation of recombinant cellobiohydrolase I (Cel7A) from Penicillium verruculosum and its effect on the enzyme activity. 27714557 5 38 gly glycoproteins 1040:1052 arg1 pharmaceutical glycoproteins pharmaceutical glycoproteins Fterm glycoproteins CONCLUSIONS This transglycosylation method using SG-oxazoline and Endo-CCN180H is beneficial for producing pharmaceutical glycoproteins modified with homogenous biantennary-complex-type oligosaccharides. 25916169 6 41 gly N-glycosylated 832:845 arg2 Asn Asn(211) Asn(211) By pharmacological, biochemical and site-directed mutagenesis, we observed that ST3Gal-II is mostly N-glycosylated at Asn(211) and that this co-translational modification is critical for its exit from the endoplasmic reticulum and proper Golgi localization. 25916169 6 41 gly N-glycosylated 832:845 arg1 ST3Gal-II Asn(211) ST3Gal-II Asn(211) By pharmacological, biochemical and site-directed mutagenesis, we observed that ST3Gal-II is mostly N-glycosylated at Asn(211) and that this co-translational modification is critical for its exit from the endoplasmic reticulum and proper Golgi localization. 25916169 6 41 gly N-glycosylated 832:845 arg1 ST3Gal-II Asn(211) ST3Gal-II Asn(211) By pharmacological, biochemical and site-directed mutagenesis, we observed that ST3Gal-II is mostly N-glycosylated at Asn(211) and that this co-translational modification is critical for its exit from the endoplasmic reticulum and proper Golgi localization. 27884519 4 64 gly O-glycosylation 457:471 arg2 N- or O-glycosylation site N- or O-glycosylation site site Modified vectors were constructed by introducing N- or O-glycosylation site on the region of hIL-11 that does not belong to the core α-helical motif based on the predicted secondary structure. 25182382 8 43 gly glycosylation 1488:1500 arg2 453 glycosylation sites 453 glycosylation sites sites These intact glycopeptides revealed 1769 site-specific N-glycans on 453 glycosylation sites which demonstrated the high heterogeneity of glycosylations. 25182382 8 96 gly glycopeptides 1429:1441 arg2 These intact glycopeptides These intact glycopeptides glycopeptides These intact glycopeptides revealed 1769 site-specific N-glycans on 453 glycosylation sites which demonstrated the high heterogeneity of glycosylations. 25182382 8 99 gly N-glycans 1471:1479 arg1 453 glycosylation sites 453 glycosylation sites 453 glycosylation sites Site sites These intact glycopeptides revealed 1769 site-specific N-glycans on 453 glycosylation sites which demonstrated the high heterogeneity of glycosylations. 25094044 1 37 gly glycoprotein 302:313 arg1 glycoprotein glucosyltransferase glycoprotein glucosyltransferase Fterm glycoprotein Here we report glycan structures and their position of attachment to a carrier protein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferase (UGGT1), as detected using tandem mass spectrometry. 25449758 7 12 part_of protein 1147:1153 arg1 an engineered glycosylation motif protein an engineered glycosylation motif Fterm Site protein motif Finally, glycopeptide mass spectrometry confirmed the transfer of the assembled glycan moiety onto an engineered glycosylation motif of recombinant maltose binding protein. 25927005 5 148 gly glycoproteins 700:712 arg1 glycoproteins glycoproteins N-glycans Fterm glycoproteins N-glycans of glycoproteins can influence viral particle formation, virus binding to cell surface, and HCV pathogenesis. 25498018 7 22 gly glycoprotein 1617:1628 arg1 target glycoprotein target glycoprotein Fterm glycoprotein Because of its simplicity and sensitivity, the method explored in this work suggests that it holds promise as a method of elucidating differences in direct N-glycosylation of target glycoprotein, even in small amount of samples. 25498018 7 54 gly N-glycosylation 1591:1605 arg1 target glycoprotein target glycoprotein Fterm glycoprotein Because of its simplicity and sensitivity, the method explored in this work suggests that it holds promise as a method of elucidating differences in direct N-glycosylation of target glycoprotein, even in small amount of samples. 27791356 8 19 gly O-glycosylated 1693:1706 arg1 a highly O-glycosylated region a highly O-glycosylated region region Interestingly, the molecule was found to contain a large amount of α-helix/unordered structures and many signatures of glycosylation, pointing to a highly O-glycosylated region on the mucin. 27052379 2 76 gly glycosylation 497:509 arg1 non-carbohydrate molecules non-carbohydrate molecules However, the main glucansucrase-catalyzed reaction results in synthesis of α-glucan polysaccharides from sucrose, and this strongly impedes the efficient glycosylation of non-carbohydrate molecules and complicates downstream processing of glucosylated products. 26479949 9 9 gly glycopeptides 1675:1687 arg2 glycopeptides glycopeptides glycopeptides Moreover, the Fe3O4-DA-Maltose NPs were applied to enrich glycopeptides from human renal mesangial cells (HRMC) for identification of N-glycosylation sites. 26479949 9 28 gly N-glycosylation 1751:1765 arg2 N-glycosylation sites N-glycosylation sites sites Moreover, the Fe3O4-DA-Maltose NPs were applied to enrich glycopeptides from human renal mesangial cells (HRMC) for identification of N-glycosylation sites. 24941220 6 64 gly deglycosylated 842:855 arg1 the corresponding deglycosylated peptides the corresponding deglycosylated peptides peptides This strategy depends on the observation that glycopeptides and the corresponding deglycosylated peptides share very similar MS/MS pattern in terms of b- and y-ions that do not contain the site of glycosylation. 24941220 6 77 gly glycosylation 957:969 arg2 the site the site site This strategy depends on the observation that glycopeptides and the corresponding deglycosylated peptides share very similar MS/MS pattern in terms of b- and y-ions that do not contain the site of glycosylation. 24941220 6 79 gly glycopeptides 806:818 arg2 glycopeptides glycopeptides glycopeptides This strategy depends on the observation that glycopeptides and the corresponding deglycosylated peptides share very similar MS/MS pattern in terms of b- and y-ions that do not contain the site of glycosylation. 29016103 10 34 gly glycoproteins 1602:1614 arg1 glycoproteins glycoproteins Fterm glycoproteins It is anticipated that the use of SAX and RAX cartridges will facilitate broad applications of identifications and quantitation of glycoproteins. 24533620 0 38 gly O-glycosylation 20:34 arg1 a semiflexible peptide linker a semiflexible peptide linker peptide Effects of branched O-glycosylation on a semiflexible peptide linker. 24747898 0 91 gly N-glycosylation 40:54 arg2 the different N-glycosylation sites the different N-glycosylation sites sites Deciphering the effect of the different N-glycosylation sites on the secretion, activity, and stability of cellobiohydrolase I from Trichoderma reesei. 29019687 3 74 part_of receptors 491:499 arg1 the ligand binding domain receptors the ligand binding domain Fterm Site receptors domain We recently demonstrated that certain glycans on the ligand binding domain (LBD) of NMDA receptors (NMDARs) can serve as intramolecular potentiators, changing EC50 of NMDAR coagonists. 28246170 2 43 gly glycosylation 329:341 arg1 mucin-like proteins mucin-like proteins Fterm proteins Understanding the glycosylation of mucin-like proteins presents a particular challenge as they are modified numerous times with both the enzymes involved and the glycosylation patterns being poorly understood. 25094044 4 2 part_of site 660:663 arg1 UGGT1 UGGT1 site PUBTATOR Site UGGT1 171129 site In this study, we reveal the site of glycosylation (N269) and the glycan structures (Hex5-8HexNAc2) in UGGT1 obtained from rat (Rattus norvegicus), pig (Sus scrofa), cow (Bos taurus), and human (Homo sapiens). 24295106 2 10 gly proteins 565:572 arg1 N-glycan profiles proteins N-glycan profiles Fterm proteins Because many known disease biomarkers are membrane-bound glycoproteins with important biological functions, we chose to compare N-glycan profiles of membrane proteins from three phenotypically different CRC cell lines, LIM1215, LIM1899, and LIM2405, representing moderately differentiated metastatic, moderately differentiated primary, and poorly differentiated (aggressive) primary CRC cell lines, respectively. 24295106 2 97 gly glycoproteins 464:476 arg1 membrane-bound glycoproteins membrane-bound glycoproteins Fterm glycoproteins Because many known disease biomarkers are membrane-bound glycoproteins with important biological functions, we chose to compare N-glycan profiles of membrane proteins from three phenotypically different CRC cell lines, LIM1215, LIM1899, and LIM2405, representing moderately differentiated metastatic, moderately differentiated primary, and poorly differentiated (aggressive) primary CRC cell lines, respectively. 28620050 3 13 gly attached 597:604 arg2 the unique N-linked glycan AND Asn-297 Asn-297 the unique N-linked glycan Asn-297 The critical influence of the unique N-linked glycan attached at Asn-297 on the structure and function of IgG1-Fc is well documented; however, whether the N-linked glycan has a similarly critical role in multimeric, avidly binding Fcs, is unknown. 24212570 1 61 part_of proteins 256:263 arg1 selected Asn residues proteins selected Asn residues Fterm AminoAcid proteins Asn residues Across evolution, N-glycosylation involves oligosaccharyltransferases that transfer lipid-linked glycans to selected Asn residues of target proteins. 27585995 12 133 gly glycoproteins 2695:2707 arg1 the O-glycans glycoproteins the O-glycans Fterm glycoproteins As a type of informational molecule, the O-glycans of these glycoproteins participate directly in these biological mechanisms. 25118826 12 22 gly polysialylated 2199:2212 arg1 polysialylated N-glycans polysialylated N-glycans We demonstrated the application of these advances in the context of the human serum glycome, and for which our initial observations included the detection of a new class of heavily sialylated N-glycans, including polysialylated N-glycans. 25118826 12 86 gly sialylated 2167:2176 arg1 polysialylated N-glycans polysialylated N-glycans We demonstrated the application of these advances in the context of the human serum glycome, and for which our initial observations included the detection of a new class of heavily sialylated N-glycans, including polysialylated N-glycans. 25118826 12 86 gly sialylated 2167:2176 arg1 heavily sialylated N-glycans heavily sialylated N-glycans We demonstrated the application of these advances in the context of the human serum glycome, and for which our initial observations included the detection of a new class of heavily sialylated N-glycans, including polysialylated N-glycans. 28543513 10 23 gly fucosylated 1650:1660 arg1 the glycan isomers the glycan isomers All of the glycan isomers, which were statistically significant, were either branch fucosylated or composed of α-2,6 linked sialic acid moieties. 25462875 5 31 part_of B4GALT1 892:898 arg1 all other animal B4GALT1 sequences B4GALT1 all other animal B4GALT1 sequences PUBTATOR Site B4GALT1 2683 sequences We also noted that the B4GALT1 used in our study had a leucine at position 282, whereas all other animal B4GALT1 sequences have an aromatic amino acid at this position. 26924641 4 15 gly sialylation 984:994 arg1 core fucosylation core fucosylation Our results show that both N-glycomes exhibit highly similar glycosylation patterns, consisting mainly of diantennary and triantennary complex type N-glycans with high levels (>95 %) of galactosylation and sialylation (mostly NeuGc) and a medium degree of core fucosylation (30 %). 24549892 6 42 gly sites 1588:1592 arg1 glycan compositions sites glycan compositions sites Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. 24549892 6 49 gly glycopeptides 1289:1301 arg2 glycopeptides glycopeptides glycopeptides Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. 24549892 6 62 gly glycopeptide 1370:1381 arg2 the glycopeptide the glycopeptide glycopeptide Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. 24549892 6 84 gly occupancy 1524:1532 arg2 N-glycosylation site occupancy N-glycosylation site occupancy site Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. 24549892 6 93 gly N-glycosylation 1503:1517 arg2 N-glycosylation site occupancy N-glycosylation site occupancy site Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. 24664809 3 45 gly glycosylation 719:731 arg2 each individual glycosylation site each individual glycosylation site site Liquid chromatography-tandem mass spectrometry (LC-MS/MS) peptide mapping is frequently used for protein structural characterization and, as a bonus, can potentially provide glycan profile on each individual glycosylation site. 25359784 1 17 gly glycoproteins 175:187 arg1 some glycoproteins some glycoproteins Fterm glycoproteins N-glycosylation has been shown to be important for the stability of some glycoproteins. 25359784 1 32 gly N-glycosylation 102:116 arg1 some glycoproteins some glycoproteins Fterm glycoproteins N-glycosylation has been shown to be important for the stability of some glycoproteins. 24941220 7 51 gly glycopeptides 982:994 arg2 glycopeptides glycopeptides glycopeptides Moreover, glycopeptides with an identical peptide backbone show nearly resembling spectra regardless of the attached glycan structures. 28556908 5 8 gly enzymes 1466:1472 arg1 the mannose-6-phosphate modification enzymes the mannose-6-phosphate modification Fterm enzymes The latter represent biosynthetic intermediates during the pathway leading to formation of the methylphosphorylated mannose epitope, which may have a similar function in intracellular targeting of hydrolases as the mannose-6-phosphate modification of lysosomal enzymes in mammals. 28556908 5 36 gly have 1348:1351 arg1 the methylphosphorylated mannose epitope AND the mannose-6-phosphate modification the methylphosphorylated mannose epitope the mannose-6-phosphate modification The latter represent biosynthetic intermediates during the pathway leading to formation of the methylphosphorylated mannose epitope, which may have a similar function in intracellular targeting of hydrolases as the mannose-6-phosphate modification of lysosomal enzymes in mammals. 28375048 1 14 gly glycoproteins 175:187 arg1 recombinant glycoproteins recombinant glycoproteins Fterm glycoproteins Protein glycosylation is arguably the paramount post-translational modification on recombinant glycoproteins, and highly cited in the literature for affecting the physiochemical properties and the efficacy of recombinant glycoprotein therapeutics. 28375048 1 86 gly glycoprotein 301:312 arg1 recombinant glycoprotein therapeutics recombinant glycoprotein therapeutics Fterm glycoprotein Protein glycosylation is arguably the paramount post-translational modification on recombinant glycoproteins, and highly cited in the literature for affecting the physiochemical properties and the efficacy of recombinant glycoprotein therapeutics. 26537504 6 58 part_of fibrin 1156:1161 arg1 disseminated fibrin deposition fibrin disseminated fibrin deposition Fterm Site fibrin position The application of chemically and enzymatically modified variants of the toxin in an animal model in guinea pigs showed that the pro-inflammatory and immunological reactions, e.g. disseminated fibrin deposition and activation of neutrophils, are due to the presence of sulfate-linked groups and not on disulfide bonds, as demonstrated by the reduction and S-alkylation of the toxin. 27638310 3 22 gly O-glycosylation 608:622 arg2 O-glycosylation sites O-glycosylation sites sites However, there are no previous reports of the O-glycosylation of rhGM-CSF from plant cells, and so this study investigated O-glycans, O-glycosylation sites, and their structural role in rrhGM-CSF. 24302562 4 63 gly sialylated 708:717 arg1 sialylated RFP N-glycans sialylated RFP N-glycans Here, we describe an analytical approach providing both quantitative profiling and in-depth mass spectrometry (MS)-based structural characterization of sialylated RFP N-glycans. 26729457 5 15 gly glycopeptide 982:993 arg2 glycopeptide fragmentation glycopeptide fragmentation glycopeptide A linear dependency of m/z-ratio and optimal fragmentation energy was found, showing that with increasing m/z-ratio, more energy is required for glycopeptide fragmentation. 27194760 5 34 gly carried 790:796 arg1 The second envelope viral protein AND N-glycans The second envelope viral protein N-glycans Fterm protein The second envelope viral protein, GN, carried mostly N-glycans not recognized by the classical glycosidases peptide-N-glycosidase F (PNGase F) and endoglycosidase H (Endo H). 26190824 2 5 gly occupancy 347:355 arg2 the sequon the sequon sequon Previous studies demonstrate that a phenylalanine residue introduced at the n-2 position relative to an Asn-Xxx-Thr/Ser N-glycosylation sequon increases the glycan occupancy of the sequon in insect cells. 26190824 2 17 gly sequon 364:369 arg1 the glycan occupancy sequon the glycan occupancy sequon Previous studies demonstrate that a phenylalanine residue introduced at the n-2 position relative to an Asn-Xxx-Thr/Ser N-glycosylation sequon increases the glycan occupancy of the sequon in insect cells. 26190824 2 41 gly N-glycosylation 303:317 arg2 an Asn-Xxx-Thr/Ser N-glycosylation sequon an Asn-Xxx-Thr/Ser N-glycosylation sequon sequon Previous studies demonstrate that a phenylalanine residue introduced at the n-2 position relative to an Asn-Xxx-Thr/Ser N-glycosylation sequon increases the glycan occupancy of the sequon in insect cells. 25117693 6 70 gly contain 1226:1232 arg1 the secreted proteins AND both N-linked glycans the secreted proteins both N-linked glycans Fterm proteins The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core similar to the structure of the glycan from RNase B, and O-linked glycans bearing mannose and glucose with 1→3 and 1→6 linkages. 25117693 6 70 gly contain 1226:1232 arg1 the secreted proteins AND O-linked glycans the secreted proteins O-linked glycans Fterm proteins The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core similar to the structure of the glycan from RNase B, and O-linked glycans bearing mannose and glucose with 1→3 and 1→6 linkages. 28654715 3 36 gly motifs 570:575 arg1 trisaccharide motifs trisaccharide motifs Combining NMR structure determination based on extensive experimental data with DFT and database searches, we have identified a set of trisaccharide motifs with a similar conformation that is characterized by a non-conventional C-H⋅⋅⋅O hydrogen bond. 27216994 13 26 part_of sites 2260:2264 arg1 GluN2B GluN2B sites PUBTATOR Site GluN2B Q13224 sites Furthermore, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 27216994 13 26 part_of sites 2260:2264 arg1 GluN1 GluN1 sites PUBTATOR Site GluN1 2902 sites Furthermore, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 25016576 7 41 part_of protein 1364:1370 arg1 the extracellular domain envelope protein the extracellular domain PUBTATOR Site envelope protein 100616444 domain In this report, we describe the isolation of a mouse mAb, 4B6, after immunization with the extracellular domain of the HIV-1 envelope protein, gp140. 27869200 6 90 gly glycopeptides 1046:1058 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides Remarkably, the developed model was found to reliably distinguish between the N- and O-linked glycopeptides using the spectral features of the oxonium ions using verification spectral set. 29019687 8 38 part_of GluN1 1449:1453 arg1 the GluN1 LBD domain GluN1 the GluN1 LBD domain PUBTATOR Site GluN1 2902 domain Some of the conformational changes in the glycans correlate with the physiologically important clamshell-like opening and closing of the GluN1 LBD domain. 29197583 4 37 gly glycoprotein 868:879 arg1 model glycoprotein model glycoprotein Fterm glycoprotein In the present work, the potential of traveling wave IM (TWIMS) for the separation of isomeric glycoconjugates was evaluated, using mouse transferrin (mTf) as model glycoprotein. 25182382 4 97 gly glycopeptides 694:706 arg2 intact glycopeptides intact glycopeptides glycopeptides The Y1 ion (peptide+GlcNAc) was accurately determined from the spectra of intact glycopeptides, and the structure of glycan was then identified by searching a constructed glycan database with calculated molecular weight of glycans and their fragment ions. 28958711 3 14 gly sialylated 506:515 arg1 the N-glycans the N-glycans Previous studies suggested that the O-glycans, but not the N-glycans on BSP, are highly sialylated. 28958711 3 14 gly sialylated 506:515 arg1 the O-glycans the O-glycans Previous studies suggested that the O-glycans, but not the N-glycans on BSP, are highly sialylated. 26154505 1 56 gly glycoproteins 286:298 arg1 recombinant glycoproteins recombinant glycoproteins Fterm glycoproteins Sialic acid, a terminal residue on complex N-glycans, and branching or antennarity can play key roles in both the biological activity and circulatory lifetime of recombinant glycoproteins of therapeutic interest. 26154505 1 72 gly residue 136:142 arg1 complex N-glycans residue complex N-glycans residue Sialic acid, a terminal residue on complex N-glycans, and branching or antennarity can play key roles in both the biological activity and circulatory lifetime of recombinant glycoproteins of therapeutic interest. 28785176 4 20 gly peptides 727:734 arg1 O-fucose additions peptides O-fucose additions peptides In this paper, HILIC is used to separate peptides with O-N-acetylgalactosamine (O-GalNAc), O-N-acetylglucosamine (O-GlcNAc), and O-fucose additions from their native forms, and coefficients representing the extent of hydrophilicity were derived using linear regression analysis as a means to predict the retention times of peptides with these modifications. 28785176 4 20 gly peptides 727:734 arg1 O-GlcNAc peptides O-GlcNAc peptides In this paper, HILIC is used to separate peptides with O-N-acetylgalactosamine (O-GalNAc), O-N-acetylglucosamine (O-GlcNAc), and O-fucose additions from their native forms, and coefficients representing the extent of hydrophilicity were derived using linear regression analysis as a means to predict the retention times of peptides with these modifications. 28785176 4 20 gly peptides 727:734 arg1 O-GalNAc peptides O-GalNAc peptides In this paper, HILIC is used to separate peptides with O-N-acetylgalactosamine (O-GalNAc), O-N-acetylglucosamine (O-GlcNAc), and O-fucose additions from their native forms, and coefficients representing the extent of hydrophilicity were derived using linear regression analysis as a means to predict the retention times of peptides with these modifications. 28785176 4 20 gly peptides 727:734 arg1 O-N-acetylglucosamine peptides O-N-acetylglucosamine peptides In this paper, HILIC is used to separate peptides with O-N-acetylgalactosamine (O-GalNAc), O-N-acetylglucosamine (O-GlcNAc), and O-fucose additions from their native forms, and coefficients representing the extent of hydrophilicity were derived using linear regression analysis as a means to predict the retention times of peptides with these modifications. 28785176 4 20 gly peptides 727:734 arg1 O-N-acetylgalactosamine peptides O-N-acetylgalactosamine peptides In this paper, HILIC is used to separate peptides with O-N-acetylgalactosamine (O-GalNAc), O-N-acetylglucosamine (O-GlcNAc), and O-fucose additions from their native forms, and coefficients representing the extent of hydrophilicity were derived using linear regression analysis as a means to predict the retention times of peptides with these modifications. 24440233 2 81 gly glycopeptides 404:416 arg2 intact glycopeptides intact glycopeptides glycopeptides In this study, we employed a recent type of fragmentation termed higher energy collisional dissociation (HCD) to examine fragmentation patterns of intact glycopeptides generated from a mixture of standard glycosylated proteins. 24440233 2 101 gly glycosylated 455:466 arg1 standard glycosylated proteins standard glycosylated proteins Fterm proteins In this study, we employed a recent type of fragmentation termed higher energy collisional dissociation (HCD) to examine fragmentation patterns of intact glycopeptides generated from a mixture of standard glycosylated proteins. 25883177 9 57 gly multifucosylated 1649:1664 arg1 multifucosylated LDN multifucosylated LDN O-glycans in the mature eggs were also diverse and contained LeX- and multifucosylated LDN, but none of these were associated with miracidia in which we detected only the Galβ1-3(Galβ1-6)GalNAc core glycan. 24473128 5 14 gly N-glycosylation 597:611 arg2 All 15 N-glycosylation sites All 15 N-glycosylation sites sites All 15 N-glycosylation sites of EBOV GP1 could be removed without compromising the expression of GP. 24719303 2 15 gly glycoprotein 428:439 arg1 the glycoprotein the glycoprotein Fterm glycoprotein Spectral data of the intact glycan moiety of RNase B is obtained by subtracting high-quality spectral data of RNase A, the non-glycosylated form of the RNase, from the spectra of the glycoprotein. 27722599 2 35 gly glycosylation 238:250 arg1 serum proteins serum proteins Fterm proteins Aberrant glycosylation in serum proteins is associated with many human diseases including inflammation and various types of cancer. 26439794 8 13 gly found 1249:1253 arg1 lysosome proteins AND high-mannose lysosome proteins high-mannose Fterm proteins Several unexpected N-glycans, such as fucosylated complex-type and fucosylated high-mannose and/or fucosylated pauci-mannose types were found in ER and lysosome proteins. 26439794 8 13 gly found 1249:1253 arg2 lysosome proteins AND fucosylated pauci-mannose types lysosome proteins fucosylated pauci-mannose types Fterm proteins Several unexpected N-glycans, such as fucosylated complex-type and fucosylated high-mannose and/or fucosylated pauci-mannose types were found in ER and lysosome proteins. 26439794 8 13 gly found 1249:1253 arg2 lysosome proteins AND complex-type lysosome proteins complex-type Fterm proteins Several unexpected N-glycans, such as fucosylated complex-type and fucosylated high-mannose and/or fucosylated pauci-mannose types were found in ER and lysosome proteins. 26439794 8 13 gly found 1249:1253 arg2 lysosome proteins AND Several unexpected N-glycans lysosome proteins Several unexpected N-glycans Fterm proteins Several unexpected N-glycans, such as fucosylated complex-type and fucosylated high-mannose and/or fucosylated pauci-mannose types were found in ER and lysosome proteins. 26439794 8 48 gly fucosylated 1212:1222 arg1 fucosylated pauci-mannose types fucosylated pauci-mannose types Several unexpected N-glycans, such as fucosylated complex-type and fucosylated high-mannose and/or fucosylated pauci-mannose types were found in ER and lysosome proteins. 29268168 3 12 gly position 623:630 arg1 the IgG-Fc glycan position 162 the IgG-Fc glycan position 162 The increase in affinity for afucosylated IgG has previously been shown to depend on direct carbohydrate-carbohydrate interactions between the IgG-Fc glycan with an N-linked glycan at position 162 unique to hFcγRIIIa and hFcγRIIIb. 26082218 3 0 gly glycoprotein 443:454 arg1 the glycoprotein the glycoprotein Fterm glycoprotein Such N-glycans can complicate downstream processing, might be immunogenic or cause the rapid clearance of the glycoprotein from circulation. 27975142 2 36 gly parameters 461:470 arg1 linkage positions linkage positions positions, The extent of compositional and structural variability of their oligomers (glycans) is unsurpassed in Nature due to the unique property of independently combining the following parameters with sequence: anomeric status, linkage positions, ring size, addition of branches and site-specific introduction of substitutions. 26110648 1 15 part_of gp120 148:152 arg1 the potential N-glycosylation sites gp120 the potential N-glycosylation sites PUBTATOR Site gp120 3700 sites The co-evolution of the potential N-glycosylation sites of HIV Clade B gp120 was mapped onto the coevolution network of the protein structure using mean field direct coupling analysis (mfDCA). 26956484 1 25 gly N-glycosylation 79:93 arg1 protein function protein function Fterm protein N-glycosylation of cell surface proteins affects protein function, stability, and interaction with other proteins. 26956484 1 25 gly N-glycosylation 79:93 arg1 cell surface proteins cell surface proteins Fterm proteins N-glycosylation of cell surface proteins affects protein function, stability, and interaction with other proteins. 25629924 7 34 part_of IgA1 1215:1218 arg1 the IgA1 hinge region IgA1 the IgA1 hinge region PUBTATOR Site IgA1 P01876 region Additionally, 54 O-linked glycan compositions located at the IgA1 hinge region (HR) were identified by comparison against a theoretical O-glycopeptide library. 24632452 5 35 gly hypoglycosylation 864:880 arg1 client proteins client proteins Fterm proteins However, modifications in the lipid-linked oligosaccharide biosynthesis often result in the accumulation of intermediate structures and cause hypoglycosylation of client proteins. 27932526 5 29 gly sialylation 1034:1044 arg1 high-mannose type species.Here high-mannose type species.Here MS has the opportunity to contribute additional information on, among others, antennarity, sialylation, and the identity of high-mannose type species.Here, we have used matrix-assisted laser desorption/ionization (MALDI)-Fourier transform ion cyclotron resonance (FTICR)-MS to study the total plasma N-glycome of 2144 healthy middle-aged individuals from the Leiden Longevity Study, to allow association analysis with markers of metabolic health and inflammation. 28975713 7 15 gly glycopeptide 1314:1325 arg2 the most probable intact glycopeptide mass matches the most probable intact glycopeptide mass matches glycopeptide CONCLUSIONS AND CLINICAL RELEVANCE PepSweetener efficiently allows the selection of the most probable intact glycopeptide mass matches and speeds up the verification process. 28199092 7 17 gly sites 1675:1679 arg1 individual glycan species sites individual glycan species sites Our results demonstrate that MAM quantification of individual glycan species from both the Fab and Fc N-Linked glycosylation sites is consistent with quantification using the traditional hydrophilic interaction liquid chromatography (HILIC) analysis of enzymatically released and fluorescently labeled glycans. 28199092 7 58 gly glycosylation 1661:1673 arg2 both the Fab and Fc N-Linked glycosylation sites both the Fab and Fc N-Linked glycosylation sites sites Our results demonstrate that MAM quantification of individual glycan species from both the Fab and Fc N-Linked glycosylation sites is consistent with quantification using the traditional hydrophilic interaction liquid chromatography (HILIC) analysis of enzymatically released and fluorescently labeled glycans. 26563299 7 30 part_of IL-15 1085:1089 arg1 The two potential IL-15 N-glycosylation sites IL-15 The two potential IL-15 N-glycosylation sites PUBTATOR Site IL-15 P40933 sites The two potential IL-15 N-glycosylation sites (Asn71 and Asn112) located at the IL-2 receptor interface were unoccupied. 25261856 5 21 gly fucosylated 1006:1016 arg1 peripherally fucosylated structures peripherally fucosylated structures The N-glycans found in the CSF were predominantly complex diantennary with sialic acid in α2,3- and α2,6-linkage, and bisecting N-acetylglucosamine-containing structures as well as peripherally fucosylated structures were found. 25837443 0 32 gly glycoproteins 18:30 arg1 glycoproteins glycoproteins Fterm glycoproteins Identification of glycoproteins containing specific glycans using a lectin-chemical method. 25837443 0 18 gly containing 32:41 arg1 glycoproteins AND specific glycans glycoproteins specific glycans Fterm glycoproteins Identification of glycoproteins containing specific glycans using a lectin-chemical method. 30023556 10 14 gly glycopeptide 1421:1432 arg2 glycopeptide libraries glycopeptide libraries glycopeptide Furthermore, the strategy of using glycopeptide libraries should enable the development of novel antibodies with predesigned O-glycan specificities. 26170448 8 45 gly released 840:847 arg2 these two S-layer glycoproteins AND the N- these two S-layer glycoproteins the N- Fterm glycoproteins Moreover, the N- and O-linked glycans were released from these two S-layer glycoproteins for structural determination. 26170448 8 45 gly released 840:847 arg2 these two S-layer glycoproteins AND O-linked glycans these two S-layer glycoproteins O-linked glycans Fterm glycoproteins Moreover, the N- and O-linked glycans were released from these two S-layer glycoproteins for structural determination. 26170448 8 56 gly glycoproteins 872:884 arg1 these two S-layer glycoproteins these two S-layer glycoproteins Fterm glycoproteins Moreover, the N- and O-linked glycans were released from these two S-layer glycoproteins for structural determination. 28486782 6 39 part_of factor 717:722 arg1 the growth factor binding site factor the growth factor binding site Fterm Site factor site Several antibodies inhibit EGFR by targeting the growth factor binding site or the dimeric interfaces. 24234447 1 57 gly structures 203:212 arg1 a growing, curated database database structures Fterm database The UniCarb KnowledgeBase (UniCarbKB; http://unicarbkb.org) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. 24234447 1 63 gly database 165:172 arg1 the glycan structures database the glycan structures Fterm database The UniCarb KnowledgeBase (UniCarbKB; http://unicarbkb.org) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. 24234447 1 69 gly glycoproteins 217:229 arg1 the glycan structures glycoproteins the glycan structures Fterm glycoproteins The UniCarb KnowledgeBase (UniCarbKB; http://unicarbkb.org) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. 25117244 2 43 gly glycoproteins 322:334 arg1 glycoproteins glycoproteins Fterm glycoproteins By using evanescent-field fluorescence detection technique, it has been applied for analysis of not only glycoproteins and glycolipids secreted by eukaryotic cells but also glycoconjugates on the cell surface of live eukaryotic cells. 25638265 4 34 gly glycoproteins 1087:1099 arg1 test glycoproteins test glycoproteins Fterm glycoproteins The method was validated with respect to mobile phase parameters, reproducibility, accuracy, linearity and limit of detection/quantification (LOD/LOQ) using test glycoproteins. 28680094 8 13 gly domain 1217:1222 arg1 one unique N-glycan domain one unique N-glycan domain We identified one unique N-glycan at the βI domain of β1 subunit that negatively regulates α5β1 activation. 26784534 3 32 part_of Tryptic 355:361 arg1 Tryptic VWF-O-glycopeptides VWF Tryptic VWF-O-glycopeptides PUBTATOR Site VWF 7450 VWF-O-glycopeptides METHODS: Tryptic VWF-O-glycopeptides were isolated by lectin affinity chromatography and/or by reverse-phase high-performance liquid chromatography. 26286102 1 60 gly linked 244:249 arg1 a protein AND N-glycan a protein N-glycan Fterm protein Protein N-glycosylation consists in the synthesis and processing of the oligosaccharide moiety (N-glycan) linked to a protein and it serves several functions for the proper central nervous system (CNS) development and function. 26286102 1 60 gly linked 244:249 arg1 a protein AND the oligosaccharide moiety a protein the oligosaccharide moiety Fterm protein Protein N-glycosylation consists in the synthesis and processing of the oligosaccharide moiety (N-glycan) linked to a protein and it serves several functions for the proper central nervous system (CNS) development and function. 28956227 5 27 part_of NTPDase3/CD39L3 1088:1102 arg1 soluble enzymatic domains NTPDase3 soluble enzymatic domains PUBTATOR Site NTPDase3 956 domains To understand the mechanism of the ecto-NTPDase activity and substrate specificity, potentially impacted by N-glycans, we have generated soluble enzymatic domains of NTPDase3/CD39L3 in human embryotic kidney cells with four different glycan modifications. 24912590 3 0 gly released 467:474 arg1 proteins AND glycans proteins glycans Fterm proteins The samples were pretreated for enzymatic cleaving, and subsequently glycans released from proteins were captured on BlotGlyco H beads. 27851982 2 70 part_of domain 336:341 arg1 CDH CDH domain PUBTATOR Site CDH 55349 domain Interdomain electron transfer between the flavin and cytochrome domain in CDH, preceding the electron flow to lytic polysaccharide monooxygenase, is known to be pH dependent, but the exact mechanism of this regulation has not been experimentally proven so far. 24820161 2 5 gly C-mannosylated 383:396 arg1 some proteins some proteins Fterm proteins In the protein glycosylation, C-mannosylation was first identified in ribonuclease 2, and some proteins have been reported to be C-mannosylated; however, effects of its modifications for target proteins remain unclear. 28947169 0 36 gly proteins 20:27 arg1 Glycan profiling proteins Glycan profiling Fterm proteins Glycan profiling of proteins using lectin binding by Surface Plasmon Resonance. 25458834 8 7 part_of subunit 990:996 arg1 the C terminus subunit the C terminus Fterm Site subunit terminus Carboxyl groups from the sialic acid residue on podoplanin and from the C terminus of the rhodocytin α subunit interact differently at this "second" binding site on CLEC-2. 25458834 8 32 part_of site 1044:1047 arg1 CLEC-2 CLEC-2 site PUBTATOR Site CLEC-2 51266 site Carboxyl groups from the sialic acid residue on podoplanin and from the C terminus of the rhodocytin α subunit interact differently at this "second" binding site on CLEC-2. 26232512 0 12 gly α1,2-fucosylated 70:85 arg1 α1,2-fucosylated glycans α1,2-fucosylated glycans Hypoxia inducible factor 1α down regulates cell surface expression of α1,2-fucosylated glycans in human pancreatic adenocarcinoma cells. 29157724 8 86 gly sialylated 1118:1127 arg1 high mannose type and sialylated N-glycans high mannose type and sialylated N-glycans Our receiver operating characteristic (ROC) curve analysis shows that high mannose type and sialylated N-glycans are useful discriminators to distinguish between lung adenocarcinoma and control tissue. 28378791 1 24 gly glycoproteins 119:131 arg1 glycoproteins glycoproteins Fterm glycoproteins N-methyl-D-aspartate receptors (NMDARs) are glycoproteins in the brain central to learning and memory. 28378791 1 24 gly glycoproteins 119:131 arg1 N-methyl-D-aspartate receptors N-methyl-D-aspartate receptors Fterm receptors N-methyl-D-aspartate receptors (NMDARs) are glycoproteins in the brain central to learning and memory. 28890362 4 55 part_of receptor 804:811 arg1 the binding site CD4 receptor the binding site PUBTATOR Site CD4 receptor 920 site Network analysis showed that highly conserved glycans combined with protomer scissoring to restrict access to the binding site of the CD4 receptor. 29237727 6 24 gly N-glycopeptides 917:931 arg2 N-glycopeptides N-glycopeptides N-glycopeptides To demonstrate the precision of the approach, we also profiled N-glycopeptides from the mutant (xylt) of β-1,2-xylosyltransferase, an enzyme in the N-glycan biosynthetic pathway. 26729242 4 27 gly glycopeptide 703:714 arg2 general glycopeptide enrichment general glycopeptide enrichment glycopeptide The first lectin provides general glycopeptide enrichment, while the second specifically enriches O-linked glycopeptides with Galβ1-3GalNAcα structures. 26729242 4 13 gly glycopeptides 776:788 arg2 O-linked glycopeptides glycopeptides Galβ1-3GalNAcα structures glycopeptides The first lectin provides general glycopeptide enrichment, while the second specifically enriches O-linked glycopeptides with Galβ1-3GalNAcα structures. 24644239 1 70 gly glycosylated 151:162 arg1 a naturally glycosylated chemokine protein a naturally glycosylated chemokine protein Fterm protein CCL1 is a naturally glycosylated chemokine protein that is secreted by activated T-cells and acts as a chemoattractant for monocytes. 26479949 10 6 gly glycopeptides 1820:1832 arg2 115 different N-linked glycopeptides 115 different N-linked glycopeptides glycopeptides Finally, we identified 115 different N-linked glycopeptides, representing 93 gene products and 124 glycosylation sites in HRMC. 26479949 10 19 gly glycosylation 1873:1885 arg2 124 glycosylation sites 124 glycosylation sites sites Finally, we identified 115 different N-linked glycopeptides, representing 93 gene products and 124 glycosylation sites in HRMC. 26189796 4 16 gly modified 853:860 arg3 the key site AND β1,6 GlcNAc-branched N-glycans the key site β1,6 GlcNAc-branched N-glycans site In vitro models further indicated that, among the four potential N-glycosylation sites of E-cadherin, Asn-554 is the key site that is selectively modified with β1,6 GlcNAc-branched N-glycans catalyzed by GnT-V. 26189796 4 16 gly modified 853:860 arg1 Asn-554 AND β1,6 GlcNAc-branched N-glycans Asn-554 β1,6 GlcNAc-branched N-glycans Asn-554 In vitro models further indicated that, among the four potential N-glycosylation sites of E-cadherin, Asn-554 is the key site that is selectively modified with β1,6 GlcNAc-branched N-glycans catalyzed by GnT-V. 26189796 4 12 gly N-glycosylation 772:786 arg2 the four potential N-glycosylation sites E-cadherin sites PUBTATOR E-cadherin 999 sites In vitro models further indicated that, among the four potential N-glycosylation sites of E-cadherin, Asn-554 is the key site that is selectively modified with β1,6 GlcNAc-branched N-glycans catalyzed by GnT-V. 25359784 0 52 gly glycosylated 20:31 arg1 a glycosylated asparagine residue a glycosylated asparagine residue asparagine residue The side chain of a glycosylated asparagine residue is important for the stability of isopullulanase. 25451932 9 5 gly N-glycosylation 1186:1200 arg2 the N-glycosylation site the N-glycosylation site site We also found that the location of the N-glycosylation site in the protease domain was not critical. 24798333 0 0 gly variants 90:97 arg1 N-Glycan-dependent and -independent quality control variants N-Glycan-dependent and -independent quality control Fterm variants N-Glycan-dependent and -independent quality control of human δ opioid receptor N-terminal variants. 26908049 10 5 gly glycoproteins 1718:1730 arg1 glycoproteins glycoproteins Fterm glycoproteins CONCLUSIONS Our findings demonstrate how careful analysis using multiple advanced techniques can be used to identify and dissect the multiple potential functions of protein glycosylation and form a prerequisite for glycoengineering and drug development of glycoproteins. 26240146 8 23 gly Asn-30 1322:1327 arg1 N-linked oligosaccharides Asn-13 and Asn-30 N-linked oligosaccharides Asn-13 and Asn-30 Site-specific N-glycosylation analysis suggests that N-linked oligosaccharides at Asn-13 and Asn-30 on the β subunit affect the binding affinity of MCA1024. 26240146 8 62 gly oligosaccharides 1291:1306 arg1 the β subunit subunit oligosaccharides Fterm subunit Site-specific N-glycosylation analysis suggests that N-linked oligosaccharides at Asn-13 and Asn-30 on the β subunit affect the binding affinity of MCA1024. 26240146 8 79 gly Asn-13 1311:1316 arg1 N-linked oligosaccharides Asn-13 and Asn-30 N-linked oligosaccharides Asn-13 and Asn-30 Site-specific N-glycosylation analysis suggests that N-linked oligosaccharides at Asn-13 and Asn-30 on the β subunit affect the binding affinity of MCA1024. 26587982 5 59 gly density 741:747 arg1 the arenavirus envelope protein's globular head the arenavirus envelope protein's globular head the arenavirus envelope protein's globular head Site head NAb response kinetics in mice correlated inversely with the N-linked glycan density in the arenavirus envelope protein's globular head. 29069609 3 64 gly glycopeptide 620:631 arg2 glycopeptide analysis glycopeptide analysis glycopeptide In this study, we investigated pseudo-MRM (MRM-HR) and data-independent acquisition (DIA) as alternative acquisition strategies for glycopeptide analysis. 24533768 3 64 gly glycosylation 480:492 arg2 the native glycosylation site the native glycosylation site site We have developed a novel site-specific conjugation method by targeting the native glycosylation site on antibodies as an approach to address these limitations. 28193332 0 81 gly non-glycosylated 105:120 arg1 partially non-glycosylated enzymes partially non-glycosylated enzymes Fterm enzymes Analysis of Agaricus meleagris pyranose dehydrogenase N-glycosylation sites and performance of partially non-glycosylated enzymes. 28193332 0 95 gly N-glycosylation 54:68 arg2 Agaricus meleagris pyranose dehydrogenase N-glycosylation sites Agaricus meleagris pyranose dehydrogenase N-glycosylation sites sites Analysis of Agaricus meleagris pyranose dehydrogenase N-glycosylation sites and performance of partially non-glycosylated enzymes. 28956227 0 36 part_of NTPDase3/CD39L3 73:87 arg1 the NTPDase3/CD39L3 ecto-enzymatic domain NTPDase3 the NTPDase3/CD39L3 ecto-enzymatic domain PUBTATOR Site NTPDase3 956 domain Various N-glycoforms differentially upregulate E-NTPDase activity of the NTPDase3/CD39L3 ecto-enzymatic domain. 24511137 1 28 gly glycosylation 98:110 arg1 O-linked glycans region O-linked glycans region Deficient glycosylation of O-linked glycans in the IgA1 hinge region is associated with IgA nephropathy in humans, but the pathogenic contribution of the underlying structural aberrations remains incompletely understood. 24511137 1 94 gly glycosylation 98:110 arg1 the IgA1 hinge region region region Deficient glycosylation of O-linked glycans in the IgA1 hinge region is associated with IgA nephropathy in humans, but the pathogenic contribution of the underlying structural aberrations remains incompletely understood. 24511137 1 94 gly glycosylation 98:110 arg1 the IgA1 hinge region region O-linked glycans region Deficient glycosylation of O-linked glycans in the IgA1 hinge region is associated with IgA nephropathy in humans, but the pathogenic contribution of the underlying structural aberrations remains incompletely understood. 24981920 0 25 part_of syndecan-3 22:31 arg1 syndecan-3 glycopeptides syndecan-3 syndecan-3 glycopeptides PUBTATOR Site syndecan-3 9672 glycopeptides Chemical synthesis of syndecan-3 glycopeptides bearing two heparan sulfate glycan chains. 26082235 1 36 gly glycoproteins 126:138 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins Monoclonal antibodies (mAbs) are an important class of therapeutic glycoproteins widely used for the treatment of cancer, inflammation, and infectious diseases. 25182382 1 2 gly glycopeptides 291:303 arg2 intact glycopeptides intact glycopeptides glycopeptides The detailed characterization of site-specific glycosylation requires the identification of glycan composition and specific attachment sites on proteins, which need the identification of intact glycopeptides by mass spectrometry. 25182382 1 21 gly composition 196:206 arg1 proteins proteins composition Fterm proteins The detailed characterization of site-specific glycosylation requires the identification of glycan composition and specific attachment sites on proteins, which need the identification of intact glycopeptides by mass spectrometry. 25575808 10 9 part_of endocan 1188:1194 arg1 endocan polypeptide endocan endocan polypeptide PUBTATOR Site endocan 11082 polypeptide In tumor tissue sections, a stromal inflammatory reaction was observed only in tumors overexpressing endocan polypeptide, and depletion of CD122+ cells was able to delete partially the anti-tumor effect of endocan polypeptide. 25575808 10 63 part_of endocan 1293:1299 arg1 endocan polypeptide endocan endocan polypeptide PUBTATOR Site endocan 11082 polypeptide In tumor tissue sections, a stromal inflammatory reaction was observed only in tumors overexpressing endocan polypeptide, and depletion of CD122+ cells was able to delete partially the anti-tumor effect of endocan polypeptide. 28661444 12 49 gly glycosylated 1955:1966 arg1 B-cell epitopic lysines B-cell epitopic lysines lysines In contrast, B-cell epitopic lysines of Ag85B were found to be poorly glycosylated and, thus, the antibody interaction of Ag85B was only marginally affected after coupling with mono- or disaccharides. 26492619 10 26 part_of PDPN 1310:1313 arg1 epitopes PDPN epitopes PUBTATOR Site PDPN 10630 epitopes By using monoclonal antibodies against different Ser/Thr, including epitopes of PDPN, it becomes possible to determine whether Ser/Thr residues of PDPN are O-glycosylated. 26492619 10 57 part_of PDPN 1377:1380 arg1 Ser/Thr residues PDPN Ser/Thr residues PUBTATOR Site PDPN 10630 residues By using monoclonal antibodies against different Ser/Thr, including epitopes of PDPN, it becomes possible to determine whether Ser/Thr residues of PDPN are O-glycosylated. 25587188 10 75 gly N-glycans 1415:1423 arg1 their variable domains their variable domains their variable domains CONCLUSIONS: The vast majority of ACPA-IgG harbour N-glycans in their variable domains. 26603318 2 13 gly attached 293:300 arg1 asparagine (Asn) 66 AND complex-type glycans Asn) 66 and Asn 110 complex-type glycans Asn) 66 and Asn 110 We studied the role of complex-type glycans attached to asparagine (Asn) 66 and Asn 110 to elucidate the role of carbohydrates in lectin activity and stability. 25636227 0 47 part_of sites 83:87 arg1 human chorionic gonadotropin chorionic gonadotropin sites OGER Site chorionic gonadotropin sites From individual proteins to proteomic samples: characterization of O-glycosylation sites in human chorionic gonadotropin and human-plasma proteins. 25636227 0 47 part_of sites 83:87 arg1 human-plasma proteins proteins sites Fterm Site proteins sites From individual proteins to proteomic samples: characterization of O-glycosylation sites in human chorionic gonadotropin and human-plasma proteins. 28510654 5 44 gly glycopeptides 610:622 arg2 12 small tryptic glycopeptides 12 small tryptic glycopeptides glycopeptides The tandem mass spectrometry (MS/MS) analysis of 12 small tryptic glycopeptides confirmed the canonical N-glycosylation consensus in P. calidifontis. 25601700 0 87 gly position 100:107 arg1 oligosaccharides position oligosaccharides position Negative electrospray ionization mass spectrometry: a method for sequencing and determining linkage position in oligosaccharides from branched hemicelluloses. 27641064 2 31 gly N-glycosylations 215:230 arg1 the calf domain the calf domain domain We previously reported that the N-glycosylations of the calf domain on integrin α5 (S3-5,10-14) are essential for its inhibitory effect on EGFR signaling in regulating cell proliferation. 27957769 11 31 gly glycosylation 2185:2197 arg2 glycosylation sites glycosylation sites sites The nature of the antibody response is characteristically different for antibodies directed to glycosylation sites in either the immune-dominant PDTR or the GSTA domain. 24130173 8 88 gly tri-sialylated 1525:1538 arg1 the native protein protein tri-sialylated N-glycans Fterm protein Moreover, the efficient synthesis of carbohydrates present only in minute amounts on the native protein (tri-sialylated N-glycans) facilitates the generation of a product with superior efficacies and/or new therapeutic functions. 25479762 1 7 gly N-glycosylated 190:203 arg1 an N-glycosylated membrane protein an N-glycosylated membrane protein Fterm protein BACKGROUND γ-Glutamyl transpeptidase 1 (GGT1) is an N-glycosylated membrane protein that catabolizes extracellular glutathione and other γ-glutamyl-containing substrates. 26082228 1 30 gly glycoprotein 165:176 arg1 recombinant glycoprotein therapeutics recombinant glycoprotein therapeutics Fterm glycoprotein Plants are attractive expression hosts for the production of recombinant glycoprotein therapeutics. 26316330 9 28 gly glycoproteins 1330:1342 arg1 two particular glycoproteins two particular glycoproteins Fterm glycoproteins 2) An estimation of the number of potential glycoprotein species of two particular glycoproteins was given. 26316330 9 69 gly glycoprotein 1291:1302 arg1 potential glycoprotein species potential glycoprotein species Fterm glycoprotein 2) An estimation of the number of potential glycoprotein species of two particular glycoproteins was given. 27705835 1 40 gly epitope 342:348 arg1 a epitope(s) a epitope(s) The Japanese cedar pollen allergen (Cry j1) and the mountain cedar pollen allergen (Jun a1) are glycosylated with plant complex type N-glycans bearing Lewis a epitope(s) (Galβ1-3[Fucα1-4]GlcNAc-). 27063138 6 28 gly occupied 770:777 arg2 the active sites the active sites sites Analysis of metal content using ICP-MS revealed that 93% of the active sites were occupied by copper. 25016576 2 75 gly glycans 413:419 arg1 the first and second variable (V1/V2) domain the first and second variable (V1/V2) domain the first and second variable (V1/V2) domain Site domain These were recovered from HIV-1 infected subjects, and several (e.g., PG9, PG16, CH01, CH03) target glycans in the first and second variable (V1/V2) domain of gp120. 27151270 5 78 gly glycosylation 818:830 arg2 the 13 sites the 13 sites sites Mass spectrometry analysis provided a detailed glycosylation profile at the 13 sites of N-linked glycosylation on windmill palm tree peroxidase. 27151270 5 37 gly glycosylation 868:880 arg1 windmill palm tree peroxidase peroxidase sites Fterm peroxidase sites Mass spectrometry analysis provided a detailed glycosylation profile at the 13 sites of N-linked glycosylation on windmill palm tree peroxidase. 28486782 11 18 part_of EGFR 1533:1536 arg1 the EGFR extracellular domain EGFR the EGFR extracellular domain PUBTATOR Site EGFR 1956 domain N-glycosylation also helps maintain the dimeric interface and plays distinct roles in binding of antibodies to spatially separated epitopes of the EGFR extracellular domain. 26110648 3 38 gly N-glycosylation 486:500 arg2 the potential N-glycosylation sites the potential N-glycosylation sites sites Indications of pressure to preserve the evolving glycan shield are seen as well as strong dependencies between the majority of the potential N-glycosylation sites and the rest of the structure. 27758867 5 37 part_of flagellin 1228:1236 arg1 flagellin glycopeptides flagellin flagellin glycopeptides PUBTATOR Site flagellin 1117738 glycopeptides Finally, NMR analysis of flagellin glycopeptides provided complementary information. 24460129 3 17 gly released 696:703 arg2 ovalbumin AND 25 N-linked glycans ovalbumin 25 N-linked glycans Fterm ovalbumin By taking advantage of the special interaction between the carbon and glycans as well as size-exclusion ability, 25 N-linked glycans released from ovalbumin were observed clearly with strong MS signals and increased signal-to-noise (S/N) ratio. 26503433 1 26 gly fucosylated 134:144 arg1 fucosylated glycans fucosylated glycans A method for the detection of fucosylated glycans from haptoglobin in patient serum has been developed that provides enhanced sensitivity. 29285644 0 64 gly glycopeptides 27:39 arg2 fingerprint glycopeptides fingerprint glycopeptides glycopeptides Designation of fingerprint glycopeptides for targeted glycoproteomic analysis of serum haptoglobin: insights into gastric cancer biomarker discovery. 28295836 1 18 gly glycoproteins 337:349 arg1 glycoproteins glycoproteins Fterm glycoproteins Sea urchin eggs are surrounded by a carbohydrate-rich layer, termed the jelly coat, that consists of polysaccharides and glycoproteins. 24497634 12 5 gly sites 1546:1550 arg1 N-glycosylation sites N-glycosylation sites sites Next, we showed that the cluster of N-glycosylation sites (Asn-467, Asn-473, and Asn-494) was required for immunoreactivity in one patient. 24497634 12 44 gly N-glycosylation 1530:1544 arg2 N-glycosylation sites N-glycosylation sites sites Next, we showed that the cluster of N-glycosylation sites (Asn-467, Asn-473, and Asn-494) was required for immunoreactivity in one patient. 24497634 12 5 gly sites 1546:1550 arg1 Asn-494 Asn-467, Asn-473, and Asn-494 Asn-467, Asn-473, and Asn-494 Next, we showed that the cluster of N-glycosylation sites (Asn-467, Asn-473, and Asn-494) was required for immunoreactivity in one patient. 24497634 12 5 gly sites 1546:1550 arg1 Asn-467 Asn-467, Asn-473, and Asn-494 Asn-467, Asn-473, and Asn-494 Next, we showed that the cluster of N-glycosylation sites (Asn-467, Asn-473, and Asn-494) was required for immunoreactivity in one patient. 24497634 12 5 gly sites 1546:1550 arg1 Asn-467 Asn-467, Asn-473, and Asn-494 Asn-467, Asn-473, and Asn-494 Next, we showed that the cluster of N-glycosylation sites (Asn-467, Asn-473, and Asn-494) was required for immunoreactivity in one patient. 24497634 12 44 gly N-glycosylation 1530:1544 arg2 Asn-494 Asn-467, Asn-473, and Asn-494 Asn-467, Asn-473, and Asn-494 Next, we showed that the cluster of N-glycosylation sites (Asn-467, Asn-473, and Asn-494) was required for immunoreactivity in one patient. 24497634 12 44 gly N-glycosylation 1530:1544 arg2 Asn-473 Asn-467, Asn-473, and Asn-494 Asn-467, Asn-473, and Asn-494 Next, we showed that the cluster of N-glycosylation sites (Asn-467, Asn-473, and Asn-494) was required for immunoreactivity in one patient. 24497634 12 44 gly N-glycosylation 1530:1544 arg2 Asn-473 Asn-467, Asn-473, and Asn-494 Asn-467, Asn-473, and Asn-494 Next, we showed that the cluster of N-glycosylation sites (Asn-467, Asn-473, and Asn-494) was required for immunoreactivity in one patient. 28246170 3 4 gly serine-rich 597:607 arg1 a mucin-like serine-rich repeat protein PsrP serine a mucin-like serine-rich repeat protein PsrP serine Here we systematically explored the O-glycosylation pathway of a mucin-like serine-rich repeat protein PsrP from the human pathogen Streptococcus pneumoniae TIGR4. 26908049 10 80 part_of glycoproteins 1718:1730 arg1 a prerequisite glycoproteins a prerequisite Fterm Site glycoproteins prerequisite CONCLUSIONS Our findings demonstrate how careful analysis using multiple advanced techniques can be used to identify and dissect the multiple potential functions of protein glycosylation and form a prerequisite for glycoengineering and drug development of glycoproteins. 25849464 11 98 gly glycosylation 1951:1963 arg1 a Basidiomycete fungal laccase a Basidiomycete fungal laccase Fterm laccase This study provides new insights into the role of glycosylation in the structure and function of a Basidiomycete fungal laccase. 27758867 5 38 gly glycopeptides 1238:1250 arg2 flagellin glycopeptides flagellin glycopeptides glycopeptides Finally, NMR analysis of flagellin glycopeptides provided complementary information. 24451126 5 50 part_of IgG1 698:701 arg1 the Fc fragment IgG1 the Fc fragment OGER Site IgG1 P01857 fragment In order to understand this cross-talk, molecular dynamics simulations of the domains of the Fc fragment of human IgG1 are reported. 24451126 5 69 part_of Fc 677:678 arg1 the Fc fragment Fc the Fc fragment Cterm Site Fc fragment In order to understand this cross-talk, molecular dynamics simulations of the domains of the Fc fragment of human IgG1 are reported. 24440233 4 14 gly attached 753:760 arg2 the peptides AND the sugar chains the peptides the sugar chains peptides Our results indicated that HCD with lower NCE values preferentially fragmented the sugar chains attached to the peptides to generate a ladder of neutral loss of monosaccharides, thereby enabling the putative glycan structure characterization. 27873218 8 33 part_of bikunin 1563:1569 arg1 the bikunin CS linkage region bikunin CS the bikunin CS linkage region PUBTATOR Site bikunin CS 259 region We have demonstrated a considerable heterogeneity of the bikunin CS linkage region. 27873218 8 95 part_of CS 1571:1572 arg1 the bikunin CS linkage region bikunin CS the bikunin CS linkage region PUBTATOR Site bikunin CS 259 region We have demonstrated a considerable heterogeneity of the bikunin CS linkage region. 26170448 7 13 gly glycoproteins 738:750 arg1 these two S-layer glycoproteins these two S-layer glycoproteins Fterm glycoproteins The genes coding for these two S-layer glycoproteins were found next to each other in the genome. 24012618 2 17 gly Glycosylation 152:164 arg1 proteins proteins Fterm proteins Glycosylation of proteins and their variations significantly affect protein structure and function, thus altering numerous physiological and pathophysiological cellular processes. 26488311 4 34 gly glycosylated 621:632 arg1 glycosylated peptides glycosylated peptides peptides More detailed structural characterization of clusterin glycopeptides was also performed, demonstrating the presence of glycosylated peptides and their corresponding glycans. 26488311 4 35 gly glycopeptides 557:569 arg2 clusterin glycopeptides clusterin glycopeptides glycopeptides More detailed structural characterization of clusterin glycopeptides was also performed, demonstrating the presence of glycosylated peptides and their corresponding glycans. 25636227 3 55 gly O-glycosylation 490:504 arg1 individual proteins proteins sites Fterm proteins sites In this work, we designed a rapid and convenient workflow for characterizing the O-glycosylation sites of individual proteins and the human-plasma proteome. 28211926 2 4 gly glycopeptides 480:492 arg2 glycopeptides glycopeptides glycopeptides Glycosyl thiols produced by this method may be used to access glycoconjugates, such as glycopeptides by use of the thiol-ene click reaction. 26132640 1 7 gly glycosylation 111:123 arg1 protein recognition protein residues Fterm protein residues O-Linked glycosylation of serine/threonine residues is a posttranslational modification of proteins and is essential for protein recognition and lipid functions on cell surfaces and within cells. 27769287 7 79 gly occupancy 1435:1443 arg1 secreted glycoproteins secreted glycoproteins Fterm glycoproteins Moreover, RHO1 overexpression could also increase N-glycan site occupancy and the amount of secreted glycoproteins. 27769287 7 56 gly glycoproteins 1472:1484 arg1 secreted glycoproteins glycoproteins N-glycan site occupancy Fterm glycoproteins Moreover, RHO1 overexpression could also increase N-glycan site occupancy and the amount of secreted glycoproteins. 26082218 5 15 gly glycoforms 680:689 arg1 therapeutically relevant glycoproteins therapeutically relevant glycoproteins Fterm glycoproteins This can be of pivotal importance to generate the appropriate glycoforms of therapeutically relevant glycoproteins or to gain a better understanding of structure-function relationships.This chapter describes the methodology to create such glyco-engineered Pichia pastoris strains using the GlycoSwitch(®). 26082218 5 62 gly glycoproteins 719:731 arg1 therapeutically relevant glycoproteins therapeutically relevant glycoproteins Fterm glycoproteins This can be of pivotal importance to generate the appropriate glycoforms of therapeutically relevant glycoproteins or to gain a better understanding of structure-function relationships.This chapter describes the methodology to create such glyco-engineered Pichia pastoris strains using the GlycoSwitch(®). 25575808 0 33 part_of endocan 19:25 arg1 The non glycanated endocan polypeptide endocan The non glycanated endocan polypeptide PUBTATOR Site endocan 11082 polypeptide The non glycanated endocan polypeptide slows tumor growth by inducing stromal inflammatory reaction. 27867116 2 27 gly glycoprotein 413:424 arg1 the glycoprotein digest the glycoprotein digest Fterm glycoprotein The use of a BEH C18 nanoACQUITY column allowed the separation of the glycopeptides present in the glycoprotein digest and a baseline-resolution of the glycoforms of the same glycopeptide on the basis of the number of sialic acids. 27867116 2 31 gly glycopeptides 384:396 arg2 the glycopeptides the glycopeptides glycopeptides The use of a BEH C18 nanoACQUITY column allowed the separation of the glycopeptides present in the glycoprotein digest and a baseline-resolution of the glycoforms of the same glycopeptide on the basis of the number of sialic acids. 27867116 2 44 gly glycopeptide 489:500 arg2 the same glycopeptide the same glycopeptide glycopeptide The use of a BEH C18 nanoACQUITY column allowed the separation of the glycopeptides present in the glycoprotein digest and a baseline-resolution of the glycoforms of the same glycopeptide on the basis of the number of sialic acids. 27867116 2 49 gly glycoforms 466:475 arg1 the same glycopeptide the same glycopeptide glycopeptide The use of a BEH C18 nanoACQUITY column allowed the separation of the glycopeptides present in the glycoprotein digest and a baseline-resolution of the glycoforms of the same glycopeptide on the basis of the number of sialic acids. 27957769 10 5 part_of MUC1 2029:2032 arg1 MUC1 peptides MUC1 MUC1 peptides PUBTATOR Site MUC1 4582 peptides It is observed that the induced antibodies recognize MUC1 peptides with very high glycosylation site specificity. 24664808 10 108 part_of having 1705:1710 arg1 an interesting fragment AND an Asn residue an interesting fragment an Asn residue Asn residue When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36](-), was abundantly formed. 24664808 10 108 part_of having 1705:1710 arg1 an interesting fragment AND Asn-36 an interesting fragment Asn-36 Asn-36 When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36](-), was abundantly formed. 27773703 3 62 gly N-glycosylation 336:350 arg2 30 potential N-glycosylation sites 30 potential N-glycosylation sites sites Megalin has 30 potential N-glycosylation sites in its extracellular domain. 25837443 6 24 gly glycoproteins 916:928 arg1 novel glycoproteins glycoproteins certain glycans Fterm glycoproteins The application of the method should be useful to facilitate our understanding of how changes in glycan associate with diseases, and to discover novel glycoproteins with certain glycans that could serve as biomarkers or therapeutic targets. 26488311 5 53 part_of sites 844:848 arg1 plasma clusterin clusterin sites OGER Site clusterin P10909 sites Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we have determined the differences in the glycoforms associated at each of the different glycosylation sites in plasma clusterin obtained from subjects of low hippocampal atrophy (n = 13) and high hippocampal atrophy (n = 14). 27283789 4 17 part_of IgG 658:660 arg1 the Fc region IgG the Fc region Cterm Site IgG region Three piperidine-melamine glycodendrimers were synthesized via a chemoenzymatic route and attached to human growth hormone and the Fc region of human IgG. 27439567 3 25 gly glycopeptides 438:450 arg2 glycopeptides glycopeptides glycopeptides The workflow involves digestion of intact glycoproteins into glycopeptides, followed by double digestion with sialidase and galactosidase. 27439567 3 34 gly glycoproteins 419:431 arg1 intact glycoproteins intact glycoproteins Fterm glycoproteins The workflow involves digestion of intact glycoproteins into glycopeptides, followed by double digestion with sialidase and galactosidase. 27810711 3 1 gly glycopeptide 401:412 arg2 syndecan-3 glycopeptide syndecan-3 glycopeptide glycopeptide In this work, we give the full account of the synthesis of syndecan-3 glycopeptide (53-62) containing two different heparan sulfate chains. 28928219 2 8 gly attached 533:540 arg2 hydroxylated Pro-143 AND a unique pentasaccharide hydroxylated Pro-143 a unique pentasaccharide Pro-143 In Dictyostelium (a social amoeba), Toxoplasma gondii (the agent for human toxoplasmosis), and other protists, Skp1 is regulated by a unique pentasaccharide attached to hydroxylated Pro-143 within its C-terminal F-box-binding domain. 25759508 4 1 gly threonine 606:614 arg1 The repeat regions threonine The repeat regions threonine The repeat regions within the IgG3 hinge were found to be in part O-glycosylated at the threonine in the triple repeat motif. 25759508 4 1 gly threonine 606:614 arg1 the triple repeat motif threonine the triple repeat motif threonine The repeat regions within the IgG3 hinge were found to be in part O-glycosylated at the threonine in the triple repeat motif. 25759508 4 49 gly O-glycosylated 584:597 arg2 The repeat regions The repeat regions within the IgG3 hinge were found to be in part O-glycosylated at the threonine in the triple repeat motif. 25759508 4 49 gly O-glycosylated 584:597 arg2 the threonine threonine threonine The repeat regions within the IgG3 hinge were found to be in part O-glycosylated at the threonine in the triple repeat motif. 25759508 4 49 gly O-glycosylated 584:597 arg2 the threonine threonine threonine The repeat regions within the IgG3 hinge were found to be in part O-glycosylated at the threonine in the triple repeat motif. 25793890 0 17 part_of gp120 111:115 arg1 the V1/V2 domain gp120 the V1/V2 domain PUBTATOR Site gp120 155971 domain Glycans flanking the hypervariable connecting peptide between the A and B strands of the V1/V2 domain of HIV-1 gp120 confer resistance to antibodies that neutralize CRF01_AE viruses. 28880909 10 13 gly observed 1779:1786 arg1 Bemfola AND A different glycan profile Bemfola Asn52 A different glycan profile Cterm Bemfola Asn52 A different glycan profile was observed at Asn52 in Bemfola compared with GONAL-f (a lower proportion of bi-antennary structures [~53% vs ~77%], and a higher proportion of tri-antennary [~41% vs ~23%] and tetra-antennary structures [~5% vs <1%]). 26244886 4 42 gly Fc-glycosylation 609:624 arg2 the conserved Fc-glycosylation site the conserved Fc-glycosylation site site Relative quantitation of glycopeptides derived from the conserved Fc-glycosylation site allowed resolution of biases on the level of individual glycan compositions. 26244886 4 52 gly glycopeptides 568:580 arg2 glycopeptides glycopeptides glycopeptides Relative quantitation of glycopeptides derived from the conserved Fc-glycosylation site allowed resolution of biases on the level of individual glycan compositions. 28246170 9 61 gly glycoprotein 1813:1824 arg1 a bacterial glycoprotein a bacterial glycoprotein Fterm glycoprotein These findings define the complete glycosylation pathway of a bacterial glycoprotein and offer a testable hypothesis of how glycosyltransferase coordination facilitates glycan assembly. 24130173 4 61 gly di-sialylated 724:736 arg1 mono- and di-sialylated N-glycans mono- and di-sialylated N-glycans Site-specific sugar profiling of secreted recombinant BChE (rBChE) collected from the intercellular fluid revealed the presence of mono- and di-sialylated N-glycans, which largely resembles to the plasma-derived orthologue. 26565680 4 11 gly glycopeptides 783:795 arg2 glycopeptides glycopeptides glycopeptides Current software tools often fail to identify glycopeptides with multiple glycosylation sites, and hence we present GlycoMID, a graph-based spectral alignment algorithm that can identify glycopeptides with multiple hydroxylysine O-glycosylation sites by tandem mass spectra. 26565680 4 15 gly glycosylation 670:682 arg2 multiple glycosylation sites multiple glycosylation sites sites Current software tools often fail to identify glycopeptides with multiple glycosylation sites, and hence we present GlycoMID, a graph-based spectral alignment algorithm that can identify glycopeptides with multiple hydroxylysine O-glycosylation sites by tandem mass spectra. 26565680 4 53 gly glycopeptides 642:654 arg2 glycopeptides glycopeptides glycopeptides Current software tools often fail to identify glycopeptides with multiple glycosylation sites, and hence we present GlycoMID, a graph-based spectral alignment algorithm that can identify glycopeptides with multiple hydroxylysine O-glycosylation sites by tandem mass spectra. 26565680 4 63 gly O-glycosylation 825:839 arg2 multiple hydroxylysine O-glycosylation sites multiple hydroxylysine O-glycosylation sites sites Current software tools often fail to identify glycopeptides with multiple glycosylation sites, and hence we present GlycoMID, a graph-based spectral alignment algorithm that can identify glycopeptides with multiple hydroxylysine O-glycosylation sites by tandem mass spectra. 26038399 2 6 part_of contains 325:332 arg1 The GP subunit GP2 AND N-linked glycosylation sites The GP subunit GP2 N-linked glycosylation sites PUBTATOR Site GP2 2813 sites The GP subunit GP2 of filoviruses contains 2 completely conserved N-linked glycosylation sites (NGSs) at N563 and N618, suggesting that they have been maintained through selective pressures. 27159528 6 65 gly fucosylated 855:865 arg1 plant typical complex fucosylated and xylosylated GnGnXF structures plant typical complex fucosylated and xylosylated GnGnXF structures N-glycan profiling revealed the predominant presence of plant typical complex fucosylated and xylosylated GnGnXF structures on sec-Ab while vac-Abs carried mainly oligomannosidic (Man 7-9) next to GnGnXF forms. 26482295 1 35 part_of residues 307:314 arg1 target proteins proteins residues Fterm AminoAcid proteins asparagine residues The central enzyme in the Campylobacter jejuni asparagine-linked glycosylation pathway is the oligosaccharyltransferase (OST), PglB, which transfers preassembled glycans to specific asparagine residues in target proteins. 28692416 7 6 gly N-glycopeptide 1444:1457 arg2 Fc N-glycopeptide profiles Fc N-glycopeptide profiles N-glycopeptide This study indicates that alteration in Fc N-glycopeptide profiles of plasma IgG subclasses is associated with blood pressure status in the Kazakh population. 28888681 0 32 part_of hemopexin 107:115 arg1 hemopexin glycopeptides hemopexin hemopexin glycopeptides PUBTATOR Site hemopexin 3263 glycopeptides Nano reversed phase versus nano hydrophilic interaction liquid chromatography on a chip in the analysis of hemopexin glycopeptides. 27773703 16 66 gly N-Glycosylation 1581:1595 arg1 megalin megalin Fterm megalin 14725 N-Glycosylation of megalin can modulate its ligand-binding activity. 25449758 0 54 gly glycosylation 64:76 arg1 initial-stage eukaryotic N-glycan initial-stage eukaryotic N-glycan Production of initial-stage eukaryotic N-glycan and its protein glycosylation in Escherichia coli. 25587188 0 39 gly glycosylation 10:22 arg1 ACPA-IgG variable domains ACPA-IgG variable domains domains Extensive glycosylation of ACPA-IgG variable domains modulates binding to citrullinated antigens in rheumatoid arthritis. 24085030 4 23 gly glycoproteins 597:609 arg1 Salivary glycoproteins Salivary glycoproteins Fterm glycoproteins METHODS Salivary glycoproteins of 31 alcohol-dependent patients and 21 healthy controls were studied by means of lectin ELISA and lectin blotting with the lectins specific for core and antennary fucose, α2,3-bound sialic acid as well as T and Tn antigens in O-glycans. 27356208 5 75 gly N-glycosylation 883:897 arg2 new N-glycosylation sites new N-glycosylation sites sites In this work, a computational approach was conducted to select suitable location(s) for introducing new N-glycosylation sites into the human coagulation factor IX (hFIX). 24806200 2 88 gly N-glycosylation 433:447 arg2 a common N-glycosylation site a common N-glycosylation site site Structurally, β-hCG shares a high degree of sequence similarity with β-hLH, including a common N-glycosylation site at the N-terminus but differs mainly in the presence of an extended C-terminal portion incorporating four closely spaced O-linked glycans. 27928741 7 0 part_of protein 1256:1262 arg1 glycopeptides protein glycopeptides Fterm Site protein glycopeptides Reverse-phase liquid chromatography tandem mass spectrometry strategies including collision induced dissociation, higher-energy collision dissociation and electron-transfer dissociation were implemented to characterise glycopeptides from the haemagglutinin-neuraminidase protein. 24947385 0 10 gly glycosylated 64:75 arg1 glycosylated proteins glycosylated proteins Fterm proteins Use of transmembrane FRET to investigate the internalization of glycosylated proteins. 28529241 7 24 part_of Sp1-binding 1278:1288 arg1 the Sp1-binding sites Sp1 the Sp1-binding sites OGER Site Sp1 P08047 sites The analysis of underlying mechanism for decreased β4-galactosylation of N-glycans showed that the gene expression level of β4-galactosyltransferase (β4GalT) 1 decreases dramatically by downregulation of Sp1 without changes in those of β4GalT2 and N-acetylglucosaminyltransferase V. Mutations in the Sp1-binding sites of the β4GalT1 gene promoter showed that the promoter activity decreases significantly, indicating that the gene expression is regulated by Sp1. 27585995 11 13 gly serine 2515:2520 arg1 residues residues residues BIOLOGICAL SIGNIFICANCE O-Linked glycoproteins, generated via a widely existing glycosylation modification process on serine (Ser) or threonine (Thr) residues of nascent proteins, play essential roles in a series of biological processes. 27585995 11 152 gly glycoproteins 2430:2442 arg1 BIOLOGICAL SIGNIFICANCE O-Linked glycoproteins BIOLOGICAL SIGNIFICANCE O-Linked glycoproteins Fterm glycoproteins BIOLOGICAL SIGNIFICANCE O-Linked glycoproteins, generated via a widely existing glycosylation modification process on serine (Ser) or threonine (Thr) residues of nascent proteins, play essential roles in a series of biological processes. 25450502 8 52 part_of OPN 1499:1501 arg1 the phosphorylation sites OPN the phosphorylation sites PUBTATOR Site OPN 6696 sites We provide a detailed, site-specific structural characterization of O-glycosylation and identify the phosphorylation sites of OPN. 28729420 6 20 part_of V3 1271:1272 arg1 a V3 polypeptide V3 a V3 polypeptide Cterm Site V3 polypeptide However, Man5GlcNAc2 glycan could be efficiently core-fucosylated by FUT8 in an appropriate protein/peptide context, such as with the erythropoietin protein, a V3 polypeptide derived from HIV-1 gp120, or a simple 9-fluorenylmethyl chloroformate-protected Asn moiety. 28661444 5 11 gly neo-glycoproteins 1096:1112 arg1 the different neo-glycoproteins the different neo-glycoproteins Fterm neo-glycoproteins The glycosylation sites and the ex vivo evaluation of the immunogenic activity of the different neo-glycoproteins were investigated. 28661444 5 83 gly glycosylation 1004:1016 arg2 The glycosylation sites The glycosylation sites sites The glycosylation sites and the ex vivo evaluation of the immunogenic activity of the different neo-glycoproteins were investigated. 27089023 4 15 gly glycopeptides 893:905 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides Here, we report that the addition of IMS to conventional glycoproteomics platforms adds additional information regarding glycan structure and is particularly useful for differentiation of sialic acid linkage isomers on both N- and O-linked glycopeptides. 27089023 4 35 gly isomers 861:867 arg1 O-linked glycopeptides O-linked glycopeptides O-linked glycopeptides Site glycopeptides Here, we report that the addition of IMS to conventional glycoproteomics platforms adds additional information regarding glycan structure and is particularly useful for differentiation of sialic acid linkage isomers on both N- and O-linked glycopeptides. 28855248 4 84 part_of inhibin 710:716 arg1 Pro-αC inhibin α-subunit Pro-αC PUBTATOR AminoAcid inhibin α-subunit 24504 Pro Native rhFSH stimulated inhibin α-subunit (Pro-αC) but did not show any effect on inhibin B (INHB) production in immature SCs isolated from 8-day-old rats. 26114652 10 21 gly core-fucosylated 1765:1780 arg1 core-fucosylated asialo diantennary structures core-fucosylated asialo diantennary structures The predominant N-linked structures were core-fucosylated asialo diantennary structures with varying galactosylation. 26114652 10 21 gly core-fucosylated 1765:1780 arg1 The predominant N-linked structures The predominant N-linked structures The predominant N-linked structures were core-fucosylated asialo diantennary structures with varying galactosylation. 25359784 10 27 gly N-glycosylation 1252:1266 arg2 N-glycosylation sites N-glycosylation sites sites Usually, the structures of N-glycosylation sites form an extended configuration in IPU; however, the Asn448 site had an atypical structure that lacked this configuration. 25188817 3 34 part_of peptides 396:403 arg1 the central sequon Pro-Asn-Gly/Ala-Thr-Trp/Ala peptides the central sequon Pro-Asn-Gly/Ala-Thr-Trp/Ala Thr We report atomically detailed replica exchange molecular dynamics simulations in explicit solvent that systematically investigate the impact of glycosylation upon peptides with the central sequon Pro-Asn-Gly/Ala-Thr-Trp/Ala. 27550041 2 73 gly positions 690:698 arg1 476 positions 137, 281 and 476 positions 137, 281 and 476 The results obtained allowed identifying 26 different glycan structures, including high mannose, complex and hybrid N-glycans, linked to the protein backbone via an amide bond to asparagine residues located at the positions 137, 281 and 476. 27550041 2 73 gly positions 690:698 arg1 281 positions 137, 281 and 476 positions 137, 281 and 476 The results obtained allowed identifying 26 different glycan structures, including high mannose, complex and hybrid N-glycans, linked to the protein backbone via an amide bond to asparagine residues located at the positions 137, 281 and 476. 27550041 2 73 gly positions 690:698 arg1 281 positions 137, 281 and 476 positions 137, 281 and 476 The results obtained allowed identifying 26 different glycan structures, including high mannose, complex and hybrid N-glycans, linked to the protein backbone via an amide bond to asparagine residues located at the positions 137, 281 and 476. 24799124 4 60 part_of detected 880:887 arg1 ceruloplasmin AND sites 138, 358, 397, and 762 ceruloplasmin sites PUBTATOR Site ceruloplasmin 1356 sites This procedure simplified the structures for further analysis by mass spectrometry, where four core-fucosylated sites (sites 138, 358, 397, and 762) were detected in ceruloplasmin. 27697163 8 51 gly glycoprotein 1534:1545 arg1 a glycoprotein a glycoprotein Fterm glycoprotein Analysis of the proteins released in the media revealed the presence of a glycoprotein with a molecular size around 32-33 kDa only for the species S. japonicus. 24508870 6 75 gly glycoprotein 1230:1241 arg1 a stage-specific glycoprotein a stage-specific glycoprotein Fterm glycoprotein Proteomic analysis revealed that the band contained several glycoproteins, including the acidic ecto-protein phosphatase AcP115, a stage-specific glycoprotein in the bloodstream form of T. brucei. 24508870 6 91 gly glycoproteins 1144:1156 arg1 several glycoproteins several glycoproteins Fterm glycoproteins Proteomic analysis revealed that the band contained several glycoproteins, including the acidic ecto-protein phosphatase AcP115, a stage-specific glycoprotein in the bloodstream form of T. brucei. 26082214 5 28 gly glycoproteins 669:681 arg1 homogeneous glycoproteins homogeneous glycoproteins Fterm glycoproteins N-linked GlcNAc can then be extended by existing methods to produce homogeneous glycoproteins. 28921966 2 51 gly glycoprotein 354:365 arg1 glycoprotein analysis glycoprotein analysis This method has the potential to simplify glycoprotein analysis by integrating glycan sequencing and glycopeptide analysis in a single experiment. 24941220 4 92 gly glycopeptides 621:633 arg2 low abundant glycopeptides gp120 glycopeptides PUBTATOR gp120 3700 glycopeptides This challenge promoted us to employ a Q-Exactive mass spectrometer to identify low abundant glycopeptides from virion-associated gp120. 24509848 10 57 gly N-glycosylation 1482:1496 arg1 the highly conserved (211)NDS motif motif motif Taken together, these data suggest that N-glycosylation at the highly conserved (211)NDS motif evolved to act as a negative repressor of DDR1 phosphorylation in the absence of ligand. 26307003 7 25 part_of enzymes 1750:1756 arg1 these common subdomains enzymes these common subdomains Fterm Site enzymes subdomains Overall, the present study reveals how family 1 CBM structures are affected by covalent attachment of monosaccharides, which are likely important post-translational modifications of these common subdomains of fungal plant cell wall degrading enzymes. 25092234 7 4 part_of hFXI 994:997 arg1 hFXI glycopeptides hFXI hFXI glycopeptides PUBTATOR Site hFXI 2160 glycopeptides Analysis of hFXI glycopeptides by LC-MS/MS enabled site-specific glycan profiling and occupancy. 27791356 5 26 part_of mucin 984:988 arg1 the heavily glycosylated central mucin domain mucin the heavily glycosylated central mucin domain PUBTATOR Site mucin 281333 domain ROA indicated that the protein backbone of MUC5B is dominated by unordered conformation, which was found to originate from the heavily glycosylated central mucin domain by isolation of MUC5B O-glycan-rich regions. 26821880 1 24 gly glycoproteins 289:301 arg1 glycoproteins glycoproteins Fterm structure of glycoproteins The enzyme UDP-N-acetylglucosamine: α-d-mannoside β-1-6 N-acetylglucosaminyltransferase V (GnT-V) catalyzes the transfer of GlcNAc from the UDP-GlcNAc donor to the α-1-6-linked mannose of the trimannosyl core structure of glycoproteins to produce the β-1-6-linked branching of N-linked oligosaccharides. 26821880 1 74 gly structure 276:284 arg1 the α-1-6-linked mannose structure of glycoproteins the α-1-6-linked mannose Fterm structure of glycoproteins The enzyme UDP-N-acetylglucosamine: α-d-mannoside β-1-6 N-acetylglucosaminyltransferase V (GnT-V) catalyzes the transfer of GlcNAc from the UDP-GlcNAc donor to the α-1-6-linked mannose of the trimannosyl core structure of glycoproteins to produce the β-1-6-linked branching of N-linked oligosaccharides. 25358049 4 1 gly glycopeptides 912:924 arg2 glycopeptides glycopeptides glycopeptides Through analysis of beam-type CID spectra and ion trap CID spectra of synthetic and natively derived N- and O-glycopeptides, we found that the fragmentation patterns of oxonium ions characteristically differ between glycopeptides terminally substituted with GalNAcα1-O-, GlcNAcβ1-O-, Galβ3GalNAcα1-O-, Galβ4GlcNAcβ-O-, and Galβ3GlcNAcβ-O- structures. 25358049 4 42 gly O-glycopeptides 804:818 arg2 O-glycopeptides O-glycopeptides O-glycopeptides Through analysis of beam-type CID spectra and ion trap CID spectra of synthetic and natively derived N- and O-glycopeptides, we found that the fragmentation patterns of oxonium ions characteristically differ between glycopeptides terminally substituted with GalNAcα1-O-, GlcNAcβ1-O-, Galβ3GalNAcα1-O-, Galβ4GlcNAcβ-O-, and Galβ3GlcNAcβ-O- structures. 29268168 4 5 gly glycosylation 700:712 arg2 the N162 glycosylation site the N162 glycosylation site site Here we report that the N162 glycosylation site is also found in the orthologous mouse FcγR, mFcγRIV. 25265424 4 9 gly fucosylation 561:572 arg1 the proteins the proteins Fterm proteins Our exoglycosidase-assisted LC-MS/MS analysis confirms the high degree of fucosylation of some of the proteins but shows that microheterogeneity is protein- and site-specific. 29062024 2 20 gly fucosylation 363:374 arg1 IgG1-Fc N-glycans IgG1-Fc N-glycans In particular, core fucosylation of IgG1-Fc N-glycans negatively affects this interaction and thereby compromises ADCC activity. 24855066 0 56 gly glycosylation 9:21 arg1 membrane proteins membrane proteins Fterm proteins Specific glycosylation of membrane proteins in epithelial ovarian cancer cell lines: glycan structures reflect gene expression and DNA methylation status. 26492619 0 23 gly Non-glycosylated 56:71 arg1 Non-glycosylated PLAG1/2 Domain Non-glycosylated PLAG1/2 Domain Fterm Domain Development of Monoclonal Antibody LpMab-10 Recognizing Non-glycosylated PLAG1/2 Domain Including Thr34 of Human Podoplanin. 26599081 6 9 gly glycosylation 950:962 arg2 numerous sites numerous sites sites Protein glycosylation occurred at numerous sites on surface-exposed lipoproteins with no apparent amino acid sequence specificity. 26598643 11 12 gly O-glycosylation 1775:1789 arg2 11 novel O-glycosylation sites 11 novel O-glycosylation sites sites Strikingly, also 11 novel O-glycosylation sites and regions were identified. 28800497 0 39 gly core-fucosylated 35:50 arg1 a core-fucosylated N-glycan trisaccharide a core-fucosylated N-glycan trisaccharide Glycoconjugate probes containing a core-fucosylated N-glycan trisaccharide for fucose lectin identification and purification. 24668806 2 10 part_of IgG 300:302 arg1 the Fc region IgG the Fc region Cterm Site IgG region EndoS preferentially hydrolyzes the N-linked glycans from the Fc region of IgG during infection. 28186137 11 14 gly glycoproteins 1513:1525 arg1 glycoproteins glycoproteins Fterm glycoproteins Taken together, this study demonstrates that GlcNAc6ST-1 modulates PNS myelination and myelinated axonal survival through the GlcNAc-6-O-sulfation of N-glycans on glycoproteins. 28186137 11 57 gly GlcNAc-6-O-sulfation 1476:1495 arg1 glycoproteins glycoproteins GlcNAc-6-O-sulfation Fterm glycoproteins Taken together, this study demonstrates that GlcNAc6ST-1 modulates PNS myelination and myelinated axonal survival through the GlcNAc-6-O-sulfation of N-glycans on glycoproteins. 28585084 1 8 gly glycoproteins 93:105 arg1 glycoproteins glycoproteins Fterm glycoproteins The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. 29255015 3 2 gly glycoprotein 413:424 arg1 the complete glycoprotein the complete glycoprotein Fterm glycoprotein A detailed description of the complete glycoprotein was achieved by combining crystallographic data with molecular modeling. 26784534 8 1 gly glycopeptides 949:961 arg2 the glycopeptides the glycopeptides glycopeptides Analysis of the glycopeptides flanking the A1 domain revealed that generally more core-2-type O-glycan was present on the C-terminal Cluster 2 glycopeptide (encompassing T(1468) , T(1477) , S(1486) and T(1487) ) compared with the N-terminal Cluster 1 glycopeptide (encompassing T(1248) , T(1255) , T(1256) and S(1263) ). 26784534 8 14 gly glycopeptide 1184:1195 arg2 the N-terminal Cluster 1 glycopeptide the N-terminal Cluster 1 glycopeptide glycopeptide Analysis of the glycopeptides flanking the A1 domain revealed that generally more core-2-type O-glycan was present on the C-terminal Cluster 2 glycopeptide (encompassing T(1468) , T(1477) , S(1486) and T(1487) ) compared with the N-terminal Cluster 1 glycopeptide (encompassing T(1248) , T(1255) , T(1256) and S(1263) ). 26784534 8 23 gly glycopeptide 1076:1087 arg2 the C-terminal Cluster 2 glycopeptide the C-terminal Cluster 2 glycopeptide glycopeptide Analysis of the glycopeptides flanking the A1 domain revealed that generally more core-2-type O-glycan was present on the C-terminal Cluster 2 glycopeptide (encompassing T(1468) , T(1477) , S(1486) and T(1487) ) compared with the N-terminal Cluster 1 glycopeptide (encompassing T(1248) , T(1255) , T(1256) and S(1263) ). 26784534 8 55 gly present 1040:1046 arg2 the C-terminal Cluster 2 glycopeptide AND generally more core-2-type O-glycan glycopeptide generally more core-2-type O-glycan glycopeptide Analysis of the glycopeptides flanking the A1 domain revealed that generally more core-2-type O-glycan was present on the C-terminal Cluster 2 glycopeptide (encompassing T(1468) , T(1477) , S(1486) and T(1487) ) compared with the N-terminal Cluster 1 glycopeptide (encompassing T(1248) , T(1255) , T(1256) and S(1263) ). 26729242 6 28 gly glycosylation 987:999 arg2 52 unique glycosylation sites 52 unique glycosylation sites sites Altogether, 52 unique glycosylation sites in 20 proteins were identified in this study. 26231935 8 45 part_of AChE 1346:1349 arg1 AChE sequence AChE AChE sequence PUBTATOR Site AChE 43 sequence Although the three glycosylation sites within AChE sequence have different extent in affecting the enzymatic activity, their glycan compositions are very similar. 28258464 3 90 gly glycopeptides 422:434 arg2 tryptic glycopeptides tryptic glycopeptides glycopeptides In the first step, tryptic glycopeptides were enriched using ZIC-HILIC. 26599081 3 8 gly glycoproteins 632:644 arg1 glycoproteins glycoproteins Fterm glycoproteins The murine pathogens Mycoplasma arthritidis and Mycoplasma pulmonis have only a single gene annotated as coding for a glycosyltransferase but synthesize glycolipid, polysaccharide and glycoproteins. 25902405 1 25 gly N-glycoproteins 137:151 arg1 N-glycoproteins N-glycoproteins Fterm N-glycoproteins Due to the important roles of N-glycoproteins in various biological processes, the global N-glycoproteome analysis has been paid much attention. 25533529 8 51 gly positions 1828:1836 arg1 the N-glycans positions 77, 81 and 100 the N-glycans positions 77, 81 and 100 Taken together, all the glycans contribute to the pharmacokinetics of acutobin and ATB-wt in vivo, and the microenvironment around the Asn(229)-glycan appears to regulate the fibrinogen-chain specificity of acutobin while the N-glycans at positions 77, 81 and 100 are crucial for its folding. 27503803 4 34 gly found 677:681 arg2 the Gc1S protein AND the same linear trisaccharide the Gc1S protein the same linear trisaccharide Fterm protein Results demonstrate that the O-glycan from the Gc1F protein is the same linear trisaccharide found on the Gc1S protein and that the hexose residue is galactose. 27503803 4 34 gly found 677:681 arg2 the Gc1S protein AND the O-glycan the Gc1S protein the O-glycan Fterm protein Results demonstrate that the O-glycan from the Gc1F protein is the same linear trisaccharide found on the Gc1S protein and that the hexose residue is galactose. 27503803 4 55 gly protein 636:642 arg1 the O-glycan protein the O-glycan Fterm protein Results demonstrate that the O-glycan from the Gc1F protein is the same linear trisaccharide found on the Gc1S protein and that the hexose residue is galactose. 27503803 4 55 gly protein 636:642 arg1 the same linear trisaccharide protein the same linear trisaccharide Fterm protein Results demonstrate that the O-glycan from the Gc1F protein is the same linear trisaccharide found on the Gc1S protein and that the hexose residue is galactose. 27928741 3 84 gly present 455:461 arg1 these proteins AND the N-linked glycans these proteins the N-linked glycans Fterm proteins Previous studies have shown that the N-linked glycans present on these proteins can modulate the ability of the virus to infect host cells and stimulate the host immune system. 28534482 1 1 gly glycopeptides 182:194 arg2 N-linked glycopeptides N-linked glycopeptides glycopeptides A method for selective and comprehensive enrichment of N-linked glycopeptides was developed to facilitate detection of micro-heterogeneity of N-glycosylation. 25378480 5 13 part_of β-glycosidase 923:935 arg1 the subsite -1 β-glycosidase the subsite -1 Fterm Site β-glycosidase subsite Using molecular modeling, we first showed that the docking of N-acetyl-d-glucosamine in the subsite -1 of the β-glycosidase from Thermus thermophilus (TtβGly) suggested several steric conflicts with active site amino-acids (N163, E338) induced by the N-acetyl group. 26729457 2 6 gly O-glycopeptide 311:324 arg2 O-glycopeptide O-glycopeptide O-glycopeptide Mass spectrometry-based N- and O-glycopeptide analyses enable determination of the glycosylation site, site occupancy, as well as glycan varieties present on a particular site. 26729457 2 21 gly occupancy 388:396 arg1 the glycosylation site, site occupancy the glycosylation site, site occupancy site, site Mass spectrometry-based N- and O-glycopeptide analyses enable determination of the glycosylation site, site occupancy, as well as glycan varieties present on a particular site. 26729457 2 43 gly present 427:433 arg2 a particular site AND glycan varieties a particular site glycan varieties site Mass spectrometry-based N- and O-glycopeptide analyses enable determination of the glycosylation site, site occupancy, as well as glycan varieties present on a particular site. 26729457 2 109 gly glycosylation 363:375 arg2 the glycosylation site, site occupancy the glycosylation site, site occupancy site, site Mass spectrometry-based N- and O-glycopeptide analyses enable determination of the glycosylation site, site occupancy, as well as glycan varieties present on a particular site. 29404022 7 30 gly glycoproteins 1033:1045 arg1 four different well-studied glycoproteins glycoproteins N-glycans Fterm glycoproteins N-glycans from four different well-studied glycoproteins were analyzed by this strategy. 27574189 1 16 gly glycoprotein 173:184 arg1 the plasma glycoprotein ADAMTS13 the plasma glycoprotein ADAMTS13 Fterm glycoprotein Patients suffering from acquired thrombotic thrombocytopenic purpura develop autoantibodies directed toward the plasma glycoprotein ADAMTS13. 26991339 3 31 gly sialylated 877:886 arg1 8 different neutral and sialylated glycans 8 different neutral and sialylated glycans The heterogeneous mixture of the proteoforms derives from the combination of 8 different neutral and sialylated glycans O-linked to Threonine 50, and 33 different glycans N-linked to Asparagine residues at positions 66, 87, 108, 129, 150, 171, 192, and 213. 28975713 1 39 gly glycopeptides 205:217 arg2 intact glycopeptides intact glycopeptides glycopeptides PURPOSE PepSweetener is a web-based visualization tool designed to facilitate the manual annotation of intact glycopeptides from MS data regardless of the instrument that produced these data. 26479949 5 13 part_of NPs 850:852 arg1 composition NPs composition OGER Site NPs P0C0P6 position The morphology, structure, and composition of Fe3O4-DA-Maltose NPs were investigated by Fourier transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM), X-ray powder diffraction (XRD), X-ray photoelectron spectrometer (XPS), and vibrating sample magnetometer (VSM). 27506355 2 17 gly glycopeptides 368:380 arg2 intact glycopeptides intact glycopeptides glycopeptides However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. 24820161 1 10 gly glycosylation 103:115 arg1 many protein functions many protein functions Fterm protein Protein glycosylation, one of the post-translational modifications, is important for many protein functions, such as protein stability, folding and secretion. 28199092 7 96 part_of Fab 1641:1643 arg1 both the Fab and Fc N-Linked glycosylation sites Fab both the Fab and Fc N-Linked glycosylation sites PUBTATOR Site Fab 2187 sites Our results demonstrate that MAM quantification of individual glycan species from both the Fab and Fc N-Linked glycosylation sites is consistent with quantification using the traditional hydrophilic interaction liquid chromatography (HILIC) analysis of enzymatically released and fluorescently labeled glycans. 26791533 2 31 part_of present 320:326 arg2 seminal plasma glycoproteins AND Epitopes seminal plasma glycoproteins Epitopes Fterm glycoproteins Epitopes such as Lewis x and y are known to be present on seminal plasma glycoproteins, which can modulate the maternal immune response. 24509848 11 42 gly presence 1630:1637 arg2 that site AND glycan moieties that site glycan moieties site The presence of glycan moieties at that site may help to lock the collagen-binding domain in the inactive state and prevent unwarranted signaling by receptor dimers. 26576925 9 9 gly sialylation 1362:1372 arg1 N-linked glycans N-linked glycans This study illustrates that sialylation of N-linked glycans creates a prion replication barrier that controls replication rate and glycoform ratios and has broad implications. 28902916 4 70 part_of CD4 624:626 arg1 the conserved CD4 binding site CD4 the conserved CD4 binding site PUBTATOR Site CD4 920 site We focused on the conserved CD4 binding site (CD4bs) since this is a known neutralizing determinant that is devoid of glycosylation to allow CD4 receptor engagement, but is ringed by surrounding N-glycans. 26797772 3 70 gly N-glycosylation 506:520 arg2 five potential N-glycosylation sites five potential N-glycosylation sites sites TNSALP has five potential N-glycosylation sites at N140, N230, N271, N303 and N430 by standard nomenclature. 25253346 13 85 part_of vulnerability 1977:1989 arg1 Env sites Env Env sites PUBTATOR Site Env 100616444 sites Fine mapping at the CD4bs indicated that conformational stabilization of the cores and addition of N-glycans altered the molecular surface of Env sites of vulnerability to neutralizing antibody, suggesting an explanation for why the elicited neutralization was not improved by this rational design strategy. 27356208 2 42 gly N-glycosylation 311:325 arg2 a new N-glycosylation site a new N-glycosylation site site Introduction of a new N-glycosylation site into a protein backbone leads to its hyper-glycosylation, and may improve the protein properties such as solubility, folding, stability, and secretion. 26488311 4 5 part_of clusterin 547:555 arg1 clusterin glycopeptides clusterin clusterin glycopeptides OGER Site clusterin P10909 glycopeptides More detailed structural characterization of clusterin glycopeptides was also performed, demonstrating the presence of glycosylated peptides and their corresponding glycans. 27793989 3 99 part_of PECAM-1 666:672 arg1 human PECAM-1 immunoglobulin homology domain 1 PECAM-1 human PECAM-1 immunoglobulin homology domain 1 PUBTATOR Site PECAM-1 5175 domain PECAM-1 glycans account for ∼30% of its molecular mass, and the newly solved crystal structure of human PECAM-1 immunoglobulin homology domain 1 reveals that a glycan emanating from the asparagine residue at position 25 (Asn-25) is located within the trans homophilic-binding interface, suggesting a role for an Asn-25-associated glycan in PECAM-1 homophilic interactions. 25450502 4 8 part_of OPN 780:782 arg1 7 O-glycosylation regions OPN 7 O-glycosylation regions PUBTATOR Site OPN 6696 regions We detected 28 O-glycopeptides from 7 O-glycosylation regions of human OPN, occupied by highly heterogeneous O-glycans. 24797265 8 3 gly glycopeptides 1021:1033 arg2 27 glycopeptides 27 glycopeptides glycopeptides By combining these approaches, 27 glycopeptides corresponding to six different segments of the N-terminal region of Srr1 [93-639] were identified. 27506355 5 57 gly glycopeptide 610:621 arg2 the glycopeptide fragmentation prediction tool the glycopeptide fragmentation prediction tool glycopeptide Methods2008, 5, 873-875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. 26571101 4 23 gly glycoprotein 956:967 arg1 glycoprotein alterations glycoprotein alterations Fterm glycoprotein The NGAG method can also be applied to quantitatively detect glycoprotein alterations in total and site-specific glycan occupancies. 25359784 9 54 gly N-glycosylated 1117:1130 arg1 only N-glycosylated Asn residue only N-glycosylated Asn residue Asn residue Our results indicate that mutation of only N-glycosylated Asn residue may lead to incorrect conclusion for the evaluation of the function of N-glycan. 29197583 9 27 gly glycopeptides 1753:1765 arg2 the glycopeptides the glycopeptides glycopeptides The impact of such a small modification in the glycan structure is more evident in smaller analytes, reason why the analysis of free glycans was easier compared to the intact protein or the glycopeptides. 29194986 4 13 gly N-glycosylated 697:710 arg1 the Asn-297 the Asn-297 Asn-297 A biochemical characterization of this recombinant antibody demonstrated that the Asn-297 is N-glycosylated by oligomannosides. 26773038 1 3 part_of factor 136:141 arg1 the von Willebrand factor (VWF) A2 domain von Willebrand factor the von Willebrand factor (VWF) A2 domain PUBTATOR Site von Willebrand factor 7450 domain Shear forces in the blood trigger a conformational transition in the von Willebrand factor (VWF) A2 domain, from its native folded to an unfolded state, in which the cryptic scissile bond (Y1605-M1606) is exposed and can then be proteolysed by ADAMTS13. 28079948 0 28 part_of Branched 41:48 arg1 Branched Core O-Mannosyl Glycopeptides-Selectivity Branched Branched Core O-Mannosyl Glycopeptides-Selectivity OGER Site Branched Glycopeptides-Selectivity Induction of Antibodies Directed Against Branched Core O-Mannosyl Glycopeptides-Selectivity Complimentary to the ConA Lectin. 29048990 9 48 gly occupied 1582:1589 arg2 the globular head the globular head head Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 29048990 9 48 gly occupied 1582:1589 arg2 the stalk region the stalk region region Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 29048990 9 92 gly glycosylation 1438:1450 arg2 Four glycosylation sequons Four glycosylation sequons Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 29048990 9 7 gly region 1473:1478 arg1 N304 N28, N40, N304 and N498 N28, N40, N304 and N498 Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 29048990 9 7 gly region 1473:1478 arg1 N40 N28, N40, N304 and N498 N28, N40, N304 and N498 Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 29048990 9 7 gly region 1473:1478 arg1 N40 N28, N40, N304 and N498 N28, N40, N304 and N498 Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 29048990 9 94 gly head 1531:1534 arg1 N104 N71, N104, N142 and N177 N71, N104, N142 and N177 Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 29048990 9 94 gly head 1531:1534 arg1 N177 N71, N104, N142 and N177 N71, N104, N142 and N177 Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 29048990 9 94 gly head 1531:1534 arg1 N177 N71, N104, N142 and N177 N71, N104, N142 and N177 Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 28486782 2 11 part_of EGFR 195:198 arg1 The extracellular domain EGFR The extracellular domain PUBTATOR Site EGFR 1956 domain The extracellular domain of EGFR is known to be heavily glycosylated. 29273683 5 79 gly N-glycosylation 502:516 arg2 conserved N-glycosylation sites conserved N-glycosylation sites sites We now show that mutations of conserved N-glycosylation sites at N238 in human CBG and N230 in rat CBG disrupt steroid binding. 27938679 2 49 part_of contains 330:337 arg1 The amino-terminal region AND conformational epitopes F, G and H The amino-terminal region conformational epitopes F, G and H epitopes The amino-terminal region of SU contains conformational epitopes F, G and H, which require a glycosylated SU to be recognized by monoclonal antibodies (MAbs) and antibodies from BLV-infected cattle. 28246170 7 28 gly serine-rich 1395:1405 arg1 the serine-rich repeats serine the serine-rich repeats serine Incorporation of different sugars to the disaccharide core structure at multiple sites along the serine-rich repeats results in a highly polymorphic product. 28556908 1 60 gly glycopeptides 298:310 arg2 radiolabeled glycopeptides radiolabeled glycopeptides glycopeptides The unusual nature of the N-glycans of the cellular slime mould Dictyostelium discoideum has been revealed by a number of studies, primarily based on examination of radiolabeled glycopeptides but more recently also by MS. The complexity of the N-glycomes of even glycosylation mutants is compounded by the occurrence of anionic modifications, which also present an analytical challenge. 28494147 2 12 gly glycopeptide 368:379 arg2 the glycopeptide the glycopeptide glycopeptide Understanding the structural changes that occur and being able to correlate those with the physical properties of the glycopeptide are valuable steps toward being able to predict how specific glycosylation patterns will affect the stability of glycoproteins. 28494147 2 13 gly glycoproteins 494:506 arg1 glycoproteins glycoproteins Fterm glycoproteins Understanding the structural changes that occur and being able to correlate those with the physical properties of the glycopeptide are valuable steps toward being able to predict how specific glycosylation patterns will affect the stability of glycoproteins. 28928219 3 43 gly glycosylation 703:715 arg2 that position position position Prolyl hydroxylation of Skp1 contributes to O2-dependent Dictyostelium development, but full glycosylation at that position is required for optimal O2 sensing. 24766575 0 28 gly glycopeptide 23:34 arg2 Efficient and accurate glycopeptide identification Efficient and accurate glycopeptide identification glycopeptide Efficient and accurate glycopeptide identification pipeline for high-throughput site-specific N-glycosylation analysis. 27052379 1 3 gly glycosylation 259:271 arg1 small non-carbohydrate molecules small non-carbohydrate molecules Glucansucrases have a broad acceptor substrate specificity and receive increased attention as biocatalysts for the glycosylation of small non-carbohydrate molecules using sucrose as donor substrate. 28193043 4 79 gly glycoproteins 696:708 arg1 N-linked glycoproteins N-linked glycoproteins Fterm glycoproteins N-linked glycoproteins however pose a challenge for HDX-MS. 24403418 3 31 gly glycosylated 376:387 arg1 Cardiac ion channels Cardiac ion channels Fterm channels Cardiac ion channels are heavily glycosylated, with up to 30% of a mature protein's mass comprised of glycan structures. 24549892 2 41 gly glycopeptides 527:539 arg2 glycopeptides glycopeptides glycopeptides Indeed, multiple peptide and glycan combinations can readily match the same mass of glycopeptides even with mass errors less than 5 ppm providing considerably ambiguity and analysis of complex mixtures of glycopeptides becomes quite challenging in the case of large proteins. 24549892 2 60 gly glycopeptides 648:660 arg2 glycopeptides glycopeptides glycopeptides Indeed, multiple peptide and glycan combinations can readily match the same mass of glycopeptides even with mass errors less than 5 ppm providing considerably ambiguity and analysis of complex mixtures of glycopeptides becomes quite challenging in the case of large proteins. 25895110 2 49 part_of Fc 335:336 arg1 the immunoglobulin G (IgG) Fc fragment Fc the immunoglobulin G (IgG) Fc fragment Cterm Site Fc fragment Alterations in N-glycans attached to the immunoglobulin G (IgG) Fc fragment can affect molecular structure and immunological function. 25895110 2 67 part_of G 327:327 arg1 the immunoglobulin G (IgG) Fc fragment immunoglobulin G the immunoglobulin G (IgG) Fc fragment Cterm Site immunoglobulin G fragment Alterations in N-glycans attached to the immunoglobulin G (IgG) Fc fragment can affect molecular structure and immunological function. 24668806 2 55 gly region 290:295 arg1 the N-linked glycans region the N-linked glycans region EndoS preferentially hydrolyzes the N-linked glycans from the Fc region of IgG during infection. 27956708 4 3 part_of F 723:723 arg1 Fc and F(ab')2 fragments F(ab')2 Fc and F(ab')2 fragments PUBTATOR Site F(ab')2 2187 fragments The N-linked glycosylation of total, Fc and F(ab')2 fragments, as well as heavy and light chains of ACPA-IgG and control IgG were analyzed by UHPLC and MALDI-TOF mass spectrometry. 27956708 4 34 part_of ACPA-IgG 779:786 arg1 Fc and F(ab')2 fragments ACPA Fc and F(ab')2 fragments PUBTATOR Site ACPA 5657 fragments The N-linked glycosylation of total, Fc and F(ab')2 fragments, as well as heavy and light chains of ACPA-IgG and control IgG were analyzed by UHPLC and MALDI-TOF mass spectrometry. 27956708 4 35 part_of IgG 800:802 arg1 Fc and F(ab')2 fragments IgG Fc and F(ab')2 fragments Cterm Site IgG fragments The N-linked glycosylation of total, Fc and F(ab')2 fragments, as well as heavy and light chains of ACPA-IgG and control IgG were analyzed by UHPLC and MALDI-TOF mass spectrometry. 27458127 6 17 part_of IgG 1202:1204 arg1 each IgG attachment site IgG each IgG attachment site Cterm Site IgG site Moreover, the method is highly amenable to automation and because no digestion steps are involved, it provides direct relative quantitative information of both glycans on each IgG attachment site. 26086522 7 45 gly glycoproteins 963:975 arg1 serum glycoproteins serum glycoproteins Fterm glycoproteins This serum glycan library, significantly expanded from a previous one covering glycans released from a handful of serum glycoproteins, has more than 170 complete and partial structures and constructed instead from whole serum. 25927005 6 13 gly glycoprotein 864:875 arg1 ofthe E2 glycoprotein ofthe E2 glycoprotein Fterm glycoprotein We studied the effect of glycans on the folding ofthe E2 glycoprotein, formation of functional glycoprotein complexes and virus particles in insect and mammalian cells. 25927005 6 69 gly glycoprotein 902:913 arg1 functional glycoprotein complexes functional glycoprotein complexes Fterm glycoprotein We studied the effect of glycans on the folding ofthe E2 glycoprotein, formation of functional glycoprotein complexes and virus particles in insect and mammalian cells. 26598643 1 69 gly glycoproteins 166:178 arg1 glycoproteins glycoproteins Fterm glycoproteins Site-specific glycosylation analysis is key to investigate structure-function relationships of glycoproteins, e.g. in the context of antigenicity and disease progression. 24233973 0 73 gly structures 99:108 arg1 mucin-type fusion proteins proteins structures Fterm proteins Avian influenza H5 hemagglutinin binds with high avidity to sialic acid on different O-linked core structures on mucin-type fusion proteins. 28091715 1 47 gly protein 174:180 arg1 glycans protein glycans Fterm protein When developing biopharmaceuticals, glycans are the most important posttranslational protein modifications that must be addressed because they affect the between-protein interactions that maintain homeostasis. 25698222 11 2 gly derived 1613:1619 arg1 glycoproteins AND glycans glycoproteins glycans Fterm glycoproteins Thus, the described MRM method of permethylated N-glycan enables a rapid and reliable identification and quantitation of glycans derived from glycoproteins purified or present in complex biological samples. 25698222 11 11 gly glycoproteins 1626:1638 arg1 glycoproteins glycoproteins Fterm glycoproteins Thus, the described MRM method of permethylated N-glycan enables a rapid and reliable identification and quantitation of glycans derived from glycoproteins purified or present in complex biological samples. 27928741 4 28 gly heterogeneity 601:613 arg1 these glycans these glycans However, site-specific heterogeneity of these glycans has not been defined. 26784534 5 57 gly occupied 671:678 arg2 all 10 predicted O-glycosylation sites all 10 predicted O-glycosylation sites sites RESULTS: We found that all 10 predicted O-glycosylation sites in VWF are occupied. 26784534 5 89 gly O-glycosylation 638:652 arg2 all 10 predicted O-glycosylation sites all 10 predicted O-glycosylation sites sites RESULTS: We found that all 10 predicted O-glycosylation sites in VWF are occupied. 24689986 8 52 part_of strain 1335:1340 arg1 the body region strain the body region Fterm Site strain region Regarding the canine antral mucosa, H. heilmannii s.s. presented the highest adhesion score whereas in the body region the SabA-positive H. pylori strain was the strain that adhered more. 26956484 6 10 part_of Orai1 901:905 arg1 the only glycosylation site Orai1 the only glycosylation site PUBTATOR Site Orai1 84876 site Ca(2+) imaging experiments and patch-clamp experiments revealed that mutation of the only glycosylation site of Orai1 (Orai1N223A) enhanced SOCE in Jurkat T cells. 28035807 7 54 gly glycoforms 1321:1330 arg1 intact O-GalNAc glycoforms intact O-GalNAc glycoforms Up until now, this is the largest data set of intact O-GalNAc glycoforms from complex biological samples at the proteome level. 24286971 0 20 gly site 110:113 arg1 the intracellular lipid-linked oligosaccharide distribution site the intracellular lipid-linked oligosaccharide distribution site The availability of glucose to CHO cells affects the intracellular lipid-linked oligosaccharide distribution, site occupancy and the N-glycosylation profile of a monoclonal antibody. 24286971 0 38 gly occupancy 115:123 arg2 site occupancy site occupancy site The availability of glucose to CHO cells affects the intracellular lipid-linked oligosaccharide distribution, site occupancy and the N-glycosylation profile of a monoclonal antibody. 27558752 6 62 gly glycoproteins 1273:1285 arg1 glycoproteins glycoproteins Fterm glycoproteins Quantitative measurements provided a molecular signature specific to glycoproteins for determining the degree of plant stress at low temperature. 26272370 9 33 gly sialylated 1700:1709 arg1 complex and highly sialylated N-glycan structures complex and highly sialylated N-glycan structures The cell line's ability to synthesize complex and highly sialylated N-glycan structures has been shown. 27550041 4 34 gly non-fucosylated 886:900 arg1 10 neutral non-fucosylated complex/hybrid N-glycans 10 neutral non-fucosylated complex/hybrid N-glycans Indeed, 10 neutral non-fucosylated complex/hybrid N-glycans and 4 neutral fucosylated complex/hybrid N-glycans were found. 27550041 4 39 gly fucosylated 941:951 arg1 4 neutral fucosylated complex/hybrid N-glycans 4 neutral fucosylated complex/hybrid N-glycans Indeed, 10 neutral non-fucosylated complex/hybrid N-glycans and 4 neutral fucosylated complex/hybrid N-glycans were found. 28888681 1 55 gly glycosylation 148:160 arg1 proteins proteins Fterm proteins Analysis of the glycosylation of proteins is a challenge that requires orthogonal methods to achieve separation of the diverse glycoforms. 26492619 0 39 part_of PLAG1/2 73:79 arg1 Non-glycosylated PLAG1/2 Domain Non-glycosylated PLAG1 Non-glycosylated PLAG1/2 Domain PUBTATOR Non-glycosylated PLAG1 5324 Development of Monoclonal Antibody LpMab-10 Recognizing Non-glycosylated PLAG1/2 Domain Including Thr34 of Human Podoplanin. 26492619 0 42 part_of Non-glycosylated 56:71 arg1 Non-glycosylated PLAG1/2 Domain Non-glycosylated PLAG1 Non-glycosylated PLAG1/2 Domain PUBTATOR Non-glycosylated PLAG1 5324 Development of Monoclonal Antibody LpMab-10 Recognizing Non-glycosylated PLAG1/2 Domain Including Thr34 of Human Podoplanin. 27743372 3 96 gly glycoproteins 471:483 arg1 glycoproteins glycoproteins Fterm glycoproteins In addition, more than half of the biopharmaceuticals are glycoproteins representing multibillion dollar worldwide business, further emphasizing the importance of their analysis. 24393138 2 29 gly glycoproteins 445:457 arg1 intact glycoproteins intact glycoproteins Fterm glycoproteins We demonstrate that glycan compositions can easily be determined directly by LC-ESI/TOF-MS from intact glycoproteins even with a very complex glycosylation pattern. 24806200 7 89 gly O-glycosylation 1469:1483 arg2 closely spaced O-glycosylation sites closely spaced O-glycosylation sites sites Key steps in these syntheses include a successful double Lansbury glycosylation en route to the N-terminal fragment of β-hCG and the sequential installation of four O-linked glycosyl-amino acid cassettes into closely spaced O-glycosylation sites in a single, high-yielding solid-supported synthesis to access the C-terminal portion of the molecule. 28188786 1 11 gly N-glycosylated 234:247 arg1 N-glycosylated protein N-glycosylated protein Fterm protein Escherichia coli cells have been considered as promising hosts for producing N-glycosylated proteins since the successful production of N-glycosylated protein in E. coli with the pgl (N-linked protein glycosylation) locus from Campylobacter jejuni. 28188786 1 76 gly N-glycosylated 175:188 arg1 N-glycosylated proteins N-glycosylated proteins Fterm proteins Escherichia coli cells have been considered as promising hosts for producing N-glycosylated proteins since the successful production of N-glycosylated protein in E. coli with the pgl (N-linked protein glycosylation) locus from Campylobacter jejuni. 24028868 5 95 gly glycoprotein 733:744 arg1 glycoprotein enrichment glycoprotein enrichment Fterm glycoprotein Label-free shotgun proteomics was applied without glycoprotein enrichment. 28860626 4 76 gly glycopeptides 1041:1053 arg2 ~300 glycopeptides ~300 glycopeptides glycopeptides A total of ~300 glycopeptides were analyzed and manually validated by tandem mass spectrometry. 28745859 7 3 gly O-glycoproteins 1302:1316 arg1 O-glycoproteins O-glycoproteins Fterm O-glycoproteins This work is a first step toward quantitative understanding of how O-glycosylation might control, through intrinsic means, the folding of O-glycoproteins. 26701617 3 73 part_of sites 478:482 arg1 recombinant human platelet-derived growth factor-BB platelet-derived growth factor sites OGER Site platelet-derived growth factor sites The aim of this study was to identify glycosylation sites on recombinant human platelet-derived growth factor-BB (rhPDGF-BB) secreted by P. pastoris, and investigate possible effects of O-linked glycans on PDGF-BB functional activity. 26701617 3 73 part_of sites 478:482 arg1 rhPDGF-BB rhPDGF sites OGER Site rhPDGF sites The aim of this study was to identify glycosylation sites on recombinant human platelet-derived growth factor-BB (rhPDGF-BB) secreted by P. pastoris, and investigate possible effects of O-linked glycans on PDGF-BB functional activity. 26929048 5 8 gly sialylated 826:835 arg1 the two sialylated disaccharides the two sialylated disaccharides Protection of the amide groups in the sialic acid residues significantly increased the yield of the glycosylation reaction between the two sialylated disaccharides, thus suggesting that the presence of hydrogen bonds on the sialic acid residues diminished their reactivity. 24417605 5 56 gly sialylated 667:676 arg1 the N-glycans the N-glycans Most of the N-glycans (∼90%) from HDL glycoproteins were sialylated with one or two neuraminic acids (Neu5Ac). 25781883 4 8 gly presence 494:501 arg2 two extracellular domains AND at least one glycan domains at least one glycan domains The presence of at least one glycan on each of its two extracellular domains, the vWA and Ig-like domains, is indeed necessary for efficient trafficking to the cell surface. 28749929 3 28 gly glycosylated 479:490 arg1 native heterogeneously glycosylated IgG N-glycans native heterogeneously glycosylated IgG N-glycans In this protocol, native heterogeneously glycosylated IgG N-glycans are first deglycosylated with a wild-type endoglycosidase. 28749929 3 71 gly deglycosylated 516:529 arg1 native heterogeneously glycosylated IgG N-glycans native heterogeneously glycosylated IgG N-glycans In this protocol, native heterogeneously glycosylated IgG N-glycans are first deglycosylated with a wild-type endoglycosidase. 25002537 6 76 gly α-Galp 1637:1642 arg1 important sites important sites important sites Site sites These and other recent findings identify linkages from α-Galp to ribitol-5-phosphate and from this residue to adjacent Gal furanoside (Galf) as important sites of CPS structural and genetic diversity. 25300029 2 14 gly glycosylation 503:515 arg1 α3 integrin subunit α3 integrin subunit Fterm subunit In this study we have utilized a powerful nano-HPLC-mass spectrometric approach to characterize patterns of normal and abnormal N-linked glycosylation of α3 integrin subunit in Pkd1(-/-) cells derived from mouse kidneys. 26240146 10 10 gly glycoprotein 1575:1586 arg1 glycoprotein biomarker-based cancer diagnostics glycoprotein biomarker-based cancer diagnostics Fterm glycoprotein It is promising to improve glycoprotein biomarker-based cancer diagnostics by developing combined immunoassays that can determine the level of protein and measure the degree of N-glycosylation simultaneously. 25551295 5 78 part_of G1 900:901 arg1 the immunoglobulin G1 fragment G1 the immunoglobulin G1 fragment Cterm Site G1 fragment To address this technological gap, immature glycoforms of the immunoglobulin G1 fragment crystallizable (Fc) were isolated in a homogeneous state and enzymatically remodeled with [(13)C,(15)N]-N-acetylglucosamine (GlcNAc). 25732693 8 55 gly fucosylated 1672:1682 arg1 fucosylated glycans fucosylated glycans Pancreatic cancer samples clearly showed an increase in the abundance of fucosylated glycans as the stage of the disease increases and this was unlike to samples from chronic pancreatitis. 24085030 8 63 gly glycoproteins 1230:1242 arg1 some glycoproteins some glycoproteins Fterm glycoproteins In some glycoproteins the tendency to correct the glycosylation profile was observed after 7 weeks of abstinence. 25554420 2 27 gly glycosylated 492:503 arg1 glutamine residues glutamine residues glutamine residues To investigate the relative importance of the individual N-glycans of CR3 for toxin activity, the asparagine residues of the consensus N-glycosylation sites of CR3 were substituted with glutamine residues that cannot be glycosylated. 25554420 2 12 gly N-glycosylation 407:421 arg2 the consensus N-glycosylation sites CR3 sites OGER CR3 sites To investigate the relative importance of the individual N-glycans of CR3 for toxin activity, the asparagine residues of the consensus N-glycosylation sites of CR3 were substituted with glutamine residues that cannot be glycosylated. 25092234 8 58 gly glycosylated 1114:1125 arg1 N335 N335 N335 It was evidenced that N335 was not glycosylated and that N72 and N108 were fully occupied, whereas N432 and N473 were occupied at about 92 and 95%, respectively. 25092234 8 7 gly occupied 1160:1167 arg2 N72 N72 and N108 N72 and N108 It was evidenced that N335 was not glycosylated and that N72 and N108 were fully occupied, whereas N432 and N473 were occupied at about 92 and 95%, respectively. 25092234 8 65 gly occupied 1197:1204 arg2 N432 N432 and N473 N432 and N473 It was evidenced that N335 was not glycosylated and that N72 and N108 were fully occupied, whereas N432 and N473 were occupied at about 92 and 95%, respectively. 25598335 0 36 gly glycoproteins 38:50 arg1 human glycoproteins: human glycoproteins: Fterm glycoproteins Engineering yeast for producing human glycoproteins: where are we now? 24632142 0 12 gly glycoprotein 63:74 arg1 a glycoprotein a glycoprotein Fterm glycoprotein Reexamination of aspartoacylase: is this human enzyme really a glycoprotein? 27216994 13 5 gly N-glycosylation 2244:2258 arg2 11 out of 12 predicted N-glycosylation sites 11 out of 12 predicted N-glycosylation sites sites Furthermore, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 27216994 13 29 gly occupied 2326:2333 arg2 11 out of 12 predicted N-glycosylation sites 11 out of 12 predicted N-glycosylation sites sites Furthermore, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 27216994 13 46 gly 7 N-glycosylation 2288:2304 arg2 7 N-glycosylation sites 7 N-glycosylation sites sites Furthermore, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 26565680 5 2 gly glycopeptides 1095:1107 arg2 many glycopeptides many glycopeptides glycopeptides GlycoMID was tested on mass spectrometry data sets of the bovine collagen α-(II) chain protein, and experimental results showed that it identified more glycopeptide-spectrum matches than other existing tools, including many glycopeptides with two glycosylation sites. 26565680 5 6 gly glycosylation 1118:1130 arg2 two glycosylation sites two glycosylation sites sites GlycoMID was tested on mass spectrometry data sets of the bovine collagen α-(II) chain protein, and experimental results showed that it identified more glycopeptide-spectrum matches than other existing tools, including many glycopeptides with two glycosylation sites. 27932460 1 11 gly glycosylation 212:224 arg1 α-dystroglycan α-dystroglycan Disruption of the O-mannosylation pathway involved in functional glycosylation of α-dystroglycan gives rise to congenital muscular dystrophies. 28314774 4 16 part_of N-terminal 856:865 arg1 an N-terminal acyltransferase domain N-terminal an N-terminal acyltransferase domain Cterm Site N-terminal domain Bioinformatic analyses indicated that the L142 protein contains an N-terminal acyltransferase domain and a predicted C-terminal glycosyltransferase. 28314774 4 25 part_of acyltransferase 867:881 arg1 an N-terminal acyltransferase domain acyltransferase an N-terminal acyltransferase domain Fterm Site acyltransferase domain Bioinformatic analyses indicated that the L142 protein contains an N-terminal acyltransferase domain and a predicted C-terminal glycosyltransferase. 28314774 4 6 part_of contains 844:851 arg1 the L142 protein AND an N-terminal acyltransferase domain the L142 protein an N-terminal acyltransferase domain Fterm Site protein domain Bioinformatic analyses indicated that the L142 protein contains an N-terminal acyltransferase domain and a predicted C-terminal glycosyltransferase. 27038031 3 32 gly glycosylation 435:447 arg2 60 glycosylation sites 60 glycosylation sites sites IgM can exist as a pentamer with a connecting singly N-glycosylated J-chain (with a total of 51 glycosylation sites) or as a hexamer (60 glycosylation sites). 27038031 3 88 gly glycosylation 394:406 arg2 51 glycosylation sites 51 glycosylation sites sites IgM can exist as a pentamer with a connecting singly N-glycosylated J-chain (with a total of 51 glycosylation sites) or as a hexamer (60 glycosylation sites). 28797655 5 60 gly N-glycosylation 757:771 arg2 six and five highly conserved N-glycosylation sites six and five highly conserved N-glycosylation sites sites As a result, HA and NA of H9N2 viruses prossess six and five highly conserved N-glycosylation sites, respectively. 26082231 4 1 gly glycoproteins 603:615 arg1 glycoproteins glycoproteins Fterm glycoproteins There are often good reasons, therefore, for wanting to engineer and predefine the N-glycans present on glycoproteins, e.g., in order to characterize the functions of the glycans or facilitate their subsequent removal. 26082231 4 48 gly present 592:598 arg2 glycoproteins AND the N-glycans glycoproteins the N-glycans Fterm glycoproteins There are often good reasons, therefore, for wanting to engineer and predefine the N-glycans present on glycoproteins, e.g., in order to characterize the functions of the glycans or facilitate their subsequent removal. 25484058 4 17 gly glycoproteins 573:585 arg1 highly complex glycoproteins highly complex glycoproteins Fterm glycoproteins As highly complex glycoproteins with a wide range of micro-variants, mAbs require extensive characterization through multiple analytical methods for structure assessment rendering manufacturing control and biosimilarity studies particularly product and time-consuming. 28630087 7 125 gly glycosylated 1318:1329 arg1 Asn185 Asn185 Asn185 Asn185 was not glycosylated. 27558752 4 50 part_of containing 755:764 arg1 Arabidopsis glycoproteins AND Asn-X-Ser/Thr/Cys motifs Arabidopsis glycoproteins Asn-X-Ser/Thr/Cys motifs Fterm Site glycoproteins motifs In-house databases of Arabidopsis glycoproteins and glycopeptides containing Asn-X-Ser/Thr/Cys motifs were constructed by reducing 20% and 90% of the public database size, respectively, to enable a rapid analysis of large datasets for comprehensive identification and quantification of glycoproteins and heterogeneous N-glycans in a complex mixture. 28170415 1 2 gly glycoproteins 157:169 arg1 the most abundant bioactive glycoproteins the most abundant bioactive glycoproteins Fterm glycoproteins Lactoferrin (LF) is one of the most abundant bioactive glycoproteins in human milk. 25916169 2 0 gly N-glycosylation 318:332 arg2 two putative N-glycosylation sites two putative N-glycosylation sites sites It contains two putative N-glycosylation sites (Asn(92) and Asn(211)). 25916169 2 64 gly sites 334:338 arg1 two putative N-glycosylation sites two putative N-glycosylation sites sites It contains two putative N-glycosylation sites (Asn(92) and Asn(211)). 25916169 2 0 gly N-glycosylation 318:332 arg2 Asn Asn(92) and Asn(211) Asn(92) and Asn(211) It contains two putative N-glycosylation sites (Asn(92) and Asn(211)). 25916169 2 64 gly sites 334:338 arg1 92 Asn(92) and Asn(211) Asn(92) and Asn(211) It contains two putative N-glycosylation sites (Asn(92) and Asn(211)). 25916169 2 64 gly sites 334:338 arg1 Asn Asn(92) and Asn(211) Asn(92) and Asn(211) It contains two putative N-glycosylation sites (Asn(92) and Asn(211)). 25916169 2 64 gly sites 334:338 arg1 Asn Asn(92) and Asn(211) Asn(92) and Asn(211) It contains two putative N-glycosylation sites (Asn(92) and Asn(211)). 25916169 2 64 gly sites 334:338 arg1 Asn Asn(92) and Asn(211) Asn(92) and Asn(211) It contains two putative N-glycosylation sites (Asn(92) and Asn(211)). 25916169 2 64 gly sites 334:338 arg1 Asn Asn(92) and Asn(211) Asn(92) and Asn(211) It contains two putative N-glycosylation sites (Asn(92) and Asn(211)). 25916169 2 64 gly sites 334:338 arg1 Asn Asn(92) and Asn(211) Asn(92) and Asn(211) It contains two putative N-glycosylation sites (Asn(92) and Asn(211)). 25568322 4 11 part_of protein 616:622 arg1 protein and cDNA sequences protein protein and cDNA sequences Fterm Site protein sequences Based on protein and cDNA sequences for purified WGA16, it is a homologue of human zymogen granule protein 16 (ZG16) belonging to the Jacalin-related lectin (JRL) family in crystal and primary structures. 27718394 4 68 gly glycosylation 785:797 arg1 individual proteins individual proteins Fterm proteins In this paper, we present a rapid and efficient method for glycosylation analysis of individual proteins focusing on changes in the degree of fucosylation or other alterations to the core structure of the glycans, such as the presence of bisecting N-acetylglucosamines and a modified degree of branching. 27574189 7 91 gly attached 828:835 arg2 Asn614 AND A high mannose-containing glycan Asn614 A high mannose-containing glycan Asn614 A high mannose-containing glycan was attached to Asn614 in the spacer domain. 27574189 7 91 gly attached 828:835 arg2 A high mannose-containing glycan AND the spacer domain the spacer domain A high mannose-containing glycan domain A high mannose-containing glycan was attached to Asn614 in the spacer domain. 25629924 8 40 part_of site 1487:1490 arg1 milk sIgA IgA site Cterm Site IgA P11912 site This represents the most comprehensive report to date detailing the complexity of glycan micro-heterogeneity with relative quantitation of glycoforms for each glycosylation site on milk sIgA. 26572920 1 45 gly glycoproteins 214:226 arg1 N-linked glycans glycoproteins N-linked glycans Fterm glycoproteins In this study, N-linked glycans from intact, formalin treated and formalin fixed paraffin embedded (FFPE) standard glycoproteins, human serum and mouse tumor tissue samples were investigated in respect to their susceptibility for formaldehyde treatment mediated changes. 24644239 0 20 gly chemokines 101:110 arg1 Ser-CCL1 Ser-CCL1 Ser Total chemical synthesis and biological activities of glycosylated and non-glycosylated forms of the chemokines CCL1 and Ser-CCL1. 26855252 0 26 gly Regions 110:116 arg1 Distinct Polysaccharide Composition Distinct Polysaccharide Composition Nonenzymatic Transglycosylation Reactions Induced by Roasting: New Insights from Models Mimicking Coffee Bean Regions with Distinct Polysaccharide Composition. 26208004 6 62 gly heterogeneity 1000:1012 arg1 DENV N-glycans DENV N-glycans By combining these methods, a high heterogeneity of DENV N-glycans was found. 28221766 7 8 gly N-glycosylation 1349:1363 arg2 a third novel, albeit low abundant, N-glycosylation site a third novel, albeit low abundant, N-glycosylation site site Additionally, next to the two known glycosylation sites, a third novel, albeit low abundant, N-glycosylation site on C9 is identified, which surprisingly does not possess the canonical N-glycosylation sequence N-X-S/T. 28221766 7 79 gly glycosylation 1292:1304 arg2 the two known glycosylation sites the two known glycosylation sites sites Additionally, next to the two known glycosylation sites, a third novel, albeit low abundant, N-glycosylation site on C9 is identified, which surprisingly does not possess the canonical N-glycosylation sequence N-X-S/T. 28529241 1 50 gly proteins 233:240 arg1 the glycan structures proteins the glycan structures Fterm proteins Dramatic changes in the glycan structures of cell surface proteins have been observed upon malignant transformation of cells as induced by the altered expression levels of glycosyltransferases. 27649061 2 102 gly glycoforms 353:362 arg1 site specific glycoforms IgG site Cterm IgG site Multiple analytical methods have been designed for the determination of the IgG N-glycan microheterogeneity, including MS methods for the analysis of site specific glycoforms of IgG. 28717478 0 38 gly glycopeptides 53:65 arg2 mannosylated glycopeptides mannosylated glycopeptides glycopeptides Convergent chemo-enzymatic synthesis of mannosylated glycopeptides; targeting of putative vaccine candidates to antigen presenting cells. 28717478 0 86 gly mannosylated 40:51 arg1 mannosylated glycopeptides mannosylated glycopeptides glycopeptides Convergent chemo-enzymatic synthesis of mannosylated glycopeptides; targeting of putative vaccine candidates to antigen presenting cells. 26059692 3 11 part_of neuropilin-1 365:376 arg1 The c/MAM domain neuropilin-1 The c/MAM domain PUBTATOR Site neuropilin-1 O14786 domain The c/MAM domain of human neuropilin-1 has been recombinantly expressed to allow for investigation of its propensity to engage in molecular interactions with other protein or carbohydrate components on a cell surface. 26059692 3 25 part_of c/MAM 343:347 arg1 The c/MAM domain MAM The c/MAM domain PUBTATOR Site MAM 6445 domain The c/MAM domain of human neuropilin-1 has been recombinantly expressed to allow for investigation of its propensity to engage in molecular interactions with other protein or carbohydrate components on a cell surface. 27867113 2 60 gly attached 326:333 arg2 proteins AND oligosaccharide structures proteins oligosaccharide structures Fterm proteins Even though oligosaccharide structures attached to proteins are conserved among eukaryotes, many differences have been found between therapeutic glycoproteins expressed in hamster and human derived cells. 27867113 2 72 gly glycoproteins 432:444 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins Even though oligosaccharide structures attached to proteins are conserved among eukaryotes, many differences have been found between therapeutic glycoproteins expressed in hamster and human derived cells. 26646445 2 11 gly bifucosylated 205:217 arg1 bifucosylated N-glycans bifucosylated N-glycans The aim of this study was to compare bifucosylated N-glycans in sera obtained from healthy controls and breast cancer patients, with the goal of identifying a potential indicator for monitoring the recurrence and metastasis of breast cancer. 28255882 3 35 gly glycosylation 441:453 arg1 recombinant fusion proteins recombinant fusion proteins Fterm proteins Here we present a mass spectrometry based protocol with a "bottom up" approach to characterize glycosylation in recombinant fusion proteins with α/β TCR constant domains expressed in mammalian cells. 27124023 1 48 gly have 207:210 arg1 More than half of all known proteins, and almost all membrane and extra-cellular proteins AND glycans More than half of all known proteins, and almost all membrane and extra-cellular proteins glycans Fterm proteins More than half of all known proteins, and almost all membrane and extra-cellular proteins have oligosaccharide structures or glycans attached to them. 27124023 1 48 gly have 207:210 arg1 More than half of all known proteins, and almost all membrane and extra-cellular proteins AND oligosaccharide structures More than half of all known proteins, and almost all membrane and extra-cellular proteins oligosaccharide structures Fterm proteins More than half of all known proteins, and almost all membrane and extra-cellular proteins have oligosaccharide structures or glycans attached to them. 24917611 6 51 gly glycoproteins 990:1002 arg1 the 26 glycoproteins the 26 glycoproteins Fterm glycoproteins Comparison of the 26 glycoproteins identified revealed that different A. baumannii strains target similar protein substrates, both in characteristics of the sites of O-glycosylation and protein identity. 24917611 6 84 gly O-glycosylation 1135:1149 arg2 the sites the sites sites Comparison of the 26 glycoproteins identified revealed that different A. baumannii strains target similar protein substrates, both in characteristics of the sites of O-glycosylation and protein identity. 26132640 6 5 gly glycoproteins 984:996 arg1 model glycoproteins model glycoproteins Fterm glycoproteins Following optimization of the reaction conditions, the MW-assisted BEP reaction substantially improved the recovery of total O-glycans from model glycoproteins (PSM) and the reaction time was reduced from 16 to 2 h. Combined with sequential solid-phase extractions, this MW-assisted BEP procedure enabled O-glycomic analyses of various biological samples. 28188786 3 34 gly N-glycosylated 531:544 arg1 N-glycosylated proteins N-glycosylated proteins Fterm proteins In this study, we developed a strategy for the production of N-glycosylated proteins with high efficiency via an optimized auto-induction method. 25995273 7 44 gly O-glycosylation 1110:1124 arg2 13 O-glycosylation sites 13 O-glycosylation sites sites We present comparative brain/liver glycosylation data on 50 N-glycosylation sites from 34 proteins and 13 O-glycosylation sites from seven proteins. 25995273 7 49 gly N-glycosylation 1064:1078 arg2 50 N-glycosylation sites 50 N-glycosylation sites sites We present comparative brain/liver glycosylation data on 50 N-glycosylation sites from 34 proteins and 13 O-glycosylation sites from seven proteins. 26105115 4 21 gly glycosylation 599:611 arg2 individual glycosylation sites individual glycosylation sites sites Here we investigate the contribution of individual glycosylation sites in the formation of this so-called intrinsic mannose patch. 24028868 8 71 gly sialylated 1212:1221 arg1 complex galactosylated and sialylated forms complex galactosylated and sialylated forms Significant differences (p ≤ 0.05) were found, with a lower abundance of complex galactosylated and sialylated forms in AD. 29019687 1 52 gly glycosylated 262:273 arg1 key neuronal receptors receptors Fterm receptors N-Methyl-d-aspartate (NMDA) receptors, key neuronal receptors playing the central role in learning and memory, are heavily glycosylated in vivo. 25182382 9 0 gly N-glycopeptides 1693:1707 arg2 intact N-glycopeptides intact N-glycopeptides N-glycopeptides BIOLOGICAL SIGNIFICANCE We presented a fully automated software platform for the high throughput characterization of intact N-glycopeptides derived from complex proteome samples. 25799047 0 29 gly glycosylated 104:115 arg1 the extracellular protein the extracellular protein Fterm protein Homologous expression of the Caldicellulosiruptor bescii CelA reveals that the extracellular protein is glycosylated. 26576925 2 54 gly sialylated 266:275 arg1 two sialylated N-linked carbohydrates two sialylated N-linked carbohydrates PrP(C) has two sialylated N-linked carbohydrates. 25501957 0 86 gly N-glycosylation 45:59 arg1 a novel β-fructosidase a novel β-fructosidase Fterm β-fructosidase Purification, cloning, characterization, and N-glycosylation analysis of a novel β-fructosidase from Aspergillus oryzae FS4 synthesizing levan- and neolevan-type fructooligosaccharides. 25546301 2 36 gly position 326:333 arg1 The glycan position Asn262 The glycan position Asn262 The glycan at position Asn262 had the most extensive and well-ordered electron density, and a GlcNAc(2)Man(7) was modeled. 29212317 7 46 gly glycoprotein 1128:1139 arg1 glycoprotein concentrations glycoprotein concentrations Fterm glycoprotein A targeted method (UHPLC-QQQ) was used to measure the glycoprotein concentrations and site-specific glycovariations of the proteins in human plasma and compared with HDL particles isolated from the same plasma samples. 28486782 10 28 part_of factor 1278:1283 arg1 the growth factor binding site factor the growth factor binding site Fterm Site factor site This stabilizes the growth factor binding site, resulting in stronger interactions (electrostatic) between the growth factor and EGFR. 26582203 5 57 part_of protease 804:811 arg1 protease cleavage sites protease protease cleavage sites Fterm Site protease sites The specificity patterns obtained by the PICS (proteomic identification of protease cleavage sites) method are similar for both KLK2 variants, with a major preference for P1-Arg. 26182462 4 81 gly N-glycoproteins 574:588 arg1 the N-glycoproteins the N-glycoproteins Fterm N-glycoproteins However, the low abundance of the N-glycoproteins and the heterogeneity of the N-glycans make it a challenge to analyse the protein glycosylation sensitively. 26182462 4 59 gly heterogeneity 598:610 arg1 the N-glycans N-glycoproteins the N-glycans Fterm N-glycoproteins However, the low abundance of the N-glycoproteins and the heterogeneity of the N-glycans make it a challenge to analyse the protein glycosylation sensitively. 26059692 7 9 gly glycosylation 1097:1109 arg2 the four different glycosylation sites the four different glycosylation sites sites ETD-MS/MS revealed a hierarchical order of the initial O-GalNAc addition to the four different glycosylation sites. 26869352 1 70 gly fucosylated 263:273 arg1 fucosylated proteins fucosylated proteins Fterm proteins Fucosylation is an important type of glycosylation involved in cancer, and fucosylated proteins could be employed as cancer biomarkers. 28729420 6 36 gly core-fucosylated 1160:1175 arg1 Man5GlcNAc2 glycan Man5GlcNAc2 glycan However, Man5GlcNAc2 glycan could be efficiently core-fucosylated by FUT8 in an appropriate protein/peptide context, such as with the erythropoietin protein, a V3 polypeptide derived from HIV-1 gp120, or a simple 9-fluorenylmethyl chloroformate-protected Asn moiety. 26231935 1 22 part_of possessing 151:160 arg1 Acetylcholinesterase AND three conserved N-linked glycosylation sites Acetylcholinesterase three conserved N-linked glycosylation sites PUBTATOR Site Acetylcholinesterase 43 sites Acetylcholinesterase (AChE; EC 3.1.1.7) is a glycoprotein possessing three conserved N-linked glycosylation sites in mammalian species, locating at 296, 381, and 495 residues of the human sequence. 26231935 1 22 part_of possessing 151:160 arg1 a glycoprotein AND three conserved N-linked glycosylation sites a glycoprotein three conserved N-linked glycosylation sites Fterm Site glycoprotein sites Acetylcholinesterase (AChE; EC 3.1.1.7) is a glycoprotein possessing three conserved N-linked glycosylation sites in mammalian species, locating at 296, 381, and 495 residues of the human sequence. 25709024 0 62 gly glycosylated 42:53 arg1 glycosylated Bacillus cereus cyclodextrin glycosyltransferase glycosylated Bacillus cereus cyclodextrin glycosyltransferase Fterm glycosyltransferase Catalytic and thermodynamic properties of glycosylated Bacillus cereus cyclodextrin glycosyltransferase. 28039139 4 101 gly glycoprotein 795:806 arg1 the surface layer (S-layer) glycoprotein the surface layer (S-layer) glycoprotein Fterm glycoprotein Cryo-electron microscopy was used to examine right-side-out membrane vesicles prepared from cells of a parent strain and from strains lacking genes encoding glycosyltransferases involved in assembling the N-linked pentasaccharide decorating the surface layer (S-layer) glycoprotein, the sole component of the S-layer surrounding H. volcanii cells. 24747898 4 89 gly glycosylation 1015:1027 arg2 Asn384 glycosylation site Asn384 glycosylation site site Further characterization of the purified CBH1 variants showed that, compared to Asn270, the thermal reactivity of CBH1 was significantly decreased by removal of either Asn45 or Asn384 glycosylation site during the catalyzed hydrolysis of soluble substrate. 25837443 4 12 gly glycoproteins 518:530 arg1 glycoproteins glycoproteins Fterm glycoproteins Here, we report a novel method for rapid and quantitative identification of glycoproteins containing specific glycans. 25837443 4 44 gly containing 532:541 arg1 glycoproteins AND specific glycans glycoproteins specific glycans Fterm glycoproteins Here, we report a novel method for rapid and quantitative identification of glycoproteins containing specific glycans. 26509638 5 56 part_of LAM 893:895 arg1 seven arabinomannan fragments LAM (1-7 seven arabinomannan fragments PUBTATOR Site LAM (1-7 6402 fragments To access these compounds, we developed an efficient orthogonal protection strategy that allowed access to seven arabinomannan fragments of LAM (1-7). 28887379 6 67 gly glycopeptides 1011:1023 arg2 glycopeptides glycopeptides glycopeptides The program includes three major advances: (1) "SmallGlyPep," a minimal linear representation of glycopeptides for MSn data analysis. 25234305 5 21 gly glycoproteins 1000:1012 arg1 standard glycoproteins standard glycoproteins Fterm glycoproteins In this work, we identified 32 linkage and positional glycan isomers in healthy human serum using exoglycosidase digestions as well as standard glycoproteins, for which we report the assignment of novel structures. 28729420 3 5 gly core-fucosylated 646:661 arg1 the oligomannose substrate Man5GlcNAc2 the oligomannose substrate Man5GlcNAc2 In contrast, we have recently shown that expression of erythropoietin in a GnTI knock-out, FUT8-overexpressing cell line results in the production of fully core-fucosylated glycoforms of the oligomannose substrate Man5GlcNAc2, suggesting that FUT8 can catalyze core fucosylation of N-glycans lacking an α1,3-arm GlcNAc in cells. 28729420 3 5 gly core-fucosylated 646:661 arg1 fully core-fucosylated glycoforms fully core-fucosylated glycoforms In contrast, we have recently shown that expression of erythropoietin in a GnTI knock-out, FUT8-overexpressing cell line results in the production of fully core-fucosylated glycoforms of the oligomannose substrate Man5GlcNAc2, suggesting that FUT8 can catalyze core fucosylation of N-glycans lacking an α1,3-arm GlcNAc in cells. 28729420 3 56 gly glycoforms 663:672 arg1 the oligomannose substrate Man5GlcNAc2 the oligomannose substrate Man5GlcNAc2 In contrast, we have recently shown that expression of erythropoietin in a GnTI knock-out, FUT8-overexpressing cell line results in the production of fully core-fucosylated glycoforms of the oligomannose substrate Man5GlcNAc2, suggesting that FUT8 can catalyze core fucosylation of N-glycans lacking an α1,3-arm GlcNAc in cells. 28729420 3 89 gly fucosylation 756:767 arg1 N-glycans N-glycans In contrast, we have recently shown that expression of erythropoietin in a GnTI knock-out, FUT8-overexpressing cell line results in the production of fully core-fucosylated glycoforms of the oligomannose substrate Man5GlcNAc2, suggesting that FUT8 can catalyze core fucosylation of N-glycans lacking an α1,3-arm GlcNAc in cells. 26059044 9 8 gly composition 1401:1411 arg1 other positions other positions other positions Site positions However, we do show that the presence of a N-glycan on Asn54 contributes to the atypical N-glycan composition of plant-produced IL-22 and influences the N-glycan composition of N-glycans on other positions. 26059044 9 21 gly presence 1268:1275 arg2 Asn54 AND a N-glycan Asn54 a N-glycan Asn54 However, we do show that the presence of a N-glycan on Asn54 contributes to the atypical N-glycan composition of plant-produced IL-22 and influences the N-glycan composition of N-glycans on other positions. 28737213 1 30 gly N-glycoproteins 193:207 arg1 the N-glycan structures N-glycoproteins the N-glycan structures Fterm N-glycoproteins In contrast to mammals and vascular plants, microalgae show a high diversity in the N-glycan structures of complex N-glycoproteins. 25155433 7 67 gly O-glycosylation 1403:1417 arg2 known O-glycosylation sites known O-glycosylation sites sites Here, we present a systematic analysis of the activity of 10 human GalNAc-T isoenzymes with 195 peptide substrates covering known O-glycosylation sites and provide a comprehensive dataset for evaluating isoform-specific contributions to the O-glycoproteome. 29119347 2 36 gly N-glycosylation 918:932 arg1 the human enzyme the human enzyme Both strategies effectively prevented N-glycan maturation and the resultant N-glycan structures on the consensus sites for N-glycosylation of the human enzyme revealed high-mannose N-glycans of predominantly Man5 (cgl-IDUA) or Man6-8 (gm1-IDUA) structures. 24797265 6 5 gly glycopeptides 868:880 arg2 glycopeptides glycopeptides glycopeptides The approach was then refined using higher energy collisional dissociation fragmentation which led to the simultaneous loss of sugar residues, production of diagnostic oxonium ions and backbone fragmentation for glycopeptides. 26082231 3 22 gly glycoproteins 484:496 arg1 glycoproteins glycoproteins Fterm glycoproteins On the other hand, the presence of large amounts of carbohydrate can often hinder the structural and functional analysis of glycoproteins. 27638310 6 39 gly attached 993:1000 arg1 Thr 10 AND the O-glycans Thr 10 the O-glycans Thr 10 residues Analysis of pronase-digested glycopeptides indicated that the O-glycans are partially attached to Ser 5, Ser 7, Ser 9, or Thr 10 residues, and glycan heterogeneity was confirmed at each site. 27638310 6 50 gly Ser 1005:1007 arg1 residues residues Thr 10 residues Analysis of pronase-digested glycopeptides indicated that the O-glycans are partially attached to Ser 5, Ser 7, Ser 9, or Thr 10 residues, and glycan heterogeneity was confirmed at each site. 27638310 6 64 gly glycopeptides 936:948 arg2 pronase-digested glycopeptides pronase-digested glycopeptides glycopeptides Analysis of pronase-digested glycopeptides indicated that the O-glycans are partially attached to Ser 5, Ser 7, Ser 9, or Thr 10 residues, and glycan heterogeneity was confirmed at each site. 27638310 6 39 gly attached 993:1000 arg1 Ser 5 AND the O-glycans Ser 5, Ser 7, Ser 9 the O-glycans Ser 5, Ser 7, Ser 9 Analysis of pronase-digested glycopeptides indicated that the O-glycans are partially attached to Ser 5, Ser 7, Ser 9, or Thr 10 residues, and glycan heterogeneity was confirmed at each site. 27638310 6 39 gly attached 993:1000 arg1 Ser 7 AND the O-glycans Ser 5, Ser 7, Ser 9 the O-glycans Ser 5, Ser 7, Ser 9 Analysis of pronase-digested glycopeptides indicated that the O-glycans are partially attached to Ser 5, Ser 7, Ser 9, or Thr 10 residues, and glycan heterogeneity was confirmed at each site. 27638310 6 39 gly attached 993:1000 arg1 Ser 7 AND the O-glycans Ser 5, Ser 7, Ser 9 the O-glycans Ser 5, Ser 7, Ser 9 Analysis of pronase-digested glycopeptides indicated that the O-glycans are partially attached to Ser 5, Ser 7, Ser 9, or Thr 10 residues, and glycan heterogeneity was confirmed at each site. 24685714 9 19 part_of PAC 1445:1447 arg1 its PAC domain PAC its PAC domain OGER Site PAC Q9H813 domain KEY RESULTS It was demonstrated that AGP31 interacts through its PAC domain with galactans that are branches of rhamnogalacturonan I. 29069609 9 34 gly glycoforms 1490:1499 arg1 IgG1 glycopeptides IgG1 glycopeptides glycopeptides 21 glycoforms of IgG1 glycopeptides were identified including two truncated structures that are rarely reported. 29069609 9 92 gly glycopeptides 1509:1521 arg2 IgG1 glycopeptides IgG1 glycopeptides glycopeptides 21 glycoforms of IgG1 glycopeptides were identified including two truncated structures that are rarely reported. 28258464 0 31 gly glycopeptides 88:100 arg2 intact glycopeptides intact glycopeptides glycopeptides Sequential fragment ion filtering and endoglycosidase-assisted identification of intact glycopeptides. 28186137 9 10 gly glycoprotein 1006:1017 arg1 the most abundant glycoprotein the most abundant glycoprotein Fterm glycoprotein P0 protein, the most abundant glycoprotein in PNS myelin and mutations in which at the glycosylation site cause Charcot-Marie-Tooth neuropathy, has abundant GlcNAc-6-O-sulfated N-glycans. 28186137 9 10 gly glycoprotein 1006:1017 arg1 P0 protein P0 protein Fterm protein P0 protein, the most abundant glycoprotein in PNS myelin and mutations in which at the glycosylation site cause Charcot-Marie-Tooth neuropathy, has abundant GlcNAc-6-O-sulfated N-glycans. 28186137 9 27 gly glycosylation 1063:1075 arg2 the glycosylation site the glycosylation site site P0 protein, the most abundant glycoprotein in PNS myelin and mutations in which at the glycosylation site cause Charcot-Marie-Tooth neuropathy, has abundant GlcNAc-6-O-sulfated N-glycans. 28186137 9 62 gly has 1120:1122 arg1 the most abundant glycoprotein AND abundant GlcNAc-6-O-sulfated N-glycans the most abundant glycoprotein abundant GlcNAc-6-O-sulfated N-glycans Fterm glycoprotein P0 protein, the most abundant glycoprotein in PNS myelin and mutations in which at the glycosylation site cause Charcot-Marie-Tooth neuropathy, has abundant GlcNAc-6-O-sulfated N-glycans. 28186137 9 62 gly has 1120:1122 arg1 P0 protein AND abundant GlcNAc-6-O-sulfated N-glycans P0 protein abundant GlcNAc-6-O-sulfated N-glycans Fterm protein P0 protein, the most abundant glycoprotein in PNS myelin and mutations in which at the glycosylation site cause Charcot-Marie-Tooth neuropathy, has abundant GlcNAc-6-O-sulfated N-glycans. 26169737 1 8 gly glycoprotein 205:216 arg1 glycoprotein isolation glycoprotein isolation Fterm glycoprotein Glycan analysis of virion-derived glycoproteins is challenging due to the difficulties in glycoprotein isolation and low sample abundance. 26169737 1 21 gly glycoproteins 149:161 arg1 virion-derived glycoproteins virion-derived glycoproteins Fterm glycoproteins Glycan analysis of virion-derived glycoproteins is challenging due to the difficulties in glycoprotein isolation and low sample abundance. 25113421 9 89 gly glycopeptides 1163:1175 arg2 intact glycopeptides intact glycopeptides glycopeptides However, the spectral data cannot be readily analyzed because of the lack of software specifically designed for the identification of intact glycopeptides. 26051934 2 57 gly heterogeneity 186:198 arg1 the glycans the glycans The high density and heterogeneity of the glycans shield Env from recognition by the immune system, but paradoxically, many potent broadly neutralizing antibodies (bNAbs) recognize epitopes involving this glycan shield. 28672164 0 34 gly subunit 29:35 arg1 N-glycan structures subunit N-glycan structures Fterm subunit N-glycan structures of β-HlH subunit of Helix lucorum hemocyanin. 25902405 3 0 gly N-glycopeptides 526:540 arg2 N-glycopeptides N-glycopeptides N-glycopeptides However, theoretically, PGANs occupy 10% of N-glycopeptides in the typical tryptic digests. 26088564 1 63 part_of positions 223:231 arg1 an abundant human plasma glycoprotein glycoprotein positions Fterm Site glycoprotein positions Human α1-acid glycoprotein (AGP) is an abundant human plasma glycoprotein that may be N-glycosylated at five positions. 27558752 0 76 gly glycoproteins 74:86 arg1 cold-upregulated glycoproteins glycoproteins Endoplasmic reticulum-associated N-glycan degradation Fterm glycoproteins Endoplasmic reticulum-associated N-glycan degradation of cold-upregulated glycoproteins in response to chilling stress in Arabidopsis. 24812685 3 51 gly sialylated 499:508 arg1 sialylated N-glycans sialylated N-glycans However,sialylated N-glycans have short migration times due to their negative charge. 25730103 3 33 gly attachment 488:497 arg1 protein residues AND sugars protein residues sugars residues N-Linked glycosylation is a common protein modification resulting from the attachment of sugars to protein residues and is important in cell signaling and immune response. 24840237 5 27 gly sialylated 1109:1118 arg1 sialylated N-glycans sialylated N-glycans The use of TFA provided distinct advantages over conventional ammonium formate as a mobile phase additive, such as, optimal elution order for sialylated N-glycans, reproducible chromatographic profiles, and matching total ion current chromatograms, as well as minimal signal splitting, analyte adduction, and fragmentation during HILIC/MS, maximizing sensitivity for trace-level species. 28939751 1 9 part_of EGF 157:159 arg1 36 extracellular EGF domains EGF 36 extracellular EGF domains OGER Site EGF P01133 domains The transmembrane signaling protein Notch, which is crucial for embryonic cell fate decisions, has 36 extracellular EGF domains that are glycosylated in variable and complex ways. 27873468 6 53 gly glycopeptide 1270:1281 arg2 glycopeptide library glycopeptide library glycopeptide These results encourage further synthetic elaboration of the glycopeptide library and testing of the network of natural galectins and rationally engineered variants of the lectins. 24279413 4 57 gly attached 819:826 arg1 their glycosylation sites AND N-linked glycans their glycosylation sites N-linked glycans sites This paper introduces a computational framework for identifying intact N-linked glycopeptides, i.e. glycopeptides with N-linked glycans attached to their glycosylation sites, in complex proteome samples. 24279413 4 59 gly glycopeptides 763:775 arg2 intact N-linked glycopeptides intact N-linked glycopeptides glycopeptides This paper introduces a computational framework for identifying intact N-linked glycopeptides, i.e. glycopeptides with N-linked glycans attached to their glycosylation sites, in complex proteome samples. 24279413 4 63 gly glycosylation 837:849 arg2 their glycosylation sites their glycosylation sites sites This paper introduces a computational framework for identifying intact N-linked glycopeptides, i.e. glycopeptides with N-linked glycans attached to their glycosylation sites, in complex proteome samples. 24279413 4 13 gly glycopeptides 783:795 arg2 glycopeptides glycopeptides N-linked glycans glycopeptides This paper introduces a computational framework for identifying intact N-linked glycopeptides, i.e. glycopeptides with N-linked glycans attached to their glycosylation sites, in complex proteome samples. 24780636 1 19 gly Asn630 161:166 arg1 N-glycans Asn432 and Asn630 N-glycans Asn432 and Asn630 Transferrin is an iron-transport protein which possesses N-glycans at Asn432 and Asn630 in humans. 24780636 1 21 gly Asn432 150:155 arg1 N-glycans Asn432 and Asn630 N-glycans Asn432 and Asn630 Transferrin is an iron-transport protein which possesses N-glycans at Asn432 and Asn630 in humans. 24780636 1 1 gly possesses 127:135 arg1 an iron-transport protein AND N-glycans an iron-transport protein N-glycans Fterm protein Transferrin is an iron-transport protein which possesses N-glycans at Asn432 and Asn630 in humans. 26170448 6 3 gly glycoproteins 635:647 arg1 two different glycoproteins two different glycoproteins Fterm glycoproteins The S-layer was found containing two different glycoproteins which shared highly similar amino acid sequences. 26784534 9 13 gly glycopeptides 1293:1305 arg2 both glycopeptides both glycopeptides glycopeptides Disialosyl motifs were present on both glycopeptides flanking the A1 domain and on the glycosylation site T(2298) in the C1 domain. 26784534 9 53 gly glycosylation 1341:1353 arg2 the glycosylation site T(2298) the glycosylation site T(2298) T(2298) Disialosyl motifs were present on both glycopeptides flanking the A1 domain and on the glycosylation site T(2298) in the C1 domain. 26784534 9 70 gly site 1355:1358 arg1 2298 T(2298) T(2298) Disialosyl motifs were present on both glycopeptides flanking the A1 domain and on the glycosylation site T(2298) in the C1 domain. 25533529 4 49 gly glycosylation 812:824 arg2 each glycosylation site each glycosylation site site Based on homology modeling of acutobin and multiple sequence alignment with various venom thrombin-like enzymes, the importance of a hydrophilic environment at each glycosylation site to the enzyme folding could be rationalized. 26687240 6 41 gly detected 1035:1042 arg1 Asn99 AND non-fucosylated complex glycans Asn99 non-fucosylated complex glycans Asn99 No glycosylation was found at Asn264, whilst high mannose glycans were only detected at Asn275, tri-antennary glycans were exclusively observed at Asn99 and Asn252, and non-fucosylated complex glycans were detected at Asn99. 26687240 6 47 gly detected 905:912 arg2 Asn275 AND high mannose glycans Asn275 high mannose glycans Asn275 No glycosylation was found at Asn264, whilst high mannose glycans were only detected at Asn275, tri-antennary glycans were exclusively observed at Asn99 and Asn252, and non-fucosylated complex glycans were detected at Asn99. 26687240 6 51 gly non-fucosylated 998:1012 arg1 non-fucosylated complex glycans non-fucosylated complex glycans No glycosylation was found at Asn264, whilst high mannose glycans were only detected at Asn275, tri-antennary glycans were exclusively observed at Asn99 and Asn252, and non-fucosylated complex glycans were detected at Asn99. 26687240 6 5 gly observed 964:971 arg2 Asn99 AND tri-antennary glycans Asn99 and Asn252 tri-antennary glycans Asn99 and Asn252 No glycosylation was found at Asn264, whilst high mannose glycans were only detected at Asn275, tri-antennary glycans were exclusively observed at Asn99 and Asn252, and non-fucosylated complex glycans were detected at Asn99. 26687240 6 46 gly glycosylation 832:844 arg1 Asn264 Asn264 Asn264 No glycosylation was found at Asn264, whilst high mannose glycans were only detected at Asn275, tri-antennary glycans were exclusively observed at Asn99 and Asn252, and non-fucosylated complex glycans were detected at Asn99. 25452313 1 20 gly glycoproteins 142:154 arg1 glycans glycoproteins glycans Fterm glycoproteins All human cells are covered by glycans, the carbohydrate units of glycoproteins, glycolipids, and proteoglycans. 25452313 1 20 gly glycoproteins 142:154 arg1 the carbohydrate units glycoproteins the carbohydrate units Fterm glycoproteins All human cells are covered by glycans, the carbohydrate units of glycoproteins, glycolipids, and proteoglycans. 26254006 0 85 gly N-glycosylation 57:71 arg1 cell wall glycans cell wall glycans Comparative proteomic analyses reveal that Gnt2-mediated N-glycosylation affects cell wall glycans and protein content in Fusarium oxysporum. 26254006 0 85 gly N-glycosylation 57:71 arg1 protein content protein cell wall glycans Fterm protein Comparative proteomic analyses reveal that Gnt2-mediated N-glycosylation affects cell wall glycans and protein content in Fusarium oxysporum. 26254006 0 85 gly N-glycosylation 57:71 arg1 protein content protein cell wall glycans Fterm protein Comparative proteomic analyses reveal that Gnt2-mediated N-glycosylation affects cell wall glycans and protein content in Fusarium oxysporum. 24085030 10 57 gly glycoproteins 1476:1488 arg1 salivary glycoproteins salivary glycoproteins Fterm glycoproteins Some of salivary glycoproteins, such as α-amylase, clusterin, haptoglobin, heavy and light chains of immunoglobulins, and transferrin, seem to be worthy of detailed glycosylation analysis in the detection of alcohol dependence. 24085030 10 57 gly glycoproteins 1476:1488 arg1 α-amylase α-amylase Fterm α-amylase Some of salivary glycoproteins, such as α-amylase, clusterin, haptoglobin, heavy and light chains of immunoglobulins, and transferrin, seem to be worthy of detailed glycosylation analysis in the detection of alcohol dependence. 26983412 1 10 gly glycoprotein 315:326 arg1 alternative, non-mammalian glycoprotein expression systems alternative, non-mammalian glycoprotein expression systems Fterm glycoprotein N-glycosylation is an important feature of therapeutic and other industrially relevant proteins, and engineering of the N-glycosylation pathway provides opportunities for developing alternative, non-mammalian glycoprotein expression systems. 28452462 4 30 gly glycoform 989:997 arg1 an unusual Man5GlcNAc2Fuc an unusual Man5GlcNAc2Fuc We found that the generation of a HEK293S GnT I knockout FUT8 overexpressing cell line enabled the production of an unusual Man5GlcNAc2Fuc glycoform, which could be converted to the core-fucosylated GlcNAc-EPO intermediate acceptor for enzymatic transglycosylation. 28452462 4 55 gly core-fucosylated 1032:1047 arg1 the core-fucosylated GlcNAc-EPO intermediate acceptor the core-fucosylated GlcNAc-EPO intermediate acceptor We found that the generation of a HEK293S GnT I knockout FUT8 overexpressing cell line enabled the production of an unusual Man5GlcNAc2Fuc glycoform, which could be converted to the core-fucosylated GlcNAc-EPO intermediate acceptor for enzymatic transglycosylation. 28060516 5 82 gly glycosylation 1030:1042 arg2 glycosylation site microheterogeneity glycosylation site microheterogeneity site We performed two semiquantitative analyses including MALDI-TOF MS permethylation analysis of released glycans and LC-MSE analysis of glycosylation site microheterogeneity. 27932526 9 74 gly sialylation 2221:2231 arg1 high-mannose species high-mannose species Overall, the bisection, galactosylation, and sialylation of diantennary species, the sialylation of tetraantennary species, and the size of high-mannose species proved to be important plasma characteristics associated with inflammation and metabolic health. 27932526 9 100 gly sialylation 2261:2271 arg1 high-mannose species high-mannose species Overall, the bisection, galactosylation, and sialylation of diantennary species, the sialylation of tetraantennary species, and the size of high-mannose species proved to be important plasma characteristics associated with inflammation and metabolic health. 28056108 3 51 gly protein 668:674 arg1 the glycan protein the glycan Fterm protein The human pathogen Streptococcus pneumoniae depolymerizes complex N-glycans with enzymes that sequentially trim a complex N-glycan down to the Man3GlcNAc2 core prior to the release of the glycan from the protein by endo-β-N-acetylglucosaminidase (EndoD), which cleaves between the two GlcNAc residues. 25251695 2 8 gly glycoproteins 474:486 arg1 improperly-folded glycoproteins improperly-folded glycoproteins Fterm glycoproteins 6400 Specific oligosaccharide structures recruit molecular chaperones that promote folding or mannose-binding lectins that assist in the clearance of improperly-folded glycoproteins by delivery to ER-associated degradation (ERAD). 25895110 7 75 gly sialylated 1163:1172 arg1 sialylated structures sialylated structures Both UC and CD were associated with significantly decreased IgG galactosylation (digalactosylation, UC: odds ratio [OR] = 0.71; 95% confidence interval [CI], 0.5-0.9; P = 0.01; CD: OR = 0.41; CI, 0.3-0.6; P = 1.4 × 10) and significant decrease in the proportion of sialylated structures in CD (OR = 0.46, CI, 0.3-0.6, P = 8.4 × 10). 25113421 3 47 gly glycoproteins 444:456 arg1 glycoproteins glycoproteins Fterm glycoproteins To reveal the biological functions of protein-linked glycans involved in numerous biological processes, the high-throughput identification of both glycoproteins and the attached glycan structures becomes fundamentally important. 28905229 5 6 gly proteins 705:712 arg1 N-linked glycans proteins N-linked glycans Fterm proteins METHODS Using a chromatographic approach, we analysed N-linked glycans from plasma proteins in two populations comprising individuals with registered hyperglycaemia during critical illness (increased risk for development of type 2 diabetes) and individuals who stayed normoglycaemic during the same condition: AcuteInflammation (59 cases vs 49 controls) and AcuteInflammation Replication (52 cases vs 14 controls) populations. 26749838 0 34 gly Anthocyanin 17:27 arg1 a Linear Trisaccharide Anthocyanin a Linear Trisaccharide Fterm Anthocyanin A Novel Acylated Anthocyanin with a Linear Trisaccharide from Flowers of Convolvulus althaeoides. 26576925 1 15 gly sialoglycoprotein 201:217 arg1 sialoglycoprotein sialoglycoprotein Fterm sialoglycoprotein Prion or PrP(Sc) is a proteinaceous infectious agent that consists of a misfolded and aggregated form of a sialoglycoprotein called prion protein or PrP(C). 24508870 1 73 gly glycoproteins 235:247 arg1 procyclin surface glycoproteins procyclin surface glycoproteins Fterm glycoproteins The procyclic form of Trypanosoma brucei expresses procyclin surface glycoproteins with unusual glycosylphosphatidylinositol-anchor side chain structures that contain branched N-acetyllactosamine and lacto-N-biose units. 24821760 7 39 gly Ser3 1198:1201 arg1 a mannose disaccharide at Ser3 Ser3 a mannose disaccharide at Ser3 Ser3 O-Mannosylation also increases the thermostability of CBM glycoforms up to 16 °C, and a mannose disaccharide at Ser3 seems to have the largest themostabilizing effect. 24821760 7 39 gly Ser3 1198:1201 arg1 a mannose disaccharide at Ser3 Ser3 a mannose disaccharide at Ser3 Ser3 O-Mannosylation also increases the thermostability of CBM glycoforms up to 16 °C, and a mannose disaccharide at Ser3 seems to have the largest themostabilizing effect. 24821760 7 39 gly Ser3 1198:1201 arg1 a mannose disaccharide at Ser3 Ser3 a mannose disaccharide at Ser3 Ser3 O-Mannosylation also increases the thermostability of CBM glycoforms up to 16 °C, and a mannose disaccharide at Ser3 seems to have the largest themostabilizing effect. 26512079 8 66 part_of coreceptor 1729:1738 arg1 the CD4bs and coreceptor binding region CD4 the CD4bs and coreceptor binding region PUBTATOR Site CD4 920 region These findings indicate that the N7 glycan plays an important and conserved role modulating the structure, stability, or accessibility of bNAb epitopes in the CD4bs and coreceptor binding region, thus representing a potential target for the design of immunogens and therapeutics. 24424471 2 31 gly glycoprotein 281:292 arg1 a glycoprotein hormone a glycoprotein hormone Fterm glycoprotein Analysis of human chorionic gonadotropin, a glycoprotein hormone produced by placental trophoblasts and trophoblastic tumors, has contributed to the diagnosis and treatment of trophoblastic disease, resulting in reduced incidence and mortality. 24840237 0 10 gly glycoproteins 135:147 arg1 related glycoproteins related glycoproteins Fterm glycoproteins Development and application of a robust N-glycan profiling method for heightened characterization of monoclonal antibodies and related glycoproteins. 25700513 4 32 part_of Delta/Serrate/Lag-2 455:473 arg1 DLL4 Delta/Serrate/Lag-2 (DSL) domain Lag-2 DLL4 Delta/Serrate/Lag-2 (DSL) domain OGER Site Lag-2 P22749 domain Notch1 epidermal growth factor-like repeats 11 and 12 interact with the DLL4 Delta/Serrate/Lag-2 (DSL) domain and module at the N-terminus of Notch ligands (MNNL) domains, respectively. 25700513 4 35 part_of DLL4 450:453 arg1 DLL4 Delta/Serrate/Lag-2 (DSL) domain DLL4 DLL4 Delta/Serrate/Lag-2 (DSL) domain OGER Site DLL4 Q9NR61 domain Notch1 epidermal growth factor-like repeats 11 and 12 interact with the DLL4 Delta/Serrate/Lag-2 (DSL) domain and module at the N-terminus of Notch ligands (MNNL) domains, respectively. 25700513 4 37 part_of DSL 476:478 arg1 DLL4 Delta/Serrate/Lag-2 (DSL) domain DSL DLL4 Delta/Serrate/Lag-2 (DSL) domain Cterm Site DSL P22749 domain Notch1 epidermal growth factor-like repeats 11 and 12 interact with the DLL4 Delta/Serrate/Lag-2 (DSL) domain and module at the N-terminus of Notch ligands (MNNL) domains, respectively. 24440233 0 105 gly glycopeptides 43:55 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides Characterization of intact N- and O-linked glycopeptides using higher energy collisional dissociation. 26773038 3 24 gly Glycosylation 409:421 arg2 N1574 N1574 N1574 Glycosylation at N1574 has previously been suggested to modulate VWF A2 domain interaction with ADAMTS13 through steric hindrance by the bulky carbohydrate structure. 28860626 6 0 gly fucosylation 1314:1325 arg1 the two influenza proteins proteins N-glycans Fterm proteins Interestingly, sulfation, fucosylation and bisecting N-acetylglucosamine of N-glycans were also reliably identified at the specific glycosylation sites of the two influenza proteins that may serve a crucial role in regulating the protein structure and increasing the protein abundance of the influenza virus reassortants. 28860626 6 0 gly fucosylation 1314:1325 arg1 the specific glycosylation sites sites N-glycans sites Interestingly, sulfation, fucosylation and bisecting N-acetylglucosamine of N-glycans were also reliably identified at the specific glycosylation sites of the two influenza proteins that may serve a crucial role in regulating the protein structure and increasing the protein abundance of the influenza virus reassortants. 28860626 6 0 gly fucosylation 1314:1325 arg1 the specific glycosylation sites proteins sites Fterm proteins sites Interestingly, sulfation, fucosylation and bisecting N-acetylglucosamine of N-glycans were also reliably identified at the specific glycosylation sites of the two influenza proteins that may serve a crucial role in regulating the protein structure and increasing the protein abundance of the influenza virus reassortants. 28860626 6 59 gly glycosylation 1420:1432 arg1 the two influenza proteins proteins sites Fterm proteins sites Interestingly, sulfation, fucosylation and bisecting N-acetylglucosamine of N-glycans were also reliably identified at the specific glycosylation sites of the two influenza proteins that may serve a crucial role in regulating the protein structure and increasing the protein abundance of the influenza virus reassortants. 25182382 13 76 gly glycopeptides 2135:2147 arg2 2249 intact glycopeptides 2249 intact glycopeptides glycopeptides In total, 2249 intact glycopeptides were identified which is by the far the largest dataset among the studies of N-glycoproteomics. 24451549 7 45 gly Glycosylation 1165:1177 arg2 Thr Thr(268) Thr(268) Glycosylation of MOMP at Thr(268) promoted cell-to-cell binding, biofilm formation and adhesion to Caco-2 cells, and was required for the optimal colonization of chickens by C. jejuni, confirming the significance of this O-glycosylation in pathogenesis. 24747898 8 55 part_of CBH1 1656:1659 arg1 specific functional regions CBH1 specific functional regions Cterm Site CBH1 regions These data implicate differential roles of N-glycosylation modifications in contributing to the stability of specific functional regions of CBH1 and highlight the potential of improving the thermostability of CBH1 by tuning proper interactions between glycans and functional residues. 27287011 2 57 gly glycosylated 339:350 arg1 the approved therapeutic proteins the approved therapeutic proteins Fterm proteins More than 60 % of the approved therapeutic proteins are glycosylated. 27873468 0 21 part_of Mucin-Like 10:19 arg1 Synthetic Mucin-Like Glycopeptides Mucin Synthetic Mucin-Like Glycopeptides PUBTATOR Site Mucin 100508689 Glycopeptides Synthetic Mucin-Like Glycopeptides as Versatile Tools to Measure Effects of Glycan Structure/Density/Position on the Interaction with Adhesion/Growth-Regulatory Galectins in Arrays. 28922740 2 69 part_of PglB 476:479 arg1 the active site PglB the active site OGER Site PglB Q99645 site Using available crystal structures and sequence alignments, we identified a DGGK motif near the active site of PglB that is conserved among all Campylobacter species. 27458127 5 45 gly glycopeptide 1003:1014 arg2 glycopeptide analysis glycopeptide analysis glycopeptide The method is able to detect hypoglycosylation, i.e. the lack of whole glycans, which is an important advantage over the well-established methods for free N-glycan or glycopeptide analysis. 26160412 7 34 gly N-glycosylation 1212:1226 arg1 CSF glycoproteins CSF glycoproteins Fterm glycoproteins RESULTS: We describe the development of a versatile approach for obtaining site-specific information on the N-glycosylation of CSF glycoproteins. 26160412 7 96 gly glycoproteins 1235:1247 arg1 CSF glycoproteins CSF glycoproteins Fterm glycoproteins RESULTS: We describe the development of a versatile approach for obtaining site-specific information on the N-glycosylation of CSF glycoproteins. 26160412 2 78 gly glycosylation 467:479 arg1 CSF proteins CSF proteins Fterm proteins The alteration of glycans bound to proteins from cerebrospinal fluid (CSF) in relation to disorders of the central nervous system is a highly relevant subject, but only few studies have focused on the glycosylation of CSF proteins. 25265424 0 64 gly glycoproteins 63:75 arg1 liver-secreted glycoproteins liver-secreted glycoproteins Fterm glycoproteins Protein and site specificity of fucosylation in liver-secreted glycoproteins. 26869421 3 6 gly glycoproteins 764:776 arg1 the Fc glycoproteins the Fc glycoproteins Fterm glycoproteins Using multiple high-throughput biophysical techniques, the physical stability of the Fc glycoproteins was then measured in 2 formulations (NaCl and sucrose) across a wide range of temperatures (10°C-90°C) and pH (4.0-7.5) conditions. 28880909 11 87 gly Asn52 2020:2024 arg1 the Asn52 glycan profile Asn52 the Asn52 glycan profile Asn52 These differences in the Asn52 glycan profile might potentially lead to differences in FSHR activation. 26929048 3 24 gly disialylated 532:543 arg1 the as-described disialylated structure the as-described disialylated structure This synthetic route enabled the synthesis of the as-described disialylated structure. 24424471 1 5 gly attachment 147:156 arg1 proteins AND glycans proteins glycans Fterm proteins Glycosylation is an important post-translational modification, in which attachment of glycans to proteins has effects on biological functions and carcinogenesis. 27287011 7 51 gly glycoproteins 1065:1077 arg1 other glycoproteins other glycoproteins Fterm glycoproteins Glycosylation changes were analyzed in human plasma immunoglobulin G samples which had previously been artificially modified by adding other glycoproteins (such as ribonuclease B and fetuin) or by digesting with enzyme (neuraminidase). 27629418 7 31 part_of immunoglobulin 1218:1231 arg1 the immunoglobulin G-derived core-fucosylated glycopeptides immunoglobulin G-derived the immunoglobulin G-derived core-fucosylated glycopeptides Cterm Site immunoglobulin G-derived glycopeptides W251N mutants could act on the immunoglobulin G-derived core-fucosylated glycopeptides and human lactoferrin glycoproteins. 27629418 7 74 part_of G-derived 1233:1241 arg1 the immunoglobulin G-derived core-fucosylated glycopeptides immunoglobulin G-derived the immunoglobulin G-derived core-fucosylated glycopeptides Cterm Site immunoglobulin G-derived glycopeptides W251N mutants could act on the immunoglobulin G-derived core-fucosylated glycopeptides and human lactoferrin glycoproteins. 26598643 3 79 gly glycoproteins 445:457 arg1 many human blood plasma glycoproteins many human blood plasma glycoproteins Fterm glycoproteins In consequence, despite their clinical and biopharmaceutical importance, many human blood plasma glycoproteins have not been characterized comprehensively with respect to their O-glycosylation. 26657071 5 22 gly aglycosylated 848:860 arg1 the aglycosylated enzyme the aglycosylated enzyme Fterm enzyme Crystal structures of hCES1 a catalytically inactive mutant (S221A) and the aglycosylated enzyme were determined in the absence of any ligand or substrate to high resolutions (1.86 Å, 1.48 Å and 2.01 Å, respectively). 25227423 6 22 gly N-glycosylation 1107:1121 arg2 an N-glycosylation site an N-glycosylation site site Fifteen of these residues occur within 10 Å of an N-glycosylation site. 28489325 2 20 part_of EGF-like 423:430 arg1 the C-type lectin and EGF-like domains EGF the C-type lectin and EGF-like domains OGER Site EGF P01133 domains In order to obtain the crystal structure of human L-selectin, we expressed a shortened version of L-selectin comprising the C-type lectin and EGF-like domains (termed LE) and systematically analysed mutations of the three glycosylation sites (Asn22, Asn66 and Asn139) in order to reduce macroheterogeneity. 27867116 9 5 part_of protein 1716:1722 arg1 protein glycosites protein protein glycosites Fterm Site protein glycosites SIGNIFICANCE We propose a simple and high-throughput glycoproteomics-based methodology that allows the separation of glycopeptide glycoforms on the basis of the number of sialic acids, and their automatic and rapid identification without prior knowledge of protein glycosites or type and structure of the glycans. 25450502 0 9 part_of osteopontin 120:130 arg1 phosphorylation sites osteopontin phosphorylation sites PUBTATOR Site osteopontin 6696 sites Site-specific structural characterization of O-glycosylation and identification of phosphorylation sites of recombinant osteopontin. 28433761 5 12 gly glycopeptides 721:733 arg2 the glycopeptides the glycopeptides glycopeptides Further nanoHPLC-ESI analysis of the glycopeptides showed two O-glycosylated peptides: the peptide sequence SSASSASSA already identified as a signature glycosylation motif in L. buchneri, substituted on average with eight glucose residues and decorated with galacturonic acid and another O-glycosylated site on peptide 471-476, with a Glc5-8GalA2 structure. 28433761 5 16 gly O-glycosylated 972:985 arg1 another O-glycosylated site another O-glycosylated site site Further nanoHPLC-ESI analysis of the glycopeptides showed two O-glycosylated peptides: the peptide sequence SSASSASSA already identified as a signature glycosylation motif in L. buchneri, substituted on average with eight glucose residues and decorated with galacturonic acid and another O-glycosylated site on peptide 471-476, with a Glc5-8GalA2 structure. 28433761 5 22 gly O-glycosylated 746:759 arg1 two O-glycosylated peptides two O-glycosylated peptides peptides Further nanoHPLC-ESI analysis of the glycopeptides showed two O-glycosylated peptides: the peptide sequence SSASSASSA already identified as a signature glycosylation motif in L. buchneri, substituted on average with eight glucose residues and decorated with galacturonic acid and another O-glycosylated site on peptide 471-476, with a Glc5-8GalA2 structure. 28433761 5 61 gly glycosylation 836:848 arg2 a signature glycosylation motif a signature glycosylation motif motif Further nanoHPLC-ESI analysis of the glycopeptides showed two O-glycosylated peptides: the peptide sequence SSASSASSA already identified as a signature glycosylation motif in L. buchneri, substituted on average with eight glucose residues and decorated with galacturonic acid and another O-glycosylated site on peptide 471-476, with a Glc5-8GalA2 structure. 24803430 5 42 part_of site 1081:1084 arg1 hN1 EGF12 hN1 site PUBTATOR Site hN1 51155 site Collectively, these data demonstrate a role for GlcNAc in modulating the ligand-binding site in hN1 EGF12, resulting in an increased affinity of this region for ligands Jagged1 and DLL1. 29062024 1 17 gly N-glycosylation 303:317 arg1 these glycoproteins these glycoproteins Fterm glycoproteins Antibody-dependent cellular cytotoxicity (ADCC) is promoted through interaction between the Fc region of immunoglobulin G1 (IgG1) and Fcγ receptor IIIa (FcγRIIIa), depending on N-glycosylation of these glycoproteins. 29062024 1 40 gly glycoproteins 328:340 arg1 these glycoproteins these glycoproteins Fterm glycoproteins Antibody-dependent cellular cytotoxicity (ADCC) is promoted through interaction between the Fc region of immunoglobulin G1 (IgG1) and Fcγ receptor IIIa (FcγRIIIa), depending on N-glycosylation of these glycoproteins. 28620050 6 21 gly glycosylation 1202:1214 arg2 an additional fully occupied N-linked glycosylation site an additional fully occupied N-linked glycosylation site site We also found that introduction of an additional fully occupied N-linked glycosylation site at the N terminus at position 1 (equivalent to Asp-221 in the Fc of IgG1) dramatically enhances overall sialic acid content of the Fc multimers. 28620050 6 21 gly glycosylation 1202:1214 arg2 the N terminus the N terminus terminus We also found that introduction of an additional fully occupied N-linked glycosylation site at the N terminus at position 1 (equivalent to Asp-221 in the Fc of IgG1) dramatically enhances overall sialic acid content of the Fc multimers. 27525954 5 19 gly N-glycosylation 680:694 arg2 five potential N-glycosylation sites five potential N-glycosylation sites sites Bioinformatic analysis showed that a signal peptide composed of 17 amino acids located at the N-terminal of SeCBP66 contained seven tandem putative Type-II functional chitin-binding domains and five potential N-glycosylation sites, but no O-linked glycosylation sites. 27525954 5 33 gly glycosylation 719:731 arg2 O-linked glycosylation sites O-linked glycosylation sites sites Bioinformatic analysis showed that a signal peptide composed of 17 amino acids located at the N-terminal of SeCBP66 contained seven tandem putative Type-II functional chitin-binding domains and five potential N-glycosylation sites, but no O-linked glycosylation sites. 28443077 1 38 gly N-glycosylation 452:466 arg2 N-glycosylation site profile (HA) site Cterm (HA) site Increasing evidence suggests that the antigenic change occasionally occurred concomitant with the alterations of the N-glycosylation site profile and hemagglutination activity of the virion surface protein hemagglutinin (HA). 28443077 1 38 gly N-glycosylation 452:466 arg2 N-glycosylation site profile hemagglutinin site Fterm hemagglutinin site Increasing evidence suggests that the antigenic change occasionally occurred concomitant with the alterations of the N-glycosylation site profile and hemagglutination activity of the virion surface protein hemagglutinin (HA). 27743372 1 84 gly glycoproteins 119:131 arg1 N-glycan profiling glycoproteins N-glycan profiling Fterm glycoproteins N-glycan profiling of therapeutic glycoproteins is essential to ensure the activity and efficacy of these promising new-generation drugs. 27743354 2 10 gly proteins 126:133 arg1 glycan parts proteins glycan parts Fterm proteins The attached glycans provide proteins with important structural and functional properties and glycan parts of glycoproteins have essential roles in many key biological processes. 27743354 2 37 gly glycoproteins 207:219 arg1 glycan parts glycoproteins glycan parts Fterm glycoproteins The attached glycans provide proteins with important structural and functional properties and glycan parts of glycoproteins have essential roles in many key biological processes. 28489325 6 17 part_of Ca2+ 1094:1097 arg1 The Ca2+ -binding site Ca2 The Ca2+ -binding site OGER Site Ca2 P00918 site The Ca2+ -binding site reflects the binding mode seen in E- and P-selectin structures co-crystallised with ligands. 24794851 0 36 gly residues 33:40 arg1 plant N-glycans residues in plant N-glycans residues in Deletion of plant-specific sugar residues in plant N-glycans by repression of GDP-D-mannose 4,6-dehydratase and β-1,2-xylosyltransferase genes. 28446609 3 5 gly glycosylation 550:562 arg2 glycosylation sites glycosylation sites sites Previous attempts to alter glycosylation sites in Env typically involved mutating the glycosylated asparagine residues to structurally similar glutamines or alanines. 28446609 3 67 gly glycosylated 609:620 arg1 the glycosylated asparagine residues the glycosylated asparagine residues asparagine residues Previous attempts to alter glycosylation sites in Env typically involved mutating the glycosylated asparagine residues to structurally similar glutamines or alanines. 27145274 4 46 gly glycosylated 879:890 arg1 both F(ab')2 arms both F(ab')2 arms arms In addition to asymmetric IgG, there are also detectable level of IgG with both F(ab')2 arms glycosylated that has not been reported previously. 27873218 0 41 gly Sulfate-Glycopeptides 53:73 arg1 Glycan Structures Sulfate-Glycopeptides Glycan Structures Sulfate-Glycopeptides Characterization of Glycan Structures of Chondroitin Sulfate-Glycopeptides Facilitated by Sodium Ion-Pairing and Positive Mode LC-MS/MS. 27124023 5 62 part_of IgG 1272:1274 arg1 IgG glycome composition IgG IgG glycome composition Cterm Site IgG position The present study demonstrated for the 1st time an association between hypertension and IgG glycome composition. 25698222 4 58 gly fucosylated 668:678 arg1 either fucosylated or sialylated N-glycans either fucosylated or sialylated N-glycans Optimum normalized collision energy (CE) for both sialylated and fucosylated N-glycan was determined to be 30%, whereas it was found to be 35% for either fucosylated or sialylated N-glycans. 25698222 4 59 gly fucosylated 579:589 arg1 both sialylated and fucosylated N-glycan both sialylated and fucosylated N-glycan Optimum normalized collision energy (CE) for both sialylated and fucosylated N-glycan was determined to be 30%, whereas it was found to be 35% for either fucosylated or sialylated N-glycans. 25698222 4 60 gly sialylated 683:692 arg1 either fucosylated or sialylated N-glycans either fucosylated or sialylated N-glycans Optimum normalized collision energy (CE) for both sialylated and fucosylated N-glycan was determined to be 30%, whereas it was found to be 35% for either fucosylated or sialylated N-glycans. 25698222 4 67 gly sialylated 564:573 arg1 both sialylated and fucosylated N-glycan both sialylated and fucosylated N-glycan Optimum normalized collision energy (CE) for both sialylated and fucosylated N-glycan was determined to be 30%, whereas it was found to be 35% for either fucosylated or sialylated N-glycans. 24549892 1 9 gly glycopeptide 155:166 arg2 Site-specific glycopeptide Site-specific glycopeptide glycopeptide Site-specific glycopeptide mapping for simultaneous glycan and peptide characterization by MS is difficult because of the heterogeneity and diversity of glycosylation in proteins and the lack of complete fragmentation information for either peptides or glycans with current fragmentation technologies. 24549892 1 54 gly peptide 204:210 arg1 simultaneous glycan and peptide characterization simultaneous glycan and peptide characterization Site-specific glycopeptide mapping for simultaneous glycan and peptide characterization by MS is difficult because of the heterogeneity and diversity of glycosylation in proteins and the lack of complete fragmentation information for either peptides or glycans with current fragmentation technologies. 26572920 4 19 gly glycoprotein 788:799 arg1 glycoprotein glycoprotein Fterm glycoprotein No significant alterations were found in the N-glycome profile at any of the investigated complexation levels (i.e., glycoprotein, serum and tissue samples) of the study. 28630087 6 39 gly glycosylation 1261:1273 arg2 low glycosylation site solvent accessibility low glycosylation site solvent accessibility site In contrast, the mostly unoccupied Asn88 carried nonfucosylated paucimannosidic N-glycans probably resulting from low glycosylation site solvent accessibility. 28630087 6 121 gly nonfucosylated 1192:1205 arg1 nonfucosylated paucimannosidic N-glycans nonfucosylated paucimannosidic N-glycans In contrast, the mostly unoccupied Asn88 carried nonfucosylated paucimannosidic N-glycans probably resulting from low glycosylation site solvent accessibility. 28381551 7 13 gly glycoprotein 1626:1637 arg1 glycoprotein preparation glycoprotein preparation Fterm glycoprotein We then employed the most efficient mutant (Q469A) other than the wild-type ApNGT to produce a homogeneous glycoprotein carrying multiple (up to 10) N-glycans, demonstrating that this construct is a promising biocatalyst for potentially addressing the issue of macroheterogeneity in glycoprotein preparation. 28381551 7 38 gly glycoprotein 1450:1461 arg1 a homogeneous glycoprotein a homogeneous glycoprotein Fterm glycoprotein We then employed the most efficient mutant (Q469A) other than the wild-type ApNGT to produce a homogeneous glycoprotein carrying multiple (up to 10) N-glycans, demonstrating that this construct is a promising biocatalyst for potentially addressing the issue of macroheterogeneity in glycoprotein preparation. 28381551 7 9 gly carrying 1463:1470 arg1 a homogeneous glycoprotein AND multiple (up to 10) N-glycans a homogeneous glycoprotein multiple (up to 10) N-glycans Fterm glycoprotein We then employed the most efficient mutant (Q469A) other than the wild-type ApNGT to produce a homogeneous glycoprotein carrying multiple (up to 10) N-glycans, demonstrating that this construct is a promising biocatalyst for potentially addressing the issue of macroheterogeneity in glycoprotein preparation. 28921955 2 28 gly glycosylation 272:284 arg1 hemagglutinin hemagglutinin Fterm hemagglutinin Understanding site specific glycosylation of hemagglutinin will increase our knowledge about virus evolution and can improve the design and quality of vaccines. 24820161 5 11 gly C-mannosylated 778:791 arg1 intracellular HYAL1 HYAL1 Trp³²¹ PUBTATOR HYAL1 3373 Trp³²¹ Using mass spectrometry, we first demonstrated that intracellular HYAL1 is C-mannosylated at Trp¹³⁰ but not at Trp³²¹. 24820161 5 11 gly C-mannosylated 778:791 arg1 intracellular HYAL1 HYAL1 Trp¹³⁰ PUBTATOR HYAL1 3373 Trp¹³⁰ Using mass spectrometry, we first demonstrated that intracellular HYAL1 is C-mannosylated at Trp¹³⁰ but not at Trp³²¹. 26663535 5 15 gly glycopeptides 742:754 arg2 deuterium-labelled glycopeptides deuterium-labelled glycopeptides glycopeptides To acquire a mechanistic insight, deuterium-labelled glycopeptides were prepared and analysed. 24747898 3 22 gly N-glycosylation 542:556 arg2 one or two N-glycosylation sites one or two N-glycosylation sites sites While the removal of one or two N-glycosylation sites hardly affected the extracellular secretion of CBH1, eliminating all of the glycosylation sites did induce expression of the unfolded protein response (UPR) target genes, and secretion of this CBH1 variant was severely compromised in a calnexin gene deletion strain. 24747898 3 24 gly glycosylation 640:652 arg2 the glycosylation sites the glycosylation sites sites While the removal of one or two N-glycosylation sites hardly affected the extracellular secretion of CBH1, eliminating all of the glycosylation sites did induce expression of the unfolded protein response (UPR) target genes, and secretion of this CBH1 variant was severely compromised in a calnexin gene deletion strain. 25029371 2 70 gly attached 275:282 arg1 nascent polypeptides AND N-Glycans nascent polypeptides N-Glycans polypeptides N-Glycans are attached to nascent polypeptides at consensus sites, N-X-T/S (X ≠ P), by one of two enzymatic isoforms of the oligosaccharyltransferase (OST), STT3A or STT3B. 26544759 1 23 gly fucosylated 278:288 arg1 core fucosylated biantennary IgG glycans core fucosylated biantennary IgG glycans Temperature dependent differential migration shifts were studied in capillary electrophoresis between linear (maltooligosaccharides) and branched (sialylated, neutral and core fucosylated biantennary IgG glycans) carbohydrates. 29224385 8 68 gly glycopeptides 1366:1378 arg2 eight glycopeptides eight glycopeptides glycopeptides The whole serum glycosylation analysis yielded 14 N-glycan compositions and multiple reaction monitoring yielded eight glycopeptides that were altered between cases and controls with statistical significance. 24549892 4 26 gly deglycopeptides 1021:1035 arg2 deglycopeptides deglycopeptides deglycopeptides This approach leverages an experimental pipeline with parallel analysis of glyco- and deglycopeptides. 29042829 3 57 gly glycopeptides 883:895 arg2 glycopeptides glycopeptides glycopeptides The importance of obtaining complete glycan release for accurate quantitation led us to investigate the kinetics of this de-glycosylation reaction for IgG glycopeptides and to determine the effect of glycan structure and amino acid sequence on the rate of glycan release from glycopeptides of IgGs. 29042829 3 67 gly glycopeptides 762:774 arg2 IgG glycopeptides IgG glycopeptides glycopeptides The importance of obtaining complete glycan release for accurate quantitation led us to investigate the kinetics of this de-glycosylation reaction for IgG glycopeptides and to determine the effect of glycan structure and amino acid sequence on the rate of glycan release from glycopeptides of IgGs. 24912705 3 23 gly contained 500:508 arg1 The modified protein AND glucosamine The modified protein glucosamine Fterm protein The modified protein contained glucosamine at a concentration of 12.1 g kg(-1) protein. 26132161 6 95 gly fucosylated 1620:1630 arg1 fucosylated N-glycans fucosylated N-glycans The sequential introduction of hTERT, SV40ER, H-RasV12, and myrAKT led to (i) temporal expression of pauci-mannose/mono-antennary type N-glycans and GD3 (hTERT); (ii) switching from ganglio- to globo-series glycosphingolipids and the appearance of Neu5Gc (hTERT and SV40ER); (iii) temporal expression of bisecting GlcNAc residues, α2,6-sialylation, and stage-specific embryonic antigen-4, accompanied by suppression of core 2 O-glycan biosynthesis (hTERT, SV40ER and Ras); and (iv) increased expression of (neo)lacto-series glycosphingolipids and fucosylated N-glycans (hTERT, SV40ER, Ras and AKT). 26132161 6 98 gly α2,6-sialylation 1404:1419 arg1 bisecting GlcNAc residues bisecting GlcNAc residues The sequential introduction of hTERT, SV40ER, H-RasV12, and myrAKT led to (i) temporal expression of pauci-mannose/mono-antennary type N-glycans and GD3 (hTERT); (ii) switching from ganglio- to globo-series glycosphingolipids and the appearance of Neu5Gc (hTERT and SV40ER); (iii) temporal expression of bisecting GlcNAc residues, α2,6-sialylation, and stage-specific embryonic antigen-4, accompanied by suppression of core 2 O-glycan biosynthesis (hTERT, SV40ER and Ras); and (iv) increased expression of (neo)lacto-series glycosphingolipids and fucosylated N-glycans (hTERT, SV40ER, Ras and AKT). 28433761 6 115 part_of S-layer 1107:1113 arg1 the S-layer amino acid sequence S-layer the S-layer amino acid sequence Cterm Site S-layer sequence As ten characteristic sequons (Asn-X-Ser/Thr) are present in the S-layer amino acid sequence, we performed a PNGase F digestion to release N-linked oligosaccharides. 25406038 11 1 gly glycoproteins 1432:1444 arg1 complex glycoproteins complex glycoproteins Fterm glycoproteins The presented method of protein digestion can be used to gain better insights into the density and complexity of glycosylation of complex glycoproteins such as mucins. 25406038 11 14 gly glycosylation 1407:1419 arg1 complex glycoproteins complex glycoproteins Fterm glycoproteins The presented method of protein digestion can be used to gain better insights into the density and complexity of glycosylation of complex glycoproteins such as mucins. 26492619 7 15 part_of PDPN 913:916 arg1 The minimum epitope PDPN The minimum epitope PUBTATOR Site PDPN 10630 epitope The minimum epitope of LpMab-10 was identified as Glu33-Gly45 of PDPN using Western blot and flow cytometry. 24632452 2 44 gly N-glycosylated 266:279 arg1 N-glycosylated proteins N-glycosylated proteins Fterm proteins N-glycan structures and N-glycosylation efficiency are crucial parameters in the production of N-glycosylated proteins. 26537504 0 68 gly N-glycans 68:76 arg1 a serine protease protease N-glycans Fterm protease Structural characterization and biological implications of sulfated N-glycans in a serine protease from the neotropical moth Hylesia metabus (Cramer [1775]) (Lepidoptera: Saturniidae). 25629924 2 0 gly glycosylated 241:252 arg1 a highly glycosylated protein a highly glycosylated protein Fterm protein Although it is a highly glycosylated protein, its site-specific glycosylation and associated glycan micro-heterogeneity have still not been fully elucidated. 27529638 5 3 gly glycopeptide/glycoprotein 794:818 arg1 homogeneous glycopeptide/glycoprotein bearing eukaryotic N-glycans homogeneous glycopeptide/glycoprotein bearing eukaryotic N-glycans In summary, the coupled approach provides a general strategy to produce homogeneous glycopeptide/glycoprotein bearing eukaryotic N-glycans. 27020775 0 54 part_of lactoferrin 80:90 arg1 glycosylation sites lactoferrin glycosylation sites PUBTATOR Site lactoferrin P02788 sites Sequence characterization and glycosylation sites identification of donkey milk lactoferrin by multiple enzyme digestions and mass spectrometry. 28630087 5 14 gly fucosylated 1044:1054 arg1 The equally unusual core fucosylated monoantenna complex-type N-sialoglycans The equally unusual core fucosylated monoantenna complex-type N-sialoglycans The equally unusual core fucosylated monoantenna complex-type N-sialoglycans also decorated these two fully occupied sites. 26088564 10 57 gly linked 1521:1526 arg2 Asn75 AND glycan chains Asn54 and Asn75 glycan chains Asn54 and Asn75 By examining the influence of fucosylation on AGP structure and binding to selectins, it is proposed that the latter may bind to glycan chains linked to Asn54 and Asn75, and that this binding may involve other glycans, such as the one attached to Asn15. 28336547 3 78 gly N-glycosylation 491:505 arg2 the individual N-glycosylation site N50 site N50 site N50 Mutagenesis-induced disruption of the individual N-glycosylation site N50, which is highly conserved among mammals, was detected to significantly enhance the PEPT1-mediated inward transport of peptides. 24685714 2 85 gly motifs 549:554 arg1 the Pro-rich domain the Pro-rich domain the Pro-rich domain Site domain AGP31 displays different O-glycosylation patterns with arabinogalactans on the AGP domain and Hyp-O-Gal/Ara-rich motifs on the Pro-rich domain. 24497634 10 10 part_of contactin 1375:1383 arg1 Ig domain 5 contactin Ig domain 5 Fterm Site contactin domain We found that the mutation of three sites (N467Q/N473Q/N494Q) in Ig domain 5 of contactin prevented soluble NF155-Fc binding. 25118826 1 61 gly glycoproteins 202:214 arg1 The N-glycan diversity glycoproteins The N-glycan diversity Fterm glycoproteins The N-glycan diversity of human serum glycoproteins, i.e., the human blood serum N-glycome, is both complex and constrained by the range of glycan structures potentially synthesizable by human glycosylation enzymes. 26773038 9 55 gly domain 1345:1350 arg1 Glycan stabilization domain Glycan stabilization domain Glycan stabilization of the VWF A2 domain acts together with the Ca(2+)binding site and vicinal cysteine disulfide bond to control unfolding and ADAMTS13 proteolysis. 26132161 5 18 gly N- 894:895 arg1 glycoproteins glycoproteins N- Fterm glycoproteins More than 160 glycans derived from three major classes of cell surface glycoconjugates (N- and O-glycans on glycoproteins, and glycosphingolipids) were quantitatively explored, and specific glycosylation patterns related to malignancy were systematically identified. 26132161 5 30 gly O-glycans 901:909 arg1 glycoproteins glycoproteins O-glycans Fterm glycoproteins More than 160 glycans derived from three major classes of cell surface glycoconjugates (N- and O-glycans on glycoproteins, and glycosphingolipids) were quantitatively explored, and specific glycosylation patterns related to malignancy were systematically identified. 26132161 5 73 gly glycoproteins 914:926 arg1 glycoproteins glycoproteins Fterm glycoproteins More than 160 glycans derived from three major classes of cell surface glycoconjugates (N- and O-glycans on glycoproteins, and glycosphingolipids) were quantitatively explored, and specific glycosylation patterns related to malignancy were systematically identified. 28711789 10 3 gly glycoproteins 1468:1480 arg1 the glycoproteins the glycoproteins Fterm glycoproteins The present study provided an insight into the glycoproteins related to drought stress in common bean at the proteome level, which is important for further understanding of molecular mechanisms of drought response in this important legume. 28246170 0 18 gly serine-rich 83:93 arg1 the pneumococcal serine-rich repeat protein PsrP serine the pneumococcal serine-rich repeat protein PsrP serine Defining the enzymatic pathway for polymorphic O-glycosylation of the pneumococcal serine-rich repeat protein PsrP. 28246170 0 86 gly O-glycosylation 47:61 arg1 the pneumococcal serine-rich repeat protein PsrP the pneumococcal serine-rich repeat protein PsrP Defining the enzymatic pathway for polymorphic O-glycosylation of the pneumococcal serine-rich repeat protein PsrP. 27283789 1 0 gly glycosylated 96:107 arg1 homogeneously glycosylated proteins homogeneously glycosylated proteins Fterm proteins The generation of homogeneously glycosylated proteins is essential for defining glycoform-specific activity and improving protein-based therapeutics. 25628020 2 0 gly N-glycosylation 296:310 arg2 a novel N-glycosylation site a novel N-glycosylation site site The acquisition of a novel N-glycosylation site may have significant effect on protein structure and function, and therefore, on the phenotype. 25422509 1 14 gly glycosylation 167:179 arg2 five glycosylation sites five glycosylation sites sites Human serum IgM Abs are composed of heavily glycosylated polymers with five glycosylation sites on the μ (heavy) chain and one glycosylation site on the J chain. 25422509 1 26 gly glycosylation 218:230 arg2 one glycosylation site one glycosylation site site Human serum IgM Abs are composed of heavily glycosylated polymers with five glycosylation sites on the μ (heavy) chain and one glycosylation site on the J chain. 26603318 3 7 gly lectin 507:512 arg1 high-mannose oligosaccharides lectin high-mannose oligosaccharides Fterm lectin Apart from the native lectin, the characteristics of a deglycosylated Escherichia coli expressed lectin, high-mannose oligosaccharides at both asparagines and its glycosylation mutants N66Q and N110Q expressed in Pichia pastoris, were compared to understand the relationship between glycosylation and activity. 26603318 3 15 gly asparagines 553:563 arg1 high-mannose oligosaccharides asparagines high-mannose oligosaccharides asparagines Apart from the native lectin, the characteristics of a deglycosylated Escherichia coli expressed lectin, high-mannose oligosaccharides at both asparagines and its glycosylation mutants N66Q and N110Q expressed in Pichia pastoris, were compared to understand the relationship between glycosylation and activity. 26603318 3 23 gly deglycosylated 465:478 arg1 a deglycosylated Escherichia coli expressed lectin a deglycosylated Escherichia coli expressed lectin Fterm lectin Apart from the native lectin, the characteristics of a deglycosylated Escherichia coli expressed lectin, high-mannose oligosaccharides at both asparagines and its glycosylation mutants N66Q and N110Q expressed in Pichia pastoris, were compared to understand the relationship between glycosylation and activity. 27810711 4 17 gly glycopeptides 638:650 arg2 syndecan-3 glycopeptides syndecan-3 glycopeptides glycopeptides For assembly of glycans, a convergent 3+2+3 approach was developed producing two different octasaccharide amino acid cassettes, which were utilized towards syndecan-3 glycopeptides. 24664808 11 60 part_of Observed 1799:1806 arg1 Observed fragments Observed Observed fragments Cterm Site Observed fragments Observed fragments are reasonably explained by a combination of existing fragmentation rules suggested for N-glycans and peptides. 27697163 1 46 gly origin 294:299 arg1 polysaccharides origin polysaccharides Fterm origin The present work demonstrates that yeasts belonging to the Schizosaccharomyces genus release a high quantity of polysaccharides of cell wall origin starting from the onset of the alcoholic fermentation. 28516782 8 16 gly occupied 1298:1305 arg2 the proline-rich hinge region the proline-rich hinge region region Moreover, the proline-rich hinge region from HEK293-6E cell-derived IgA1 was occupied with mucin-type O-glycans, whereas IgA1 from N. benthamiana displayed numerous plant-specific modifications. 25697358 9 61 part_of HUB 1306:1308 arg1 the HUB domain HUB the HUB domain OGER Site HUB Q12926 domain TarM assembles into a trimer using a novel trimerization domain, here termed the HUB domain. 28074929 6 3 part_of domains 942:948 arg1 GnTV GnTV domains OGER GnTV Q09328 Two domains in GnTV are restricted to specific eukaryotic domains, while 10 domains distribute not only in species where certain unique PNG reactions occur and thus genes harboring these domains are supoosed to be present, but in other ehkaryotic lineages. 25587188 11 17 gly N-glycosylation 1656:1670 arg2 the N-glycosylation sites the N-glycosylation sites sites As N-linked glycosylation requires glycosylation consensus sites in the protein sequence and as these are lacking in the 'germline-counterparts' of identified variable domains, our data indicate that the N-glycosylation sites in ACPA variable domains have been introduced by somatic hypermutation. 25587188 11 29 gly glycosylation 1487:1499 arg2 glycosylation consensus sites glycosylation consensus sites sites As N-linked glycosylation requires glycosylation consensus sites in the protein sequence and as these are lacking in the 'germline-counterparts' of identified variable domains, our data indicate that the N-glycosylation sites in ACPA variable domains have been introduced by somatic hypermutation. 27585995 1 120 gly glycoprotein 292:303 arg1 glycoprotein O-glycans glycoprotein O-glycans Rapid, simple and versatile methods for quantitative analysis of glycoprotein O-glycans are urgently required for current studies on protein O-glycosylation patterns and the search for disease O-glycan biomarkers. 26189796 0 52 gly N-glycosylation 31:45 arg1 Asn-554 Asn-554 Asn-554 Preventing E-cadherin aberrant N-glycosylation at Asn-554 improves its critical function in gastric cancer. 26618856 6 56 gly glycosylated 1119:1130 arg1 O-linked glycosylated and unglycosylated forms O-linked glycosylated and unglycosylated forms We simulate these IDPs in aqueous solution for O-linked glycosylated and unglycosylated forms by employing two modern all-atom force fields for which glycan parameters are also available. 26618856 6 60 gly unglycosylated 1136:1149 arg1 O-linked glycosylated and unglycosylated forms O-linked glycosylated and unglycosylated forms We simulate these IDPs in aqueous solution for O-linked glycosylated and unglycosylated forms by employing two modern all-atom force fields for which glycan parameters are also available. 25995273 7 0 part_of proteins 1143:1150 arg1 13 O-glycosylation sites proteins 13 O-glycosylation sites Fterm Site proteins sites We present comparative brain/liver glycosylation data on 50 N-glycosylation sites from 34 proteins and 13 O-glycosylation sites from seven proteins. 26492619 10 35 gly O-glycosylated 1386:1399 arg1 Ser/Thr residues PDPN residues PUBTATOR PDPN 10630 residues By using monoclonal antibodies against different Ser/Thr, including epitopes of PDPN, it becomes possible to determine whether Ser/Thr residues of PDPN are O-glycosylated. 29124306 3 24 gly proteins 430:437 arg1 tag glycan structures proteins tag glycan structures Fterm proteins In this work, we have developed a new metal labeling strategy to tag glycan structures of proteins, more particularly antibodies. 25458834 1 35 gly O-glycoprotein 149:162 arg1 a transmembrane O-glycoprotein a transmembrane O-glycoprotein Fterm O-glycoprotein Podoplanin is a transmembrane O-glycoprotein that binds to C-type lectin-like receptor 2 (CLEC-2). 29233759 2 13 part_of -1 522:523 arg1 the -3 and -1 subsites -3 and -1 the -3 and -1 subsites OGER Site -3 and -1 O75717 subsites Three independent mutants were created, targeting Trp residues from the -3 and -1 subsites and the central catalytic Asp from the DxDxE motif of StmChiA. 29233759 2 25 part_of -3 515:516 arg1 the -3 and -1 subsites -3 and -1 the -3 and -1 subsites OGER Site -3 and -1 O75717 subsites Three independent mutants were created, targeting Trp residues from the -3 and -1 subsites and the central catalytic Asp from the DxDxE motif of StmChiA. 29233759 2 42 part_of motif 579:583 arg1 Trp residues motif Trp residues Trp residues Three independent mutants were created, targeting Trp residues from the -3 and -1 subsites and the central catalytic Asp from the DxDxE motif of StmChiA. 29233759 2 42 part_of motif 579:583 arg1 the central catalytic Asp motif the central catalytic Asp Asp Three independent mutants were created, targeting Trp residues from the -3 and -1 subsites and the central catalytic Asp from the DxDxE motif of StmChiA. 26646445 0 84 gly glycoprotein 24:35 arg1 serum glycoprotein bifucosylation serum glycoprotein bifucosylation Elevated level of serum glycoprotein bifucosylation and prognostic value in Chinese breast cancer. 28711789 0 18 gly N-glycoproteins 96:110 arg1 N-glycoproteins N-glycoproteins Fterm N-glycoproteins Towards a better understanding of protein changes in common bean under drought: A case study of N-glycoproteins. 29273683 11 29 gly sites 1711:1715 arg1 N-glycans sites N-glycans sites Moreover, while glycosylation of N347 in the RCL limits these activities, N-glycans at other sites also appear to protect CBG from neutrophil elastase or chymotrypsin. 29273683 11 13 gly glycosylation 1634:1646 arg1 N347 RCL N347 OGER RCL O43598 N347 Moreover, while glycosylation of N347 in the RCL limits these activities, N-glycans at other sites also appear to protect CBG from neutrophil elastase or chymotrypsin. 26339047 0 50 gly Asparagine-Linked 16:32 arg1 Asparagine-Linked Glycan Density Asparagine Asparagine-Linked Glycan Density Asparagine Modification of Asparagine-Linked Glycan Density for the Design of Hepatitis B Virus Virus-Like Particles with Enhanced Immunogenicity. 24965454 2 18 gly position 479:486 arg1 a glycan position N332 a glycan position N332 2G12 is a unique, domain-exchanged antibody that binds exclusively to conserved N-linked glycans that form the high-mannose patch on the gp120 outer domain centered on a glycan at position N332. 24965454 2 50 gly patch 423:427 arg1 the gp120 outer domain the gp120 outer domain the gp120 outer domain Site domain 2G12 is a unique, domain-exchanged antibody that binds exclusively to conserved N-linked glycans that form the high-mannose patch on the gp120 outer domain centered on a glycan at position N332. 25303961 9 62 gly types 1309:1313 arg1 basal tear proteins proteins types Fterm proteins These results suggest the conservation of glycan types on basal tear proteins between individuals and point to only small changes in glycan expression on the proteins in tears with the development of diabetes and DR. 25303961 9 66 gly expression 1400:1409 arg1 the proteins proteins expression Fterm proteins These results suggest the conservation of glycan types on basal tear proteins between individuals and point to only small changes in glycan expression on the proteins in tears with the development of diabetes and DR. 25437919 0 51 gly glycoproteins 30:42 arg1 membrane glycoproteins membrane glycoproteins Fterm glycoproteins Glycomic analysis of membrane glycoproteins with bisecting glycosylation from ovarian cancer tissues reveals novel structures and functions. 24475074 1 51 gly glycoprotein 168:179 arg1 glycoprotein folding glycoprotein folding Fterm glycoprotein Protein N-glycosylation is found in all domains of life and has a conserved role in glycoprotein folding and stability. 24475074 1 82 gly N-glycosylation 92:106 arg1 all domains all domains domains Protein N-glycosylation is found in all domains of life and has a conserved role in glycoprotein folding and stability. 26512079 4 4 gly glycans 863:869 arg1 the conserved regions the conserved regions the conserved regions Site regions However, it is not clear if the role of the N7 glycan is conserved among diverse HIV-1 isolates and if other glycans in the conserved regions of HIV-1 Env display similar functions. 27023912 6 36 gly Asn19-linked 945:956 arg1 the Asn19-linked glycan Asn19 the Asn19-linked glycan Asn19 In the case of the Asn19-linked glycan, it also occurred around region 438-444, where one of the most prevalent GCase mutations is found. 28887379 2 97 gly site 464:467 arg1 glycans site glycans site The structural analysis of this PTM is challenging because of the diverse monosaccharides which are not conserved among organisms, the branched nature of glycans, their isomeric structures, and heterogeneity in the glycan distribution at a given site. 28887379 2 97 gly site 464:467 arg1 the diverse monosaccharides site the diverse monosaccharides site The structural analysis of this PTM is challenging because of the diverse monosaccharides which are not conserved among organisms, the branched nature of glycans, their isomeric structures, and heterogeneity in the glycan distribution at a given site. 29187599 2 11 gly N-glycosylation 238:252 arg2 multiple N-glycosylation sites multiple N-glycosylation sites sites Human diamine oxidase (hDAO), required for histamine catabolism, has multiple N-glycosylation sites, but their roles, for example in DAO secretion, are unclear. 24632452 3 56 gly glycoproteins 364:376 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins Yeast cells can be seen as an attractive production host for therapeutic glycoproteins and pioneering work of glycoengineering was performed in Pichia pastoris, realizing yeast strains capable of producing defined, human-type N-glycans. 27884519 4 24 part_of hIL-11 495:500 arg1 the region hIL-11 the region PUBTATOR Site hIL-11 3589 region Modified vectors were constructed by introducing N- or O-glycosylation site on the region of hIL-11 that does not belong to the core α-helical motif based on the predicted secondary structure. 26956484 2 1 gly N-glycosylated 275:288 arg1 N-glycosylated subunits N-glycosylated subunits Fterm subunits Orai channels, which mediate store-operated Ca(2+) entry (SOCE), are composed of N-glycosylated subunits. 24475074 9 52 part_of sites 1726:1730 arg1 proteins proteins sites Fterm AminoAcid proteins Lys sites An examination of acetyl-Lys sites in proteins indicated similar evolutionary dynamics, consistent with asymmetry of the target and recognition portions of modified sites. 24108499 0 30 part_of glucoamylase 65:76 arg1 starch binding domain glucoamylase starch binding domain Fterm Site glucoamylase domain Crystal structures of starch binding domain from Rhizopus oryzae glucoamylase in complex with isomaltooligosaccharide: insights into polysaccharide binding mechanism of CBM21 family. 28322444 5 4 gly N229-glycosylated 854:870 arg1 the N229-glycosylated Kv3.1b protein the N229-glycosylated Kv3.1b protein Fterm protein Mass spectrometry analysis revealed a complex type Hex3 HexNAc4 Fuc1 glycan as the major glycan component of the N229-glycosylated Kv3.1b protein, as opposed to a high-mannose type Man8 GlcNAc2 glycan for N220-glycosylated Kv3.1b. Taken together, these results suggest that trafficking-dependent roles of the Kv3.1b potassium channel are dependent on N229 site-specific glycosylation and N-glycan structure, and operate through a mechanism whereby specific N-glycan structures regulate cell surface expression. 28322444 5 14 gly protein 879:885 arg1 the major glycan component protein the major glycan component Fterm protein Mass spectrometry analysis revealed a complex type Hex3 HexNAc4 Fuc1 glycan as the major glycan component of the N229-glycosylated Kv3.1b protein, as opposed to a high-mannose type Man8 GlcNAc2 glycan for N220-glycosylated Kv3.1b. Taken together, these results suggest that trafficking-dependent roles of the Kv3.1b potassium channel are dependent on N229 site-specific glycosylation and N-glycan structure, and operate through a mechanism whereby specific N-glycan structures regulate cell surface expression. 28322444 5 14 gly protein 879:885 arg1 a complex type Hex3 HexNAc4 Fuc1 glycan protein a complex type Hex3 HexNAc4 Fuc1 glycan Fterm protein Mass spectrometry analysis revealed a complex type Hex3 HexNAc4 Fuc1 glycan as the major glycan component of the N229-glycosylated Kv3.1b protein, as opposed to a high-mannose type Man8 GlcNAc2 glycan for N220-glycosylated Kv3.1b. Taken together, these results suggest that trafficking-dependent roles of the Kv3.1b potassium channel are dependent on N229 site-specific glycosylation and N-glycan structure, and operate through a mechanism whereby specific N-glycan structures regulate cell surface expression. 26773038 4 59 part_of VWF 624:626 arg1 the VWF A2 domain VWF the VWF A2 domain PUBTATOR Site VWF 7450 domain We investigated how the N-linked glycans of the VWF A2 domain affect thermostability and regulate both the exposure of the ADAMTS13 binding sites and the scissile bond. 27145274 2 12 part_of Fab 524:526 arg1 Fab fragment Fab Fab fragment PUBTATOR Site Fab 2187 fragment In this study, applying affinity chromatography, silver stain, Western blot and lectin stain techniques, N- linked oligosaccharide attached to Fab fragment was demonstrated to be exposed on the surface of the protein and be accessible by ConA. 28489325 1 40 gly N-glycosylation 258:272 arg2 seven N-glycosylation sites seven N-glycosylation sites sites L-Selectin, a cell-adhesion receptor on the surface of most leukocytes, contains seven N-glycosylation sites. 28905148 6 78 gly glycoproteins 1516:1528 arg1 glycoproteins glycoproteins Fterm glycoproteins Consequently, this platform should serve as a valuable resource for facilitating the detailed analysis of the glycosylation of both purified recombinant, and complex mixtures of, glycoproteins using established workflows. 27489265 3 70 gly it 578:579 arg1 a site a site site Previous studies have shown that the removal of a particular conserved glycan at N197 increases the neutralization sensitivity of the virus to antibodies targeting the CD4 binding site (CD4bs), making it a site of significant interest from the perspective of vaccine design. 27199480 6 60 gly glycosyltransferase 773:791 arg1 the β-Kdo counterparts glycosyltransferase the β-Kdo counterparts Fterm glycosyltransferase In contrast, the β-Kdo counterparts were not identified as glycosyltransferase enzymes by bioinformatics tools and were not represented among the 98 currently recognized glycosyltransferase families in the Carbohydrate-Active Enzymes database. 25110774 6 6 gly glycopeptides 994:1006 arg2 glycopeptides glycopeptides glycopeptides The LCD-MOFs performance for the selective enrichment of glycopeptides from the complex biological samples were investigated with a digested mixture of human immunoglobulin G (IgG) that was used as standard samples. 28482115 7 26 gly glycoprotein 1386:1397 arg1 a soluble glycoprotein a soluble glycoprotein Fterm glycoprotein FLA4 functions as a soluble glycoprotein via its carboxy-proximal Fas1 domain and its normal cellular trafficking depends on N- and O-glycosylation. 27038031 5 68 gly N-glycosylation 733:747 arg2 all putative N-glycosylation sites all putative N-glycosylation sites sites The occupancy of all putative N-glycosylation sites on the pentameric and hexameric IgM were able to be determined. 27038031 5 72 gly occupancy 707:715 arg2 all putative N-glycosylation sites all putative N-glycosylation sites sites The occupancy of all putative N-glycosylation sites on the pentameric and hexameric IgM were able to be determined. 25629924 6 63 gly heterogeneity 1007:1019 arg1 each composition each composition position Site-specific heterogeneity and relative quantitation of each composition and the extent of occupation at each site were determined using nonspecific proteases. 28109443 1 15 gly O-glycans 204:212 arg1 its hinge region its hinge region its hinge region Site region Human immunoglobulin A1 (IgA1), which carries four to six mucin-type O-glycans (O-glycans) on its hinge region (HR), is the most abundant O-glycoprotein in plasma or serum. 28109443 1 63 gly O-glycoprotein 273:286 arg1 the most abundant O-glycoprotein the most abundant O-glycoprotein Fterm O-glycoprotein Human immunoglobulin A1 (IgA1), which carries four to six mucin-type O-glycans (O-glycans) on its hinge region (HR), is the most abundant O-glycoprotein in plasma or serum. 28109443 1 109 gly carries 173:179 arg1 the most abundant O-glycoprotein AND O-glycans the most abundant O-glycoprotein O-glycans Fterm O-glycoprotein Human immunoglobulin A1 (IgA1), which carries four to six mucin-type O-glycans (O-glycans) on its hinge region (HR), is the most abundant O-glycoprotein in plasma or serum. 28109443 1 109 gly carries 173:179 arg1 the most abundant O-glycoprotein AND four to six mucin-type O-glycans the most abundant O-glycoprotein four to six mucin-type O-glycans Fterm O-glycoprotein Human immunoglobulin A1 (IgA1), which carries four to six mucin-type O-glycans (O-glycans) on its hinge region (HR), is the most abundant O-glycoprotein in plasma or serum. 28104755 11 76 part_of peptide 1783:1789 arg1 SMPDL3A SMPDL3A peptide PUBTATOR Site SMPDL3A Q92484 peptide We provide the first experimental evidence for a predicted 22 residue N-terminal signal peptide in SMPDL3A, which is essential for facilitating glycosylation and is removed from the mature protein secreted from CHO cells. 27663739 0 34 gly O-fucosylated 0:12 arg1 O-fucosylated glycoproteins O-fucosylated glycoproteins Fterm glycoproteins O-fucosylated glycoproteins form assemblies in close proximity to the nuclear pore complexes of Toxoplasma gondii. 27663739 0 37 gly glycoproteins 14:26 arg1 O-fucosylated glycoproteins O-fucosylated glycoproteins Fterm glycoproteins O-fucosylated glycoproteins form assemblies in close proximity to the nuclear pore complexes of Toxoplasma gondii. 25697358 7 55 part_of GT-B-type 1022:1030 arg1 a GT-B-type glycosyltransferase domain GT-B-type a GT-B-type glycosyltransferase domain Cterm Site GT-B-type domain The protein assembles into a propeller-like homotrimer in which each blade contains a GT-B-type glycosyltransferase domain with a typical Rossmann fold. 25697358 7 60 part_of glycosyltransferase 1032:1050 arg1 a GT-B-type glycosyltransferase domain glycosyltransferase a GT-B-type glycosyltransferase domain Fterm Site glycosyltransferase domain The protein assembles into a propeller-like homotrimer in which each blade contains a GT-B-type glycosyltransferase domain with a typical Rossmann fold. 25697358 7 3 part_of contains 1011:1018 arg1 a propeller-like homotrimer AND a GT-B-type glycosyltransferase domain a propeller-like homotrimer a GT-B-type glycosyltransferase domain Fterm Site homotrimer domain The protein assembles into a propeller-like homotrimer in which each blade contains a GT-B-type glycosyltransferase domain with a typical Rossmann fold. 29279989 9 44 gly glycoprotein 1207:1218 arg1 Two glycoprotein standards Two glycoprotein standards Fterm glycoprotein Two glycoprotein standards were deglycosylated through hydrazinolysis and tagged at the optimized conditions. 27111718 9 30 gly structures 1721:1730 arg1 glycopeptides glycopeptides glycopeptides Site glycopeptides Hence, GlycoSeq is ready to be used for the characterization of glycan structures in glycopeptides from MS/MS analysis. 27111718 9 61 gly glycopeptides 1735:1747 arg2 glycopeptides glycopeptides glycopeptides Hence, GlycoSeq is ready to be used for the characterization of glycan structures in glycopeptides from MS/MS analysis. 28745859 5 19 gly glycosylation 937:949 arg2 the glycosylation site the glycosylation site site The strongest effect, a 6-fold increase in overall folding rate, was observed when a single O-mannose was the glycan, and the glycosylation site was near the N-terminus of the peptide sequence. 25636227 1 29 gly heterogeneity 250:262 arg1 O-glycan core structures O-glycan core structures O-glycosylation-site characterization of individual glycoproteins is a major challenge because of the heterogeneity of O-glycan core structures. 25636227 1 61 gly glycoproteins 200:212 arg1 individual glycoproteins individual glycoproteins Fterm glycoproteins O-glycosylation-site characterization of individual glycoproteins is a major challenge because of the heterogeneity of O-glycan core structures. 24931470 4 20 part_of gp120 652:656 arg1 the gp120 inner domain gp120 the gp120 inner domain PUBTATOR Site gp120 3700 domain CD4 activation induces the reorganization of bridging sheet elements, V1/V2 and V3, much of the gp120 inner domain, and the gp41 fusion subunit. 27810711 3 27 part_of syndecan-3 390:399 arg1 syndecan-3 glycopeptide syndecan-3 syndecan-3 glycopeptide OGER Site syndecan-3 O75056 glycopeptide In this work, we give the full account of the synthesis of syndecan-3 glycopeptide (53-62) containing two different heparan sulfate chains. 28039392 4 8 gly N-glycans 684:692 arg1 Lea epitopes Lea epitopes Lea epitopes It substantially hydrolyzed the non-reducing terminal α1,3-fucose residue on LNFP III and α1,4-fucose residues of Lea epitopes on plant complex-type N-glycans, but not the α1,2-fucose residue on LNFP I or the α1,3-fucose residue on pyridylaminated Fucα1-3GlcNAc. 28039392 4 21 gly epitopes 653:660 arg1 plant complex-type N-glycans plant complex-type N-glycans It substantially hydrolyzed the non-reducing terminal α1,3-fucose residue on LNFP III and α1,4-fucose residues of Lea epitopes on plant complex-type N-glycans, but not the α1,2-fucose residue on LNFP I or the α1,3-fucose residue on pyridylaminated Fucα1-3GlcNAc. 28039392 4 32 gly epitopes 653:660 arg1 Lea epitopes Lea epitopes It substantially hydrolyzed the non-reducing terminal α1,3-fucose residue on LNFP III and α1,4-fucose residues of Lea epitopes on plant complex-type N-glycans, but not the α1,2-fucose residue on LNFP I or the α1,3-fucose residue on pyridylaminated Fucα1-3GlcNAc. 28039392 4 32 gly epitopes 653:660 arg1 the α1,3-fucose residue the α1,3-fucose residue It substantially hydrolyzed the non-reducing terminal α1,3-fucose residue on LNFP III and α1,4-fucose residues of Lea epitopes on plant complex-type N-glycans, but not the α1,2-fucose residue on LNFP I or the α1,3-fucose residue on pyridylaminated Fucα1-3GlcNAc. 28039392 4 32 gly epitopes 653:660 arg1 the non-reducing terminal α1,3-fucose residue the non-reducing terminal α1,3-fucose residue It substantially hydrolyzed the non-reducing terminal α1,3-fucose residue on LNFP III and α1,4-fucose residues of Lea epitopes on plant complex-type N-glycans, but not the α1,2-fucose residue on LNFP I or the α1,3-fucose residue on pyridylaminated Fucα1-3GlcNAc. 28039392 4 32 gly epitopes 653:660 arg1 the α1,2-fucose residue the α1,2-fucose residue It substantially hydrolyzed the non-reducing terminal α1,3-fucose residue on LNFP III and α1,4-fucose residues of Lea epitopes on plant complex-type N-glycans, but not the α1,2-fucose residue on LNFP I or the α1,3-fucose residue on pyridylaminated Fucα1-3GlcNAc. 28039392 4 32 gly epitopes 653:660 arg1 α1,4-fucose residues α1,4-fucose residues It substantially hydrolyzed the non-reducing terminal α1,3-fucose residue on LNFP III and α1,4-fucose residues of Lea epitopes on plant complex-type N-glycans, but not the α1,2-fucose residue on LNFP I or the α1,3-fucose residue on pyridylaminated Fucα1-3GlcNAc. 26085185 1 77 gly glycoprotein 262:273 arg1 glycoprotein markers glycoprotein markers Fterm glycoprotein Glycomics may assist in uncovering the structure-function relationships of protein glycosylation and identify glycoprotein markers in colorectal cancer (CRC) research. 26701617 3 25 gly glycosylation 464:476 arg2 glycosylation sites glycosylation sites sites The aim of this study was to identify glycosylation sites on recombinant human platelet-derived growth factor-BB (rhPDGF-BB) secreted by P. pastoris, and investigate possible effects of O-linked glycans on PDGF-BB functional activity. 25265424 6 70 gly glycopeptides 1064:1076 arg2 select glycopeptides select glycopeptides glycopeptides Core fucosylation is detectable in only trace amounts in haptoglobin but with confidence on hemopexin and complement factor H, where core fucosylation of the bi-antennary glycans on select glycopeptides reaches 15-20% intensity. 25265424 6 85 gly fucosylation 1013:1024 arg1 select glycopeptides glycopeptides select glycopeptides Site glycopeptides Core fucosylation is detectable in only trace amounts in haptoglobin but with confidence on hemopexin and complement factor H, where core fucosylation of the bi-antennary glycans on select glycopeptides reaches 15-20% intensity. 25265424 6 85 gly fucosylation 1013:1024 arg1 select glycopeptides glycopeptides the bi-antennary glycans glycopeptides Core fucosylation is detectable in only trace amounts in haptoglobin but with confidence on hemopexin and complement factor H, where core fucosylation of the bi-antennary glycans on select glycopeptides reaches 15-20% intensity. 25552259 0 31 gly site 84:87 arg1 glycophorin C N-glycans site glycophorin C N-glycans site The structures of glycophorin C N-glycans, a putative component of the GPC receptor site for Plasmodium falciparum EBA-140 ligand. 29164281 9 26 gly non-sialylated 1232:1245 arg1 non-sialylated N-glycans non-sialylated N-glycans About 100 N-glycans were identified, profiled, and structurally elucidated by nano LC/MS and tandem MS. Sialylated N-glycans were exclusively present in abundance in live rat saliva whereas non-sialylated N-glycans including LacdiNAc disaccharides were detected in high level following death. 29164281 9 26 gly non-sialylated 1232:1245 arg1 LacdiNAc disaccharides LacdiNAc disaccharides About 100 N-glycans were identified, profiled, and structurally elucidated by nano LC/MS and tandem MS. Sialylated N-glycans were exclusively present in abundance in live rat saliva whereas non-sialylated N-glycans including LacdiNAc disaccharides were detected in high level following death. 26372017 3 46 gly linked 700:705 arg3 β-glucose moieties AND C20-position C20-position β-glucose moieties position The results showed that rice seed α-glucosidase transfers α-glucosyl group from maltose to G-Rg1 by forming either α-1,3 (α-nigerosyl)-, α-1,4 (α-maltosyl)-, or α-1,6 (α-isomaltosyl)-glucosidic linkages in β-glucose moieties linked at the C6- and C20-position of protopanaxatriol (PPT)-type aglycone. 26075384 1 22 gly O-glycosylated 158:171 arg1 heavily O-glycosylated proteins heavily O-glycosylated proteins Fterm proteins BACKGROUND Mucins are heavily O-glycosylated proteins where the glycosylation has been shown to play an important role in cancer. 26077366 9 72 part_of protein 1315:1321 arg1 SER225 protein residues VAL161, PRO182 and SER225 Fterm AminoAcid protein residues VAL161, PRO182 and SER225 The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. 26077366 9 72 part_of protein 1315:1321 arg1 the protein residues VAL161, PRO182 and SER225 protein residues VAL161, PRO182 and SER225 Fterm AminoAcid protein residues VAL161, PRO182 and SER225 The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. 26077366 9 72 part_of protein 1315:1321 arg1 PRO182 protein residues VAL161, PRO182 and SER225 Fterm AminoAcid protein residues VAL161, PRO182 and SER225 The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. 26077366 9 72 part_of protein 1315:1321 arg1 the protein residues VAL161, PRO182 and SER225 protein residues VAL161, PRO182 and SER225 Fterm AminoAcid protein residues VAL161, PRO182 and SER225 The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. 26077366 9 72 part_of protein 1315:1321 arg1 PRO182 protein residues VAL161, PRO182 and SER225 Fterm AminoAcid protein residues VAL161, PRO182 and SER225 The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. 26077366 9 72 part_of protein 1315:1321 arg1 PRO182 protein residues VAL161, PRO182 and SER225 Fterm AminoAcid protein residues VAL161, PRO182 and SER225 The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. 25554420 2 54 part_of CR3 432:434 arg1 the consensus N-glycosylation sites CR3 the consensus N-glycosylation sites OGER Site CR3 sites To investigate the relative importance of the individual N-glycans of CR3 for toxin activity, the asparagine residues of the consensus N-glycosylation sites of CR3 were substituted with glutamine residues that cannot be glycosylated. 27751954 5 13 gly fucosylated 862:872 arg1 core fucosylated N-glycans core fucosylated N-glycans RESULTS Whereas the L3 N-glycome was simpler and more dominated by phosphorylcholine-modified structures, the male and female worms express a wide range of core fucosylated N-glycans with up to three fucose residues. 28714086 7 4 part_of sites 1269:1273 arg1 each subunit subunit sites Fterm Site subunit sites ABSTRACT: Ionotropic glutamate receptors (iGluRs) are tetrameric proteins with between four and 12 consensus sites for N-glycosylation on each subunit, which potentially allows for a high degree of structural diversity conferred by this post-translational modification. 28277614 7 121 gly glycopeptides 1318:1330 arg2 glycopeptides glycopeptides glycopeptides Positive mode C18-LC/ESI-MS/MS was used to identify and characterise glycopeptides found to be modified with this class of O-glycans, identifying cellobiohydrolase I as a carrier of these novel O-glycans. 28186137 4 38 gly glycoproteins 370:382 arg1 Many glycoproteins Many glycoproteins Fterm glycoproteins Many glycoproteins have been identified in myelin, and a lack of one myelin glycoprotein results in abnormal myelin structures in many cases. 28186137 4 55 gly glycoprotein 441:452 arg1 one myelin glycoprotein one myelin glycoprotein Fterm glycoprotein Many glycoproteins have been identified in myelin, and a lack of one myelin glycoprotein results in abnormal myelin structures in many cases. 25449758 4 63 part_of Hex 712:714 arg1 2 HexNAc and 3 Hex residues Hex 2 HexNAc and 3 Hex residues OGER Site Hex residues Mass spectrometric analysis of the fluorescently labeled N-glycan indicated a glycan signal composed of 2 HexNAc and 3 Hex residues. 28188786 2 94 gly N-glycosylated 380:393 arg1 N-glycosylated proteins N-glycosylated proteins Fterm proteins However, one hurdle in producing N-glycosylated proteins in large scale using E. coli is inefficient glycan glycosylation. 29016103 6 5 gly glycopeptides 816:828 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides It was found that removal of N-glycans prior to enrichment of O-linked glycopeptides by HILIC improved identification of O-linked glycopeptides by mass spectrometry. 29016103 6 69 gly glycopeptides 875:887 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides It was found that removal of N-glycans prior to enrichment of O-linked glycopeptides by HILIC improved identification of O-linked glycopeptides by mass spectrometry. 24511137 1 68 part_of IgA1 139:142 arg1 the IgA1 hinge region IgA1 the IgA1 hinge region PUBTATOR Site IgA1 P01876 region Deficient glycosylation of O-linked glycans in the IgA1 hinge region is associated with IgA nephropathy in humans, but the pathogenic contribution of the underlying structural aberrations remains incompletely understood. 28752594 2 12 gly glycoproteins 311:323 arg1 glycoproteins glycoproteins Fterm glycoproteins Specific alterations in N-glycosylation of glycoproteins are considered a key component in cancer progression, which can serve as a distinct molecular signature for cancer detection. 28752594 2 24 gly N-glycosylation 292:306 arg1 glycoproteins glycoproteins Fterm glycoproteins Specific alterations in N-glycosylation of glycoproteins are considered a key component in cancer progression, which can serve as a distinct molecular signature for cancer detection. 25995273 1 38 gly glycopeptides 140:152 arg2 intact glycopeptides intact glycopeptides glycopeptides This manuscript describes the enrichment and mass spectrometric analysis of intact glycopeptides from mouse liver, which yielded site-specific N- and O-glycosylation data for ∼ 130 proteins. 26891276 4 12 gly glycosylated 607:618 arg1 β-O-linked glycosylated variants β-O-linked glycosylated variants Fterm variants Using β-O-linked glycosylated variants of the highly studied Tau-derived hexapeptide motif VQIVYK, which served as a simplified amyloid model, we demonstrate that amyloid formation and toxicity can be strongly attenuated by a glycan unit, depending on the nature of the glycan itself. 28978918 2 53 gly asparagine 296:305 arg1 asparagine(N)297-linked glycans asparagine asparagine(N)297-linked glycans asparagine The composition of asparagine(N)297-linked glycans can modulate the binding affinity of IgG1 Fc to Fc γ receptors, but it is unclear how the structural modifications of N-glycan termini, which are distal from the binding interface, contribute to the affinity. 27489265 11 94 gly glycoprotein 1802:1813 arg1 The HIV-1 Env glycoprotein The HIV-1 Env glycoprotein Fterm glycoprotein The HIV-1 Env glycoprotein presents a dense patchwork of host cell-derived N-linked glycans. 25279697 0 7 gly glycosylation 64:76 arg1 α-dystroglycan α-dystroglycan B4GAT1 is the priming enzyme for the LARGE-dependent functional glycosylation of α-dystroglycan. 25036289 4 12 part_of Fc 454:455 arg1 the Fc effector domain Fc the Fc effector domain Cterm Site Fc domain Recent studies have indicated that the Fc effector domain also displays considerable heterogeneity, accounting for its complex effector functions of inflammation, modulation, and immune suppression. 25623399 4 51 part_of LLT1 991:994 arg1 LLT1 ectodomain LLT1 LLT1 ectodomain PUBTATOR Site LLT1 29121 ectodomain Here we report transient expression and characterization of soluble His176Cys mutant of LLT1 ectodomain in an eukaryotic expression system of human suspension-adapted HEK293S GnTI(-) cell line with uniform N-glycans. 28935113 6 89 gly glycopeptide 970:981 arg2 glycopeptide libraries glycopeptide libraries glycopeptide Recently, we reported a novel system for the directed evolution of glycopeptide libraries, which could in principle be decorated with any desired glycan. 26316330 10 38 gly glycoprotein 1430:1441 arg1 glycoprotein species glycoprotein species Fterm glycoprotein 3) The influence of production conditions for recombinant glycoproteins on glycoprotein species generation was displayed. 26316330 10 41 gly glycoproteins 1413:1425 arg1 recombinant glycoproteins recombinant glycoproteins Fterm glycoproteins 3) The influence of production conditions for recombinant glycoproteins on glycoprotein species generation was displayed. 26729242 1 31 gly glycopeptides 110:122 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides In this work O-linked glycopeptides bearing mucin core-1 type structures were enriched from human serum. 25094044 0 5 gly structure 7:15 arg1 the ER-resident glycoprotein glycoprotein structure Fterm glycoprotein Glycan structure and site of glycosylation in the ER-resident glycoprotein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferases 1 from rat, porcine, bovine, and human. 25094044 0 23 gly glycoprotein 108:119 arg1 glycoprotein glucosyltransferases 1 glycoprotein glucosyltransferases 1 Fterm glycoprotein Glycan structure and site of glycosylation in the ER-resident glycoprotein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferases 1 from rat, porcine, bovine, and human. 25094044 0 42 gly site 21:24 arg1 uridine 5'-diphosphate-glucose site uridine 5'-diphosphate-glucose site Glycan structure and site of glycosylation in the ER-resident glycoprotein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferases 1 from rat, porcine, bovine, and human. 25094044 0 10 gly glycoprotein 62:73 arg1 uridine 5'-diphosphate-glucose glycoprotein uridine 5'-diphosphate-glucose Fterm glycoprotein Glycan structure and site of glycosylation in the ER-resident glycoprotein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferases 1 from rat, porcine, bovine, and human. 25094044 0 30 gly glycoprotein 62:73 arg1 Glycan structure glycoprotein Glycan structure Fterm glycoprotein Glycan structure and site of glycosylation in the ER-resident glycoprotein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferases 1 from rat, porcine, bovine, and human. 25094044 0 36 gly glycosylation 29:41 arg1 the ER-resident glycoprotein glycoprotein site Fterm glycoprotein site Glycan structure and site of glycosylation in the ER-resident glycoprotein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferases 1 from rat, porcine, bovine, and human. 25094044 0 36 gly glycosylation 29:41 arg1 uridine 5'-diphosphate-glucose site uridine 5'-diphosphate-glucose site Glycan structure and site of glycosylation in the ER-resident glycoprotein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferases 1 from rat, porcine, bovine, and human. 25094044 0 36 gly glycosylation 29:41 arg1 uridine 5'-diphosphate-glucose glycoprotein uridine 5'-diphosphate-glucose Fterm glycoprotein Glycan structure and site of glycosylation in the ER-resident glycoprotein, uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferases 1 from rat, porcine, bovine, and human. 28487369 1 36 gly glycoproteins 126:138 arg1 highly O-glycosylated glycoproteins highly O-glycosylated glycoproteins Fterm glycoproteins Transmembrane mucins are highly O-glycosylated glycoproteins that coat the apical glycocalyx on mucosal surfaces and represent the first line of cellular defense against infection and injury. 28487369 1 42 gly O-glycosylated 111:124 arg1 highly O-glycosylated glycoproteins highly O-glycosylated glycoproteins Fterm glycoproteins Transmembrane mucins are highly O-glycosylated glycoproteins that coat the apical glycocalyx on mucosal surfaces and represent the first line of cellular defense against infection and injury. 29065342 4 5 gly glycopeptides 747:759 arg2 diverse O-linked LeX glycopeptides diverse O-linked LeX glycopeptides glycopeptides The presence of an Fmoc-threonine amino acid facilitates incorporation of the pentasaccharide in solid phase peptide synthesis, providing a route to diverse O-linked LeX glycopeptides. 25451932 7 50 gly N-glycosylation 881:895 arg2 Asn-231 Asn-231 Asn-231 Similarly, N-glycosylation at Asn-231 protected corin from autocleavage in the frizzled-1 domain. 26850169 5 14 part_of Fc 806:807 arg1 Fc regions Fc Fc regions Cterm Site Fc regions For example, Fc regions with afucosylated glycans bind more tightly to FcγRIIIa than fucosylated Fc, and afucosylated Fcs exhibit enhanced ADCC activity in vivo and in vitro. 28104755 10 36 gly Glycosylation 1497:1509 arg1 Asn356 Asn356 Asn356 Glycosylation of Asn356 in SMPDL3A, an N-linked site conserved throughout the aSMase-like family, was critical for protection against proteasomal degradation and preservation of enzymatic activity. 27604319 5 62 gly glycosylation 949:961 arg1 gp120 gp120 site PUBTATOR gp120 Q14624 site While most prior studies have focused on glycan analysis of recombinant forms of gp120, here we report the first systematic glycosylation site analysis of gp120 derived from virions produced by infected T lymphoid cells and show that a single site is exclusively substituted with complex glycans. 27780868 4 54 gly contains 618:625 arg1 A tunnel-shaped active site AND 10 glucose unit binding sites A tunnel-shaped active site 10 glucose unit binding sites site A tunnel-shaped active site rests in the CD and contains 10 glucose unit binding sites. 26082231 1 41 gly glycoproteins 161:173 arg1 glycoproteins glycoproteins Fterm glycoproteins Some of the most important and interesting molecules in metazoan biology are glycoproteins. 28486782 9 8 part_of EGF 1233:1235 arg1 the EGF binding site EGF the EGF binding site PUBTATOR Site EGF 1950 site N-glycosylation results in the formation of several noncovalent interactions between the glycans and EGFR extracellular domain near the EGF binding site. 28486782 9 30 part_of EGFR 1198:1201 arg1 EGFR extracellular domain EGFR EGFR extracellular domain PUBTATOR Site EGFR 1956 domain N-glycosylation results in the formation of several noncovalent interactions between the glycans and EGFR extracellular domain near the EGF binding site. 24161615 1 51 gly glycoproteins 293:305 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins The principal aim of this study was to demonstrate the optimization and fine-tuning of quantitative and nonselective analysis of O-linked glycans released from therapeutic glycoproteins. 24161615 1 58 gly released 267:274 arg2 therapeutic glycoproteins AND O-linked glycans therapeutic glycoproteins O-linked glycans Fterm glycoproteins The principal aim of this study was to demonstrate the optimization and fine-tuning of quantitative and nonselective analysis of O-linked glycans released from therapeutic glycoproteins. 25451932 11 33 gly sites 1403:1407 arg1 N-glycans sites N-glycans sites Together, our results show that N-glycans at different sites may play distinct roles in regulating the cell membrane targeting, zymogen activation, and ectodomain shedding of corin. 24451126 1 53 part_of IgG1 217:220 arg1 the crystallizable fragment IgG1 the crystallizable fragment OGER Site IgG1 P01857 fragment An interesting format in the development of therapeutic monoclonal antibodies uses the crystallizable fragment of IgG1 as starting scaffold. 28446609 1 17 part_of gp120 340:344 arg1 the remaining core gp120 region gp120 the remaining core gp120 region PUBTATOR Site gp120 3700 region The gp120 subunit of the HIV-1 envelope (Env) protein is heavily glycosylated at ∼25 glycosylation sites, of which ∼7-8 are located in the V1/V2 and V3 variable loops and the others in the remaining core gp120 region. 25341402 5 17 gly N-glycosylation 666:680 arg2 one conserved and one non-conserved potential N-glycosylation site one conserved and one non-conserved potential N-glycosylation site site It contains one conserved and one non-conserved potential N-glycosylation site (N-X-S/T) at the residues N95 and N198, respectively. 25341402 5 62 gly residues 704:711 arg1 N198 residues N95 and N198 residues N95 and N198 It contains one conserved and one non-conserved potential N-glycosylation site (N-X-S/T) at the residues N95 and N198, respectively. 25341402 5 62 gly residues 704:711 arg1 N95 residues N95 and N198 residues N95 and N198 It contains one conserved and one non-conserved potential N-glycosylation site (N-X-S/T) at the residues N95 and N198, respectively. 25341402 5 62 gly residues 704:711 arg1 N95 residues N95 and N198 residues N95 and N198 It contains one conserved and one non-conserved potential N-glycosylation site (N-X-S/T) at the residues N95 and N198, respectively. 26355101 6 29 gly sialylated 1130:1139 arg1 sialylated complex/hybrid type glycans sialylated complex/hybrid type glycans As Caco-2 cells differentiate to form a brush border membrane, a decrease in high mannose type glycans and a concurrent increase in fucosylated and sialylated complex/hybrid type glycans were observed. 28928219 0 68 part_of subunit 95:101 arg1 the F-box-combining site Dictyostelium Skp1 subunit the F-box-combining site PUBTATOR Site Dictyostelium Skp1 subunit 6500 site O2 sensing-associated glycosylation exposes the F-box-combining site of the Dictyostelium Skp1 subunit in E3 ubiquitin ligases. 29237727 4 23 gly N-glycopeptides 631:645 arg2 complementary and triggered fragmentation to profile Arabidopsis N-glycopeptides complementary and triggered fragmentation to profile Arabidopsis N-glycopeptides N-glycopeptides In this study, we use hydrophilic enrichment, high-resolution tandem mass spectrometry with complementary and triggered fragmentation to profile Arabidopsis N-glycopeptides from microsomal membranes of aerial tissues. 25546301 0 41 gly Asn262 104:109 arg1 the glycan Asn262 the glycan Asn262 Crystal structure of a fully glycosylated HIV-1 gp120 core reveals a stabilizing role for the glycan at Asn262. 25110774 10 24 gly glycopeptides 1964:1976 arg2 identifying and enriching low-abundant glycopeptides identifying and enriching low-abundant glycopeptides glycopeptides The results clearly demonstrated that when used in a HILIC matrix, LCD-MOFs have great potential for identifying and enriching low-abundant glycopeptides in complex biological samples. 28258464 4 99 gly glycopeptides 494:506 arg2 the glycopeptides the glycopeptides glycopeptides Secondly, a portion of the glycopeptides was treated with endoglycosidase H (Endo H) to remove high-mannose (Man) and hybrid N-linked glycans. 27773703 3 0 part_of potential 326:334 arg1 30 potential N-glycosylation sites Megalin 30 potential N-glycosylation sites PUBTATOR Site Megalin 14725 sites Megalin has 30 potential N-glycosylation sites in its extracellular domain. 27773703 3 29 part_of has 319:321 arg1 Megalin AND 30 potential N-glycosylation sites Megalin 30 potential N-glycosylation sites Fterm Site Megalin 14725 sites Megalin has 30 potential N-glycosylation sites in its extracellular domain. 25551295 8 51 part_of polypeptide 1566:1576 arg1 polypeptide residues polypeptide polypeptide residues Fterm Site polypeptide residues Two-dimensional heteronuclear single-quantum coherence spectra of the Gnt1 product, containing a single [(13)C,(15)N]GlcNAc residue on each N-glycan, showed that the N-glycan is stabilized through interactions with polypeptide residues. 27313494 9 45 gly glycosylated 1805:1816 arg1 corresponding glycosylated proteins corresponding glycosylated proteins Fterm proteins The integrated strategy described here allows detailed examination of glycomes subcellular fraction with high resolution and sensitivity, and will be useful for elucidation of the functional roles of glycans and corresponding glycosylated proteins in distinct organelles. 25110774 0 45 gly glycopeptides 24:36 arg2 glycopeptides glycopeptides glycopeptides Efficient enrichment of glycopeptides using metal-organic frameworks by hydrophilic interaction chromatography. 25406038 4 17 gly glycosylation 578:590 arg1 these regions these regions regions However, glycosylation of these regions of the MUC2 has not been extensively studied. 27506355 11 30 gly glycoprotein 1481:1492 arg1 glycoprotein datasets glycoprotein datasets Fterm glycoprotein We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. 27506355 11 60 gly glycoprotein 1365:1376 arg1 a standard glycoprotein a standard glycoprotein Fterm glycoprotein We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. 26598643 10 68 gly O-glycosylation 1632:1646 arg2 31 O-glycosylation sites 31 O-glycosylation sites sites Overall, 31 O-glycosylation sites and regions belonging to 22 proteins were identified, the majority being acute-phase proteins. 26554003 7 44 gly O-glycosylation 1442:1456 arg1 ectodomain shedding ectodomain shedding ectodomain The study provides compelling evidence for a wider role of site-specific O-glycosylation in ectodomain shedding. 26929048 4 4 gly sialylated 614:623 arg1 two sialylated disaccharides two sialylated disaccharides A more-convergent route based on the glycosylation of two sialylated disaccharides was also established to scale up the synthesis. 26929048 4 19 gly glycosylation 593:605 arg1 two sialylated disaccharides two sialylated disaccharides A more-convergent route based on the glycosylation of two sialylated disaccharides was also established to scale up the synthesis. 26929048 1 10 gly disialylated 115:126 arg1 Neu5Ac(α2,3)Gal(β1,3)[Neu5Ac(α2,6)]GlcNAc (1), which is found at the termini of some N-glycans Neu5Ac(α2,3)Gal(β1,3)[Neu5Ac(α2,6)]GlcNAc (1), which is found at the termini of some N-glycans A disialylated tetrasaccharide, Neu5Ac(α2,3)Gal(β1,3)[Neu5Ac(α2,6)]GlcNAc (1), which is found at the termini of some N-glycans, has been synthesized. 26929048 1 10 gly disialylated 115:126 arg1 A disialylated tetrasaccharide A disialylated tetrasaccharide A disialylated tetrasaccharide, Neu5Ac(α2,3)Gal(β1,3)[Neu5Ac(α2,6)]GlcNAc (1), which is found at the termini of some N-glycans, has been synthesized. 26110648 1 28 gly N-glycosylation 111:125 arg2 the potential N-glycosylation sites gp120 sites PUBTATOR gp120 3700 sites The co-evolution of the potential N-glycosylation sites of HIV Clade B gp120 was mapped onto the coevolution network of the protein structure using mean field direct coupling analysis (mfDCA). 29190644 4 28 gly attached 643:650 arg1 ASN241 AND the glycan ASN241 the glycan ASN241 From our investigation, we found that the glycan attached to ASN241 is both structurally and functionally important due to its close proximity to the BChE tetramerization domain and the active site gorge. 26335373 2 18 gly heterogeneity 260:272 arg1 glycans glycans In view of the general complexity and heterogeneity of glycans, improved depth-of-coverage and sensitivity are required for glycosylation analysis. 28381551 4 34 gly N-glycosylation 780:794 arg2 N-glycosylation sequon N-glycosylation sequon sequon In this study we found that ApNGT, a newly discovered cytoplasmic N-glycosyltransferase from Actinobacillus pleuropneumoniae, has strict selectivity toward the residues around the Asn of N-glycosylation sequon by screening a small library of synthetic peptides. 25793407 3 32 gly glycosylation 489:501 arg1 proteins proteins Fterm proteins As glucose levels can affect the pathways leading to glycosylation of proteins, we investigated whether metabolic syndrome (MS) and type 2 diabetes mellitus (T2DM), pathological conditions characterized by altered glucose levels, are associated with specific modifications in serum N-glycome. 25700513 5 2 part_of residues 585:592 arg1 Notch1 Notch1 residues PUBTATOR AminoAcid Notch1 4851 Threonine and serine residues Threonine and serine residues on Notch1 are functionalized with O-fucose and O-glucose, which act as surrogate amino acids by making specific, and essential, contacts to residues on DLL4. 25406038 2 50 part_of mucin 257:261 arg1 The protein's central mucin domain mucin The protein's central mucin domain PUBTATOR Site mucin 100508689 domain The protein's central mucin domain is highly O-glycosylated and binds water to provide lubrication and prevent dehydration, binds bacteria, and separates the bacteria from the epithelial cells. 26307003 1 62 gly enzymes 190:196 arg1 UNLABELLED Family 1 carbohydrate-binding modules enzymes UNLABELLED Family 1 carbohydrate-binding modules Fterm enzymes UNLABELLED Family 1 carbohydrate-binding modules (CBMs) are ubiquitous components of multimodular fungal enzymes that degrade plant cell wall polysaccharides and bind specifically to cellulose. 28177314 1 8 gly glycoproteins 202:214 arg1 glycoproteins glycoproteins Fterm glycoproteins The close-range interactions provided by covalently linked glycans are essential for the correct folding of glycoproteins and also play a pivotal role in recognition processes. 26239923 4 2 gly sialylated 668:677 arg1 sialylated complex/hybrid glycans sialylated complex/hybrid glycans The N-glycan microheterogeneity was established based on chemoselective glycoblotting technique with the identification of high mannose, neutral complex/hybrid and sialylated complex/hybrid glycans. 26189796 4 13 part_of E-cadherin 797:806 arg1 the four potential N-glycosylation sites E-cadherin the four potential N-glycosylation sites PUBTATOR Site E-cadherin 999 sites In vitro models further indicated that, among the four potential N-glycosylation sites of E-cadherin, Asn-554 is the key site that is selectively modified with β1,6 GlcNAc-branched N-glycans catalyzed by GnT-V. 27151270 7 48 gly contained 1012:1020 arg1 Site Asn211 AND 30 different glycans Site Asn211 30 different glycans Asn211 Site Asn211 was the most heterogeneous and contained 30 different glycans. 26479949 7 60 part_of peroxidase 1285:1294 arg1 glycopeptides peroxidase glycopeptides Fterm Site peroxidase glycopeptides The hydrophilic Fe3O4-DA-Maltose NPs were applied in isolation and enrichment of glycopeptides from horseradish peroxidase (HRP), immunoglobulin (IgG) digests. 26869352 5 21 gly glycosylation 1138:1150 arg2 all glycosylation sites all glycosylation sites sites In all cancer samples, monofucosylated N-glycans were significantly increased at all glycosylation sites. 26869352 5 65 gly monofucosylated 1076:1090 arg1 monofucosylated N-glycans monofucosylated N-glycans In all cancer samples, monofucosylated N-glycans were significantly increased at all glycosylation sites. 26554003 4 5 gly O-glycosites 968:979 arg2 O-glycosites O-glycosites O-glycosites We analyzed 25 membrane proteins that are known to undergo ADAM17 shedding and where the processing sites included Ser/Thr residues within ± 4 residues that could represent O-glycosites. 28489544 5 13 gly glycopeptides 808:820 arg2 glycopeptides glycopeptides glycopeptides The proposed approach is implemented as a software tool, GlycoNovoDB, for automated glycan structure identification from HCD MS/MS of glycopeptides. 26924641 2 89 gly glycosylation 367:379 arg1 proteins proteins Fterm proteins Among these events, it is becoming increasingly evident that changes in glycosylation of proteins, especially in the plasma and at the site of inflammation, play an important role in the inflammatory response. 28717478 3 48 part_of pp65 573:576 arg1 A peptide pp65 A peptide Cterm Site pp65 peptide A peptide from the human cytomegalovirus (CMV) tegument protein pp65 that incorporates a well-characterised T cell epitope, containing N-acetylglucosamine at specific Asn residues, was accessed by solid phase peptide synthesis, and used as an acceptor substrate. 25305020 3 30 gly residues 736:743 arg1 20-612 20-612 residues 20-612 In the present study, we purified the glycosylated extracellular domain of calcium-sensing receptor (CaSR) (ECD) (residues 20-612), containing either complex or high mannose N-glycan structures depending on the host cell line employed for recombinant expression. 25305020 3 72 gly glycosylated 660:671 arg1 calcium-sensing receptor calcium-sensing receptor domain PUBTATOR calcium-sensing receptor 846 domain In the present study, we purified the glycosylated extracellular domain of calcium-sensing receptor (CaSR) (ECD) (residues 20-612), containing either complex or high mannose N-glycan structures depending on the host cell line employed for recombinant expression. 26631508 9 35 gly disialylated 1794:1805 arg1 the extended core 2 disialylated structure the extended core 2 disialylated structure This was primarily due to the loss of the extended core 2 disialylated structure, with and without fucosylation. 24668806 5 63 part_of IgG1 529:532 arg1 fragments IgG1 fragments OGER Site IgG1 P01857 fragments We expressed fragments of IgG1 and demonstrated that EndoS was catalytically active against all of them including the isolated CH2 domain of the Fc domain. 28539451 5 34 part_of trimers 925:931 arg1 the V3 region trimers the V3 region Fterm Site trimers region Accordingly, we have assessed how to minimize the exposure of V3 non-NAb epitopes and thereby reduce their immunogenicity by introducing N-glycans within the V3 region of BG505 SOSIP trimers. 25451932 2 76 part_of has 238:240 arg1 Human corin AND 19 predicted N-glycosylation sites Human corin 19 predicted N-glycosylation sites PUBTATOR Site Human corin 10699 sites Human corin has 19 predicted N-glycosylation sites in its extracellular domains. 28314774 6 13 part_of L142 1244:1247 arg1 the L142 N-terminal domain L142 the L142 N-terminal domain Cterm Site L142 domain Using mass spectrometry and NMR analyses, we confirmed that the L142 N-terminal domain is a sugar acetyltransferase, catalyzing the transfer of an acetyl moiety from acetyl-CoA to the C-4 amino group of UDP-d-viosamine. 25883177 10 12 gly glycoproteins 1945:1957 arg1 glycoproteins glycoproteins Fterm glycoproteins Immature eggs also exhibited short O-glycan core structures only, suggesting that complex fucosylated O-glycans of schistosome eggs are derived primarily from glycoproteins produced by the subshell envelope in the developed egg. 25883177 10 93 gly derived 1922:1928 arg2 glycoproteins AND complex fucosylated O-glycans glycoproteins complex fucosylated O-glycans Fterm glycoproteins Immature eggs also exhibited short O-glycan core structures only, suggesting that complex fucosylated O-glycans of schistosome eggs are derived primarily from glycoproteins produced by the subshell envelope in the developed egg. 25883177 10 112 gly fucosylated 1876:1886 arg1 complex fucosylated O-glycans complex fucosylated O-glycans Immature eggs also exhibited short O-glycan core structures only, suggesting that complex fucosylated O-glycans of schistosome eggs are derived primarily from glycoproteins produced by the subshell envelope in the developed egg. 29162910 4 9 gly deglycosylation 866:880 arg1 these biosynthetic precursors these biosynthetic precursors Fterm precursors Following deglycosylation of these biosynthetic precursors, the resulting microbial oligosaccharides are subjected to a greatly simplified purification scheme followed by structural remodeling using commercially available and recombinantly produced glycosyltransferases including key N-acetylglucosaminyltransferases (e.g., GnTI, GnTII, and GnTIV) involved in early remodeling of glycans in the mammalian glycosylation pathway. 25253346 2 4 part_of primary 314:320 arg1 the gp120 primary receptor CD4 binding site gp120 the gp120 primary receptor CD4 binding site PUBTATOR Site gp120 3700 site Env possesses conserved antigenic determinants, such as the gp120 primary receptor CD4 binding site (CD4bs), a known neutralization target. 25253346 2 79 part_of receptor 322:329 arg1 the gp120 primary receptor CD4 binding site gp120 the gp120 primary receptor CD4 binding site PUBTATOR Site gp120 3700 site Env possesses conserved antigenic determinants, such as the gp120 primary receptor CD4 binding site (CD4bs), a known neutralization target. 25253346 2 130 part_of known 359:363 arg1 the gp120 primary receptor CD4 binding site CD4 the gp120 primary receptor CD4 binding site PUBTATOR Site CD4 920 site Env possesses conserved antigenic determinants, such as the gp120 primary receptor CD4 binding site (CD4bs), a known neutralization target. 24085030 1 76 gly Glycosylation 102:114 arg1 serum proteins serum proteins Fterm proteins AIM Glycosylation of serum proteins is affected with prolonged heavy drinking, and carbohydrate deficient transferrin (CDT) is well established and highly specific biomarker of sustained alcohol consumption. 26773038 0 22 part_of VWF 37:39 arg1 the VWF A2 domain VWF the VWF A2 domain PUBTATOR Site VWF 7450 domain N-linked glycan stabilization of the VWF A2 domain. 27873218 8 42 gly heterogeneity 1542:1554 arg1 the bikunin CS linkage region the bikunin CS linkage region region We have demonstrated a considerable heterogeneity of the bikunin CS linkage region. 28417175 3 43 gly glycoproteins 714:726 arg1 two standard glycoproteins two standard glycoproteins Fterm glycoproteins After further validation with other two standard glycoproteins (ovalbumin and bovine fetuin), the proposed strategy was applied to human serum for preliminary pathological analysis of N-glycans between healthy and lung cancer individuals. 28417175 3 43 gly glycoproteins 714:726 arg1 bovine fetuin bovine fetuin Fterm fetuin After further validation with other two standard glycoproteins (ovalbumin and bovine fetuin), the proposed strategy was applied to human serum for preliminary pathological analysis of N-glycans between healthy and lung cancer individuals. 29190644 4 9 part_of BChE 744:747 arg1 the BChE tetramerization domain BChE the BChE tetramerization domain PUBTATOR Site BChE 590 domain From our investigation, we found that the glycan attached to ASN241 is both structurally and functionally important due to its close proximity to the BChE tetramerization domain and the active site gorge. 28958711 7 22 gly termini 1143:1149 arg1 sialylation termini sialylation termini Removal of all terminal SAs has a greater effect in reversing the effect of rhiBSP on osteogenesis, especially on mineralization, suggesting that sialylation at the termini of both N-glycans and O-glycans plays an important role in this regulation. 28958711 7 63 gly sialylation 1124:1134 arg1 the termini the termini termini Removal of all terminal SAs has a greater effect in reversing the effect of rhiBSP on osteogenesis, especially on mineralization, suggesting that sialylation at the termini of both N-glycans and O-glycans plays an important role in this regulation. 28486782 0 81 gly N-glycosylation 8:22 arg1 EGFR ectodomain ligand binding EGFR ectodomain PUBTATOR EGFR 1956 ectodomain Role of N-glycosylation in EGFR ectodomain ligand binding. 27594301 4 51 gly glycoproteins 785:797 arg1 human glycoproteins human glycoproteins Fterm glycoproteins Detailed chromatographic and mass spectrometric analysis revealed afucosylated, oligomannose-type glycans, which, as a whole, displayed isomeric structures that deviate from the typical human counterparts, but whose branches were equivalent to fragments of metabolic intermediates observed in human glycoproteins. 27594301 4 60 gly afucosylated 552:563 arg1 afucosylated, oligomannose-type glycans afucosylated, oligomannose-type glycans Detailed chromatographic and mass spectrometric analysis revealed afucosylated, oligomannose-type glycans, which, as a whole, displayed isomeric structures that deviate from the typical human counterparts, but whose branches were equivalent to fragments of metabolic intermediates observed in human glycoproteins. 26773038 8 39 part_of VWF 1285:1287 arg1 the VWF A2 domain VWF the VWF A2 domain PUBTATOR Site VWF 7450 domain Substitution of the surface-exposed Y1544 to aspartic acid is able to stabilize the domain in the absence of glycosylation and protect against ADAMTS13 proteolysis in both the VWF A2 domain and FLVWF. 25451932 8 52 part_of protease 1061:1068 arg1 the protease domain protease the protease domain Fterm Site protease domain Moreover, N-glycosylation at Asn-697 in the scavenger receptor domain and at Asn-1022 in the protease domain is important for corin cell surface targeting and zymogen activation. 25406038 4 64 part_of MUC2 616:619 arg1 these regions MUC2 these regions PUBTATOR Site MUC2 Q02817 regions However, glycosylation of these regions of the MUC2 has not been extensively studied. 25110774 8 70 gly glycopeptide 1550:1561 arg2 glycopeptide enrichment glycopeptide enrichment glycopeptide In addition, the resulting LCD-MOFs demonstrated the lower detection limit (3.3 fmol) with a satisfactory recovery yield (84-103%) for glycopeptide enrichment from a digest of IgG. 25071157 1 44 part_of IgA1 284:287 arg1 the deposition IgA1 the deposition PUBTATOR Site IgA1 P01876 position Immunoglobulin A nephropathy (IgAN) is the most common form of glomerulonephritis worldwide and is histologically characterized by the deposition of IgA1 and consequent inflammation in the glomerular mesangium. 27500750 7 59 gly glycopeptides 1233:1245 arg2 glycopeptides glycopeptides subtly variable glycan structures glycopeptides This brings another attractive feature that our materials can discriminate subtly variable glycan structures of glycopeptides, especially, isomeric glycosidic linkages. 27928741 12 54 gly glycopeptide 1811:1822 arg2 a previously undocumented O-linked glycopeptide a previously undocumented O-linked glycopeptide glycopeptide In addition, a previously undocumented O-linked glycopeptide was identified from the stalk domain of the haemagglutinin-neuraminidase protein. 25188817 6 32 gly glycoproteins 958:970 arg1 the intraprotein and protein-glycan interactions glycoproteins the intraprotein and protein-glycan interactions Fterm glycoproteins These structures corroborate the simulations and also suggest a remarkable consistency between the intraprotein and protein-glycan interactions of natural glycoproteins. 26990841 6 56 gly glycoproteins 1066:1078 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins This significantly larger number of glycans than found in any other glycoanalysis of therapeutic glycoproteins is due to both the improved separation of sialylated versus asialylated species in the first (high-pH) dimension and the ability to inject large amounts of glycosylated peptides in the 2D studies. 26990841 6 62 gly glycosylated 1236:1247 arg1 glycosylated peptides glycosylated peptides peptides This significantly larger number of glycans than found in any other glycoanalysis of therapeutic glycoproteins is due to both the improved separation of sialylated versus asialylated species in the first (high-pH) dimension and the ability to inject large amounts of glycosylated peptides in the 2D studies. 27506355 0 92 gly glycopeptides 57:69 arg1 Direct glycan structure determination glycopeptides Direct glycan structure determination glycopeptides Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching. 25092234 2 90 gly N-glycosylation 306:320 arg2 N473 N473 N432 , N473 Its deficiency results in bleeding diathesis referred to as hemophilia C. hFXI bears five N-glycosylation consensus sites per monomer, N72 , N108 , N335 on the heavy chain and N432 , N473 on the light chain. 25092234 2 90 gly N-glycosylation 306:320 arg2 five N-glycosylation consensus sites five N-glycosylation consensus sites sites Its deficiency results in bleeding diathesis referred to as hemophilia C. hFXI bears five N-glycosylation consensus sites per monomer, N72 , N108 , N335 on the heavy chain and N432 , N473 on the light chain. 25092234 2 90 gly N-glycosylation 306:320 arg2 N335 N72 , N108 , N335 N72 , N108 , N335 Its deficiency results in bleeding diathesis referred to as hemophilia C. hFXI bears five N-glycosylation consensus sites per monomer, N72 , N108 , N335 on the heavy chain and N432 , N473 on the light chain. 28193043 8 64 gly glycoproteins 1818:1830 arg1 glycoproteins glycoproteins Fterm glycoproteins In summary, the HDX-MS workflow with integrated PNGase A deglycosylation enables analysis of the native HDX of protein regions containing N-linked glycan sites and should thus significantly improve our ability to study the conformational properties of glycoproteins. 28193043 8 90 gly containing 1693:1702 arg1 protein regions AND N-linked glycan sites protein regions N-linked glycan sites regions In summary, the HDX-MS workflow with integrated PNGase A deglycosylation enables analysis of the native HDX of protein regions containing N-linked glycan sites and should thus significantly improve our ability to study the conformational properties of glycoproteins. 26082218 8 54 gly proteins 1560:1567 arg1 humanized N-glycans proteins humanized N-glycans Fterm proteins The steps described in this chapter can be followed in an iterative fashion in order to generate clones of Pichia pastoris expressing heterologous proteins with humanized N-glycans. 24821760 3 58 gly glycosylation 558:570 arg2 three glycosylation sites three glycosylation sites sites Here, the effects of O-mannosylation are examined on the Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase at three glycosylation sites. 27094473 6 43 gly glycoproteins 1039:1051 arg1 mature cell wall glycoproteins mature cell wall glycoproteins Fterm glycoproteins We measured glycan structures and occupancy on mature cell wall glycoproteins, and relative protein abundance, in the different mutants. 27094473 6 87 gly structures 994:1003 arg1 mature cell wall glycoproteins glycoproteins structures Fterm glycoproteins We measured glycan structures and occupancy on mature cell wall glycoproteins, and relative protein abundance, in the different mutants. 26482026 3 68 gly glycosylated 542:553 arg1 covalently attaching native and glycosylated bilirubin oxidase covalently attaching native and glycosylated bilirubin oxidase Fterm oxidase A series of bioconjugates was constructed using two different strategies: adsorbing or covalently attaching native and glycosylated bilirubin oxidase (BOD) to GO. 28905280 2 7 gly fucose 401:406 arg1 a commercial β-galactosidase β-galactosidase fucose Fterm β-galactosidase This study employed a commercial β-galactosidase in the production of fucose-containing galacto-oligosaccharides (fGOS) from lactose and fucose. 28905280 2 32 gly β-galactosidase 297:311 arg1 fucose β-galactosidase fucose Fterm β-galactosidase This study employed a commercial β-galactosidase in the production of fucose-containing galacto-oligosaccharides (fGOS) from lactose and fucose. 28947169 7 39 gly variants 1123:1130 arg1 mannose composition variants mannose composition Fterm variants We further applied this method to measure the fucose composition of glycan engineered mouse antibodies, as well as to determine mannose composition of human antibody variants with depletion or enrichment of high mannose. 24473128 17 97 gly glycoprotein 2632:2643 arg1 glycoprotein glycosylation glycoprotein glycosylation Fterm glycoprotein Therefore, our studies provide evidence that filoviruses maintain glycoprotein glycosylation to protect against proteases and antibody neutralization at the expense of efficient entry. 26156869 7 71 gly Fc-glycosylation 1644:1659 arg2 the Fc-glycosylation site the Fc-glycosylation site site We conclude that EndoS and EndoS2 hydrolyze different glycoforms from the Fc-glycosylation site on therapeutic mAbs and that this can be used for rapid quantification of high mannose content. 26891276 5 0 gly glycosylated 973:984 arg1 the glycosylated peptides the glycosylated peptides peptides Importantly, we show for the first time that not only do glycans hinder self-aggregation, but the glycosylated peptides are capable of inhibiting aggregation of the non-modified corresponding amyloid scaffold. 27845725 2 11 part_of antithrombin-binding 302:321 arg1 the heparin antithrombin-binding domain antithrombin the heparin antithrombin-binding domain PUBTATOR Site antithrombin 462 domain Idraparinux is a synthetic anticoagulant pentasaccharide based on the heparin antithrombin-binding domain. 26114652 2 17 gly sialylated 600:609 arg1 typical neutral and sialylated glycans typical neutral and sialylated glycans For chromatography, the N-glycans were removed enzymatically from the mAbs using PNGase F. Native glycans were determined by HPAEC-PAD using a panel of 21 N-glycan standards and a multi-stage linear gradient eluent profile for sequential analyses of typical neutral and sialylated glycans in one chromatographic run. 25598335 3 1 gly glycans 458:464 arg1 recombinant proteins proteins glycans Fterm proteins This is of great value for therapeutic protein production and indispensable to determine the structure-function relationships of glycans on recombinant proteins. 28994411 0 48 gly glycosylated 38:49 arg1 a natively glycosylated HIV-1 envelope trimer a natively glycosylated HIV-1 envelope trimer Fterm trimer X-ray and EM structures of a natively glycosylated HIV-1 envelope trimer. 28745859 3 56 gly O-glycoproteins 416:430 arg1 O-glycoproteins O-glycoproteins Fterm O-glycoproteins One gap remaining in our understanding of O-glycoproteins is how O-glycans might affect the folding of proteins. 28630087 2 58 gly glycoprotein 371:382 arg1 LC-MS/MS-based glycan, glycopeptide and glycoprotein profiling LC-MS/MS-based glycan, glycopeptide and glycoprotein profiling Herein, LC-MS/MS-based glycan, glycopeptide and glycoprotein profiling were utilized to first determine the heterogeneous N-glycosylation of HNE purified from neutrophil lysates and then from isolated neutrophil granules of healthy individuals. 25036289 2 15 part_of IgGs 271:274 arg1 distinct regions IgGs distinct regions Cterm Site IgGs regions The recognition and effector responses are encoded on distinct regions of IgGs. 28277614 3 117 part_of proteins 535:542 arg1 glycopeptides proteins glycopeptides Fterm Site proteins glycopeptides METHODS O-Glycans and glycopeptides from secreted proteins were separated by porous graphitised carbon and C-18 liquid chromatography, respectively. 28752594 7 47 gly bifucosylated 1100:1112 arg1 the bifucosylated triantennary N-glycan the bifucosylated triantennary N-glycan Quantitative analyses showed that among 13 N-glycan structures, the bifucosylated triantennary N-glycan (peak10, NA3F2) presented the best diagnostic performance for distinguishing ECCA from BBD and HC. 24475074 3 0 gly glycoproteins 657:669 arg1 glycoproteins glycoproteins Fterm glycoproteins Here we ask whether the natural tension between increasing diversity (glycan-protein interactions) and site multiplicity (backup and status quo) might be revealed by a phylogenic examination of glycoproteins and NXS/T(X ≠ P) N-glycosylation sites. 24475074 3 93 gly N-glycosylation 688:702 arg2 N-glycosylation sites N-glycosylation sites sites Here we ask whether the natural tension between increasing diversity (glycan-protein interactions) and site multiplicity (backup and status quo) might be revealed by a phylogenic examination of glycoproteins and NXS/T(X ≠ P) N-glycosylation sites. 24475074 3 99 gly examination 642:652 arg1 N-glycosylation sites N-glycosylation sites sites Here we ask whether the natural tension between increasing diversity (glycan-protein interactions) and site multiplicity (backup and status quo) might be revealed by a phylogenic examination of glycoproteins and NXS/T(X ≠ P) N-glycosylation sites. 26747427 0 20 gly nonfucosylated 93:106 arg1 high-mannose or complex-type nonfucosylated N-linked oligosaccharides high-mannose or complex-type nonfucosylated N-linked oligosaccharides Comparison of biological activities of human antithrombins with high-mannose or complex-type nonfucosylated N-linked oligosaccharides. 24941220 11 107 gly glycosite 1808:1816 arg2 the O-linked glycosite the O-linked glycosite glycosite Core 1 O-linked glycan Gal1GalNAc1 was seen for the O-linked glycosite at Thr499. 27842516 2 30 gly glycosylation 295:307 arg1 the main structural protein the main structural protein Fterm protein Post-translational glycosylation of flagellin, the main structural protein of the flagellum, is a common characteristic among many Gram-negative bacteria and Archaea. 26489654 6 65 gly proteins 1117:1124 arg1 N-glycan ligand recognition proteins N-glycan ligand recognition Fterm proteins Subsequently, endocytic lectins with distinct binding specificities, including the Ashwell-Morell receptor, integrin αM, and macrophage mannose receptor, are engaged in N-glycan ligand recognition and the turnover of secreted proteins. 26765751 2 97 gly glycosylations 428:441 arg1 the Notch extracellular EGF-like domain the Notch extracellular EGF-like domain domain Notch signaling is modified by posttranslational glycosylations of the Notch extracellular EGF-like domain. 26940363 9 19 gly glycoproteins 1798:1810 arg1 mammalian glycoproteins mammalian glycoproteins Fterm glycoproteins CONCLUSIONS: Updates and improvements to UniCarbKB have introduced unique features for storing and displaying glycosylation features of mammalian glycoproteins. 27629418 10 55 gly glycoproteins 1879:1891 arg1 core-fucosylated glycoproteins core-fucosylated glycoproteins Fterm glycoproteins These findings not only give insights into the substrate recognition mechanism of glycoside hydrolase family 85 enzymes but also widen their scope of application in preparing homogeneous glycoforms of core-fucosylated glycoproteins for the production of potent glycoprotein-based therapeutics. 27629418 10 70 gly core-fucosylated 1862:1877 arg1 core-fucosylated glycoproteins core-fucosylated glycoproteins Fterm glycoproteins These findings not only give insights into the substrate recognition mechanism of glycoside hydrolase family 85 enzymes but also widen their scope of application in preparing homogeneous glycoforms of core-fucosylated glycoproteins for the production of potent glycoprotein-based therapeutics. 27629418 10 75 gly glycoforms 1848:1857 arg1 core-fucosylated glycoproteins core-fucosylated glycoproteins Fterm glycoproteins These findings not only give insights into the substrate recognition mechanism of glycoside hydrolase family 85 enzymes but also widen their scope of application in preparing homogeneous glycoforms of core-fucosylated glycoproteins for the production of potent glycoprotein-based therapeutics. 28935113 4 33 gly site 539:542 arg1 Glycan structure site Glycan structure site Glycan structure at each glycosylation site is not genetically encoded, and yeast and mammalian cells produce a heterogeneous mixture of glycoforms at each site on the protein. 28935113 4 66 gly glycosylation 525:537 arg2 each glycosylation site each glycosylation site site Glycan structure at each glycosylation site is not genetically encoded, and yeast and mammalian cells produce a heterogeneous mixture of glycoforms at each site on the protein. 28696719 3 13 gly O-glycosites 422:433 arg2 O-glycosites O-glycosites O-glycosites However, comprehensive characterization of all probable N-glycosites simultaneous with O-glycosites is still not fully revealed. 28696719 3 26 gly N-glycosites 391:402 arg2 all probable N-glycosites all probable N-glycosites N-glycosites However, comprehensive characterization of all probable N-glycosites simultaneous with O-glycosites is still not fully revealed. 24824609 12 48 part_of antithrombin 1789:1800 arg1 a new region antithrombin a new region PUBTATOR Site antithrombin 462 region Our results suggest the C-sheet of antithrombin as a new region that is relevant for proper maturation of the N-glycans. 28489325 2 12 gly glycosylation 503:515 arg2 the three glycosylation sites the three glycosylation sites sites In order to obtain the crystal structure of human L-selectin, we expressed a shortened version of L-selectin comprising the C-type lectin and EGF-like domains (termed LE) and systematically analysed mutations of the three glycosylation sites (Asn22, Asn66 and Asn139) in order to reduce macroheterogeneity. 28489325 2 52 gly sites 517:521 arg1 the three glycosylation sites the three glycosylation sites sites In order to obtain the crystal structure of human L-selectin, we expressed a shortened version of L-selectin comprising the C-type lectin and EGF-like domains (termed LE) and systematically analysed mutations of the three glycosylation sites (Asn22, Asn66 and Asn139) in order to reduce macroheterogeneity. 28489325 2 12 gly glycosylation 503:515 arg2 Asn139 Asn22, Asn66 and Asn139 Asn22, Asn66 and Asn139 In order to obtain the crystal structure of human L-selectin, we expressed a shortened version of L-selectin comprising the C-type lectin and EGF-like domains (termed LE) and systematically analysed mutations of the three glycosylation sites (Asn22, Asn66 and Asn139) in order to reduce macroheterogeneity. 28489325 2 52 gly sites 517:521 arg1 Asn66 Asn22, Asn66 and Asn139 Asn22, Asn66 and Asn139 In order to obtain the crystal structure of human L-selectin, we expressed a shortened version of L-selectin comprising the C-type lectin and EGF-like domains (termed LE) and systematically analysed mutations of the three glycosylation sites (Asn22, Asn66 and Asn139) in order to reduce macroheterogeneity. 24632452 1 0 gly glycosylation 86:98 arg1 proteins proteins Fterm proteins N-linked glycosylation of proteins is one of the most common posttranslational modifications. 29048990 10 42 gly glycosite 1711:1719 arg2 each glycosite each glycosite glycosite Our results revealed a broad glycan microheterogeneity, i.e., a great diversity of glycan compositions present on each glycosite. 29048990 10 95 gly present 1695:1701 arg2 each glycosite AND glycan compositions each glycosite glycan compositions glycosite Our results revealed a broad glycan microheterogeneity, i.e., a great diversity of glycan compositions present on each glycosite. 26603318 6 10 gly deglycosylated 1478:1491 arg1 deglycosylated proteins deglycosylated proteins Fterm proteins Reversibility experiments after thermal denaturation reveal that deglycosylated proteins tend to aggregate during thermal inactivation but the wild type shows a much greater recovery to the native state upon refolding. 25451932 10 2 gly N-Glycosylation 1248:1262 arg2 Asn-1022 Asn-1022 Asn-1022 N-Glycosylation at Asn-1022 may be switched to different sites to promote corin zymogen activation. 26940363 2 80 gly glycoproteins 560:572 arg1 single purified glycoproteins single purified glycoproteins The database comprises two levels of annotation (i) global-specific data of oligosaccharides released and characterised from single purified glycoproteins and (ii) information pertaining to site-specific glycan heterogeneity. 25452312 4 11 gly glycopeptide 331:342 arg2 glycopeptide glycopeptide glycopeptide This makes the glycopeptide analysis of exosomes important. 27791356 6 4 part_of mucin 1237:1241 arg1 the central mucin domain mucin the central mucin domain PUBTATOR Site mucin 281333 domain In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D'-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. 27791356 6 46 part_of MUC5B 1253:1257 arg1 the central mucin domain MUC5B the central mucin domain PUBTATOR Site MUC5B Q9HC84 domain In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D'-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. 27791356 6 50 part_of MUC5B 1166:1170 arg1 the Cys-domain MUC5B the Cys-domain PUBTATOR AminoAcid MUC5B Q9HC84 Cys In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D'-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. 27791356 6 91 part_of MUC5B 1110:1114 arg1 the Cys-domain MUC5B the Cys-domain PUBTATOR AminoAcid MUC5B Q9HC84 Cys In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D'-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. 27791356 6 50 part_of MUC5B 1166:1170 arg1 D4-B-C-CK domains MUC5B domains PUBTATOR Site MUC5B Q9HC84 domains In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D'-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. 27791356 6 50 part_of MUC5B 1166:1170 arg1 the N-terminal region MUC5B region PUBTATOR Site MUC5B Q9HC84 region In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D'-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. 27791356 6 91 part_of MUC5B 1110:1114 arg1 D4-B-C-CK domains MUC5B domains PUBTATOR Site MUC5B Q9HC84 domains In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D'-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. 27791356 6 91 part_of MUC5B 1110:1114 arg1 the N-terminal region MUC5B region PUBTATOR Site MUC5B Q9HC84 region In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D'-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. 28096352 4 31 gly glycosylated 1022:1033 arg1 the glycosylated residue the glycosylated residue residue The three peptidases showed selectivity for different glycans, revealing protein-specific adaptations to particular glycan modifications, yet always cleaved the peptide bond immediately preceding the glycosylated residue. 25406038 2 8 gly O-glycosylated 280:293 arg1 The protein's central mucin domain The protein's central mucin domain domain The protein's central mucin domain is highly O-glycosylated and binds water to provide lubrication and prevent dehydration, binds bacteria, and separates the bacteria from the epithelial cells. 25740940 6 58 gly found 1118:1122 arg2 other parasites AND potentially immunogenic glycan epitopes other parasites potentially immunogenic glycan epitopes parasites Thus, the N-glycans of Haemonchus contain a number of potentially immunogenic glycan epitopes also found in other parasites and our proposed structures are in line with the previously defined specificity of nematode glycosyltransferases as we show that distal fucosylation and the presence of an α1,6-mannose are apparently mutually exclusive. 25740940 6 73 gly fucosylation 1279:1290 arg1 an α1,6-mannose an α1,6-mannose Thus, the N-glycans of Haemonchus contain a number of potentially immunogenic glycan epitopes also found in other parasites and our proposed structures are in line with the previously defined specificity of nematode glycosyltransferases as we show that distal fucosylation and the presence of an α1,6-mannose are apparently mutually exclusive. 27956708 4 7 gly glycosylation 692:704 arg1 Fc and F(ab')2 fragments Fc and F(ab')2 fragments fragments The N-linked glycosylation of total, Fc and F(ab')2 fragments, as well as heavy and light chains of ACPA-IgG and control IgG were analyzed by UHPLC and MALDI-TOF mass spectrometry. 25916169 0 74 gly glycosylation 42:54 arg1 Asn211 Asn211 Asn211 Critical role of evolutionarily conserved glycosylation at Asn211 in the intracellular trafficking and activity of sialyltransferase ST3Gal-II. 25916169 0 74 gly glycosylation 42:54 arg1 sialyltransferase ST3Gal-II sialyltransferase Asn211 Fterm sialyltransferase Asn211 Critical role of evolutionarily conserved glycosylation at Asn211 in the intracellular trafficking and activity of sialyltransferase ST3Gal-II. 25916169 0 74 gly glycosylation 42:54 arg1 sialyltransferase ST3Gal-II sialyltransferase Asn211 Fterm sialyltransferase Asn211 Critical role of evolutionarily conserved glycosylation at Asn211 in the intracellular trafficking and activity of sialyltransferase ST3Gal-II. 24821760 9 59 gly glycoprotein 1533:1544 arg1 chemical glycoprotein synthesis chemical glycoprotein synthesis Fterm glycoprotein Overall, by combining chemical glycoprotein synthesis and functional studies, we show that specific glycosylation events confer multiple beneficial properties on Family 1 CBMs. 25182382 6 113 gly N-glycopeptides 1223:1237 arg2 the intact N-glycopeptides the intact N-glycopeptides N-glycopeptides The fully automated software platform integrates all of the above processes involved in the identification of the intact N-glycopeptides. 27574189 16 21 gly containing 1662:1671 arg1 immune- or clearance receptors AND carbohydrate recognition domains immune- or clearance receptors carbohydrate recognition domains Fterm receptors Overall, our findings highlight the complexity of glycan modifications on ADAMTS13, which may have implications for its interaction with immune- or clearance receptors containing carbohydrate recognition domains. 25916169 9 25 part_of containing 1371:1380 arg1 the N-terminal ST3Gal-II domain AND the cytosolic, transmembrane and stem region retain region Fterm Site retain region Lastly, we demonstrated that the N-terminal ST3Gal-II domain containing the cytosolic, transmembrane and stem region (amino acids 1-51) is able to drive a protein reporter out of the endoplasmic reticulum and to retain it in the Golgi complex. 24201825 7 24 gly proteases 1434:1442 arg1 exosite 2 exosite 2 exosite Finally, the enzymes catalytic triad organization was disrupted due to a strong glycosaminoglycan binding to the proteases exosite 2. 28314774 5 56 part_of L142 987:990 arg1 the L142 N-terminal domain L142 the L142 N-terminal domain Cterm Site L142 domain Sequence analysis of the structural model of the L142 N-terminal domain indicated significant homology with some characterized sugar acetyltransferases that modify the C-4 amino group in the bacillosamine or perosamine biosynthetic pathways. 28091715 5 40 gly glycoproteins 867:879 arg1 the glycoproteins the glycoproteins Fterm glycoproteins We developed a highly sensitive protocol using RapiFluor-MS to label glycosylamines for O-glycan analysis combined with a non-enzyme treatment for efficient release of the reduced O-glycans from the glycoproteins. 24644239 2 48 gly N-glycosylation 335:349 arg2 one N-glycosylation site one N-glycosylation site site Originally, CCL1 was identified as a 73 amino acid protein having one N-glycosylation site, and a variant 74 residue non-glycosylated form, Ser-CCL1, has also been described. 26208004 1 46 gly glycoprotein 121:132 arg1 DENV envelope glycoprotein DENV envelope glycoprotein Fterm glycoprotein DENV envelope glycoprotein (E) is responsible for interacting with host cell receptors and is the main target for the development of a dengue vaccine based on an induction of neutralizing antibodies. 25551295 5 96 gly glycoforms 867:876 arg1 the immunoglobulin G1 fragment the immunoglobulin G1 fragment fragment To address this technological gap, immature glycoforms of the immunoglobulin G1 fragment crystallizable (Fc) were isolated in a homogeneous state and enzymatically remodeled with [(13)C,(15)N]-N-acetylglucosamine (GlcNAc). 27194760 4 99 gly glycoprotein 668:679 arg1 The glycoprotein GC The glycoprotein GC Fterm glycoprotein The glycoprotein GC was mainly highly mannosylated on tick cell-derived viral progeny. 25341402 9 52 gly attached 1252:1259 arg2 the residue N95 AND only one N-glycan the residue N95 only one N-glycan N95 Site-directed mutagenesis revealed PelA has only one N-glycan attached to the residue N95. 26075384 3 58 gly glycoproteins 520:532 arg1 acidic glycoproteins acidic glycoproteins Fterm glycoproteins The cyst fluids were shown to be a rich source for acidic glycoproteins. 26316330 5 10 gly glycoproteins 619:631 arg1 two recombinant glycoproteins two recombinant glycoproteins Fterm glycoproteins In this study, we further determined the theoretical numbers of glycoprotein species of two recombinant glycoproteins - a therapeutical antibody and the human protease inhibitor alpha-1-antitrypsin (A1AT) - based on structural analysis of their N-glycans. 26316330 5 39 gly glycoprotein 579:590 arg1 glycoprotein species glycoprotein species Fterm glycoprotein In this study, we further determined the theoretical numbers of glycoprotein species of two recombinant glycoproteins - a therapeutical antibody and the human protease inhibitor alpha-1-antitrypsin (A1AT) - based on structural analysis of their N-glycans. 27696564 3 25 gly serine 786:791 arg1 residues residues threonine residues The identified glycan of mass 450.2 Da is composed of a monoacetylated nonulosonic acid (Non) with a novel extended N7 acyl modification, a 2-methoxy-4,5,6-trihydroxy-hexanoyl residue in which the Non has a pseudaminic acid configuration (L-glycero-L-manno) and is β-linked to serine or threonine residues. 28890404 4 12 gly N-glycosylated 769:782 arg2 asparagine 83 enzyme asparagine 83 Fterm enzyme asparagine 83 The gene AN7908 was cloned and transformed in A. nidulans for homologous production of AnAbf62Awt, and we confirmed that the enzyme is N-glycosylated at asparagine 83 by mass spectrometry analysis. 26082235 5 23 gly glycosylation 981:993 arg2 the glycosylation site the glycosylation site site The protocol includes the deglycosylation of a mAb by an endoglycosidase (such as wild type EndoS) to remove the heterogeneous Fc N-glycans, leaving only the innermost GlcNAc or the core-fucosylated GlcNAc at the glycosylation site. 26082235 5 44 gly core-fucosylated 950:965 arg1 the core-fucosylated GlcNAc the core-fucosylated GlcNAc The protocol includes the deglycosylation of a mAb by an endoglycosidase (such as wild type EndoS) to remove the heterogeneous Fc N-glycans, leaving only the innermost GlcNAc or the core-fucosylated GlcNAc at the glycosylation site. 27151270 3 2 gly microheterogeneity 435:452 arg1 windmill palm tree (Trachycarpus fortunei) peroxidase windmill palm tree (Trachycarpus fortunei) peroxidase Fterm peroxidase Herein, site-specific glycosylation and microheterogeneity of windmill palm tree (Trachycarpus fortunei) peroxidase are reported. 27151270 3 10 gly glycosylation 417:429 arg1 windmill palm tree (Trachycarpus fortunei) peroxidase windmill palm tree (Trachycarpus fortunei) peroxidase Fterm peroxidase Herein, site-specific glycosylation and microheterogeneity of windmill palm tree (Trachycarpus fortunei) peroxidase are reported. 29404022 9 16 gly present 1230:1236 arg1 the membrane glycoproteins AND the N-glycans the membrane glycoproteins the N-glycans Fterm glycoproteins This strategy was then used to analyze the N-glycans present on the membrane glycoproteins of gastric carcinoma cells with different degrees of differentiation. 29404022 9 39 gly glycoproteins 1254:1266 arg1 the membrane glycoproteins the membrane glycoproteins Fterm glycoproteins This strategy was then used to analyze the N-glycans present on the membrane glycoproteins of gastric carcinoma cells with different degrees of differentiation. 24533620 6 13 gly glycosylated 989:1000 arg1 glycosylated serines glycosylated serines serines At the residue level, glycans are found to introduce a bias for the formation of more extended secondary structural elements for glycosylated serines. 25737449 4 46 part_of E2 485:486 arg1 the E2 region E2 the E2 region Cterm Site E2 region Antibodies to the E2 region comprising residues 412-423 (E2(412-423)) have broadly neutralizing activities. 25437919 6 55 gly glycoproteins 919:931 arg1 the membrane glycoproteins the membrane glycoproteins Fterm glycoproteins We use a lectin capture strategy coupled to nano-ESI-RPLC-MS/MS to isolate and identify the membrane glycoproteins and unique glycan structures associated with GnT-III amplification in human ovarian cancer tissues. 26699903 1 2 gly glycoprotein 174:185 arg1 a secreted and membrane-bound glycoprotein a secreted and membrane-bound glycoprotein Fterm glycoprotein SCUBE1 (S1), a secreted and membrane-bound glycoprotein, has a modular protein structure composed of an N-terminal signal peptide sequence followed by nine epidermal growth factor (EGF)-like repeats, a spacer region and three cysteine-rich (CR) motifs with multiple potential N-linked glycosylation sites, and one CUB domain at the C-terminus. 26699903 1 70 gly glycosylation 416:428 arg2 multiple potential N-linked glycosylation sites multiple potential N-linked glycosylation sites sites SCUBE1 (S1), a secreted and membrane-bound glycoprotein, has a modular protein structure composed of an N-terminal signal peptide sequence followed by nine epidermal growth factor (EGF)-like repeats, a spacer region and three cysteine-rich (CR) motifs with multiple potential N-linked glycosylation sites, and one CUB domain at the C-terminus. 28039139 10 56 gly attachment 2084:2093 arg1 select asparagine residues AND sugars select asparagine residues sugars asparagine residues These findings suggest that H. volcanii could adapt to changes in its surroundings by modulating N-glycosylation so as to affect S-layer architecture and function.IMPORTANCE Long held to be a process unique to eukaryotes, it is now accepted that bacteria and archaea also perform N-glycosylation, namely, the covalent attachment of sugars to select asparagine residues of target proteins. 28039139 10 89 gly asparagine 2115:2124 arg1 select asparagine residues asparagine residues select asparagine residues asparagine residues These findings suggest that H. volcanii could adapt to changes in its surroundings by modulating N-glycosylation so as to affect S-layer architecture and function.IMPORTANCE Long held to be a process unique to eukaryotes, it is now accepted that bacteria and archaea also perform N-glycosylation, namely, the covalent attachment of sugars to select asparagine residues of target proteins. 28039139 10 89 gly asparagine 2115:2124 arg1 target proteins asparagine residues target proteins asparagine residues These findings suggest that H. volcanii could adapt to changes in its surroundings by modulating N-glycosylation so as to affect S-layer architecture and function.IMPORTANCE Long held to be a process unique to eukaryotes, it is now accepted that bacteria and archaea also perform N-glycosylation, namely, the covalent attachment of sugars to select asparagine residues of target proteins. 28193332 4 9 gly N-glycosylation 829:843 arg2 N-glycosylation site mutants N-glycosylation site mutants site For a better understanding of the role of N-glycosylation of AmPDH1, a systematic set of N-glycosylation site mutants was investigated in this work, regarding expression efficiency, enzyme activity and stability. 28711789 2 57 gly Glycosylation 206:218 arg1 proteins proteins Fterm proteins Glycosylation of proteins is very important post-translational modification that is involved in many physiological functions and biological pathways. 27928741 8 38 gly residues 1338:1345 arg1 433 asparagine residues 341, 433 and 481 asparagine residues 341, 433 and 481 Overall 63, 58, and 37 glycan compositions were identified at asparagine residues 341, 433 and 481, respectively. 27928741 8 38 gly residues 1338:1345 arg1 341 asparagine residues 341, 433 and 481 asparagine residues 341, 433 and 481 Overall 63, 58, and 37 glycan compositions were identified at asparagine residues 341, 433 and 481, respectively. 27928741 8 38 gly residues 1338:1345 arg1 341 asparagine residues 341, 433 and 481 asparagine residues 341, 433 and 481 Overall 63, 58, and 37 glycan compositions were identified at asparagine residues 341, 433 and 481, respectively. 27151270 8 80 gly glycosylation 1087:1099 arg2 each glycosylation site each glycosylation site site Relative quantitation revealed 90% of each glycosylation site was occupied by three or fewer glycans, and two of the 13 sites were partially unoccupied. 25462875 1 1 gly glycoprotein 191:202 arg1 glycoprotein glycans glycoprotein glycans β1,4-galactosyltransferase I (B4GALT1) is a Golgi-resident enzyme that elongates glycoprotein glycans, but a subpopulation of this enzyme is secreted following proteolytic cleavage in its stem domain. 25300029 0 16 gly structures 50:59 arg1 α3 integrin integrin structures Fterm integrin Identification of novel glycans with disialylated structures in α3 integrin from mouse kidney cells with the phenotype of polycystic kidney disease. 25300029 0 61 gly disialylated 37:48 arg1 disialylated structures disialylated structures Identification of novel glycans with disialylated structures in α3 integrin from mouse kidney cells with the phenotype of polycystic kidney disease. 24616211 3 13 gly L-asparagine 474:485 arg1 the archaeal L-asparagine linked hexasaccharide asparagine the archaeal L-asparagine linked hexasaccharide asparagine Herein the first total synthesis of the archaeal L-asparagine linked hexasaccharide from Methanothermus fervidus is reported using a highly convergent [3+3] glycosylation approach in high overall yields. 28258464 13 17 gly glycopeptide 2085:2096 arg2 each glycopeptide each glycopeptide glycopeptide We quantified the site-specific glycoforms occupancy ratios through the MS response signaling of each glycopeptide at the same time. 27052379 0 31 gly glycosylation 99:111 arg1 non-carbohydrate molecules non-carbohydrate molecules Glucansucrase Gtf180-ΔN of Lactobacillus reuteri 180: enzyme and reaction engineering for improved glycosylation of non-carbohydrate molecules. 27558752 5 80 gly N-glycoproteins 1095:1109 arg1 c. 100 stress-related N-glycoproteins c. 100 stress-related N-glycoproteins Fterm N-glycoproteins Proteome-wide analysis identified c. 100 stress-related N-glycoproteins, of which the endoplasmic reticulum (ER) resident proteins were examined to be up-regulated. 25230686 8 41 part_of GnTI 1343:1346 arg1 the transmembrane domain GnTI the transmembrane domain OGER Site GnTI P26572 domain Our results suggest that sequence-specific features in the transmembrane domain of GnTI account for its steady-state distribution in the cis/medial-Golgi in plants, which is a prerequisite for efficient N-glycan processing in vivo. 27558752 3 37 gly glycopeptides 610:622 arg2 glycopeptides glycopeptides glycopeptides We describe a highly sensitive proteomics method for large-scale identification and quantification of glycoproteins in Arabidopsis through (15) N-metabolic labeling, selective enrichment of glycopeptides, data-dependent MS/MS analysis and automated database searching. 27558752 3 58 gly glycoproteins 522:534 arg1 glycoproteins glycoproteins Fterm glycoproteins We describe a highly sensitive proteomics method for large-scale identification and quantification of glycoproteins in Arabidopsis through (15) N-metabolic labeling, selective enrichment of glycopeptides, data-dependent MS/MS analysis and automated database searching. 25117244 3 49 gly peptide 552:558 arg1 the peptide glycans the peptide glycans Bacterial cells are known to be decorated with polysaccharides, teichoic acids, and proteins in the peptide glycans of their cell wall and lipoteichoic acids in their phospholipid bilayer. 24664809 8 84 gly glycoproteins 1572:1584 arg1 simple N-glycans glycoproteins simple N-glycans Fterm glycoproteins The LC-MS/MS peptide mapping method with fully automated data analysis requires less sample preparation, provides site-specific information, and may serve as an alternative method for routine profiling of N-glycans on immunoglobulins as well as other glycoproteins with simple N-glycans. 24798328 10 27 gly glycosylation 1596:1608 arg1 three of four linker regions three of four linker regions regions This was supported by expression of LDLR in HEK293 cells, where knock-out of the GalNAc-T11 isoform resulted in the loss of glycosylation of three of four linker regions. 26059692 2 44 part_of neuropilin-1 189:200 arg1 The membrane proximal domain neuropilin-1 The membrane proximal domain PUBTATOR Site neuropilin-1 O14786 domain The membrane proximal domain of neuropilin-1, called c or MAM domain based on its sequence conservation, has been implicated in neuropilin oligomerization required for its function. 26059692 2 57 part_of MAM 215:217 arg1 c or MAM domain MAM c or MAM domain PUBTATOR Site MAM 6445 domain The membrane proximal domain of neuropilin-1, called c or MAM domain based on its sequence conservation, has been implicated in neuropilin oligomerization required for its function. 28258464 2 105 gly N-glycopeptides 350:364 arg2 intact N-glycopeptides intact N-glycopeptides N-glycopeptides In this work, we developed an analytical strategy for characterization of intact N-glycopeptides in complex proteome samples. 25048706 1 106 part_of strain 301:306 arg1 VP8* domains strain VP8* domains Fterm Site strain domains We have shown that recombinant forms of VP8* domains of the human rotavirus outer capsid spike protein VP4 from human neonatal strains (N155(G10P[11]) and RV3(G3P[6]) and a bovine strain (B223) recognize unique glycans within the repertoire of human milk glycans. 28170415 6 4 gly sialylated 747:756 arg1 fucosylated and sialylated complex glycans fucosylated and sialylated complex glycans The results revealed a high diversity of N-glycan structures, including fucosylated and sialylated complex glycans that may contribute additional bioactivities. 28170415 6 14 gly fucosylated 731:741 arg1 fucosylated and sialylated complex glycans fucosylated and sialylated complex glycans The results revealed a high diversity of N-glycan structures, including fucosylated and sialylated complex glycans that may contribute additional bioactivities. 26286102 2 97 gly glycoprotein 445:456 arg1 proper glycoprotein sialylation proper glycoprotein sialylation Previous experimental and clinical studies have shown the importance of proper glycoprotein sialylation for the synaptic function and the occurrence of autism spectrum disorders (ASD) in the presence of sialylation deficiency in the CNS. 27956708 6 82 gly sialylated 1025:1034 arg1 highly sialylated glycans highly sialylated glycans The structural analyses revealed that ACPA-IgG molecules contain highly sialylated glycans in their Fab-domain. 27956708 6 40 gly contain 1010:1016 arg1 their Fab-domain AND highly sialylated glycans their Fab-domain highly sialylated glycans Fab-domain The structural analyses revealed that ACPA-IgG molecules contain highly sialylated glycans in their Fab-domain. 27932460 5 5 gly O-mannosylated 1090:1103 arg1 the O-mannosylated peptide the O-mannosylated peptide peptide We define a POMGNT2 acceptor motif, conserved among 59 vertebrate species, in α-dystroglycan that when engineered into a POMGNT1-only site is sufficient to convert the O-mannosylated peptide to a substrate for POMGNT2. 27932460 5 20 gly motif 951:955 arg1 α-dystroglycan motif α-dystroglycan motif We define a POMGNT2 acceptor motif, conserved among 59 vertebrate species, in α-dystroglycan that when engineered into a POMGNT1-only site is sufficient to convert the O-mannosylated peptide to a substrate for POMGNT2. 24130173 2 89 gly sialylated 334:343 arg1 sialylated structures sialylated structures However, the presence and functional necessity of complex N-glycans (i.e. sialylated structures) is a challenging issue in respect to its recombinant expression. 24130173 2 89 gly sialylated 334:343 arg1 complex N-glycans complex N-glycans However, the presence and functional necessity of complex N-glycans (i.e. sialylated structures) is a challenging issue in respect to its recombinant expression. 26301455 1 52 gly N-glycosylation 214:228 arg2 four potential N-glycosylation sites four potential N-glycosylation sites sites Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 60 gly sites 230:234 arg1 four potential N-glycosylation sites four potential N-glycosylation sites sites Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 52 gly N-glycosylation 214:228 arg2 Asn388 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 52 gly N-glycosylation 214:228 arg2 Asn430 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 52 gly N-glycosylation 214:228 arg2 Asn45 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 52 gly N-glycosylation 214:228 arg2 Asn430 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 52 gly N-glycosylation 214:228 arg2 Asn45 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 52 gly N-glycosylation 214:228 arg2 Asn45 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 60 gly sites 230:234 arg1 Asn430 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 60 gly sites 230:234 arg1 Asn194 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 60 gly sites 230:234 arg1 Asn45 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 60 gly sites 230:234 arg1 Asn194 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 60 gly sites 230:234 arg1 Asn45 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 26301455 1 60 gly sites 230:234 arg1 Asn45 Asn45, Asn194, Asn388, and Asn430 Asn45, Asn194, Asn388, and Asn430 Cellobiohydrolase I from Penicillium verruculosum (PvCel7A) has four potential N-glycosylation sites at its catalytic module: Asn45, Asn194, Asn388, and Asn430. 25205566 5 39 gly glycoproteins 672:684 arg1 glycans glycoproteins glycans Fterm glycoproteins In this protocol, we describe a novel and high-throughput method for isolation and modification of glycans from glycoproteins using a chemoenzymatic approach on solid-phase. 26267136 1 44 part_of neuraminidase 127:139 arg1 the most conserved glycosylation sites neuraminidase the most conserved glycosylation sites Fterm Site neuraminidase sites One of the most conserved glycosylation sites of neuraminidase (NA) is 146-N-glycan. 27810711 5 38 gly glycopeptides 657:669 arg2 The glycopeptides The glycopeptides glycopeptides The glycopeptides presented many obstacles for post-glycosylation manipulation, peptide elongation, and deprotection. 30023556 8 64 part_of 20-mer 1226:1231 arg1 20-mer glycopeptide mer 20-mer glycopeptide OGER Site mer Q12866 glycopeptide Furthermore, 1B2 and 12D10 showed a strong binding to not only native MUC1 but also 20-mer glycopeptide with a monovalent epitope. 28193043 2 86 gly glycoproteins 427:439 arg1 glycoproteins glycoproteins Fterm glycoproteins Glycosylation covers a wide subset of modifications involving many types of complex oligosaccharide structures, making structural analysis of glycoproteins and their glycans challenging for most analytical techniques. 25113421 13 31 gly glycopeptide 1927:1938 arg2 the N-linked glycopeptide sequon the N-linked glycopeptide sequon glycopeptide sequon When only HCD spectra are available, GlycoMaster DB can still help to identify the glycans, and a list of possible peptide sequences are reported according to the accurate precursor mass and the N-linked glycopeptide sequon. 28400175 11 18 gly glycosylation 1379:1391 arg1 recombinant proteins recombinant proteins Fterm proteins Targeted glycosylation of recombinant proteins may provide an advantage in therapeutic applications. 26304114 9 59 part_of acid/base 1795:1803 arg1 the general acid/base catalytic residue acid/base the general acid/base catalytic residue Fterm Site acid/base residue On the basis of these structural observations we propose a new variation of the retaining glycoside hydrolase mechanism wherein the intervening water molecule enables a Grotthuss proton shuttle between Glu-796 and the glycosidic oxygen, permitting this residue to serve as the general acid/base catalytic residue. 25004930 1 65 gly glycosylation 165:177 arg1 the constant fragment the constant fragment fragment The N-linked glycosylation of the constant fragment (Fc) of immunoglobulin G has been shown to change during pathological and physiological events and to strongly influence antibody inflammatory properties. 27869200 3 13 gly glycopeptides 611:623 arg2 glycopeptides glycopeptides glycopeptides Here, we investigated the link between glycan structures and the intensity of oxonium ions in the spectra of glycopeptides and utilized this information to improve the identification of glycopeptides in biological samples. 27869200 3 28 gly glycopeptides 534:546 arg2 glycopeptides glycopeptides glycopeptides Here, we investigated the link between glycan structures and the intensity of oxonium ions in the spectra of glycopeptides and utilized this information to improve the identification of glycopeptides in biological samples. 25124522 0 60 gly sialylglycopeptide 52:69 arg2 sialylglycopeptide sialylglycopeptide sialylglycopeptide A simplified procedure for gram-scale production of sialylglycopeptide (SGP) from egg yolks and subsequent semi-synthesis of Man3GlcNAc oxazoline. 24509848 8 31 part_of DDR1 1279:1282 arg1 the wild-type DDR1 ectodomain DDR1 the wild-type DDR1 ectodomain PUBTATOR Site DDR1 Q08345 ectodomain The N211Q traffics to the cell surface, and its ectodomain displays collagen I binding with an affinity similar to that of the wild-type DDR1 ectodomain. 26066491 7 28 gly shorter 860:866 arg1 2-6 residues 2-6 residues residues Skin O-glycans were shorter (2-6 residues) and less diverse (33 structures) than intestinal O-glycans (2-13 residues, 93 structures). 26066491 7 29 gly O-glycans 932:940 arg1 2-13 residues 2-13 residues residues Skin O-glycans were shorter (2-6 residues) and less diverse (33 structures) than intestinal O-glycans (2-13 residues, 93 structures). 27975142 4 35 gly glycans 759:765 arg1 proteins proteins glycans Fterm proteins These 'words' are part of the glycans on proteins and lipids, and the glycome represented by these 'words' in their entirety has cell type-dependent features. 25450502 6 2 gly O-glycopeptides 1094:1108 arg2 the generated O-glycopeptides the generated O-glycopeptides O-glycopeptides MS(3) spectra of the generated O-glycopeptides showed cleavages of the peptide backbone and provided essential information on the peptide sequence. 28842505 5 42 gly glycosylated 904:915 arg1 the heavily glycosylated Notch receptor the heavily glycosylated Notch receptor Fterm receptor More specifically, we found that GnT-III expression regulates the levels and activation of the heavily glycosylated Notch receptor involved in normal and malignant development. 26439794 7 18 gly monosialo-fucosylated 1061:1081 arg1 monosialo-fucosylated biantennary oligosaccharides monosialo-fucosylated biantennary oligosaccharides The most frequently occurring forms at N-glycosylation site were high-mannose type containing nine mannose residues (M9) and monosialo-fucosylated biantennary oligosaccharides. 26439794 7 42 gly site 991:994 arg1 high-mannose type site high-mannose type site The most frequently occurring forms at N-glycosylation site were high-mannose type containing nine mannose residues (M9) and monosialo-fucosylated biantennary oligosaccharides. 26439794 7 47 gly N-glycosylation 975:989 arg2 N-glycosylation site N-glycosylation site site The most frequently occurring forms at N-glycosylation site were high-mannose type containing nine mannose residues (M9) and monosialo-fucosylated biantennary oligosaccharides. 26503433 5 30 gly nonfucosylated 865:878 arg1 their corresponding nonfucosylated forms their corresponding nonfucosylated forms The ratio of the fucosylated peaks to their corresponding nonfucosylated forms shows that the fucosylated glycans are upregulated in the case of hepatocellular carcinoma (HCC) samples versus cirrhosis samples, where the relatively low abundance bifucosylated tetra-antennary form can be detected and may be a particularly good marker for HCC. 26503433 5 31 gly bifucosylated 1052:1064 arg1 the relatively low abundance bifucosylated tetra-antennary form the relatively low abundance bifucosylated tetra-antennary form The ratio of the fucosylated peaks to their corresponding nonfucosylated forms shows that the fucosylated glycans are upregulated in the case of hepatocellular carcinoma (HCC) samples versus cirrhosis samples, where the relatively low abundance bifucosylated tetra-antennary form can be detected and may be a particularly good marker for HCC. 26503433 5 37 gly fucosylated 901:911 arg1 the fucosylated glycans the fucosylated glycans The ratio of the fucosylated peaks to their corresponding nonfucosylated forms shows that the fucosylated glycans are upregulated in the case of hepatocellular carcinoma (HCC) samples versus cirrhosis samples, where the relatively low abundance bifucosylated tetra-antennary form can be detected and may be a particularly good marker for HCC. 27928741 2 19 gly glycoproteins 280:292 arg1 oligomeric type II integral membrane proteins oligomeric type II integral membrane proteins Fterm proteins These glycoproteins are oligomeric type II integral membrane proteins, which possess haemagglutination and sialidase activity. 27928741 2 19 gly glycoproteins 280:292 arg1 These glycoproteins These glycoproteins Fterm glycoproteins These glycoproteins are oligomeric type II integral membrane proteins, which possess haemagglutination and sialidase activity. 28444691 3 27 gly undersialylated 384:398 arg1 undersialylated glycoforms apoC-III undersialylated glycoforms PUBTATOR apoC-III 345 In COG-CDG, isoelectric focusing separation of undersialylated glycoforms of serum transferrin and apolipoprotein C-III (apoC-III) allows to detect N-glycosylation and O-glycosylation defects, respectively. 28444691 3 27 gly undersialylated 384:398 arg1 serum transferrin transferrin undersialylated glycoforms OGER transferrin P02787 In COG-CDG, isoelectric focusing separation of undersialylated glycoforms of serum transferrin and apolipoprotein C-III (apoC-III) allows to detect N-glycosylation and O-glycosylation defects, respectively. 28444691 3 27 gly undersialylated 384:398 arg1 apolipoprotein C-III apolipoprotein C-III undersialylated glycoforms PUBTATOR apolipoprotein C-III 345 In COG-CDG, isoelectric focusing separation of undersialylated glycoforms of serum transferrin and apolipoprotein C-III (apoC-III) allows to detect N-glycosylation and O-glycosylation defects, respectively. 24766575 2 26 gly N-glycopeptide 410:423 arg2 high-throughput N-glycopeptide profiling high-throughput N-glycopeptide profiling N-glycopeptide Here we have developed a novel approach for high-throughput N-glycopeptide profiling based on a network-centric algorithm for deciphering glycan fragmentation in mass spectrometry. 26959726 0 16 gly glycoproteins 77:89 arg1 human blood serum glycoproteins human blood serum glycoproteins Fterm glycoproteins LC-MS/MS of permethylated N-glycans derived from model and human blood serum glycoproteins. 26321095 5 45 gly trisialylated 811:823 arg1 tri antennary trigalactosylated trisialylated glycans tri antennary trigalactosylated trisialylated glycans We identified tri antennary trigalactosylated trisialylated glycans in serum as being associated with lower levels of tumour transcripts involved in focal adhesion and integrin-mediated cell adhesion. 25251695 0 0 part_of STRUBBELIG 96:105 arg1 the misfolded extracellular domain STRUBBELIG the misfolded extracellular domain PUBTATOR Site STRUBBELIG 837654 domain A context-independent N-glycan signal targets the misfolded extracellular domain of Arabidopsis STRUBBELIG to endoplasmic-reticulum-associated degradation. 25601700 8 44 gly fucosylated 1593:1603 arg1 fucosylated side-chains fucosylated side-chains Resonant activation in the LTQ Orbitrap allowed not only determining the type of all linkages but also the O-acetyl group location on fucosylated side-chains. 27867116 9 5 gly protein 1716:1722 arg1 the glycans protein the glycans Fterm protein SIGNIFICANCE We propose a simple and high-throughput glycoproteomics-based methodology that allows the separation of glycopeptide glycoforms on the basis of the number of sialic acids, and their automatic and rapid identification without prior knowledge of protein glycosites or type and structure of the glycans. 27867116 9 35 gly glycopeptide 1576:1587 arg2 glycopeptide glycoforms glycopeptide glycoforms glycopeptide SIGNIFICANCE We propose a simple and high-throughput glycoproteomics-based methodology that allows the separation of glycopeptide glycoforms on the basis of the number of sialic acids, and their automatic and rapid identification without prior knowledge of protein glycosites or type and structure of the glycans. 27867116 9 82 gly glycoforms 1589:1598 arg1 glycopeptide glycoforms glycopeptide glycoforms glycopeptide SIGNIFICANCE We propose a simple and high-throughput glycoproteomics-based methodology that allows the separation of glycopeptide glycoforms on the basis of the number of sialic acids, and their automatic and rapid identification without prior knowledge of protein glycosites or type and structure of the glycans. 27867116 9 2 gly glycosites 1724:1733 arg1 the glycans glycosites the glycans glycosites SIGNIFICANCE We propose a simple and high-throughput glycoproteomics-based methodology that allows the separation of glycopeptide glycoforms on the basis of the number of sialic acids, and their automatic and rapid identification without prior knowledge of protein glycosites or type and structure of the glycans. 29048990 8 79 gly occupancy 1305:1313 arg2 glycosylation sites glycosylation sites sites We confirmed experimentally the occupancy of glycosylation sites identified by primary sequence analysis and determined the heterogeneity of glycan structures. 29048990 8 82 gly glycosylation 1318:1330 arg2 glycosylation sites glycosylation sites sites We confirmed experimentally the occupancy of glycosylation sites identified by primary sequence analysis and determined the heterogeneity of glycan structures. 29048990 8 103 gly heterogeneity 1397:1409 arg1 glycan structures glycan structures We confirmed experimentally the occupancy of glycosylation sites identified by primary sequence analysis and determined the heterogeneity of glycan structures. 26657071 4 11 gly aglycosylated 608:620 arg1 The purified aglycosylated enzyme The purified aglycosylated enzyme Fterm enzyme The purified aglycosylated enzyme was found to be more active than glycosylated hCES1 and analysis of enzyme kinetics revealed that both enzymes exhibit positive cooperativity. 25927005 9 22 gly glycosylation 1618:1630 arg2 the N1 and N8 glycosylation sites the N1 and N8 glycosylation sites sites The level of synthesis of HCV glycoprotein E2 in human HEK293T cells depended on the presence of glycans at the N1 and N8 glycosylation sites in contrast to Sf9 cells. 25927005 9 66 gly sites 1632:1636 arg1 glycans sites glycans sites The level of synthesis of HCV glycoprotein E2 in human HEK293T cells depended on the presence of glycans at the N1 and N8 glycosylation sites in contrast to Sf9 cells. 25927005 9 71 gly glycoprotein 1526:1537 arg1 HCV glycoprotein E2 HCV glycoprotein E2 Fterm glycoprotein The level of synthesis of HCV glycoprotein E2 in human HEK293T cells depended on the presence of glycans at the N1 and N8 glycosylation sites in contrast to Sf9 cells. 26182462 9 14 gly proteins 1443:1450 arg1 N-linked glycans proteins N-linked glycans Fterm proteins Finally, pGMAG-SiO2 was applied to the enrichment of N-linked glycans from human plasma proteins and 47 glycoforms were successfully identified after enrichment. 26701617 7 11 gly glycosylation 1217:1229 arg2 glycosylation sites glycosylation sites sites Although O-glycosylation resulted in heterogeneous protein expression, the removal of glycosylation sites did not affect rhPDGF-BB mitogenic activity. 24702330 3 29 gly glycosylation 408:420 arg2 the internal glycosylation site the internal glycosylation site site Here, we report the installation of a genetically encoded aldehyde tag at the internal glycosylation site of the crystallizable fragment (Fc) of IgG1. 24702330 3 38 gly site 422:425 arg1 a genetically encoded aldehyde tag site a genetically encoded aldehyde tag site Here, we report the installation of a genetically encoded aldehyde tag at the internal glycosylation site of the crystallizable fragment (Fc) of IgG1. 24702330 3 29 gly glycosylation 408:420 arg2 the crystallizable fragment fragment fragment Here, we report the installation of a genetically encoded aldehyde tag at the internal glycosylation site of the crystallizable fragment (Fc) of IgG1. 26056814 8 9 gly glycosylation 1544:1556 arg2 a glycosylation site a glycosylation site site The K123N mutation which introduces a glycosylation site proximal to the receptor binding site, did not impact the α2,3/α2,6 glycan selectivity, however, it lowered the overall glycan binding affinity of the HA; suggesting glycosylation may interfere with receptor binding. 25927005 4 106 gly glycosylation 502:514 arg1 the virus envelope proteins the virus envelope proteins Fterm proteins It is believed that virion properties depend on glycosylation of the virus envelope proteins in a cell, while glycansat several glycosylation sites of these proteins play a pivotal role in protein functioning and the HCV life cycle. 25927005 4 77 gly glycosylation 582:594 arg1 these proteins proteins sites Fterm proteins sites It is believed that virion properties depend on glycosylation of the virus envelope proteins in a cell, while glycansat several glycosylation sites of these proteins play a pivotal role in protein functioning and the HCV life cycle. 27489265 13 89 gly glycans 2024:2030 arg1 specific positions specific positions While the positions of many N-linked glycans are isolate specific, some are highly conserved and are believed to play key functional roles. 25552259 1 49 gly glycosylated 163:174 arg1 highly glycosylated integral sialoglycoproteins highly glycosylated integral sialoglycoproteins Fterm sialoglycoproteins Glycophorins C and D are highly glycosylated integral sialoglycoproteins of human red blood cell membranes carrying the Gerbich blood group antigens. 25552259 1 52 gly sialoglycoproteins 185:202 arg1 highly glycosylated integral sialoglycoproteins highly glycosylated integral sialoglycoproteins Fterm sialoglycoproteins Glycophorins C and D are highly glycosylated integral sialoglycoproteins of human red blood cell membranes carrying the Gerbich blood group antigens. 26307003 3 7 gly attached 702:709 arg2 both Thr1 AND a mannose group both Thr1 a mannose group Thr1 and Ser3 To gain molecular insights into the changes in CBM properties upon glycosylation, solution structures of two glycoforms of a Trichoderma reesei family 1 CBM were studied by NMR spectroscopy: a glycosylated family 1 CBM with a mannose group attached to both Thr1 and Ser3 and a second family 1 CBM with single mannose groups attached to Thr1, Ser3 and Ser14. 26307003 3 95 gly attached 786:793 arg1 Thr1 AND single mannose groups Thr1, Ser3 and Ser14 single mannose groups Thr1, Ser3 and Ser14 To gain molecular insights into the changes in CBM properties upon glycosylation, solution structures of two glycoforms of a Trichoderma reesei family 1 CBM were studied by NMR spectroscopy: a glycosylated family 1 CBM with a mannose group attached to both Thr1 and Ser3 and a second family 1 CBM with single mannose groups attached to Thr1, Ser3 and Ser14. 26307003 3 95 gly attached 786:793 arg1 Ser3 AND single mannose groups Thr1, Ser3 and Ser14 single mannose groups Thr1, Ser3 and Ser14 To gain molecular insights into the changes in CBM properties upon glycosylation, solution structures of two glycoforms of a Trichoderma reesei family 1 CBM were studied by NMR spectroscopy: a glycosylated family 1 CBM with a mannose group attached to both Thr1 and Ser3 and a second family 1 CBM with single mannose groups attached to Thr1, Ser3 and Ser14. 26307003 3 95 gly attached 786:793 arg1 Ser3 AND single mannose groups Thr1, Ser3 and Ser14 single mannose groups Thr1, Ser3 and Ser14 To gain molecular insights into the changes in CBM properties upon glycosylation, solution structures of two glycoforms of a Trichoderma reesei family 1 CBM were studied by NMR spectroscopy: a glycosylated family 1 CBM with a mannose group attached to both Thr1 and Ser3 and a second family 1 CBM with single mannose groups attached to Thr1, Ser3 and Ser14. 26784534 6 12 gly structures 708:717 arg1 all glycosylation sites all glycosylation sites all glycosylation sites Site sites The majority of the glycan structures on all glycosylation sites is represented by disialyl core 1 O-glycan. 26784534 6 45 gly glycosylation 726:738 arg2 all glycosylation sites all glycosylation sites sites The majority of the glycan structures on all glycosylation sites is represented by disialyl core 1 O-glycan. 28378791 4 36 gly attached 496:503 arg1 residue GluN1-N440 AND the glycan residue GluN1-N440 the glycan residue Our simulations predict that intra-domain interactions involving the glycan attached to residue GluN1-N440 stabilize closed-clamshell conformations of the GluN1 LBD. 28231413 4 27 gly glycoprotein 842:853 arg1 glycoprotein glycoprotein Fterm glycoprotein For example, they are incorporated substoichiometrically into glycans, and most MCRs are not selective for one class (e.g., O-GlcNAcylation) of glycoprotein. 28193843 6 78 part_of containing 866:875 arg1 domain A AND the catalytic site domain A the catalytic site Cterm Site domain A site The enzyme consists of four domains, including domain N, carbohydrate-binding module family 48 (CBM48), domain A containing the catalytic site, and domain C. 26257376 2 29 gly level 618:622 arg1 a 2-deoxy motif a 2-deoxy motif a 2-deoxy motif Site motif For the introduction of the 2'- and 2"-deoxy motifs the most efficient way was to use a 1,2-di-bromo-mannosyl donor in silver triflate-promoted couplings to construct the α-glycosidic linkage followed by reduction of the 2-bromo-function to a 2-deoxy motif at the di- or trisaccharide level. 24440233 10 93 gly glycoproteins 1852:1864 arg1 glycoproteins glycoproteins Fterm glycoproteins This approach provided concurrent characterization of both the peptide and the glycan, thereby enabling comprehensive structural characterization of glycoproteins in a single LC-MS/MS analysis. 24692304 4 48 gly glycosylated 723:734 arg1 the glycosylated L-protein the glycosylated L-protein Fterm L-protein Facile crystal formation occurred from a quasi-racemic mixture consisting of glycosylated L-protein and non-glycosylated-D-protein, while no crystals were obtained from the glycosylated L-protein alone. 24692304 4 54 gly glycosylated 627:638 arg1 L-protein L-protein Fterm L-protein Facile crystal formation occurred from a quasi-racemic mixture consisting of glycosylated L-protein and non-glycosylated-D-protein, while no crystals were obtained from the glycosylated L-protein alone. 25016576 0 15 part_of protein 120:126 arg1 the V1/V2 domain envelope protein the V1/V2 domain PUBTATOR Site envelope protein 100616444 domain Characterization of a monoclonal antibody to a novel glycan-dependent epitope in the V1/V2 domain of the HIV-1 envelope protein, gp120. 24308457 5 52 gly receptors 1115:1123 arg1 the sialylation receptors the sialylation Fterm receptors We demonstrated the capability of this cis-membrane FRET imaging method by visualizing the sialylation of several important cell surface receptors including integrin αXβ2, epidermal growth factor receptor, and transforming growth factor-beta receptor type I. Furthermore, our imaging experiments revealed that the sialylation might be important for β2 integrin activation. 24308457 5 61 gly sialylation 1292:1302 arg1 β2 integrin activation β2 integrin activation Fterm integrin We demonstrated the capability of this cis-membrane FRET imaging method by visualizing the sialylation of several important cell surface receptors including integrin αXβ2, epidermal growth factor receptor, and transforming growth factor-beta receptor type I. Furthermore, our imaging experiments revealed that the sialylation might be important for β2 integrin activation. 24308457 5 67 gly sialylation 1069:1079 arg1 several important cell surface receptors several important cell surface receptors Fterm receptors We demonstrated the capability of this cis-membrane FRET imaging method by visualizing the sialylation of several important cell surface receptors including integrin αXβ2, epidermal growth factor receptor, and transforming growth factor-beta receptor type I. Furthermore, our imaging experiments revealed that the sialylation might be important for β2 integrin activation. 24854630 2 36 gly glycoprotein 402:413 arg1 glycoprotein synthetic enzymes glycoprotein synthetic enzymes Fterm glycoprotein We hypothesized that altered glycosylation could be related to differences in gene expression levels of glycoprotein synthetic enzymes between normal and malignant prostate tissues. 28277614 2 61 gly N-glycosylation 334:348 arg1 secreted proteins secreted proteins Fterm proteins The N-glycosylation of secreted proteins of RUT-C30 is known to vary depending on culture nutrients but O-glycosylation has been less extensively studied. 28837324 1 50 gly glycoproteins 236:248 arg1 glycoproteins glycoproteins Fterm glycoproteins Pseudaminic acid (Pse) is a nonulosonic acid unique to bacterial species, found as a component of important cell surface glycans and glycoproteins in various pathogenic species, such as the critical hospital threat Pseudomonas aeruginosa. 27038031 8 43 gly glycosylation 1119:1131 arg2 Asn563 Asn563 Asn563 Asn563, a high mannose-rich glycosylation site that locates in the center of the IgM polymer, was only approximately 60% occupied in both the pentameric and hexameric IgM forms, with a difference in relative abundance of the glycan structures between the pentamer and hexamer. 26439794 5 45 part_of glycoproteins 821:833 arg1 63 sites glycoproteins 63 sites Fterm Site glycoproteins sites The glycoproteomic approach to the human fetal lung fibroblasts membrane fraction resulted in the identification of over 272 glycoforms on 63 sites of the 44 glycoproteins. 28264742 6 19 gly fucosylated 1455:1465 arg1 α1,2-linked fucosylated oligosaccharides α1,2-linked fucosylated oligosaccharides Both MPS and NMPS microarrays reacted with all the lectins and revealed that the expression of (i) O-glycans with NeuNAcα2-3Galβ1,3(±NeuNAcα2-6)GalNAc, Galβ1,3GalNAc and GalNAcα1,3(l-Fucα1,2)Galβ1,3/4GlcNAcβ1 was not season dependent; (ii) O-linked glycans terminating with GalNAc, asialo N-linked glycans terminating with Galβ1,4GlcNAc, GlcNAc, as well as α1,6 and α1,2-linked fucosylated oligosaccharides was predominant in MPS; (iii) high mannose- and biantennary complex types N-glycans terminating with α2,6 sialic acids and terminal galactose were lower in MPS. 24616211 0 18 gly asparagine-linked 22:38 arg1 asparagine-linked archaeal N-glycan asparagine asparagine-linked archaeal N-glycan asparagine Chemical synthesis of asparagine-linked archaeal N-glycan from Methanothermus fervidus. 27209430 1 3 gly glycoproteins 189:201 arg1 serum glycoproteins serum glycoproteins Fterm glycoproteins BACKGROUND Nearly all secreted proteins are glycosylated, and serum glycoproteins that exhibit disease-associated glycosylation changes have potential to be biomarkers. 27209430 1 20 gly glycosylated 165:176 arg1 Nearly all secreted proteins Nearly all secreted proteins Fterm proteins BACKGROUND Nearly all secreted proteins are glycosylated, and serum glycoproteins that exhibit disease-associated glycosylation changes have potential to be biomarkers. 27751954 7 50 gly fucosylated 1110:1120 arg1 the fucosylated paucimannosidic glycans the fucosylated paucimannosidic glycans On the other hand, while many of the fucosylated paucimannosidic glycans are identical with examples from other nematode species, but simpler than the tetrafucosylated glycans of C. elegans, there is a wide range of phosphorylcholine-modified glycans with extended HexNAc2-4PC2-4 motifs not observed in our previous studies on other nematodes. 27751954 7 92 gly tetrafucosylated 1224:1239 arg1 the tetrafucosylated glycans the tetrafucosylated glycans On the other hand, while many of the fucosylated paucimannosidic glycans are identical with examples from other nematode species, but simpler than the tetrafucosylated glycans of C. elegans, there is a wide range of phosphorylcholine-modified glycans with extended HexNAc2-4PC2-4 motifs not observed in our previous studies on other nematodes. 28975713 2 63 gly glycopeptide 348:359 arg2 a theoretical glycopeptide dataset a theoretical glycopeptide dataset glycopeptide EXPERIMENTAL DESIGN This exploratory tool uses a theoretical glycopeptide dataset to visualize all peptide-glycan combinations that fall within the error range of the query precursor ion. 25927005 7 15 gly N-glycosylation 1040:1054 arg1 HCV protein E2 E2 sites Cterm E2 sites In order to investigate these processes, point mutations of the N-glycosylation sites of HCV protein E2 (genotype 1b strain 274933RU) were generated and the mutant proteins were further analyzed in the baculovirus expression system. 28966766 5 28 gly glycosylation 971:983 arg2 the glycosylation site the glycosylation site site Going forward, this study suggests the possibility of designing proteins with multiple improved properties by simultaneously varying the structures of O-glycans and amino acids local to the glycosylation site. 25231986 8 68 part_of precursor 1554:1562 arg1 ∼10-12 mannosyl residues precursor ∼10-12 mannosyl residues Fterm Site precursor residues Analysis of the number of arabinans attached to the mannan core of LM in two other mutants (ΔembC and ΔMSMEG_4247) demonstrated exactly one arabinosyl substitution of the mannan core suggestive of the arabinosylation of a linear LM precursor with ∼10-12 mannosyl residues followed by additional mannosylation of the core and arabinosylation of a single arabinosyl "primer." 28800497 4 40 gly core-fucosylated 702:717 arg1 core-fucosylated trisaccharide core-fucosylated trisaccharide An affinity chromatography column stuffed with the agarose beads carrying core-fucosylated trisaccharide exhibited a good specificity in purification of AAL than non-fucose disaccharide agarose beads. 27818199 10 64 gly glycosylation 1433:1445 arg1 the asparagine the asparagine asparagine Finally, to determine whether glycosylation of the asparagine proximal to the Pro1199-Leu polymorphism in sACE affected shedding, the equivalent P623L mutation in tACE was investigated. 25188817 1 44 gly Asparagine-linked 36:52 arg1 Asparagine-linked carbohydrates Asparagine Asparagine-linked carbohydrates Asparagine Asparagine-linked carbohydrates profoundly impact glycoprotein folding, stability, and structure. 25188817 1 46 gly glycoprotein 86:97 arg1 impact glycoprotein folding impact glycoprotein folding Fterm glycoprotein Asparagine-linked carbohydrates profoundly impact glycoprotein folding, stability, and structure. 26599081 0 56 gly Glycosylation 23:35 arg1 Exogenous Oligosaccharide Lipoproteins Exogenous Oligosaccharide Fterm Lipoproteins General N-and O-Linked Glycosylation of Lipoproteins in Mycoplasmas and Role of Exogenous Oligosaccharide. 24803430 6 8 part_of Notch 1418:1422 arg1 other regions Notch other regions PUBTATOR Site Notch 4851 regions We propose that this finding explains the Fringe-catalyzed enhancement of Notch-Delta signaling observed in flies and humans, but suggest that the inhibitory effect of Fringe on Jagged/Serrate mediated signaling involves other regions of Notch. 28818784 2 38 gly glycoprotein 224:235 arg1 glycoprotein glycoprotein Fterm glycoprotein The glycosylated complex of glycoprotein was used as template to construct a glycosyl imprinted sensor. 26925665 9 90 gly glycoproteins 1690:1702 arg1 disease-related glycoproteins disease-related glycoproteins Fterm glycoproteins Our structural analyses of glycans may provide important information regarding physiology of disease-related glycoproteins in CCA. 26482295 7 22 part_of sequon 1406:1411 arg1 human immunoglobulin G human immunoglobulin G sequon Cterm Site human immunoglobulin G sequon One notable example is D. gigas PglB, which was the only bacterial OST to glycosylate the Fc domain of human immunoglobulin G at its native 'QYNST' sequon. 26482295 7 22 part_of sequon 1406:1411 arg1 the Fc domain sequon the Fc domain domain One notable example is D. gigas PglB, which was the only bacterial OST to glycosylate the Fc domain of human immunoglobulin G at its native 'QYNST' sequon. 26482295 7 26 part_of G 1382:1382 arg1 the Fc domain human immunoglobulin G the Fc domain Cterm Site human immunoglobulin G domain One notable example is D. gigas PglB, which was the only bacterial OST to glycosylate the Fc domain of human immunoglobulin G at its native 'QYNST' sequon. 26482295 7 36 part_of domain 1351:1356 arg1 its native 'QYNST' sequon domain its native 'QYNST' sequon sequon One notable example is D. gigas PglB, which was the only bacterial OST to glycosylate the Fc domain of human immunoglobulin G at its native 'QYNST' sequon. 26993603 3 7 part_of GP73 560:563 arg1 three GP73 N-glycosylation sites GP73 three GP73 N-glycosylation sites PUBTATOR Site GP73 51280 sites We identified three GP73 N-glycosylation sites: Asn109, Asn144 and Asn398. 25341402 0 20 gly N-glycosylation 119:133 arg2 the highly conserved N-glycosylation site the highly conserved N-glycosylation site site Biochemical characteristics of an alkaline pectate lyase PelA from Volvariella volvacea: roles of the highly conserved N-glycosylation site in its secretion and activity. 28188786 4 4 part_of fibronectin 631:641 arg1 The 10th human fibronectin type III domain fibronectin The 10th human fibronectin type III domain PUBTATOR Site fibronectin 2335 domain The 10th human fibronectin type III domain (FN3) was engineered with native glycosylation sequon DFNRSK and optimized DQNAT sequon in C-terminus with flexible linker as acceptor protein models. 28188786 4 4 part_of fibronectin 631:641 arg1 DQNAT sequon fibronectin DQNAT sequon PUBTATOR Site fibronectin 2335 sequon The 10th human fibronectin type III domain (FN3) was engineered with native glycosylation sequon DFNRSK and optimized DQNAT sequon in C-terminus with flexible linker as acceptor protein models. 28188786 4 81 part_of protein 794:800 arg1 The 10th human fibronectin type III domain protein The 10th human fibronectin type III domain Fterm Site protein domain The 10th human fibronectin type III domain (FN3) was engineered with native glycosylation sequon DFNRSK and optimized DQNAT sequon in C-terminus with flexible linker as acceptor protein models. 28188786 4 81 part_of protein 794:800 arg1 DQNAT sequon protein DQNAT sequon Fterm Site protein sequon The 10th human fibronectin type III domain (FN3) was engineered with native glycosylation sequon DFNRSK and optimized DQNAT sequon in C-terminus with flexible linker as acceptor protein models. 28482115 4 1 gly sites 889:893 arg1 a highly conserved N-glycan sites a highly conserved N-glycan sites The activity of FLA4 was resistant against deletion of the amino-proximal fasciclin 1 domain and was unaffected by removal of the GPI-modification signal, a highly conserved N-glycan or the deletion of predicted O-glycosylation sites. 28482115 4 16 gly O-glycosylation 873:887 arg2 predicted O-glycosylation sites predicted O-glycosylation sites sites The activity of FLA4 was resistant against deletion of the amino-proximal fasciclin 1 domain and was unaffected by removal of the GPI-modification signal, a highly conserved N-glycan or the deletion of predicted O-glycosylation sites. 27638310 0 44 part_of GM-CSF 57:62 arg1 O-glycosylation sites GM-CSF O-glycosylation sites PUBTATOR Site GM-CSF 1437 sites O-glycans and O-glycosylation sites of recombinant human GM-CSF derived from suspension-cultured rice cells, and their structural role. 25452312 9 37 gly N-glycopeptides 1046:1060 arg2 the N-glycopeptides the N-glycopeptides N-glycopeptides Here, we have enriched and identified the N-glycopeptides from these vesicles. 27604319 4 63 gly glycopeptide 774:785 arg2 glycopeptide antigens glycopeptide antigens glycopeptide Knowing the site-specific glycosylation of gp120 can facilitate the rational design of glycopeptide antigens for HIV vaccine development. 25660649 9 105 gly glycosylated 1392:1403 arg1 both asparagine residues 67 and 153 both asparagine residues 67 and 153 asparagine residues 67 and 153 Site-specific N-glycosylation analysis of CYDs using nanoLC-ESI-MS/MS demonstrates that both asparagine residues 67 and 153 are glycosylated. 27732771 10 8 gly asialoglycoprotein 1295:1312 arg1 asialoglycoprotein receptor asialoglycoprotein receptor Fterm asialoglycoprotein In vivo clearance of these glycoforms was then assessed in VWF-/- mice in the presence or absence of inhibitors of asialoglycoprotein receptor (ASGPR), or following clodronate-induced macrophage depletion. 27223297 8 18 gly N-glycosylated 1104:1117 arg1 Gc N1077 Gc N1077 N1077 Gc N1077 was heterogeneously N-glycosylated. 25978763 5 22 part_of Y1 1007:1008 arg1 the normal Y1 fragment Y1 the normal Y1 fragment Cterm Site Y1 fragment However, the carbamidomethylation of Met residues leads to sulfonium ether formation, and the resulting fixed positive charge triggers a characteristic fragmentation, that eliminates the normal Y1 fragment from the HCD spectra of N-linked glycopeptides, producing an abundant Y1-48 Da ion instead (the nominal mass difference is given relative to the unmodified amino acid sequence), that easily can be mistaken for the side chain loss from Met sulfoxide. 25883177 5 122 gly multifucosylated 1135:1150 arg1 mono- and multifucosylated LDN-motifs mono- and multifucosylated LDN-motifs LeX-motifs were present on glycolipids up to 2 weeks of schistosomula development, whereas glycolipids with mono- and multifucosylated LDN-motifs remained present up to the adult worm stage. 25092234 4 24 gly A2 740:741 arg1 complex biantennary mono-α2,6-sialylated (A2 S1 , 20%) and bis-α2,6-sialylated structures A2-S2 complex biantennary mono-α2,6-sialylated (A2 S1 , 20%) and bis-α2,6-sialylated structures A2-S2 Hydrophilic interaction LC and MS characterization and quantification of the N-glycans showed that the two major forms are complex biantennary mono-α2,6-sialylated (A2 S1 , 20%) and bis-α2,6-sialylated structures (A2 S2 , 66%). 25092234 4 15 gly mono-α2,6-sialylated 669:688 arg1 A2 S2 A2-S2 complex biantennary mono-α2,6-sialylated (A2 S1 , 20%) and bis-α2,6-sialylated structures A2-S2 Hydrophilic interaction LC and MS characterization and quantification of the N-glycans showed that the two major forms are complex biantennary mono-α2,6-sialylated (A2 S1 , 20%) and bis-α2,6-sialylated structures (A2 S2 , 66%). 25092234 4 66 gly bis-α2,6-sialylated 708:726 arg1 A2 S2 A2-S2 complex biantennary mono-α2,6-sialylated (A2 S1 , 20%) and bis-α2,6-sialylated structures A2-S2 Hydrophilic interaction LC and MS characterization and quantification of the N-glycans showed that the two major forms are complex biantennary mono-α2,6-sialylated (A2 S1 , 20%) and bis-α2,6-sialylated structures (A2 S2 , 66%). 25748215 0 43 gly N-glycosylation 11:25 arg1 protein conformation protein conformation Fterm protein Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study. 27714557 1 29 gly glycoproteins 258:270 arg1 N-linked oligosaccharide chains glycoproteins N-linked oligosaccharide chains Fterm glycoproteins OBJECTIVES To establish an efficient method of chemoenzymatic modification for making N-linked oligosaccharide chains of glycoproteins structurally homogeneous, which crucially affects their bioactivities. 25737449 0 28 gly glycoprotein 78:89 arg1 hepatitis C virus E2 glycoprotein glycoprotein the glycan shield Fterm glycoprotein Structural basis for penetration of the glycan shield of hepatitis C virus E2 glycoprotein by a broadly neutralizing human antibody. 24798328 5 49 part_of sites 718:722 arg1 recombinant LDLR LDLR sites PUBTATOR Site LDLR 3949 sites Herein, we have systematically characterized O-glycosylation sites on recombinant LDLR shed from HEK293 SimpleCells and CHO wild-type cells. 27506355 8 40 gly glycopeptides 922:934 arg2 intact glycopeptides intact glycopeptides glycopeptides Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. 26791533 5 12 gly glycoproteins 717:729 arg1 the glycoproteins the glycoproteins Fterm glycoproteins This analysis provides identification of the glycoproteins, glycosylation sites, glycan compositions, and proposed structures from the original sample. 26791533 5 41 gly glycosylation 732:744 arg2 glycosylation sites glycosylation sites sites This analysis provides identification of the glycoproteins, glycosylation sites, glycan compositions, and proposed structures from the original sample. 27722232 5 43 gly sialylated 1130:1139 arg1 labile sialylated glycans labile sialylated glycans Abundant generation of diagnostic glycosidic (Y-, and B-type ions) and cross-ring cleavage (A-type ions) ions permits unambiguous determination of the composition, sequence, branching, and linkage of labile sialylated glycans. 27743354 3 42 gly glycosylation 313:325 arg1 proteins proteins Fterm proteins This chapter describes the effect of glycosylation on the structure and function of proteins, with emphasis on regulation of protein half-life and modulation of protein function by alternative glycosylation. 26231935 3 48 part_of AChE 598:601 arg1 wild-type human AChE(T) sequence AChE wild-type human AChE(T) sequence PUBTATOR Site AChE 43 sequence In order to determine the role of three N-glycosylation sites in AChE activity and glycan composition, the site-directed mutagenesis of N-glycosylation sites in wild-type human AChE(T) sequence was employed to generate the single-site mutants (i.e., AChE(T) (N296Q), AChET (N381Q), and AChE(T) (N495Q)) and all site mutant (i.e., AChE(T) (3N→3Q)). 26231935 3 70 part_of T 603:603 arg1 wild-type human AChE(T) sequence T wild-type human AChE(T) sequence Cterm Site T 43 sequence In order to determine the role of three N-glycosylation sites in AChE activity and glycan composition, the site-directed mutagenesis of N-glycosylation sites in wild-type human AChE(T) sequence was employed to generate the single-site mutants (i.e., AChE(T) (N296Q), AChET (N381Q), and AChE(T) (N495Q)) and all site mutant (i.e., AChE(T) (3N→3Q)). 29069609 11 18 gly glycopeptides 1848:1860 arg2 glycopeptides glycopeptides glycopeptides The novelty is that this approach does not require glycan composition to be pre-defined, thereby allowing glycopeptides carrying unexpected glycans to be identified. 29069609 11 66 gly carrying 1862:1869 arg1 glycopeptides AND unexpected glycans glycopeptides unexpected glycans glycopeptides The novelty is that this approach does not require glycan composition to be pre-defined, thereby allowing glycopeptides carrying unexpected glycans to be identified. 27283789 2 6 gly glycoprotein 347:358 arg1 'N-glycosylated' glycoprotein mimics 'N-glycosylated' glycoprotein mimics Fterm glycoprotein We present a novel glycodendron prosthetic which can be site-selectively appended to recombinant proteins to create 'N-glycosylated' glycoprotein mimics. 24326091 9 80 gly glycosylated 2010:2021 arg1 5-carboxyfluorescein labeled high mannose glycosylated asparagine 5-carboxyfluorescein labeled high mannose glycosylated asparagine asparagine As an example of a biochemical study using functionalized high mannose glycosylated asparagine, a fluorescence polarization assay has been utilized to study the binding of the lectin Concanavalin A (ConA) using 5-carboxyfluorescein labeled high mannose glycosylated asparagine. 24326091 9 83 gly glycosylated 1828:1839 arg1 functionalized high mannose glycosylated asparagine functionalized high mannose glycosylated asparagine asparagine As an example of a biochemical study using functionalized high mannose glycosylated asparagine, a fluorescence polarization assay has been utilized to study the binding of the lectin Concanavalin A (ConA) using 5-carboxyfluorescein labeled high mannose glycosylated asparagine. 28711789 4 66 gly N-glycoproteins 580:594 arg1 N-glycoproteins N-glycoproteins Fterm N-glycoproteins Quantification of N-glycoproteins was performed using MaxQuant with a label free quantification approach. 24473128 1 98 gly glycoprotein 138:149 arg1 the virion surface-associated glycoprotein the virion surface-associated glycoprotein Fterm glycoprotein Ebola virus (EBOV) entry requires the virion surface-associated glycoprotein (GP) that is composed of a trimer of heterodimers (GP1/GP2). 26083631 0 0 gly Glycan 12:17 arg1 the C2 Domain Domain Glycan Fterm Domain A Conserved Glycan in the C2 Domain of HIV-1 Envelope Acts as a Molecular Switch to Control X4 Utilization by Clonal Variants with Identical V3 Loops. 25251695 4 16 gly domain 760:765 arg1 a misfolded variant a misfolded variant In the present study, we provide evidence that a misfolded variant of the STRUBBELIG (SUB) extracellular domain (SUBEX-C57Y) is degraded in a glycan-dependent manner in plants. 25907685 10 61 gly N-glycosylation 1562:1576 arg1 mAbs mAbs sites Cterm mAbs sites BIOLOGICAL SIGNIFICANCE The characterization of the N-glycosylation sites of therapeutic recombinant monoclonal antibodies (mAbs) is usually one of the most critical and time consuming steps in the developing process of biosimilars or any other glycosylated drug. 24794851 8 16 gly plants 1409:1414 arg1 total soluble protein protein plants Fterm protein The proportion of N-glycans with deleted plant-specific sugar residues found in total soluble protein from ΔGMDΔXylT plants increased by 82.41%. 24794851 8 24 gly found 1363:1367 arg2 total soluble protein AND deleted plant-specific sugar residues total soluble protein deleted plant-specific sugar residues Fterm protein The proportion of N-glycans with deleted plant-specific sugar residues found in total soluble protein from ΔGMDΔXylT plants increased by 82.41%. 28966766 3 22 gly glycoprotein 391:402 arg1 a small model glycoprotein a small model glycoprotein Fterm glycoprotein Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. 28966766 3 31 gly glycosylation 476:488 arg2 the glycosylation site the glycosylation site site Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. 29048990 6 53 gly glycosylation 1036:1048 arg2 predicted glycosylation sites predicted glycosylation sites sites Due to experimental challenges, experimental confirmation of the occupation of predicted glycosylation sites has only been carried out for a few strains. 25406038 3 39 part_of mucin 455:459 arg1 the mucin domain mucin the mucin domain PUBTATOR Site mucin 100508689 domain Glycosylation outside the mucin domain is suggested to be important for proper protein folding and protection against intestinal proteases. 28328971 2 10 gly N-glycosylation 136:150 arg1 proteins proteins Fterm proteins N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. 26831718 3 37 part_of IgG 516:518 arg1 IgG glycome composition IgG IgG glycome composition Cterm Site IgG position EXPERIMENTAL DESIGN Using recently developed high-throughput UPLC technology for IgG glycosylation analysis, we analyzed IgG glycome composition in 760 patients with colorectal cancer and 538 matching controls. 26240146 3 2 gly heterogeneity 455:467 arg1 carbohydrates carbohydrates However, developing an immunoassay directly against the N-linked oligosaccharides is unlikely because of the heterogeneity and low immunogenicity of carbohydrates. 30023556 5 66 gly O-glycosylation 822:836 arg2 an O-glycosylation site an O-glycosylation site site Both antibodies recognized specific O-glycan structures at the PDT*R motif (the asterisk represents an O-glycosylation site). 24326091 4 15 gly glycosylated 851:862 arg1 N-linked high mannose glycosylated asparagine N-linked high mannose glycosylated asparagine asparagine By using a convergent on-resin glycosylamine coupling strategy, an N-glycosidic linkage is successfully formed on the free side chain of the resin bound aspartic acid with a large high mannose oligosaccharide, Man8GlcNAc2, to yield N-linked high mannose glycosylated asparagine. 24326091 4 74 gly acid 759:762 arg1 Man8GlcNAc2 aspartic acid Man8GlcNAc2 aspartic acid By using a convergent on-resin glycosylamine coupling strategy, an N-glycosidic linkage is successfully formed on the free side chain of the resin bound aspartic acid with a large high mannose oligosaccharide, Man8GlcNAc2, to yield N-linked high mannose glycosylated asparagine. 24326091 4 74 gly acid 759:762 arg1 a large high mannose oligosaccharide aspartic acid a large high mannose oligosaccharide aspartic acid By using a convergent on-resin glycosylamine coupling strategy, an N-glycosidic linkage is successfully formed on the free side chain of the resin bound aspartic acid with a large high mannose oligosaccharide, Man8GlcNAc2, to yield N-linked high mannose glycosylated asparagine. 26101185 8 35 gly sialylated 1206:1215 arg1 more sialylated N-glycans more sialylated N-glycans In general, more sialylated N-glycans were released at lower temperatures and pH values. 25799047 6 47 gly Histidine 1302:1310 arg1 a Histidine tag Histidine a Histidine tag Histidine The protein, which contains a Histidine tag, was active and excreted from the cell. 25799047 6 79 gly contains 1291:1298 arg1 The protein AND a Histidine tag The protein a Histidine tag Fterm protein The protein, which contains a Histidine tag, was active and excreted from the cell. 24780636 6 86 gly modified 1033:1040 arg1 Asn432 AND single GlcNAc Asn432 single GlcNAc Asn432 On the other hand, Tf-1 is site-specifically modified: Asn630 has biantennary agalacto-complex-type glycan with bisecting N-acetylglucosamine (GlcNAc) and core fucose while Asn432 is modified with complex/high mannose-type glycans and possibly single GlcNAc. 24780636 6 86 gly modified 1033:1040 arg1 Asn432 AND complex/high mannose-type glycans Asn432 complex/high mannose-type glycans Asn432 On the other hand, Tf-1 is site-specifically modified: Asn630 has biantennary agalacto-complex-type glycan with bisecting N-acetylglucosamine (GlcNAc) and core fucose while Asn432 is modified with complex/high mannose-type glycans and possibly single GlcNAc. 24766575 4 0 gly glycopeptide 920:931 arg2 glycopeptide profiling glycopeptide profiling glycopeptide The results revealed a similar level of glycan microheterogeneity to that of conventional glycomics approach on individual proteins and provided the unique in-depth site-specific information that could only be studied through glycopeptide profiling. 28231413 3 32 gly glycoproteins 640:652 arg1 glycoproteins glycoproteins Fterm glycoproteins These metabolic chemical reporters (MCRs) have proven to be powerful for the unbiased identification of glycoproteins; however, they do have certain limitations. 26492619 8 50 gly O-glycosylated 1102:1115 arg1 Thr34 Thr34 Thr34 The Thr34 of PLAG1 is critical for LpMab-10 recognition, and O-glycan is not included in LpMab-10 epitope, indicating that Thr34 of PLAG1 is not O-glycosylated. 26241388 7 51 gly glycoproteins 1347:1359 arg1 chemically predefined oligosaccharide side-chain structures glycoproteins chemically predefined oligosaccharide side-chain structures Fterm glycoproteins Finally, the new FDL-deficient S2 cell derivative produced in this study will enable future bottom-up glycoengineering efforts designed to isolate insect cell lines that can efficiently produce recombinant glycoproteins with chemically predefined oligosaccharide side-chain structures. 24302562 0 65 gly sialylated 34:43 arg1 sialylated N-glycans sialylated N-glycans Profiling and characterization of sialylated N-glycans by 2D-HPLC (HIAX/PGC) with online orbitrap MS/MS and offline MSn. 28745859 4 58 gly O-glycopeptides 537:551 arg2 synthetic, homogeneous O-glycopeptides synthetic, homogeneous O-glycopeptides O-glycopeptides Here, we took advantage of synthetic, homogeneous O-glycopeptides to show that certain glycosylation patterns have an intrinsic effect, independent of any cellular folding machinery, on the folding pathway of a model O-glycoprotein, a carbohydrate binding module (CBM) derived from the Trichoderma reesei cellulase TrCel7A. 28745859 4 11 gly O-glycoprotein 704:717 arg1 a model O-glycoprotein O-glycoprotein a carbohydrate binding module Fterm O-glycoprotein Here, we took advantage of synthetic, homogeneous O-glycopeptides to show that certain glycosylation patterns have an intrinsic effect, independent of any cellular folding machinery, on the folding pathway of a model O-glycoprotein, a carbohydrate binding module (CBM) derived from the Trichoderma reesei cellulase TrCel7A. 27867116 7 65 gly glycopeptide 1371:1382 arg2 certain glycopeptide species certain glycopeptide species glycopeptide Moreover, the method does not require an extra glycopeptide enrichment step, thus preventing the bias that this step could cause towards certain glycopeptide species. 27867116 7 93 gly glycopeptide 1273:1284 arg2 an extra glycopeptide enrichment step an extra glycopeptide enrichment step glycopeptide Moreover, the method does not require an extra glycopeptide enrichment step, thus preventing the bias that this step could cause towards certain glycopeptide species. 25732693 1 54 gly glycoproteins 560:572 arg1 selected glycoproteins selected glycoproteins Fterm glycoproteins In this work we demonstrate the potential of glycan reductive isotope labeling (GRIL) using [(12)C]- and [(13)C]-coded aniline and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry (μZIC-HILIC-ESI-MS) for relative quantitation of glycosylation variants in selected glycoproteins present in samples from cancer patients. 26840264 3 13 gly glycosylation 593:605 arg1 circulating glycoproteins circulating glycoproteins Fterm glycoproteins Although the biosynthesis of glycans is in general mediated by glycosyltransferases associated with internal cell membranes, the extracellular glycosylation of circulating glycoproteins mediated by plasmatic glycosyltransferases has been recently demonstrated. 26840264 3 14 gly glycoproteins 622:634 arg1 circulating glycoproteins circulating glycoproteins Fterm glycoproteins Although the biosynthesis of glycans is in general mediated by glycosyltransferases associated with internal cell membranes, the extracellular glycosylation of circulating glycoproteins mediated by plasmatic glycosyltransferases has been recently demonstrated. 25648510 1 47 gly fucosylated 149:159 arg1 Natural anionic polysaccharides fucosylated chondroitin sulfates Natural anionic polysaccharides fucosylated chondroitin sulfates Natural anionic polysaccharides fucosylated chondroitin sulfates (FCS) from sea cucumbers attract great attention nowadays due to their ability to influence various biological processes, such as blood coagulation, thrombosis, angiogenesis, inflammation, bacterial and viral adhesion. 25029371 0 100 gly N-glycosylation 48:62 arg2 cotranslational N-glycosylation consensus site cotranslational N-glycosylation consensus site site The middle X residue influences cotranslational N-glycosylation consensus site skipping. 24473128 15 42 gly glycoprotein 2182:2193 arg1 The sole viral envelope glycoprotein The sole viral envelope glycoprotein Fterm glycoprotein The sole viral envelope glycoprotein, which is a principal immunogenic target, contains a heavy shield of glycans surrounding the conserved receptor-binding domain. 27629418 7 43 gly core-fucosylated 1243:1258 arg1 the immunoglobulin G-derived core-fucosylated glycopeptides the immunoglobulin G-derived core-fucosylated glycopeptides glycopeptides W251N mutants could act on the immunoglobulin G-derived core-fucosylated glycopeptides and human lactoferrin glycoproteins. 27629418 7 73 gly glycopeptides 1260:1272 arg2 the immunoglobulin G-derived core-fucosylated glycopeptides the immunoglobulin G-derived core-fucosylated glycopeptides glycopeptides W251N mutants could act on the immunoglobulin G-derived core-fucosylated glycopeptides and human lactoferrin glycoproteins. 28749929 5 87 part_of IgG 1204:1206 arg1 a well-defined conjugation site IgG a well-defined conjugation site Cterm Site IgG site Compared with in vivo glycoengineering technologies and the glycosyltransferase-enabled in vitro engineering method, the current approach is robust and features quantitative yield, homogeneous glycoforms of produced antibodies and ADCs, compatibility with diverse natural and non-natural glycan structures, convenient exploitation of native IgG as the starting material, and a well-defined conjugation site for antibody modifications. 24308717 1 85 part_of contains 253:260 arg1 a highly glycosylated therapeutic Fc-fusion protein AND multiple N- and O-glycosylation sites a highly glycosylated therapeutic Fc-fusion protein multiple N- and O-glycosylation sites Fterm Site protein sites Etanercept is a highly glycosylated therapeutic Fc-fusion protein that contains multiple N- and O-glycosylation sites. 27311011 2 34 gly glycosylation 372:384 arg2 glycosylation sites glycosylation sites sites The vast heterogeneity of structures that exist across glycosylation sites hinders the in-depth analysis of glycan changes specific to an individual protein within a complex mixture. 28680094 8 36 part_of subunit 1230:1236 arg1 the βI domain 1 subunit the βI domain PUBTATOR Site 1 subunit 146712 domain We identified one unique N-glycan at the βI domain of β1 subunit that negatively regulates α5β1 activation. 24941220 9 73 gly glycosites 1500:1509 arg2 five N- and one O-linked glycosites five N- and one O-linked glycosites glycosites Strikingly, we were able to observe five N- and one O-linked glycosites in native gp120. 28433761 9 21 gly glycoproteins 1517:1529 arg1 S-layer glycoproteins S-layer glycoproteins Fterm glycoproteins To our knowledge, this is the first description of the structure of N-glycans in S-layer glycoproteins from Lactobacillus species. 27722232 6 18 gly sialylated 1238:1247 arg1 labile sialylated glycans labile sialylated glycans The general utility of this approach was demonstrated by the characterization of labile sialylated glycans and two sets of complicated isomeric glycans. 27108103 4 84 gly glycosylated 448:459 arg1 subunits subunits Fterm subunits Soybean agglutinin is a tetrameric legume lectin, each of whose subunits are glycosylated. 26272370 4 5 gly glycoproteins 693:705 arg1 recombinant glycoproteins recombinant glycoproteins Fterm glycoproteins Aiming to establish a novel production platform for recombinant glycoproteins, the human TE671 cell line was investigated. 27957769 5 111 part_of mucin 875:879 arg1 mucin 1 glycopeptides mucin 1 mucin 1 glycopeptides PUBTATOR Site mucin 1 4582 glycopeptides For assessment of the influence of the immune stimulant on antibody recognition, a comprehensive library of mucin 1 glycopeptides (>100 entries) is synthesized and employed in antibody microarray profiling; these range from small tumor-associated glycans (TN , STN , and T-antigen structures) to heavily extended O-glycan core structures (type-1 and type-2 elongated core 1-3 tri-, tetra-, and hexasaccharides) glycosylated in variable density at the five different sites of the MUC1 tandem repeat. 24797265 4 78 gly glycopeptides 567:579 arg2 potential glycopeptides potential glycopeptides glycopeptides After Srr1 enrichment and trypsin digestion, potential glycopeptides were identified in collision induced dissociation spectra using X! 28693729 6 8 gly α2,6-sialylated 1584:1598 arg1 both α2,3- and α2,6-sialylated glycans both α2,3- and α2,6-sialylated glycans It was demonstrated that the relative abundances of individual glycans were different in RA negative and RA positive samples, and meanwhile the RA patient/control ratios of both α2,3- and α2,6-sialylated glycans tended to elevate accompanied with the increase of sialylation. 28581490 12 88 gly peptide 1924:1930 arg1 a tandem repeat peptide antigen a tandem repeat peptide antigen These glycan changes on MUC1 were detected with high sensitivity owing to the cluster effect of immobilized lectins on a tandem repeat peptide antigen covered with highly dense glycosylation such as mucin. 26082228 3 22 gly glycoproteins 381:393 arg1 recombinant glycoproteins recombinant glycoproteins Fterm glycoproteins Consequently, approaches are needed that enable the production of recombinant glycoproteins with customized and homogenous N- and O-glycan structures. 28921966 4 35 gly glycopeptides 712:724 arg2 intact glycopeptides intact glycopeptides glycopeptides Here we present a strategy for the permethylation of intact glycopeptides, obtained via controlled protease digest, and their characterization by using advanced mass spectrometry. 26990841 5 73 gly glycopeptide 869:880 arg2 247 glycopeptide ions 247 glycopeptide ions glycopeptide The 2D studies found a total of 247 glycopeptide ions and 60 glycans of different masses, including 30 glycans found in the 1D studies. 26983412 9 75 gly glycoproteins 1714:1726 arg1 humanized glycoproteins humanized glycoproteins Fterm glycoproteins Our results represent a further step towards obtaining humanized glycoproteins with a high homogeneity in S. cerevisiae. 29164281 4 20 gly glycoproteins 548:560 arg1 various glycoproteins various glycoproteins Fterm glycoproteins Saliva, one of the vital fluids encountered at crime scenes, contains various glycoproteins that are highly affected by biochemical environment. 25118826 3 87 gly polysialylated 755:768 arg1 polysialylated N-glycans polysialylated N-glycans In this report several improvements have been implemented in sample preparation and analysis to extend ESI-MS glycan characterization and to include polysialylated N-glycans. 27108103 6 65 gly non-glycosylated 840:855 arg1 non-glycosylated dimers non-glycosylated dimers Fterm dimers In order to understand the role of glycosylation on the dimeric interface, we have carried out normal (298K), high temperatures (380K, 500K) long explicit solvent molecular dynamics (MD) simulations and compared the structural and conformational changes between the glycosylated and non-glycosylated dimers. 26729242 0 36 gly O-glycosylation 0:14 arg2 O-glycosylation sites O-glycosylation sites sites O-glycosylation sites identified from mucin core-1 type glycopeptides from human serum. 26729242 0 58 gly glycopeptides 56:68 arg2 mucin core-1 type glycopeptides mucin core-1 type glycopeptides glycopeptides O-glycosylation sites identified from mucin core-1 type glycopeptides from human serum. 27038031 4 8 gly glycopeptides 688:700 arg2 HILIC-enriched tryptic and GluC glycopeptides HILIC-enriched tryptic and GluC glycopeptides glycopeptides In this study, the N-glycosylation of recombinant pentameric and hexameric IgM produced by the same human cell type and culture conditions was site-specifically profiled by RP-LC-CID/ETD-MS/MS using HILIC-enriched tryptic and GluC glycopeptides. 25868252 1 5 gly glycosylation 193:205 arg1 repetitive sequences repetitive sequences sequences Recombinant protein SMB(PRG4) containing two Somatomedin B domains and a small amount of glycosylation of repetitive sequences of proteoglycan 4 was cloned according to PGR4 gene polymorphism. 25253346 6 3 gly glycoproteins 836:848 arg1 most glycoproteins most glycoproteins Fterm glycoproteins Following purification, most glycoproteins, except for 10G, were recognized by broadly neutralizing CD4bs-directed antibodies. 27259834 4 69 part_of Mucin-1-derived 769:783 arg1 A Mucin-1-derived acceptor peptide Mucin-1 A Mucin-1-derived acceptor peptide OGER Site Mucin-1 P15941 peptide A Mucin-1-derived acceptor peptide (MUC1ap) was expressed as an acceptor. 28039139 1 7 part_of proteins 173:180 arg1 select Asn residues proteins select Asn residues Fterm AminoAcid proteins Asn residues N-Glycosylation, the covalent linkage of glycans to select Asn residues of target proteins, is an almost universal posttranslational modification in archaea. 26646445 8 69 gly bifucosylated 1366:1378 arg1 bifucosylated N-glycan bifucosylated N-glycan We compared the potential of bifucosylated N-glycan as an indicator of breast cancer recurrence with the current clinical biomarkers, i.e., CEA, CA 15-3 and CA125. 27731363 1 16 gly N-glycosylated 244:257 arg1 N-glycosylated proteins N-glycosylated proteins Fterm proteins In holometabolous insects the transition from larva to adult requires a complete body reorganization and relies on N-glycosylated proteins. 29065342 4 22 part_of O-linked 734:741 arg1 diverse O-linked LeX glycopeptides O-linked LeX diverse O-linked LeX glycopeptides Cterm Site O-linked LeX 2526 glycopeptides The presence of an Fmoc-threonine amino acid facilitates incorporation of the pentasaccharide in solid phase peptide synthesis, providing a route to diverse O-linked LeX glycopeptides. 29065342 4 43 part_of LeX 743:745 arg1 diverse O-linked LeX glycopeptides O-linked LeX diverse O-linked LeX glycopeptides Cterm Site O-linked LeX 2526 glycopeptides The presence of an Fmoc-threonine amino acid facilitates incorporation of the pentasaccharide in solid phase peptide synthesis, providing a route to diverse O-linked LeX glycopeptides. 27503803 2 58 gly NeuNAc-Gal-GalNAc-Thr 311:331 arg1 the O-glycan Thr the O-glycan Thr Previously reported evidence indicated that the O-glycan of the Gc1S allele product is the linear core 1 NeuNAc-Gal-GalNAc-Thr trisaccharide. 27503803 2 58 gly NeuNAc-Gal-GalNAc-Thr 311:331 arg1 the linear core 1 NeuNAc-Gal-GalNAc-Thr trisaccharide Thr the linear core 1 NeuNAc-Gal-GalNAc-Thr trisaccharide Thr Previously reported evidence indicated that the O-glycan of the Gc1S allele product is the linear core 1 NeuNAc-Gal-GalNAc-Thr trisaccharide. 24981920 2 32 part_of syndecan-3 431:440 arg1 the extracellular domain syndecan-3 the extracellular domain PUBTATOR Site syndecan-3 9672 domain Herein, we report the first synthesis of a glycosaminoglycan family glycopeptide containing two different heparan sulfate chains, namely the extracellular domain of syndecan-3. 28104755 7 85 gly non-glycosylated 1140:1155 arg1 this non-glycosylated protein this non-glycosylated protein Fterm protein Proteasomal inhibition restored levels of SMPDL3A in TM-treated cells, although this non-glycosylated protein lacked phosphodiesterase activity. 26990841 8 11 gly glycopeptides 1506:1518 arg2 glycopeptides glycopeptides glycopeptides Energy-dependent changes in HCD fragmentation confirmed the proposed glycan structures and led to a peak-annotated mass spectral library to aid the analysis of glycopeptides derived from IgG1 drugs. 25305020 4 88 gly glycosylated 890:901 arg1 dimers dimers Fterm dimers Both glycosylated forms of the CaSR ECD were purified as dimers and exhibit similar secondary structures with ∼ 50% α-helix, ∼ 20% β-sheet content, and a well buried Trp environment. 26863921 3 24 part_of N-glycosylation 633:647 arg1 the seven putative S-layer glycoprotein N-glycosylation sites N-glycosylation the seven putative S-layer glycoprotein N-glycosylation sites Cterm Site N-glycosylation sites In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 45 part_of glycoprotein 620:631 arg1 the seven putative S-layer glycoprotein N-glycosylation sites glycoprotein the seven putative S-layer glycoprotein N-glycosylation sites Fterm Site glycoprotein sites In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 57 part_of S-layer 612:618 arg1 the seven putative S-layer glycoprotein N-glycosylation sites S-layer the seven putative S-layer glycoprotein N-glycosylation sites Cterm Site S-layer sites In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 45 part_of glycoprotein 620:631 arg1 Asn-279 glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 Fterm SpecificSite glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 45 part_of glycoprotein 620:631 arg1 Asn-274 glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 Fterm SpecificSite glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 45 part_of glycoprotein 620:631 arg1 Asn-83 glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 Fterm SpecificSite glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 45 part_of glycoprotein 620:631 arg1 Asn-274 glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 Fterm SpecificSite glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 45 part_of glycoprotein 620:631 arg1 Asn-83 glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 Fterm SpecificSite glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 26863921 3 45 part_of glycoprotein 620:631 arg1 Asn-83 glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 Fterm SpecificSite glycoprotein Asn-13, Asn-83, Asn-274 and Asn-279 In the present study, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy were used to define the structure of this glycan attached to at least four of the seven putative S-layer glycoprotein N-glycosylation sites, namely Asn-13, Asn-83, Asn-274 and Asn-279. 24161615 4 69 gly glycoproteins 626:638 arg1 glycoproteins glycoproteins Fterm glycoproteins Specifically, the release of O-glycans from glycoproteins was approximately 20 to 30 times more efficient with hydrazine compared with ammonia-based β-elimination reagent. 28887379 8 43 gly glycopeptides 1309:1321 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides (2) A novel scoring scheme based on calculation of the "Ensemble Score (ES)," a measure that scores and rank-orders MS/MS spectrum for N- and O-linked glycopeptides using cross-correlation and probability based analyses. 25849464 4 18 gly N-glycosylated 507:520 arg1 three N-glycosylated sites three N-glycosylated sites sites T1 and T2/T3 copper binding sites and three N-glycosylated sites at Asn75, Asn238, and Asn458 were elucidated. 28837324 4 34 gly glycosylation 826:838 arg1 the Pse glycosyl donors the Pse glycosyl donors Moreover, we have studied the glycosylation of the Pse glycosyl donors and identified the structural determinants for its glycosylation diastereoselectivity, which enabled us to complete the total synthesis of P. aeruginosa 1244 pilin trisaccharide α-5NβOHC47NFmPse-(2→4)-β-Xyl-(1→3)-FucNAc. 28620050 2 34 part_of IgG1 420:423 arg1 The Fc region IgG1 The Fc region OGER Site IgG1 P01857 region The Fc region of human IgG1 (IgG1-Fc) can be engineered into multimeric structures (hexa-Fcs) that bind their cognate receptors with high avidity. 28714086 1 96 gly contain 212:218 arg1 mature receptors AND high-mannose, hybrid and complex oligosaccharides mature receptors high-mannose, hybrid and complex oligosaccharides Fterm receptors KEY POINTS: Ionotropic glutamate receptor (iGluR) subunits are N-glycosylated at 4-12 sites, and Golgi processing produces mature receptors that contain high-mannose, hybrid and complex oligosaccharides. 28714086 1 67 gly N-glycosylated 130:143 arg1 Ionotropic glutamate receptor (iGluR) subunits subunits sites Fterm subunits sites KEY POINTS: Ionotropic glutamate receptor (iGluR) subunits are N-glycosylated at 4-12 sites, and Golgi processing produces mature receptors that contain high-mannose, hybrid and complex oligosaccharides. 25213144 4 17 gly glycoforms 671:680 arg1 unique protein-associated disaccharide glycoforms unique protein-associated disaccharide glycoforms Here, we identify unique protein-associated disaccharide glycoforms that carry N-acetylglucosamine (GlcNAc) at their non-reducing end. 27585995 9 47 gly O-glycoproteins 2117:2131 arg1 model O-glycoproteins model O-glycoproteins Fterm O-glycoproteins The good quantitation feasibility, reliability and linearity of this strategy have been verified using bovine fetuin and porcine stomach mucin as model O-glycoproteins. 26921321 2 66 gly glycoprotein 412:423 arg1 the trimerized glycoprotein BclA the trimerized glycoprotein BclA Fterm glycoprotein The major constituent of its hairlike surface, the trimerized glycoprotein BclA, is attached to the basal layer through an N-terminal domain. 27928741 13 44 part_of haemagglutinin-neuraminidase 2085:2112 arg1 N-linked glycosylation sites haemagglutinin-neuraminidase N-linked glycosylation sites Fterm Site haemagglutinin-neuraminidase sites These finding will form the basis for future quantitative glycomic studies of the distribution of glycan structures across N-linked glycosylation sites of Newcastle disease virus haemagglutinin-neuraminidase and assessment of the functional significance of the O-linked glycan in the stalk domain of this protein. 27928741 13 115 part_of protein 2211:2217 arg1 the stalk domain protein the stalk domain Fterm Site protein domain These finding will form the basis for future quantitative glycomic studies of the distribution of glycan structures across N-linked glycosylation sites of Newcastle disease virus haemagglutinin-neuraminidase and assessment of the functional significance of the O-linked glycan in the stalk domain of this protein. 27638310 0 46 gly O-glycosylation 14:28 arg1 recombinant human GM-CSF GM-CSF sites PUBTATOR GM-CSF 1437 sites O-glycans and O-glycosylation sites of recombinant human GM-CSF derived from suspension-cultured rice cells, and their structural role. 29190644 0 35 gly glycoprotein 29:40 arg1 human glycoprotein butyrylcholinesterase human glycoprotein butyrylcholinesterase Fterm glycoprotein Structural analysis of human glycoprotein butyrylcholinesterase using atomistic molecular dynamics: The importance of glycosylation site ASN241. 29190644 0 24 gly glycosylation 118:130 arg2 ASN241 site ASN241 site ASN241 Structural analysis of human glycoprotein butyrylcholinesterase using atomistic molecular dynamics: The importance of glycosylation site ASN241. 25202310 6 39 gly glycosylation 1399:1411 arg2 the glycosylation sites the glycosylation sites sites The solvent accessibility of the glycosylation sites on maturely folded proteins of the 100 most abundant putative N-glycoproteins observed uniquely in the three subcellular glycoproteomes correlated with the glycan type processing thereby mechanistically explaining the formation of subcellular-specific N-glycosylation. 25202310 6 53 gly N-glycoproteins 1481:1495 arg1 the 100 most abundant putative N-glycoproteins the 100 most abundant putative N-glycoproteins Fterm N-glycoproteins The solvent accessibility of the glycosylation sites on maturely folded proteins of the 100 most abundant putative N-glycoproteins observed uniquely in the three subcellular glycoproteomes correlated with the glycan type processing thereby mechanistically explaining the formation of subcellular-specific N-glycosylation. 28938401 8 17 gly multifucosylated 1489:1504 arg1 multifucosylated glycans multifucosylated glycans Three groups of acidic N-glycans were more abundant in metastasized tumors: multifucosylated glycans, acid ester-modified (sulfated or phosphorylated) glycans, and hybrid-type/monoantennary N-glycans. 24279413 5 0 gly glycopeptides 947:959 arg2 glycopeptides glycopeptides glycopeptides Scoring algorithms are presented for tandem mass spectra of glycopeptides resulting from collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD) fragmentation modes. 26479949 8 49 gly glycopeptides 1581:1593 arg2 glycopeptides enrichment (85-110%) glycopeptides enrichment (85-110%) glycopeptides The MALDI-TOF mass spectrometric analysis indicated that the novel NPs exhibited high detection sensitivity in enrichment from HRP digests at concentration as low as 0.05 ng μL(-1), a large binding capacity up to 43 mg g(-1), and good recovery for glycopeptides enrichment (85-110%). 26729457 10 26 gly glycopeptide 1813:1824 arg2 The Q-TOF based glycopeptide analysis platform The Q-TOF based glycopeptide analysis platform glycopeptide The Q-TOF based glycopeptide analysis platform presented here opens the way to a range of different applications in glycoproteomics research as well as biopharmaceutical development and quality control. 27869200 5 16 gly glycopeptides 937:949 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides Logistic regression was applied to this database to develop model to distinguish between the spectra of N- and O-linked glycopeptides. 26765751 3 107 gly glycosylation 752:764 arg2 the designated glycosylation sites the designated glycosylation sites sites To evaluate the structural and functional roles of various glycoforms at multiple EGF domains in the human Notch transmembrane receptor, we established a universal method for the construction of NOTCH1 EGF modules displaying the desired O-glycans at the designated glycosylation sites. 26316330 3 62 gly glycoproteins 325:337 arg1 glycoproteins glycoproteins Fterm glycoproteins The structural heterogeneity of glycoproteins was also described by the definition of glycoforms. 26316330 3 86 gly heterogeneity 308:320 arg1 glycoproteins glycoproteins Fterm glycoproteins The structural heterogeneity of glycoproteins was also described by the definition of glycoforms. 26823463 1 24 gly glycosylated 245:256 arg1 Xanthophyllomyces dendrorhousβ-fructofuranosidase Xanthophyllomyces dendrorhousβ-fructofuranosidase Fterm dendrorhousβ-fructofuranosidase Xanthophyllomyces dendrorhousβ-fructofuranosidase (XdINV)is a highly glycosylated dimeric enzyme that hydrolyzes sucrose and releases fructose from various fructooligosaccharides (FOS) and fructans. 26823463 1 24 gly glycosylated 245:256 arg1 a highly glycosylated dimeric enzyme a highly glycosylated dimeric enzyme Fterm enzyme Xanthophyllomyces dendrorhousβ-fructofuranosidase (XdINV)is a highly glycosylated dimeric enzyme that hydrolyzes sucrose and releases fructose from various fructooligosaccharides (FOS) and fructans. 25936869 0 138 gly monoglycosylated 37:52 arg1 monoglycosylated biglycan monoglycosylated biglycan UV irradiation-induced production of monoglycosylated biglycan through downregulation of xylosyltransferase 1 in cultured human dermal fibroblasts. 28672164 5 4 gly Asn-bound 831:839 arg1 the Asn-bound GlcNAc Asn the Asn-bound GlcNAc Asn The oligosaccharide chains are mostly modified at the inner core by β1-2-linked xylose to β-mannose, by α1-6-fucosylation of the innermost GlcNAc residue (the Asn-bound GlcNAc), and by methylation. 28672164 5 4 gly Asn-bound 831:839 arg1 the innermost GlcNAc residue Asn the innermost GlcNAc residue Asn The oligosaccharide chains are mostly modified at the inner core by β1-2-linked xylose to β-mannose, by α1-6-fucosylation of the innermost GlcNAc residue (the Asn-bound GlcNAc), and by methylation. 28672164 5 50 gly α1-6-fucosylation 776:792 arg1 the Asn-bound GlcNAc the Asn-bound GlcNAc The oligosaccharide chains are mostly modified at the inner core by β1-2-linked xylose to β-mannose, by α1-6-fucosylation of the innermost GlcNAc residue (the Asn-bound GlcNAc), and by methylation. 28672164 5 50 gly α1-6-fucosylation 776:792 arg1 the innermost GlcNAc residue the innermost GlcNAc residue The oligosaccharide chains are mostly modified at the inner core by β1-2-linked xylose to β-mannose, by α1-6-fucosylation of the innermost GlcNAc residue (the Asn-bound GlcNAc), and by methylation. 24803430 0 3 part_of Notch1 77:82 arg1 the ligand-binding region Notch1 the ligand-binding region PUBTATOR Site Notch1 4851 region Fringe-mediated extension of O-linked fucose in the ligand-binding region of Notch1 increases binding to mammalian Notch ligands. 26208004 2 55 part_of has 349:351 arg1 DENV E glycoprotein AND two potential N-linked glycosylation sites DENV E glycoprotein two potential N-linked glycosylation sites Fterm Site glycoprotein sites It is well known that DENV E glycoprotein has two potential N-linked glycosylation sites at Asn67 and Asn153. 28193332 3 30 gly sites 512:516 arg1 N175 sites N75 and N175 sites N75 and N175 In-vitro deglycosylated AmPDH1 as well as knock-out mutants of the N-glycosylation sites N75 and N175, near the active site entrance, were previously shown to improve achievable current densities of graphite electrodes modified with AmPDH1 and an osmium redox polymer acting as a redox mediator, up to 10-fold. 28193332 3 30 gly sites 512:516 arg1 N75 sites N75 and N175 sites N75 and N175 In-vitro deglycosylated AmPDH1 as well as knock-out mutants of the N-glycosylation sites N75 and N175, near the active site entrance, were previously shown to improve achievable current densities of graphite electrodes modified with AmPDH1 and an osmium redox polymer acting as a redox mediator, up to 10-fold. 28193332 3 30 gly sites 512:516 arg1 N75 sites N75 and N175 sites N75 and N175 In-vitro deglycosylated AmPDH1 as well as knock-out mutants of the N-glycosylation sites N75 and N175, near the active site entrance, were previously shown to improve achievable current densities of graphite electrodes modified with AmPDH1 and an osmium redox polymer acting as a redox mediator, up to 10-fold. 28193332 3 79 gly N-glycosylation 496:510 arg2 the N-glycosylation sites N75 and N175 sites N75 and N175 sites N75 and N175 In-vitro deglycosylated AmPDH1 as well as knock-out mutants of the N-glycosylation sites N75 and N175, near the active site entrance, were previously shown to improve achievable current densities of graphite electrodes modified with AmPDH1 and an osmium redox polymer acting as a redox mediator, up to 10-fold. 28193332 3 79 gly N-glycosylation 496:510 arg2 N75 sites N75 and N175 sites N75 and N175 In-vitro deglycosylated AmPDH1 as well as knock-out mutants of the N-glycosylation sites N75 and N175, near the active site entrance, were previously shown to improve achievable current densities of graphite electrodes modified with AmPDH1 and an osmium redox polymer acting as a redox mediator, up to 10-fold. 28193332 3 79 gly N-glycosylation 496:510 arg2 N75 sites N75 and N175 sites N75 and N175 In-vitro deglycosylated AmPDH1 as well as knock-out mutants of the N-glycosylation sites N75 and N175, near the active site entrance, were previously shown to improve achievable current densities of graphite electrodes modified with AmPDH1 and an osmium redox polymer acting as a redox mediator, up to 10-fold. 29187599 6 89 gly glycosylation 1065:1077 arg1 Asn-137 Asn-137 Asn-137 The related copper-containing amine oxidase human vascular adhesion protein-1 also exclusively displayed high-mannose glycosylation at Asn-137. 27758867 3 3 gly glycopeptide 619:630 arg2 a LLDGSSTEIR glycopeptide a LLDGSSTEIR glycopeptide glycopeptide Detailed analysis of a LLDGSSTEIR glycopeptide released by tryptic digestion, which carried two variant structures, revealed that the glycopeptide contained, in addition to carbohydrate moieties, a novel structural entity. 27758867 3 42 gly glycopeptide 719:730 arg2 the glycopeptide the glycopeptide glycopeptide Detailed analysis of a LLDGSSTEIR glycopeptide released by tryptic digestion, which carried two variant structures, revealed that the glycopeptide contained, in addition to carbohydrate moieties, a novel structural entity. 27038031 7 3 gly had 970:972 arg1 Asn171 AND predominantly complex type glycans Asn171, Asn332, and Asn395 predominantly complex type glycans Asn171, Asn332, and Asn395 While Asn171, Asn332, and Asn395 all had predominantly complex type glycans, differences in glycan branching and sialylation were observed between the sites. 27038031 7 3 gly had 970:972 arg1 Asn332 AND predominantly complex type glycans Asn171, Asn332, and Asn395 predominantly complex type glycans Asn171, Asn332, and Asn395 While Asn171, Asn332, and Asn395 all had predominantly complex type glycans, differences in glycan branching and sialylation were observed between the sites. 27038031 7 3 gly had 970:972 arg1 Asn332 AND predominantly complex type glycans Asn171, Asn332, and Asn395 predominantly complex type glycans Asn171, Asn332, and Asn395 While Asn171, Asn332, and Asn395 all had predominantly complex type glycans, differences in glycan branching and sialylation were observed between the sites. 28255882 0 18 part_of α/β 27:29 arg1 α/β T Cell Receptor Constant Domains /β T Cell α/β T Cell Receptor Constant Domains PUBTATOR /β T Cell 351 Glycosylation Profiling of α/β T Cell Receptor Constant Domains Expressed in Mammalian Cells. 28255882 0 26 part_of Cell 33:36 arg1 α/β T Cell Receptor Constant Domains /β T Cell α/β T Cell Receptor Constant Domains PUBTATOR /β T Cell 351 Glycosylation Profiling of α/β T Cell Receptor Constant Domains Expressed in Mammalian Cells. 28255882 0 29 part_of T 31:31 arg1 α/β T Cell Receptor Constant Domains /β T Cell α/β T Cell Receptor Constant Domains PUBTATOR /β T Cell 351 Glycosylation Profiling of α/β T Cell Receptor Constant Domains Expressed in Mammalian Cells. 29106908 3 23 gly glycosylated 369:380 arg1 large, complex and highly glycosylated proteins large, complex and highly glycosylated proteins Fterm proteins IgMs are large, complex and highly glycosylated proteins that are only stable in a limited range of conditions. 27900782 8 33 gly glycosylation 976:988 arg1 carbohydrates carbohydrates Carbohydrate-specific applications described herein include virtual glycosylation, loop-modeling of carbohydrates, and docking of glyco-ligands to antibodies. 29273683 8 20 gly glycosylation 1115:1127 arg2 only one glycosylation site only one glycosylation site site When expressed in N-acetylglucosaminyltransferase-I-deficient Lec1 cells, human and rat CBGs, and a human CBG mutant with only one glycosylation site at N238, have higher (2-4 fold) steroid-binding affinities than when produced by sialylation-deficient Lec2 cells or glycosylation-competent CHO-S cells. 27869200 2 52 gly glycopeptides 284:296 arg2 glycopeptides glycopeptides glycopeptides Higher-energy collisional dissociation (HCD) fragmentation of glycopeptides generates mono- or disaccharide ions called oxonium ions that carry information about the structure of the fragmented glycans. 28258464 1 21 gly glycosylation 195:207 arg2 the sites the sites sites Detailed characterization of glycoprotein structures requires determining both the sites of glycosylation as well as the glycan structures associated with each site. 28258464 1 33 gly glycoprotein 132:143 arg1 glycoprotein structures glycoprotein structures Fterm glycoprotein Detailed characterization of glycoprotein structures requires determining both the sites of glycosylation as well as the glycan structures associated with each site. 25629924 8 59 gly glycosylation 1473:1485 arg2 each glycosylation site each glycosylation site site This represents the most comprehensive report to date detailing the complexity of glycan micro-heterogeneity with relative quantitation of glycoforms for each glycosylation site on milk sIgA. 28074929 5 0 part_of containing 822:831 arg1 4491 sequences AND the domains 4491 sequences the domains domains From 153 species, 4491 sequences containing the domains were retrieved, based on which we analyzed distribution of domains among eukaryotic species. 27617431 0 9 part_of CD4-binding 91:101 arg1 the CD4-binding site CD4 the CD4-binding site PUBTATOR Site CD4 920 site Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site. 24651839 10 83 part_of IgA1 1737:1740 arg1 IgA1 deposition IgA1 IgA1 deposition PUBTATOR Site IgA1 P01876 position Our results of analysis in the rare case of a patient with monoclonal immunoglobulin deposition disease suggest that the formation of unusually polymerized IgA1 is caused by divergent mechanisms including multiple structural alterations of glycans, which contributes to IgA1 deposition and mesangium proliferation. 29268168 1 4 part_of IgG 233:235 arg1 the Fc-domain IgG the Fc-domain PUBTATOR Site IgG 16059 Fc-domain The binding strength between IgG and FcγR is influenced by the composition of the N-linked glycan at position N297 in the Fc-domain of IgG. 28246170 6 16 part_of GlyD 1251:1254 arg1 the GlyD GT8 domain GlyD GT8 the GlyD GT8 domain OGER Site GlyD GT8 Q2TAA5 domain Specifically, the full-length GlyE and GlyG proteins and the GlyD DUF1792 domain participate in both steps, whereas full-length GlyA and the GlyD GT8 domain catalyze only the fourth step. 28246170 6 58 part_of GT8 1256:1258 arg1 the GlyD GT8 domain GlyD GT8 the GlyD GT8 domain OGER Site GlyD GT8 Q2TAA5 domain Specifically, the full-length GlyE and GlyG proteins and the GlyD DUF1792 domain participate in both steps, whereas full-length GlyA and the GlyD GT8 domain catalyze only the fourth step. 25552259 0 27 part_of GPC 71:73 arg1 the GPC receptor site GPC the GPC receptor site PUBTATOR Site GPC 2995 site The structures of glycophorin C N-glycans, a putative component of the GPC receptor site for Plasmodium falciparum EBA-140 ligand. 28509333 3 20 gly fucosylated 512:522 arg1 fucosylated tri-mannose N-glycan core sites LCA fucosylated tri-mannose N-glycan core sites OGER LCA P08575 Lectins capturing fucosyl residues (AAL), fucosylated tri-mannose N-glycan core sites (LCA), terminal sialic acid residues (SNA) and O-glycosidically linked galactose/N-acetylgalactosamine (GalNac-L) were used. 26850169 1 66 part_of G 121:121 arg1 The Fc region Immunoglobulin G The Fc region Cterm Site Immunoglobulin G region The Fc region of Immunoglobulin G (IgG) initiates inflammatory responses such as antibody-dependent cell-mediated cytotoxicity (ADCC) through binding to activating Fc receptors (FcγRI, FcγRIIa, FcγRIIIa). 26850169 1 78 part_of Fc 93:94 arg1 The Fc region Fc The Fc region Cterm Site Fc region The Fc region of Immunoglobulin G (IgG) initiates inflammatory responses such as antibody-dependent cell-mediated cytotoxicity (ADCC) through binding to activating Fc receptors (FcγRI, FcγRIIa, FcγRIIIa). 24965454 5 28 gly glycosylated 1117:1128 arg1 its native and fully glycosylated epitope its native and fully glycosylated epitope epitope Here, we present a negative-stain single-particle electron microscopy reconstruction of 2G12 Fab2 in complex with a soluble, trimeric Env at ∼17-Å resolution that reveals the antibody's interaction with its native and fully glycosylated epitope. 27501865 5 61 gly bisialylated 926:937 arg1 bisialylated biantennary glycan bisialylated biantennary glycan In particular, we observed the increase of bisialylated biantennary glycan, A2G2S[3,6]2, 12 hours after surgery, which progressively increased until 48 postoperative hours. 27581986 4 147 part_of CD4 674:676 arg1 The initial CD4 binding site CD4 The initial CD4 binding site PUBTATOR Site CD4 920 site The initial CD4 binding site response potently neutralized the heterologous tier 2 clade B viral strain RHPA, which was used to design resurfaced gp120 antigens for single-B-cell sorting. 28039139 7 99 gly glycoprotein 1273:1284 arg1 Compromised S-layer glycoprotein N-glycosylation Compromised S-layer glycoprotein N-glycosylation Fterm glycoprotein Compromised S-layer glycoprotein N-glycosylation resulted in impaired transfer of the reporter past the S-layer and into the growth medium. 25759508 8 19 gly N-glycosylation 1214:1228 arg1 the Fc CH2 domain the Fc CH2 domain domain For IgG3 samples from six donors we found similar O-glycan structures and site occupancies, whereas for the same samples the conserved N-glycosylation of the Fc CH2 domain showed considerable interindividual variation. 28890404 5 65 gly non-glycosylated 1001:1016 arg1 the non-glycosylated enzyme the non-glycosylated enzyme Fterm enzyme The enzyme was also expressed in Escherichia coli and the studies of circular dichroism showed that the melting temperature and structural profile of AnAbf62Awt and the non-glycosylated enzyme from E. coli (AnAbf62Adeglyc) were highly similar. 28258464 12 73 gly glycopeptide 1845:1856 arg2 intact glycopeptide intact glycopeptide glycopeptide Graphical abstract Through integrating the information of intact glycopeptide, fragment ions filters and endoglycosidase digestion, the reliability of the identification could be significantly improved. 25732693 11 105 gly glycoprotein 2380:2391 arg1 novel cancer associated glycoprotein biomarkers novel cancer associated glycoprotein biomarkers Fterm glycoprotein The methodology is assumed being suitable as well for other such studies aimed at finding novel cancer associated glycoprotein biomarkers. 27957769 11 8 part_of GSTA 2247:2250 arg1 the GSTA domain GSTA the GSTA domain OGER Site GSTA domain The nature of the antibody response is characteristically different for antibodies directed to glycosylation sites in either the immune-dominant PDTR or the GSTA domain. 29062024 6 58 gly fucosylation 1136:1147 arg1 IgG1-Fc IgG1 residues OGER IgG1 P01857 residues Moreover, our simulation demonstrates that core fucosylation of IgG1-Fc affects conformational dynamics and rearrangements of surrounding amino acid residues, typified by Tyr296 of IgG1-Fc, which was more extensively involved in the interaction with sFcγRIIIa without Fc core fucosylation. 24497634 5 46 gly contactin 781:789 arg1 the molecular determinants contactin the molecular determinants Fterm contactin In the present study, we mapped the molecular determinants of contactin targeted by the autoantibodies. 25204387 10 61 part_of CGA 1748:1750 arg1 a fragment CGA a fragment OGER Site CGA P10645 fragment Moreover, two putative cellulose synthase-like D family genes (CSLDs) from the CGA species Coleochaete orbicularis and a fragment of a putative CSLA/K-like sequence from a CGA Spirogyra species were cloned, providing the first evidence that all the cellulose synthase/-like genes present in early-divergent land plants were already present in CGA. 26918373 1 13 gly attached 107:114 arg2 therapeutic glycoproteins AND Glycans therapeutic glycoproteins Glycans Fterm glycoproteins Glycans or carbohydrates attached to therapeutic glycoproteins can directly affect product quality, safety and efficacy, and therefore must be adequately analyzed and controlled throughout product life cycles. 26918373 1 28 gly glycoproteins 131:143 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins Glycans or carbohydrates attached to therapeutic glycoproteins can directly affect product quality, safety and efficacy, and therefore must be adequately analyzed and controlled throughout product life cycles. 26729457 8 2 gly O-glycopeptides 1476:1490 arg2 O-glycopeptides O-glycopeptides O-glycopeptides These optimized fragmentation parameters also enabled software-assisted glycopeptide assignment of both N- and O-glycopeptides including information about the most abundant glycan compositions, peptide sequence and putative structures. 26729457 8 101 gly glycopeptide 1437:1448 arg2 software-assisted glycopeptide assignment software-assisted glycopeptide assignment glycopeptide These optimized fragmentation parameters also enabled software-assisted glycopeptide assignment of both N- and O-glycopeptides including information about the most abundant glycan compositions, peptide sequence and putative structures. 27791356 3 24 gly glycosylation 541:553 arg1 the various mucin subdomains the various mucin subdomains subdomains Thus, key structural information, such as the secondary structure of the various mucin subdomains, and glycosylation patterns along individual molecules, remains to be elucidated. 25895110 6 61 part_of IgG 803:805 arg1 IgG glycome composition IgG IgG glycome composition Cterm Site IgG position RESULTS Statistically significant differences in IgG glycome composition between patients with UC or CD, compared with controls, were observed. 25868116 2 54 gly glycosylation 407:419 arg1 the disaccharide the disaccharide This imidate glycosylated di-O-isopropylidene-α-D-glucofuranose in high yield and glycosylation of the disaccharide after removal of the 3'-O-benzyl ether afforded the β1,3 linked trisaccharide in excellent yield. 26802542 4 31 part_of GH 761:762 arg1 Ttβ-gly GH 1 Ttβ-gly OGER AminoAcid GH 1 P01241 gly Two hyperthermostable GH 1 β-galactosidases, Ttβ-gly from Thermus thermophilus HB27 and CelB from Pyrococcus furiosus, were codon-optimized for expression in Escherichia coli along with BgaD-D, a truncated version of the GH 42 β-galactosidase from Bacillus circulans showing high transgalactosylation activity at low substrate concentrations. 26267136 1 20 gly glycosylation 104:116 arg2 the most conserved glycosylation sites neuraminidase sites Fterm neuraminidase sites One of the most conserved glycosylation sites of neuraminidase (NA) is 146-N-glycan. 25110774 9 11 gly glycoproteins 1774:1786 arg1 290 different glycoproteins 290 different glycoproteins Fterm glycoproteins Furthermore, a promising protocol was developed for the selective enrichment of glycopeptides from mouse liver, and 344 unique N-glycosylation sites that mapped to 290 different glycoproteins were identified in a single MS run. 25110774 9 54 gly N-glycosylation 1723:1737 arg2 344 unique N-glycosylation sites 344 unique N-glycosylation sites sites Furthermore, a promising protocol was developed for the selective enrichment of glycopeptides from mouse liver, and 344 unique N-glycosylation sites that mapped to 290 different glycoproteins were identified in a single MS run. 25110774 9 56 gly glycopeptides 1676:1688 arg2 glycopeptides glycopeptides glycopeptides Furthermore, a promising protocol was developed for the selective enrichment of glycopeptides from mouse liver, and 344 unique N-glycosylation sites that mapped to 290 different glycoproteins were identified in a single MS run. 26216755 3 26 gly subsite 836:842 arg1 GlcNAc subsite GlcNAc subsite The crystal structures of an inactive double mutant of CrChiA (CrChiA-G77W/E119Q) with one or two N-acetylglucosamine residues occupying subsites +1 or +1/+2, respectively, revealed that the Trp77 side chain was oriented toward +1 GlcNAc to be stacked with it face-to-face, but rotated away from subsite +1 in the absence of GlcNAc at the subsite. 27313494 7 75 gly fucosylated 1229:1239 arg1 fucosylated structures fucosylated structures Among a total of 40, 32 and 15 N-glycans in four fractions of three cells detected by MS analysis, high-mannose and fucosylated structures were predominant, 10 N-glycans in YTS1, 5 N-glycans in KK47 and 7 N-glycans in HCV29 were present in all four fractions; and 10 N-glycans in YTS1, 16 N-glycans in KK47, and 3 N-glycans in HCV29 were present in only one fraction. 28077298 6 34 gly glycoprotein 1620:1631 arg1 recombinant glycoprotein production recombinant glycoprotein production Fterm glycoprotein SIGNIFICANCE The occurrence of anionic and zwitterionic glycans in the Lepidoptera data is not only of glycoanalytical and evolutionary interest, but is of biotechnological relevance as lepidopteran cell lines are potential factories for recombinant glycoprotein production. 28452462 7 62 gly attached 1580:1587 arg3 a different N-glycan AND the third (Asn-24) site the third (Asn-24) site a different N-glycan site Finally, a different N-glycan was attached at the third (Asn-24) site by pushing the enzymatic transglycosylation with a distinct glycan oxazoline, achieving the site-selective glycosylation modification of the protein. 28452462 7 62 gly attached 1580:1587 arg3 a different N-glycan AND Asn-24 Asn-24 a different N-glycan Asn-24 Finally, a different N-glycan was attached at the third (Asn-24) site by pushing the enzymatic transglycosylation with a distinct glycan oxazoline, achieving the site-selective glycosylation modification of the protein. 28692416 4 25 gly N-glycopeptides 698:712 arg2 60 N-glycopeptides 60 N-glycopeptides N-glycopeptides The profile of 60 N-glycopeptides of IgG subclass isolated from plasma samples of 150 Kazakh study participants was analyzed by nano ultra-performance liquid chromatography with mass spectrometry. 28258464 10 60 gly glycosite 1572:1580 arg2 a specific glycosite a specific glycosite glycosite The intensity of different glycoforms at a specific glycosite was obtained to reach the occupancy ratios of site-specific glycoforms. 27506354 7 28 gly glycoprotein 1291:1302 arg1 asialofetuin asialofetuin Fterm asialofetuin The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). 27506354 7 31 gly sialylated 1236:1245 arg1 model oligosaccharides model oligosaccharides The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). 27506354 7 31 gly sialylated 1236:1245 arg1 sialylated glycan A1 sialylated glycan A1 The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). 27506354 7 45 gly glycoprotein 1291:1302 arg1 glycans glycoprotein glycans Fterm glycoprotein The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). 26492619 1 45 gly sialoglycoprotein 169:185 arg1 a type-I transmembrane sialoglycoprotein a type-I transmembrane sialoglycoprotein Fterm sialoglycoprotein Podoplanin (PDPN) is a type-I transmembrane sialoglycoprotein that possesses a platelet aggregation-stimulating (PLAG) domain in the N-terminus. 29058712 7 32 part_of OST 1055:1057 arg1 conserved OST motifs OST conserved OST motifs OGER Site OST motifs Our results define the chemistry of a ternary complex state, assign functional roles to conserved OST motifs, and provide opportunities for glycoengineering by rational design of PglB. 27933952 3 11 gly has 404:406 arg1 enoxaparin AND a reducing sugar moiety enoxaparin a reducing sugar moiety Fterm enoxaparin In particular, enoxaparin, which has a reducing sugar moiety at the end-site of polysaccharide, is prepared by alkaline depolymerization. 27145274 1 56 part_of Fab 366:368 arg1 Fab fragments Fab Fab fragments PUBTATOR Site Fab 2187 fragments Concanavalin A (ConA) chromatography has been extensively used to separate asymmetric Immunoglobulin G (IgG), which possesses oligosaccharide attached to one of the two F(ab')2 arms, from symmetric IgG with no glycan attached to Fab fragments. 28424265 11 22 gly glycoproteins 1797:1809 arg1 cell-surface glycoproteins cell-surface glycoproteins Fterm glycoproteins Notably, N-linked glycans produced by GNE-deficient cells displayed enhanced binding to galectin-1, indicating that changes in GNE activity can alter affinity of cell-surface glycoproteins for the galectin lattice. 26537504 2 30 gly glycosylated 475:486 arg1 a pro-inflammatory glycosylated protease a pro-inflammatory glycosylated protease Fterm protease The setae contain a pro-inflammatory glycosylated protease homologous to other S1A serine proteases of insects. 25451932 8 69 gly N-glycosylation 978:992 arg1 corin cell surface targeting corin domain PUBTATOR corin 10699 domain Moreover, N-glycosylation at Asn-697 in the scavenger receptor domain and at Asn-1022 in the protease domain is important for corin cell surface targeting and zymogen activation. 25451932 8 69 gly N-glycosylation 978:992 arg1 the scavenger receptor domain domain domain Moreover, N-glycosylation at Asn-697 in the scavenger receptor domain and at Asn-1022 in the protease domain is important for corin cell surface targeting and zymogen activation. 25451932 8 69 gly N-glycosylation 978:992 arg1 corin cell surface targeting corin Asn-1022 PUBTATOR corin 10699 Asn-1022 Moreover, N-glycosylation at Asn-697 in the scavenger receptor domain and at Asn-1022 in the protease domain is important for corin cell surface targeting and zymogen activation. 25451932 8 69 gly N-glycosylation 978:992 arg2 Asn-1022 Asn-1022 Asn-1022 Moreover, N-glycosylation at Asn-697 in the scavenger receptor domain and at Asn-1022 in the protease domain is important for corin cell surface targeting and zymogen activation. 25451932 8 69 gly N-glycosylation 978:992 arg2 Asn-697 corin Asn-697 PUBTATOR corin 10699 Asn-697 Moreover, N-glycosylation at Asn-697 in the scavenger receptor domain and at Asn-1022 in the protease domain is important for corin cell surface targeting and zymogen activation. 25451932 8 69 gly N-glycosylation 978:992 arg1 the scavenger receptor domain corin domain PUBTATOR corin 10699 domain Moreover, N-glycosylation at Asn-697 in the scavenger receptor domain and at Asn-1022 in the protease domain is important for corin cell surface targeting and zymogen activation. 25451932 8 69 gly N-glycosylation 978:992 arg2 Asn-1022 corin Asn-1022 PUBTATOR corin 10699 Asn-1022 Moreover, N-glycosylation at Asn-697 in the scavenger receptor domain and at Asn-1022 in the protease domain is important for corin cell surface targeting and zymogen activation. 25451932 8 69 gly N-glycosylation 978:992 arg1 Asn-697 corin Asn-697 PUBTATOR corin 10699 Asn-697 Moreover, N-glycosylation at Asn-697 in the scavenger receptor domain and at Asn-1022 in the protease domain is important for corin cell surface targeting and zymogen activation. 25451932 8 69 gly N-glycosylation 978:992 arg1 Asn-697 Asn-697 Asn-697 Moreover, N-glycosylation at Asn-697 in the scavenger receptor domain and at Asn-1022 in the protease domain is important for corin cell surface targeting and zymogen activation. 28956227 3 19 gly glycosylation 629:641 arg2 seven N-linked glycosylation sites seven N-linked glycosylation sites sites NTPDase3/CD39L3is dominantly expressed in pancreatic islet cells, where it may regulate insulin secretion, and has seven N-linked glycosylation sites with four close to five highly conserved domains called "apyrase conserved regions" (ACRs). 26515403 0 64 gly glycosylation 32:44 arg1 lipopolysaccharide lipopolysaccharide ArnT proteins that catalyze the glycosylation of lipopolysaccharide share common features with bacterial N-oligosaccharyltransferases. 28443077 3 30 gly glycosylated 707:718 arg1 the glycosylated HA trimers the glycosylated HA trimers Fterm trimers To address this issue, we performed molecular dynamics simulations of the glycosylated HA trimers of the A(H3N2), which has a novel pattern of Asn-X-Ser/Thr sequons unique in the new A(H3N2) epidemic clade 3C.2a and is characterized by attenuated ability to agglutinate nonhuman erythrocytes. 25036289 3 71 part_of Fab 318:320 arg1 the antigen recognition Fab domains Fab the antigen recognition Fab domains PUBTATOR Site Fab 2187 domains The diversity of the antigen recognition Fab domains accounts for IgG's ability to bind with high specificity to essentially any antigen. 26784534 4 56 gly glycopeptides 522:534 arg2 the purified glycopeptides the purified glycopeptides glycopeptides Subsequently, the purified glycopeptides were analyzed by glycosidase digestion and mass spectrometry. 26038399 2 21 gly glycosylation 366:378 arg2 N-linked glycosylation sites N-linked glycosylation sites sites The GP subunit GP2 of filoviruses contains 2 completely conserved N-linked glycosylation sites (NGSs) at N563 and N618, suggesting that they have been maintained through selective pressures. 29255015 0 50 gly glycoprotein 49:60 arg1 the chlorovirus PBCV-1 major capsid glycoprotein the chlorovirus PBCV-1 major capsid glycoprotein Fterm glycoprotein Structure of the chlorovirus PBCV-1 major capsid glycoprotein determined by combining crystallographic and carbohydrate molecular modeling approaches. 25533529 3 64 gly acutobin 438:445 arg1 single glycan-knockout mutants acutobin single glycan-knockout mutants Fterm acutobin The wild-type (ATB-wt) and single glycan-knockout mutants of recombinant acutobin were prepared from HEK293T, demonstrating that mutations at Asn(77), Asn(81) and Asn(100) impaired the folding while the S79A mutant and various Asn(229)-deglycosylated mutants were correctly folded. 25837443 3 3 gly glycoproteins 427:439 arg1 their affected glycoproteins their affected glycoproteins Fterm glycoproteins Due to this heterogeneity of glycosylation, it has proven difficult to study the structure-function relationship of specific glycans and their affected glycoproteins. 26850169 4 46 part_of Fc 778:779 arg1 the Fc CH2 domain Fc the Fc CH2 domain Cterm Site Fc domain The affinity of IgG Fc for binding activating Fc receptors depends on IgG subclass and the composition of N-linked glycans attached to a conserved asparagine in the Fc CH2 domain. 25230686 4 26 part_of GnTI 634:637 arg1 The individual GnTI protein domains GnTI The individual GnTI protein domains OGER Site GnTI P26572 domains The individual GnTI protein domains were replaced with those from the well-known trans-Golgi enzyme α2,6-sialyltransferase (ST) and transiently expressed in Nicotiana benthamiana. 28035807 2 57 gly O-glycopeptides 214:228 arg2 intact O-glycopeptides O-glycopeptides different glycans O-glycopeptides However, intact O-glycopeptides with different glycans are typically not well elucidated using the current methods. 26765751 2 101 part_of EGF-like 470:477 arg1 the Notch extracellular EGF-like domain EGF the Notch extracellular EGF-like domain OGER Site EGF P01133 domain Notch signaling is modified by posttranslational glycosylations of the Notch extracellular EGF-like domain. 26765751 2 104 part_of Notch 450:454 arg1 the Notch extracellular EGF-like domain Notch the Notch extracellular EGF-like domain PUBTATOR Site Notch 4851 domain Notch signaling is modified by posttranslational glycosylations of the Notch extracellular EGF-like domain. 26773038 0 51 gly domain 44:49 arg1 N-linked glycan stabilization domain N-linked glycan stabilization domain N-linked glycan stabilization of the VWF A2 domain. 26582203 3 1 gly carries 525:531 arg1 Asn-95 AND a core glycan Asn-95 a core glycan Asn-95 Mass spectrometry revealed that Asn-95 carries a core glycan, consisting of two GlcNAc and three hexoses. 26082214 1 8 gly glycoproteins 148:160 arg1 eukaryotic glycoproteins eukaryotic glycoproteins Fterm glycoproteins Glycans linked to asparagine (N) residues of eukaryotic glycoproteins are typically heterogeneous. 26082214 1 15 gly linked 100:105 arg2 eukaryotic glycoproteins AND Glycans glycoproteins residues Glycans Fterm glycoproteins residues Glycans linked to asparagine (N) residues of eukaryotic glycoproteins are typically heterogeneous. 25305020 3 24 part_of receptor 713:720 arg1 the glycosylated extracellular domain calcium-sensing receptor the glycosylated extracellular domain PUBTATOR Site calcium-sensing receptor 846 domain In the present study, we purified the glycosylated extracellular domain of calcium-sensing receptor (CaSR) (ECD) (residues 20-612), containing either complex or high mannose N-glycan structures depending on the host cell line employed for recombinant expression. 28035807 5 51 gly glycopeptides 1086:1098 arg1 93 glycoproteins 93 glycoproteins Fterm glycoproteins This strategy was applied to analyze the O-GalNAc glycoproteome of human serum, leading to identification of 407 intact O-GalNAc glycopeptides from 93 glycoproteins. 28035807 5 72 gly glycoproteins 1108:1120 arg1 93 glycoproteins glycoproteins 407 intact O-GalNAc glycopeptides Fterm glycoproteins This strategy was applied to analyze the O-GalNAc glycoproteome of human serum, leading to identification of 407 intact O-GalNAc glycopeptides from 93 glycoproteins. 25124522 1 40 gly Heterogeneity 147:159 arg1 glycan structures glycan structures Heterogeneity of glycan structures in native glycoconjugates always hampers precise studies on carbohydrate-involved biological functions. 25482815 0 28 gly flagellin 17:25 arg1 Glycan moiety flagellin Glycan moiety Fterm flagellin Glycan moiety of flagellin in Acidovorax avenae K1 prevents the recognition by rice that causes the induction of immune responses. 28973586 5 58 gly glycosylated 662:673 arg1 the oligomeric glycosylated proteins the oligomeric glycosylated proteins Fterm proteins To gain further insight on ABP1 structural biology, this study was carried out employing molecular dynamics simulations of the complete models of the oligomeric glycosylated proteins from maize and Arabidopsis thaliana with or without auxins. 26439794 3 2 gly glycopeptide 417:428 arg2 a glycopeptide enrichment method a glycopeptide enrichment method glycopeptide Previously, we developed a glycopeptide enrichment method by acetone precipitation, and it was successfully applied to human serum glycoproteomics. 26599081 6 45 part_of sites 985:989 arg1 surface-exposed lipoproteins lipoproteins sites Fterm Site lipoproteins sites Protein glycosylation occurred at numerous sites on surface-exposed lipoproteins with no apparent amino acid sequence specificity. 24747898 2 32 part_of cellobiohydrolase 405:421 arg1 the catalytic domain cellobiohydrolase I the catalytic domain Fterm Site cellobiohydrolase I domain We investigated the significance of the three N-linked glycans on the catalytic domain of cellobiohydrolase I (CBH1) from the filamentous fungus Trichoderma reesei in its secretion and activity. 29048990 4 38 gly glycosite 792:800 arg2 glycosite modifications glycosite modifications glycosite Sequence-based analysis of viral RNA has provided great insight into the role of glycosite modifications in altering virulence and pathogenicity. 26983412 5 46 gly strain 923:928 arg1 the glycan pattern strain the glycan pattern Fterm strain We improved the glycan pattern of the glycoengineered strain both in terms of glycoform homogeneity and the efficiency of complex-type glycosylation. 29187599 3 28 gly carries 475:481 arg1 Asn-110 AND only mammalian-atypical oligomannosidic glycans Asn-110 only mammalian-atypical oligomannosidic glycans Asn-110 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 34 gly N-glycosylation 351:365 arg2 the N-glycosylation sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 34 gly N-glycosylation 351:365 arg2 Asn-168 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 34 gly N-glycosylation 351:365 arg2 Asn-745 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 34 gly N-glycosylation 351:365 arg2 Asn-168 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 34 gly N-glycosylation 351:365 arg2 Asn-745 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 34 gly N-glycosylation 351:365 arg2 Asn-745 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 79 gly sites 367:371 arg1 Asn-538 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 79 gly sites 367:371 arg1 Asn-745 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 79 gly sites 367:371 arg1 Asn-168 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 79 gly sites 367:371 arg1 Asn-745 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 79 gly sites 367:371 arg1 Asn-168 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 79 gly sites 367:371 arg1 Asn-168 sites Asn-168, Asn-538, and Asn-745 sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 31 gly carry 431:435 arg1 Asn-538 AND complex-type glycans sites Asn-168, Asn-538, and Asn-745 complex-type glycans sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 31 gly carry 431:435 arg1 Asn-745 AND complex-type glycans sites Asn-168, Asn-538, and Asn-745 complex-type glycans sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 31 gly carry 431:435 arg1 Asn-168 AND complex-type glycans sites Asn-168, Asn-538, and Asn-745 complex-type glycans sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 31 gly carry 431:435 arg1 Asn-745 AND complex-type glycans sites Asn-168, Asn-538, and Asn-745 complex-type glycans sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 31 gly carry 431:435 arg1 Asn-168 AND complex-type glycans sites Asn-168, Asn-538, and Asn-745 complex-type glycans sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 29187599 3 31 gly carry 431:435 arg1 Asn-168 AND complex-type glycans sites Asn-168, Asn-538, and Asn-745 complex-type glycans sites Asn-168, Asn-538, and Asn-745 We recently reported that the N-glycosylation sites Asn-168, Asn-538, and Asn-745 in recombinant hDAO (rhDAO) carry complex-type glycans, whereas Asn-110 carries only mammalian-atypical oligomannosidic glycans. 25029481 8 80 gly fucosylated 1373:1383 arg1 fucosylated complex N-glycans fucosylated complex N-glycans The mass spectrometry images were used to study the relative abundance of oligomannose, nonfucosylated, and fucosylated complex N-glycans in different brain areas including isocortex, hippocampal formation, and brainstem and specific glycans associated with different areas of the brain were identified. 25094044 4 22 gly glycosylation 668:680 arg2 the site UGGT1 site PUBTATOR UGGT1 171129 site In this study, we reveal the site of glycosylation (N269) and the glycan structures (Hex5-8HexNAc2) in UGGT1 obtained from rat (Rattus norvegicus), pig (Sus scrofa), cow (Bos taurus), and human (Homo sapiens). 24806200 6 21 gly glycosylation 1224:1236 arg2 all native glycosylation sites all native glycosylation sites sites Using the powerful tools of chemical synthesis, the work presented herein focuses on the highly convergent syntheses of homogeneous β-hLH and β-hCG bearing model glycans at all native glycosylation sites. 28921955 4 58 gly glycopeptides 830:842 arg2 suitable glycopeptides suitable glycopeptides glycopeptides Three enzymes, trypsin, AspN, and pepsin, were used separately to generate suitable glycopeptides for online LC tandem MS analysis. 25227423 5 46 gly N-glycosylation 955:969 arg2 N-glycosylation sites N-glycosylation sites sites We identify, from an analysis of over 6000 influenza A H3N2 sequences, a set of residues adjacent to N-glycosylation sites that are highly likely to be involved in antigenic escape from host antibodies. 26598643 12 29 gly O-glycosylation 1838:1852 arg2 23 O-glycosylation sites 23 O-glycosylation sites sites In total 23 O-glycosylation sites could be pinpointed. 25629924 7 54 gly O-glycopeptide 1290:1303 arg2 a theoretical O-glycopeptide library a theoretical O-glycopeptide library O-glycopeptide Additionally, 54 O-linked glycan compositions located at the IgA1 hinge region (HR) were identified by comparison against a theoretical O-glycopeptide library. 27869200 1 9 gly glycopeptides 110:122 arg2 intact glycopeptides intact glycopeptides glycopeptides Analysis of intact glycopeptides by mass spectrometry is essential to determining the microheterogeneity of protein glycosylation. 26925665 3 50 gly glycoprotein 327:338 arg1 O-linked glycoprotein glycoprotein the glycan structures Fterm glycoprotein We identified and quantified the glycan structures of O-linked glycoprotein from cholangiocarcinoma (CCA) cell lines from different histological types and compared their profiles by nanospray ionization-linear ion trap mass spectrometry (NSI-MSn). 27356208 3 20 gly hyper-glycosylation 535:553 arg1 recombinant proteins recombinant proteins Fterm proteins Glyco-engineering is an approach to facilitate the hyper-glycosylation of recombinant proteins by application of the site-directed mutagenesis methods. 25737449 10 52 part_of E2 1600:1601 arg1 the E2(412-423) epitope E2 the E2(412-423) epitope Cterm Site E2 epitope Furthermore, our results highlight the structural flexibility of the E2(412-423) epitope, which may serve as an immune evasion strategy to impede induction of antibodies targeting this site by reducing its antigenicity. 28056108 9 46 gly glycoprotein 1589:1600 arg1 a model N-glycosylated glycoprotein a model N-glycosylated glycoprotein Fterm glycoprotein Finally, we evaluated the contribution of EndoD and ABCNG to growth of S. pneumoniae on a model N-glycosylated glycoprotein, and the contribution of these enzymes and SpGH92 to virulence in a mouse model. 28056108 9 85 gly N-glycosylated 1574:1587 arg1 a model N-glycosylated glycoprotein a model N-glycosylated glycoprotein Fterm glycoprotein Finally, we evaluated the contribution of EndoD and ABCNG to growth of S. pneumoniae on a model N-glycosylated glycoprotein, and the contribution of these enzymes and SpGH92 to virulence in a mouse model. 26483525 13 141 gly glycosylation 2366:2378 arg1 the major subunit the major subunit Fterm subunit A number of lines of evidence indicate that the glycan components in these systems are subject to diversifying selection and suggest that glycan variation may be driven in the context of glycosylation of the abundant and surface-localized pilin protein PilE, the major subunit of type IV pili. 29187599 0 73 gly Asn-110 27:33 arg1 Oligomannosidic glycans Asn-110 Oligomannosidic glycans Asn-110 Oligomannosidic glycans at Asn-110 are essential for secretion of human diamine oxidase. 27873468 3 11 gly peptide 555:561 arg1 a peptide repeat sequence motif a peptide repeat sequence motif Using a peptide repeat sequence motif of the glycoprotein mucin-1, the principle of introducing synthetic (glyco)peptides with distinct variations in these three parameters to an array-based screening of tissue lectins is illustrated. 27873468 3 33 gly sequence 570:577 arg1 a peptide repeat sequence motif a peptide repeat sequence motif Using a peptide repeat sequence motif of the glycoprotein mucin-1, the principle of introducing synthetic (glyco)peptides with distinct variations in these three parameters to an array-based screening of tissue lectins is illustrated. 27873468 3 38 gly glycoprotein 592:603 arg1 the glycoprotein mucin-1 the glycoprotein mucin-1 Fterm glycoprotein Using a peptide repeat sequence motif of the glycoprotein mucin-1, the principle of introducing synthetic (glyco)peptides with distinct variations in these three parameters to an array-based screening of tissue lectins is illustrated. 25753710 4 1 gly preferences 514:524 arg1 proteins proteins preferences Fterm proteins It centers on a glycan structure database and accumulates information such as glycan preferences of lectins, glycosylation sites in proteins, and genes related to glycan syntheses from glycoscience and related fields. 25753710 4 2 gly glycosylation 538:550 arg2 glycosylation sites glycosylation sites sites It centers on a glycan structure database and accumulates information such as glycan preferences of lectins, glycosylation sites in proteins, and genes related to glycan syntheses from glycoscience and related fields. 25732693 2 21 gly glycoprotein 673:684 arg1 Human α1-acid-glycoprotein Human α1-acid-glycoprotein Fterm α1-acid-glycoprotein Human α1-acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. 25732693 2 21 gly glycoprotein 673:684 arg1 an acute phase serum glycoprotein an acute phase serum glycoprotein Fterm glycoprotein Human α1-acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. 25732693 2 72 gly α1-acid-glycoprotein 621:640 arg1 Human α1-acid-glycoprotein Human α1-acid-glycoprotein Fterm α1-acid-glycoprotein Human α1-acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. 25732693 2 72 gly α1-acid-glycoprotein 621:640 arg1 an acute phase serum glycoprotein an acute phase serum glycoprotein Fterm glycoprotein Human α1-acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. 29194986 6 36 gly present 1019:1025 arg2 the Asn-297 AND the N-glycan structures the Asn-297 the N-glycan structures Asn-297 Interactions between IgG and FcγR are influenced by the N-glycan structures present on the Asn-297. 25252784 4 83 gly glycosylation 855:867 arg1 2-N-carbamate-protected α-GlcN-lactol 2-N-carbamate-protected α-GlcN-lactol The α,α-(1↔1) linkage was attained by the glycosylation of 2-N-carbamate-protected α-GlcN-lactol with N-phenyl-trifluoroacetimidate of 2-O-methylated mannose. 27639389 4 21 gly proteins 853:860 arg1 N-and O-linked glycans proteins N-and O-linked glycans Fterm proteins Specifically, we characterized and statistically evaluated the expression of histo-blood group (A, B, O) antigens on N-and O-linked glycans from BEC membrane proteins of various individuals that represented different blood group type and secretor status using a porous graphitic carbon liquid chromatography electrospray ionization mass spectrometry (PGC-LC-ESI-MS) based glycomics approach. 27867116 1 10 gly glycoproteins 299:311 arg1 standard glycoproteins standard glycoproteins Fterm glycoproteins Here we demonstrate the potential of nano-UPLC-LTQ-FT-MS and the Byonic™ proteomic search engine for the separation, detection, and identification of N- and O-glycopeptide glycoforms in standard glycoproteins. 27867116 1 29 gly O-glycopeptide 261:274 arg2 O-glycopeptide O-glycopeptide O-glycopeptide Here we demonstrate the potential of nano-UPLC-LTQ-FT-MS and the Byonic™ proteomic search engine for the separation, detection, and identification of N- and O-glycopeptide glycoforms in standard glycoproteins. 24981920 1 19 gly glycopeptides 203:215 arg2 glycopeptides glycopeptides glycopeptides Despite the ubiquitous presence of proteoglycans in mammalian systems, methodologies to synthesize this class of glycopeptides with homogeneous glycans are not well developed. 30023556 7 9 gly have 1087:1090 arg1 glycopeptides AND GlcNAc glycopeptides GlcNAc glycopeptides Neither of them bound to glycopeptides with core 2 O-glycans that have GlcNAc at the O-6 position of the GalNAc residue. 30023556 7 67 gly glycopeptides 1046:1058 arg2 glycopeptides glycopeptides core 2 O-glycans glycopeptides Neither of them bound to glycopeptides with core 2 O-glycans that have GlcNAc at the O-6 position of the GalNAc residue. 28975713 6 8 gly glycopeptide 1176:1187 arg2 the correct glycopeptide identification the correct glycopeptide identification glycopeptide Additionally, a visualization chart incorporates glycan composition filtering, sorting by mass and tolerance, and an in silico peptide fragmentation diagram is provided to further support the correct glycopeptide identification. 28921955 1 61 gly glycoprotein 172:183 arg1 Influenza hemagglutinin Influenza hemagglutinin Fterm hemagglutinin Influenza hemagglutinin is a surface glycoprotein related to virus invasion and host immune system response. 28921955 1 61 gly glycoprotein 172:183 arg1 a surface glycoprotein a surface glycoprotein Fterm glycoprotein Influenza hemagglutinin is a surface glycoprotein related to virus invasion and host immune system response. 25188817 5 22 gly glycoproteins 788:800 arg1 full length glycoproteins full length glycoproteins Fterm glycoproteins In addition, we compare our simulated ensembles with the known structures for full length glycoproteins. 27503803 5 20 gly Gal-GalNAc-Thr 1120:1133 arg1 a Gal-GalNAc-Thr disaccharide Thr a Gal-GalNAc-Thr disaccharide Thr In addition, the putative anti-cancer derivative of DBP known as Gc Protein-derived Macrophage Activating Factor (GcMAF, which is formed by the combined action of β-galactosidase and neuraminidase upon DBP) was analyzed intact by ESI-MS, revealing that the activating E. coli β-galactosidase cleaves nothing from the protein-leaving the glycan structure of active GcMAF as a Gal-GalNAc-Thr disaccharide, regardless of the order in which β-galactosidase and neuraminidase are applied. 25053492 4 5 part_of ECD 765:767 arg1 Notch ECD fragments Notch ECD Notch ECD fragments OGER Site Notch ECD O95905 fragments Here we describe the expression and purification of Notch ECD fragments, digestion of the fragments with proteases to prepare for mass spectral analysis, and identification of peptides modified with O-glycans using mass spectrometry. 25053492 4 7 part_of Notch 759:763 arg1 Notch ECD fragments Notch ECD Notch ECD fragments OGER Site Notch ECD O95905 fragments Here we describe the expression and purification of Notch ECD fragments, digestion of the fragments with proteases to prepare for mass spectral analysis, and identification of peptides modified with O-glycans using mass spectrometry. 25053492 4 18 part_of fragments 797:805 arg1 Notch ECD fragments fragments Notch ECD fragments Fterm Site fragments fragments Here we describe the expression and purification of Notch ECD fragments, digestion of the fragments with proteases to prepare for mass spectral analysis, and identification of peptides modified with O-glycans using mass spectrometry. 28680094 7 64 part_of I-EGF1 1106:1111 arg1 the I-EGF1 domain EGF1 the I-EGF1 domain PUBTATOR Site EGF1 85476 domain In contrast, removal of the β3-N371 N-glycan near the β3 hybrid and I-EGF3 interface, or the β3-N452 N-glycan at the I-EGF1 domain rendered β3 integrin more active than the wild type. 26255982 4 28 gly released 476:483 arg2 proteins AND labeling O-glycans proteins labeling O-glycans Fterm proteins EXPERIMENTAL DESIGN We used the method of labeling O-glycans (released from proteins) with 1-phenyl-3-methyl-5-pyrazolone followed by LC-MS analysis. 26993603 0 38 gly N-glycosylation 5:19 arg2 Asn144 Asn144 Asn144 GP73 N-glycosylation at Asn144 reduces hepatocellular carcinoma cell motility and invasiveness. 29237727 7 14 gly N-glycoproteins 1215:1229 arg1 N-glycoproteins N-glycoproteins Fterm N-glycoproteins This analysis represents the most comprehensive and unbiased collection of Arabidopsis N-glycopeptides revealing an unsurpassed level of detail on the micro-heterogeneity present in N-glycoproteins of Arabidopsis. 29237727 7 45 gly N-glycopeptides 1120:1134 arg2 Arabidopsis N-glycopeptides Arabidopsis N-glycopeptides N-glycopeptides This analysis represents the most comprehensive and unbiased collection of Arabidopsis N-glycopeptides revealing an unsurpassed level of detail on the micro-heterogeneity present in N-glycoproteins of Arabidopsis. 29069609 9 96 part_of IgG1 1504:1507 arg1 IgG1 glycopeptides IgG1 IgG1 glycopeptides OGER Site IgG1 P01857 glycopeptides 21 glycoforms of IgG1 glycopeptides were identified including two truncated structures that are rarely reported. 26088564 3 65 gly attached 364:371 arg1 Asn85 AND the glycan chains Asn54, Asn75 and Asn85 the glycan chains Asn54, Asn75 and Asn85 In such events, the glycan chains attached to Asn54, Asn75 and Asn85 may become fucosylated, originating a sialyl-Lewis X epitope. 26088564 3 65 gly attached 364:371 arg1 Asn75 AND the glycan chains Asn54, Asn75 and Asn85 the glycan chains Asn54, Asn75 and Asn85 In such events, the glycan chains attached to Asn54, Asn75 and Asn85 may become fucosylated, originating a sialyl-Lewis X epitope. 26088564 3 65 gly attached 364:371 arg1 Asn75 AND the glycan chains Asn54, Asn75 and Asn85 the glycan chains Asn54, Asn75 and Asn85 In such events, the glycan chains attached to Asn54, Asn75 and Asn85 may become fucosylated, originating a sialyl-Lewis X epitope. 28956227 9 62 gly Asn149 1869:1874 arg1 N-glycan modifications Asn149 N-glycan modifications Asn149 Structural modeling analysis based on putative structures derived from bacterial-originated CD39 domain proteins suggests that N-glycan modifications at Asn149 next to ACR2 and/or Asn454, N-terminal to ACR5 have critical roles in regulating the catalytic pocket of NTPDase3/CD39L3. 30023556 8 13 gly glycopeptide 1233:1244 arg2 20-mer glycopeptide 20-mer glycopeptide glycopeptide Furthermore, 1B2 and 12D10 showed a strong binding to not only native MUC1 but also 20-mer glycopeptide with a monovalent epitope. 27617431 2 42 gly glycoforms 369:378 arg1 high-mannose and complex-type Env glycoforms high-mannose and complex-type Env glycoforms Variability in high-mannose and complex-type Env glycoforms leads to heterogeneity that usually precludes visualization of the native glycan shield. 24854630 3 102 gly glycoprotein 583:594 arg1 glycoprotein synthetic enzymes glycoprotein synthetic enzymes Fterm glycoprotein METHODS We interrogated prostate cancer gene expression data for reproducible changes in expression of glycoprotein synthetic enzymes. 28378791 6 19 gly GluN1-N440 792:801 arg1 glycans N440 glycans N440 Based on these results, and assuming the transferability of the results of LBD simulations to the full receptor, we predict that glycans at GluN1-N440 might play a potentiator role in NMDARs. 28039139 9 58 gly glycoprotein 1744:1755 arg1 S-layer glycoprotein folding S-layer glycoprotein folding Fterm glycoprotein Perturbed N-glycosylation thus affects S-layer glycoprotein folding. 28039139 9 67 gly N-glycosylation 1707:1721 arg1 S-layer glycoprotein folding S-layer glycoprotein folding Fterm glycoprotein Perturbed N-glycosylation thus affects S-layer glycoprotein folding. 26631508 10 30 gly fucosylated 1877:1887 arg1 the extended, fucosylated core 2 disialylated structure the extended, fucosylated core 2 disialylated structure A decrease in the extended, fucosylated core 2 disialylated structure on MUC7, residual mucosal wetness, and whole mouth saliva flow rate appeared to have a negative and cumulative effect on the perception of oral dryness. 26631508 10 84 gly disialylated 1896:1907 arg1 the extended, fucosylated core 2 disialylated structure the extended, fucosylated core 2 disialylated structure A decrease in the extended, fucosylated core 2 disialylated structure on MUC7, residual mucosal wetness, and whole mouth saliva flow rate appeared to have a negative and cumulative effect on the perception of oral dryness. 26208004 4 5 gly attached 654:661 arg2 E glycoprotein AND the N-glycans E glycoprotein the N-glycans Fterm glycoprotein However, the precise structures of the N-glycans that are attached to E glycoprotein remain elusive, although the crystal structure of DENV E has been determined. 26208004 4 8 gly glycoprotein 668:679 arg1 E glycoprotein E glycoprotein Fterm glycoprotein However, the precise structures of the N-glycans that are attached to E glycoprotein remain elusive, although the crystal structure of DENV E has been determined. 25029481 5 22 gly proteins 902:909 arg1 N-linked glycans proteins N-linked glycans Fterm proteins This technique consists of sectioning FFPE tissues, deparaffinization, and rehydration of the sections, denaturing tissue proteins, releasing N-linked glycans from proteins by printing peptide-N-glycosidase F over the sections, spray-coating the tissue with matrix, and analyzing N-glycans by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). 24295789 5 43 gly N-glycosylation 1385:1399 arg2 an evolutionarily conserved N-glycosylation site an evolutionarily conserved N-glycosylation site site The primary sequence suggests that the enzyme belongs to glycosyl hydrolase family 38 and the N-glycan sequence analysis revealed high-mannose oligosaccharides, which were found to be heterogeneous with varying number of hexoses viz, Man8-9GlcNAc2 and Glc1Man9GlcNAc2 in an evolutionarily conserved N-glycosylation site. 27428423 6 23 gly enzymes 1058:1064 arg1 O-GlcNAc enzymes O-GlcNAc Fterm enzymes Androgen exposure stimulated synthesis of glycan structures downstream of this core set of regulated enzymes including sialyl-Tn (sTn), sialyl Lewis(X) (SLe(X)), O-GlcNAc and chondroitin sulphate, suggesting androgen regulation of the core set of enzymes controls key steps in glycan synthesis. 24965454 2 91 part_of gp120 436:440 arg1 the gp120 outer domain gp120 the gp120 outer domain PUBTATOR Site gp120 3700 domain 2G12 is a unique, domain-exchanged antibody that binds exclusively to conserved N-linked glycans that form the high-mannose patch on the gp120 outer domain centered on a glycan at position N332. 24105809 2 25 gly glycoprotein 247:258 arg1 glycoprotein core structures glycoprotein core structures Fterm glycoprotein The expression of PLN on glycoprotein core structures minimally requires enzyme activities for β1,4-galactosyltransferase (β4GalT) and β1,3-N-acetylglucosminyltransferase (β3GnT). 28860626 3 52 part_of hemagglutinin 844:856 arg1 9 N-glycosylation sites hemagglutinin 9 N-glycosylation sites Fterm Site hemagglutinin sites Proteomic data analyses of the full-length protein sequences determined 9 N-glycosylation sites of hemagglutinin, and defined 6 N-glycosylation sites and the glycan structures of low abundance neuraminidase, which were occupied by high-mannose, hybrid and complex-type N-glycans. 28860626 3 60 part_of neuraminidase 938:950 arg1 6 N-glycosylation sites neuraminidase 6 N-glycosylation sites Fterm Site neuraminidase sites Proteomic data analyses of the full-length protein sequences determined 9 N-glycosylation sites of hemagglutinin, and defined 6 N-glycosylation sites and the glycan structures of low abundance neuraminidase, which were occupied by high-mannose, hybrid and complex-type N-glycans. 27439567 5 44 gly glycopeptides 736:748 arg2 The glycopeptides The glycopeptides glycopeptides The glycopeptides in each fraction were treated with PNGase F and then divided into halves. 26590834 5 61 gly N-glycan 1164:1171 arg1 the threonine the threonine the threonine AminoAcid threonine The Δmmp1090 deletion mutant was archaellated when examined by electron microscopy and mass spectrometry analysis of purified archaella showed that the archaellins were modified with a truncated N-glycan in which the terminal sugar residue and the threonine linked to the third sugar residue were missing. 25282312 4 61 gly glycopeptides 1113:1125 arg2 Neo glycopeptides Neo glycopeptides glycopeptides Neo glycopeptides were purified by on-line porous graphitized carbon solid-phase extraction, separated by hydrophilic interaction liquid chromatography and analyzed by electrospray mass spectrometry (ESI-MS(n)). 28887379 12 34 gly glycopeptides 1957:1969 arg2 960 unique glycopeptides 960 unique glycopeptides glycopeptides It is also used to identify 960 unique glycopeptides in cell lysates from prostate cancer cells. 26648038 10 58 gly N-glycosylation 1270:1284 arg1 the lectin the lectin Fterm lectin The N-glycosylation of the lectin involves a plant-specific glycan while that in toxic type II RIPs of known structure involves a glycan which is animal as well as plant specific. 28849661 1 15 part_of Syndecan-1 68:77 arg1 Syndecan-1 chondroitin sulfate glycopeptide Syndecan-1 Syndecan-1 chondroitin sulfate glycopeptide PUBTATOR Site Syndecan-1 6382 glycopeptide Syndecan-1 chondroitin sulfate glycopeptide was synthesized for the first time using the cassette approach. 27295180 0 4 gly Glycans 12:18 arg1 α1-Acid Glycoprotein Glycoprotein Glycans Fterm Glycoprotein Fucosylated Glycans in α1-Acid Glycoprotein for Monitoring Treatment Outcomes and Prognosis of Cancer Patients. 26059044 10 9 gly glycoproteins 1597:1609 arg1 recombinant glycoproteins recombinant glycoproteins Fterm glycoproteins Altogether, our data demonstrate that plants offer an excellent tool to investigate the role of N-glycosylation on folding and activity of recombinant glycoproteins, such as IL-22. 26993603 3 12 gly N-glycosylation 565:579 arg2 three GP73 N-glycosylation sites three GP73 N-glycosylation sites sites We identified three GP73 N-glycosylation sites: Asn109, Asn144 and Asn398. 26993603 3 51 gly sites 581:585 arg1 three GP73 N-glycosylation sites three GP73 N-glycosylation sites sites We identified three GP73 N-glycosylation sites: Asn109, Asn144 and Asn398. 26993603 3 12 gly N-glycosylation 565:579 arg2 Asn109 Asn109, Asn144 and Asn398 Asn109, Asn144 and Asn398 We identified three GP73 N-glycosylation sites: Asn109, Asn144 and Asn398. 26993603 3 12 gly N-glycosylation 565:579 arg2 Asn398 Asn109, Asn144 and Asn398 Asn109, Asn144 and Asn398 We identified three GP73 N-glycosylation sites: Asn109, Asn144 and Asn398. 26993603 3 12 gly N-glycosylation 565:579 arg2 Asn398 Asn109, Asn144 and Asn398 Asn109, Asn144 and Asn398 We identified three GP73 N-glycosylation sites: Asn109, Asn144 and Asn398. 26993603 3 51 gly sites 581:585 arg1 Asn144 Asn109, Asn144 and Asn398 Asn109, Asn144 and Asn398 We identified three GP73 N-glycosylation sites: Asn109, Asn144 and Asn398. 26993603 3 51 gly sites 581:585 arg1 Asn109 Asn109, Asn144 and Asn398 Asn109, Asn144 and Asn398 We identified three GP73 N-glycosylation sites: Asn109, Asn144 and Asn398. 26993603 3 51 gly sites 581:585 arg1 Asn109 Asn109, Asn144 and Asn398 Asn109, Asn144 and Asn398 We identified three GP73 N-glycosylation sites: Asn109, Asn144 and Asn398. 27439567 2 26 gly antennary-fucosylated 343:363 arg1 antennary-fucosylated glycosites antennary-fucosylated glycosites glycosites This procedure is applied to the glycoprotein alpha-1-antitrypsin (A1AT), which contains both core- and antennary-fucosylated glycosites. 27439567 2 41 gly glycoprotein 272:283 arg1 the glycoprotein alpha-1-antitrypsin the glycoprotein alpha-1-antitrypsin Fterm glycoprotein This procedure is applied to the glycoprotein alpha-1-antitrypsin (A1AT), which contains both core- and antennary-fucosylated glycosites. 27439567 2 64 gly glycosites 365:374 arg2 antennary-fucosylated glycosites antennary-fucosylated glycosites glycosites This procedure is applied to the glycoprotein alpha-1-antitrypsin (A1AT), which contains both core- and antennary-fucosylated glycosites. 24719303 4 18 gly non-glycosylated 761:776 arg1 the non-glycosylated isoform the non-glycosylated isoform Fterm isoform The results show that ROA spectroscopy is able to extract detailed spectral data of the glycan moieties of proteins, provided that the non-glycosylated isoform is available. 27791356 3 89 part_of mucin 519:523 arg1 the various mucin subdomains mucin the various mucin subdomains PUBTATOR Site mucin 281333 subdomains Thus, key structural information, such as the secondary structure of the various mucin subdomains, and glycosylation patterns along individual molecules, remains to be elucidated. 24664809 1 9 gly released 362:369 arg2 the glycoprotein AND fluorescence-labeled glycans the glycoprotein fluorescence-labeled glycans Fterm glycoprotein Protein N-Glycan analysis is traditionally performed by high pH anion exchange chromatography (HPAEC), reversed phase liquid chromatography (RPLC), or hydrophilic interaction liquid chromatography (HILIC) on fluorescence-labeled glycans enzymatically released from the glycoprotein. 24664809 1 55 gly glycoprotein 380:391 arg1 the glycoprotein the glycoprotein Fterm glycoprotein Protein N-Glycan analysis is traditionally performed by high pH anion exchange chromatography (HPAEC), reversed phase liquid chromatography (RPLC), or hydrophilic interaction liquid chromatography (HILIC) on fluorescence-labeled glycans enzymatically released from the glycoprotein. 27020775 3 1 part_of lactoferrin 781:791 arg1 donkey lactoferrin sequence lactoferrin donkey lactoferrin sequence PUBTATOR Site lactoferrin P02788 sequence Our results allowed the almost complete characterization of donkey lactoferrin sequence, that, at least for the covered sequence, differs from the horse genomic deduced sequence (UniProtKB Acc. 25759508 3 37 gly O-glycosylation 402:416 arg1 the IgG3 hinge region the IgG3 hinge region region This study reports partial O-glycosylation of the IgG3 hinge region, observed with nanoLC-ESI-IT-MS(/MS) analysis after proteolytic digestion. 23581857 1 72 gly glycosylated 384:395 arg1 the glycosylated Asn350 the glycosylated Asn350 Asn350 Its deficiency results in Metachromatic Leukodystrophy, whereas a minor condition called ARSA pseudodeficiency occurs in healthy individuals, which has been associated with the substitution of the glycosylated Asn350 by a Ser and with the loss of the polyadenylation signal. 25614628 7 13 gly groove 936:941 arg1 an additional bowl-like domain an additional bowl-like domain an additional bowl-like domain Site domain Structural comparison with PNGase F revealed a relatively larger glycan-binding groove in the catalytic domain and an additional bowl-like domain with unknown function at the N terminus of the candidate protein. 25614628 7 13 gly groove 936:941 arg1 the catalytic domain the catalytic domain the catalytic domain Site domain Structural comparison with PNGase F revealed a relatively larger glycan-binding groove in the catalytic domain and an additional bowl-like domain with unknown function at the N terminus of the candidate protein. 25833378 7 10 gly attached 978:985 arg1 the acceptor peptide AND the natural C. jejuni N-glycan the acceptor peptide the natural C. jejuni N-glycan peptide A three-dimensional homology model of membrane-associated PglBCj, docked to the natural C. jejuni N-glycan attached to the acceptor peptide, was used to identify potential sugar-interacting residues as targets for mutagenesis. 25818946 0 52 gly glycosylation 13:25 arg1 S-layer proteins S-layer proteins Fterm proteins Relevance of glycosylation of S-layer proteins for cell surface properties. 26891276 0 45 part_of Tau-Derived 54:64 arg1 a Tau-Derived Peptide Tau a Tau-Derived Peptide PUBTATOR Tau 4137 Selective Inhibition of Aggregation and Toxicity of a Tau-Derived Peptide using Its Glycosylated Analogues. 26598643 8 34 gly O-glycosylation 1465:1479 arg2 the O-glycosylation sites the O-glycosylation sites sites glycopeptides To pinpoint the O-glycosylation sites glycopeptides were fragmented using electron transfer dissociation. 26598643 8 39 gly glycopeptides 1487:1499 arg2 glycopeptides glycopeptides sites glycopeptides To pinpoint the O-glycosylation sites glycopeptides were fragmented using electron transfer dissociation. 28489325 0 43 gly Microheterogeneity 20:37 arg1 N-Glycans N-Glycans Reducing Macro- and Microheterogeneity of N-Glycans Enables the Crystal Structure of the Lectin and EGF-Like Domains of Human L-Selectin To Be Solved at 1.9 Å Resolution. 29042829 5 79 gly glycopeptides 1149:1161 arg2 glycopeptides glycopeptides glycopeptides However, statistically significant differences in the deglycosylation rate constants were observed between glycopeptides differing only in glycan structure (i.e., nonfucosylated, fucosylated, bisecting-GlcNAc, sialylated, etc.). 27938679 5 3 gly glycosylated 744:755 arg1 sites sites sites To determine which sites were actually glycosylated, we generated mutated SU forms, where each N-glycosylation site was changed to alanine (A). 27938679 5 51 gly N-glycosylation 800:814 arg2 each N-glycosylation site each N-glycosylation site site To determine which sites were actually glycosylated, we generated mutated SU forms, where each N-glycosylation site was changed to alanine (A). 27439567 4 62 gly glycopeptides 530:542 arg1 truncated glycans glycopeptides truncated glycans glycopeptides The resulting glycopeptides with truncated glycans were separated using an off-line HILIC (hydrophilic interaction liquid chromatography) separation where multiple fractions were collected at various time intervals. 27038031 9 21 part_of protein 1486:1492 arg1 the site-heterogeneity protein the site-heterogeneity Fterm Site protein site-heterogeneity This study highlights the information obtained by characterization of the site-heterogeneity of a highly glycosylated protein of high molecular mass with quaternary structure, revealing differences that would not be seen by global glycan or deglycosylated peptide profiling. 29048990 9 98 part_of sequons 1452:1458 arg1 the stalk region sequons the stalk region region Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 29048990 9 98 part_of sequons 1452:1458 arg1 the globular head sequons the globular head head Four glycosylation sequons on the stalk region (N28, N40, N304 and N498) and four on the globular head (N71, N104, N142 and N177) of the protein are occupied. 25927005 4 114 part_of proteins 611:618 arg1 glycansat several glycosylation sites proteins glycansat several glycosylation sites Fterm Site proteins sites It is believed that virion properties depend on glycosylation of the virus envelope proteins in a cell, while glycansat several glycosylation sites of these proteins play a pivotal role in protein functioning and the HCV life cycle. 25452312 10 13 gly N-glycopeptides 1098:1112 arg2 These enriched N-glycopeptides These enriched N-glycopeptides N-glycopeptides These enriched N-glycopeptides were solved for their peptide sequence, glycan composition, structure, and glycosylation site using collision-induced dissociation MS/MS (CID-tandem MS) data interpreted by a publicly available software GlycopeptideId. 25452312 10 19 gly glycosylation 1189:1201 arg2 glycosylation site glycosylation site site These enriched N-glycopeptides were solved for their peptide sequence, glycan composition, structure, and glycosylation site using collision-induced dissociation MS/MS (CID-tandem MS) data interpreted by a publicly available software GlycopeptideId. 24798328 6 79 part_of contain 865:871 arg1 the short linker regions AND an evolutionarily conserved O-glycosylation site the short linker regions an evolutionarily conserved O-glycosylation site site We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position -1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. 26812091 1 19 gly glycoproteins 219:231 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins Glycosylation is an important PTM and is critical for the manufacture and efficacy of therapeutic glycoproteins. 25759508 6 57 gly O-glycosylation 907:921 arg2 the site the site site NanoLC-ESI-IT-MS/MS with electron transfer dissociation fragmentation and CE-MS/MS with CID fragmentation were used to determine the site of IgG3 O-glycosylation. 28534482 6 4 gly N-glycopeptide 1005:1018 arg2 this highly efficient N-glycopeptide enrichment method this highly efficient N-glycopeptide enrichment method N-glycopeptide Most importantly, this highly efficient N-glycopeptide enrichment method enables the simultaneous determination of N-glycan composition and N-glycosites with a deeper coverage (compared to lectin enrichment) and improves large-scale N-glycoproteomics studies due to greatly reduced sample complexity. 28534482 6 45 gly N-glycosites 1105:1116 arg2 N-glycosites N-glycosites N-glycosites Most importantly, this highly efficient N-glycopeptide enrichment method enables the simultaneous determination of N-glycan composition and N-glycosites with a deeper coverage (compared to lectin enrichment) and improves large-scale N-glycoproteomics studies due to greatly reduced sample complexity. 24664809 4 29 gly N-glycopeptides 871:885 arg2 N-glycopeptides N-glycopeptides N-glycopeptides In this work, a recently developed glycopeptide fragmentation model was used for automated identification, based on their MS/MS, of N-glycopeptides from proteolytic digestion of monoclonal antibodies (mAbs). 24664809 4 54 gly glycopeptide 774:785 arg2 a recently developed glycopeptide fragmentation model a recently developed glycopeptide fragmentation model glycopeptide In this work, a recently developed glycopeptide fragmentation model was used for automated identification, based on their MS/MS, of N-glycopeptides from proteolytic digestion of monoclonal antibodies (mAbs). 28543513 6 81 gly sialylated 1045:1054 arg1 10 sialylated structures 10 sialylated structures In the case of C18-LC-MS/MS analysis, 25 glycan structures were identified of which 10 sialylated structures were found to be statistically significant between the two cohorts. 25628020 7 40 gly N-glycosylation 1282:1296 arg2 the novel N-glycosylation sites the novel N-glycosylation sites sites CONCLUSIONS: We propose that the novel N-glycosylation sites described in this study may be useful candidates for functional analyses to identify innovative genetic modifications for beneficial phenotypes acquired in the human lineage. 28737213 4 15 gly N-glycopeptides 591:605 arg2 intact N-glycopeptides intact N-glycopeptides N-glycopeptides Thereby, the analysis of intact N-glycopeptides allowed the determination of N-glycan compositions. 27938679 0 50 gly N-glycosylation 7:21 arg2 Single N-glycosylation site Single N-glycosylation site site Single N-glycosylation site of bovine leukemia virus SU is involved in conformation and viral escape. 27269286 3 29 gly galectin-glycoprotein 423:443 arg1 galectin-glycoprotein galectin-glycoprotein Here we report that N-glycan branching deficiency triggers the Golgi to generate bioequivalent N-glycans that preserve galectin-glycoprotein interactions and cellular homeostasis. 24903886 2 83 gly glycoproteins 367:379 arg1 truncated glycans glycoproteins truncated glycans Fterm glycoproteins For example, a mammalian cell glycosylation mutant lacking a specific glycosyltransferase generates glycoproteins, and/or glycolipids, and/or proteoglycans with truncated glycans missing the sugar transferred by that glycosyltransferase, as well as those sugars that would be added subsequently. 24798333 5 57 gly non-N-glycosylated 877:894 arg1 some incompletely folded non-N-glycosylated hδOR-Cys Cys(27) Cys(27) However, the N-glycan-independent QC was unable to compensate the N-glycan-dependent pathway, and some incompletely folded non-N-glycosylated hδOR-Cys(27) reached the cell surface in conformation incompatible with ligand binding. 26537799 10 45 gly fucosylated 1894:1904 arg1 highly fucosylated glycans and CDX1 and/or villin mRNA expression highly fucosylated glycans and CDX1 and/or villin mRNA expression Finally, correlation of CRC cell line glycosylation features with cancer cell markers and phenotypes revealed an association between highly fucosylated glycans and CDX1 and/or villin mRNA expression that both correlate with cell differentiation. 26729242 0 34 part_of core-1 44:49 arg1 mucin core-1 type glycopeptides mucin core-1 mucin core-1 type glycopeptides PUBTATOR Site mucin core-1 100508689 glycopeptides O-glycosylation sites identified from mucin core-1 type glycopeptides from human serum. 26729242 0 39 part_of mucin 38:42 arg1 mucin core-1 type glycopeptides mucin core-1 mucin core-1 type glycopeptides PUBTATOR Site mucin core-1 100508689 glycopeptides O-glycosylation sites identified from mucin core-1 type glycopeptides from human serum. 27581986 11 20 part_of CD4 1953:1955 arg1 The conserved CD4 binding site CD4 The conserved CD4 binding site PUBTATOR Site CD4 920 site IMPORTANCE The conserved CD4 binding site on gp120 is a major target for HIV-1 vaccine design, but key events in the elicitation and maturation of different antibody lineages to this site remain elusive. 27581986 11 78 part_of site 1965:1968 arg1 gp120 gp120 site PUBTATOR Site gp120 155971 site IMPORTANCE The conserved CD4 binding site on gp120 is a major target for HIV-1 vaccine design, but key events in the elicitation and maturation of different antibody lineages to this site remain elusive. 24612801 4 4 gly glycosylated 556:567 arg1 the only glycosylated protein the only glycosylated protein Fterm protein Among the components of casein, κ-CN is the only glycosylated protein that has been identified. 28444691 7 52 gly undersialylated 1194:1208 arg1 undersialylated and undergalactosylated biantennary and triantennary glycans undersialylated and undergalactosylated biantennary and triantennary glycans Serum N-glycome of COG5-CDG patients was characterized by the relative abundance of undersialylated and undergalactosylated biantennary and triantennary glycans as well as slight increase of high-mannose structures and hybrid glycans. 24644239 6 66 gly glycoproteins 903:915 arg1 these glycoproteins these glycoproteins Fterm glycoproteins Chemotaxis assays of these glycoproteins and the corresponding non-glycosylated proteins were carried out. 24644239 6 67 gly non-glycosylated 939:954 arg1 the corresponding non-glycosylated proteins the corresponding non-glycosylated proteins Fterm proteins Chemotaxis assays of these glycoproteins and the corresponding non-glycosylated proteins were carried out. 28585749 1 43 gly Glycosylation 172:184 arg1 proteins proteins Fterm proteins AIM Glycosylation of proteins is altered in cancer cells and distinctive glycan structures are associated with specific cancers, but little is known about the complete glycan profile of particular tumors. 24497634 9 34 gly N-glycosylation 1258:1272 arg2 the nine consensus N-glycosylation sites the nine consensus N-glycosylation sites sites To investigate precisely the role of contactin N-glycans, we have mutated each of the nine consensus N-glycosylation sites independently. 29285644 7 5 gly glycopeptides 1282:1294 arg2 Ninety-six glycopeptides Ninety-six glycopeptides glycopeptides Ninety-six glycopeptides, each corresponding to a unique glycan/glycosite pairing, were tracked across all cancer and control samples. 27209430 13 95 gly glycoprotein 2134:2145 arg1 a glycoprotein biomarker a glycoprotein biomarker Fterm glycoprotein CONCLUSIONS This is the first report of a glycoprotein biomarker using glycan change at a local lesion to assess disease activity in autoimmune diseases. 26869352 9 79 gly fucosylated 1513:1523 arg1 Lewis-type and core-type fucosylated N-glycans Lewis-type and core-type fucosylated N-glycans Lewis-type and core-type fucosylated N-glycans were increased in gastroenterological cancer samples, but only core-type fucosylated N-glycan was relatively increased in prostate cancer samples. 26869352 9 101 gly fucosylated 1608:1618 arg1 only core-type fucosylated N-glycan only core-type fucosylated N-glycan Lewis-type and core-type fucosylated N-glycans were increased in gastroenterological cancer samples, but only core-type fucosylated N-glycan was relatively increased in prostate cancer samples. 28334636 4 49 gly position 782:789 arg1 3a 3a position 3 The additional glucose was bound directly via a transglycosylation to rhoifolin at position 3a of the sugar moiety. 28934626 3 0 gly glycosylation 539:551 arg1 1,2:3,4-di-O-isopropylidene-α-D-galactopyranose 1,2:3,4-di-O-isopropylidene-α-D-galactopyranose These glycosyl donors were examined in the model glycosylation of the primary hydroxyl group of 1,2:3,4-di-O-isopropylidene-α-D-galactopyranose in comparison with sialyl donors without O-TFA groups. 27333379 7 34 gly α2,6-sialylated 1107:1121 arg1 the prevailing glycans the prevailing glycans Here, we expand our engineering repertoire by in planta generation of galactose-deficient and α2,6-sialylated O-glycans which are the prevailing glycans detected on IgA1 from patients with IgAN. 27333379 7 34 gly α2,6-sialylated 1107:1121 arg1 galactose-deficient and α2,6-sialylated O-glycans galactose-deficient and α2,6-sialylated O-glycans Here, we expand our engineering repertoire by in planta generation of galactose-deficient and α2,6-sialylated O-glycans which are the prevailing glycans detected on IgA1 from patients with IgAN. 27356208 6 74 part_of hFIX 997:1000 arg1 the first 45 residues hFIX the first 45 residues PUBTATOR Site hFIX 2158 residues With this aim, the first 45 residues of mature hFIX were explored to find out suitable positions for introducing either Asn or Ser/Thr residues, to create new N-glycosylation site(s). 24475074 8 59 part_of PTMs 1651:1654 arg1 Lys PTMs Lys OGER AminoAcid PTMs P20962 Lys Given the topology of the genetic code, mutation of (A) is more often nonsynonomous, and Lys, another target of many PTMs, is also encoded by two (A)-rich codons. 26160412 9 73 gly glycoproteins/glycopeptides 1421:1447 arg2 glycoproteins/glycopeptides glycoproteins/glycopeptides glycoproteins/glycopeptides Special emphasis was placed on the analysis of glycoproteins/glycopeptides bearing 'brain-type' N-glycans, representing potential biologically relevant structures in the field of neurodegenerative disorders. 27529638 3 29 gly glycosylated 466:477 arg1 a model protein protein peptide Fterm protein peptide A pharmaceutical peptide, glucagon-like peptide-1 (GLP-1), and a model protein, bovine α-Crystallin, were successfully glycosylated using such an approach. 27529638 3 29 gly glycosylated 466:477 arg1 bovine α-Crystallin α-Crystallin peptide Fterm α-Crystallin peptide A pharmaceutical peptide, glucagon-like peptide-1 (GLP-1), and a model protein, bovine α-Crystallin, were successfully glycosylated using such an approach. 27529638 3 29 gly glycosylated 466:477 arg1 glucagon-like peptide-1 protein peptide-1 Fterm protein peptide-1 A pharmaceutical peptide, glucagon-like peptide-1 (GLP-1), and a model protein, bovine α-Crystallin, were successfully glycosylated using such an approach. 27529638 3 29 gly glycosylated 466:477 arg1 glucagon-like peptide-1 α-Crystallin peptide-1 Fterm α-Crystallin peptide-1 A pharmaceutical peptide, glucagon-like peptide-1 (GLP-1), and a model protein, bovine α-Crystallin, were successfully glycosylated using such an approach. 25730103 8 53 gly sialylated 1320:1329 arg1 larger (in terms of total monosaccharide count) and more sialylated glycan structures larger (in terms of total monosaccharide count) and more sialylated glycan structures Closer examination revealed the preference for larger (in terms of total monosaccharide count) and more sialylated glycan structures in the MYCN-amplified samples in comparison to smaller, nonsialylated glycans that are more dominant in the MYCN-nonamplified samples. 27743366 4 65 gly glycopeptides 854:866 arg2 glycopeptides glycopeptides the glycans glycopeptides Peptide:N-glycosidase F is sufficient to isolate N-glycans from fungi and some protists, but in most invertebrates core α1,3-fucose is present, so release of the glycans from glycopeptides with peptide:N-glycosidases A is required. 25902405 2 42 part_of peptides 314:321 arg1 glycosylated Asn peptides glycosylated Asn Asn However, by current strategies for N-glycoproteome profiling, peptides with glycosylated Asn at N-terminus (PGANs), generated by protease digestion, could hardly be identified, due to the poor deglycosylation capacity by enzymes. 26858341 8 11 gly sialylated 1475:1484 arg1 sialylated structures sialylated structures The overall abundance of H-antigen carrying structures was decreased fivefold, while H-antigen precursors and sialylated structures were relatively more abundant in pigs with the FUT1 missense mutation. 25210040 2 42 gly peptide 468:474 arg1 peptide determinants peptide determinants Whereas previous studies have revealed evidence for peptide determinants as controlling elements in LacdiNAc biosynthesis, we report here on an entirely independent conformational control of GalNAc transfer by single TFF (Trefoil factor) domains as high stringency determinants. 25182382 2 100 gly N-glycopeptides 445:459 arg2 intact N-glycopeptides intact N-glycopeptides N-glycopeptides In this study, we present an analytical and computational strategy for the high throughput characterization of intact N-glycopeptides derived from complex proteome samples. 25629924 1 52 gly glycoprotein 125:136 arg1 a major glycoprotein a major glycoprotein Fterm glycoprotein Secretory immunoglobulin A (sIgA) is a major glycoprotein in milk and plays a key role in mediating immune protection of the gut mucosa. 27791356 5 27 gly glycosylated 963:974 arg1 the heavily glycosylated central mucin domain the heavily glycosylated central mucin domain domain ROA indicated that the protein backbone of MUC5B is dominated by unordered conformation, which was found to originate from the heavily glycosylated central mucin domain by isolation of MUC5B O-glycan-rich regions. 24889612 3 7 gly sialylated 374:383 arg1 O-linked sugar T antigen sTn O-linked sugar T antigen OGER sTn Q05639 Here we show that sialylated O-linked sugar T antigen (sTn) and its attached peptide region are both required for ligand recognition by PILRα. 25636227 10 26 gly O-glycosylated 1572:1585 arg1 core 4 O-glycosylated proteins core 4 O-glycosylated proteins The approach described herein is simple, sensitive, and global for site analysis of core 1 through core 4 O-glycosylated proteins. 25849464 6 103 gly N-glycosylation 984:998 arg2 the three N-glycosylation sites the three N-glycosylation sites sites Endo H-deglycosylated nLcc4 (dLcc4), with only one GlcNAc residue remaining at each of the three N-glycosylation sites in the enzyme, exhibited similar kinetic efficiency and thermal stability to that of nLcc4. 24352591 2 25 gly glycoproteins 434:446 arg1 carrier glycoproteins carrier glycoproteins Fterm glycoproteins Although whole/core glycan structures and carrier glycoproteins for the N-linked HNK-1 epitope have been studied, carrier glycoproteins and the biosynthetic pathway of the O-mannose-linked HNK-1 epitope have not been fully characterized. 24352591 2 41 gly glycoproteins 506:518 arg1 carrier glycoproteins carrier glycoproteins Fterm glycoproteins Although whole/core glycan structures and carrier glycoproteins for the N-linked HNK-1 epitope have been studied, carrier glycoproteins and the biosynthetic pathway of the O-mannose-linked HNK-1 epitope have not been fully characterized. 25202310 3 19 gly glycoproteins 726:738 arg1 the high-mannose-rich microsomal glycoproteins the high-mannose-rich microsomal glycoproteins LC-MS/MS-based quantitative glycomics showed that the secreted glycoproteins of eight human breast epithelial cells displaying diverse geno- and phenotypes consistently displayed more processed, primarily complex type, N-glycans than the high-mannose-rich microsomal glycoproteins. 25202310 3 73 gly glycoproteins 522:534 arg1 the secreted glycoproteins the secreted glycoproteins Fterm glycoproteins LC-MS/MS-based quantitative glycomics showed that the secreted glycoproteins of eight human breast epithelial cells displaying diverse geno- and phenotypes consistently displayed more processed, primarily complex type, N-glycans than the high-mannose-rich microsomal glycoproteins. 26791533 3 28 gly glycoproteins 466:478 arg1 seminal plasma glycoproteins seminal plasma glycoproteins Fterm glycoproteins It is suggested by multiple studies that seminal plasma glycoproteins play, largely undiscovered, important roles in the process of fertilization. 29069609 8 23 gly N-glycosylation 1392:1406 arg2 59 N-glycosylation sites 59 N-glycosylation sites sites This workflow was demonstrated by detection of 59 N-glycosylation sites from 41 glycoproteins from a HILIC enriched human plasma tryptic digest. 29069609 8 27 gly glycoproteins 1422:1434 arg1 41 glycoproteins 41 glycoproteins Fterm glycoproteins This workflow was demonstrated by detection of 59 N-glycosylation sites from 41 glycoproteins from a HILIC enriched human plasma tryptic digest. 28670741 2 54 gly fucosylated 573:583 arg1 fucosylated sidechains fucosylated sidechains In Arabidopsis thaliana, a glycosyl transferase family 37 (GT37) fucosyltransferase 1 (AtFUT1) catalyzes the regiospecific transfer of terminal 1,2-fucosyl residues to xyloglucan side chains - a key step in the biosynthesis of fucosylated sidechains of galactoxyloglucan. 28323417 4 18 gly glycopeptides 897:909 arg2 individual N-linked glycopeptides individual N-linked glycopeptides glycopeptides Linear trendlines were observed for the glycoforms of individual N-linked glycopeptides, the deglycosylated peptides, and the released, deutero-reduced permethylated glycans. 28323417 4 34 gly deglycosylated 916:929 arg1 the deglycosylated peptides the deglycosylated peptides peptides Linear trendlines were observed for the glycoforms of individual N-linked glycopeptides, the deglycosylated peptides, and the released, deutero-reduced permethylated glycans. 28323417 4 39 gly glycoforms 863:872 arg1 the deglycosylated peptides peptides the released, deutero-reduced permethylated glycans peptides Linear trendlines were observed for the glycoforms of individual N-linked glycopeptides, the deglycosylated peptides, and the released, deutero-reduced permethylated glycans. 28323417 4 39 gly glycoforms 863:872 arg1 individual N-linked glycopeptides glycopeptides the released, deutero-reduced permethylated glycans glycopeptides Linear trendlines were observed for the glycoforms of individual N-linked glycopeptides, the deglycosylated peptides, and the released, deutero-reduced permethylated glycans. 27585995 13 166 gly glycoprotein 2977:2988 arg1 various glycoprotein O-glycans various glycoprotein O-glycans Thus, the characteristic differences or changes of O-glycans in expression level usually relate to pathologies of many diseases and represent an important opportunity to uncover the functional mechanisms of various glycoprotein O-glycans. 27573070 9 23 gly used 1824:1827 arg2 N-glycopeptides N-glycopeptides N-glycopeptides Thus, gFinder is a convenient, high-throughput analytical tool for interpreting the tandem mass spectra of N-glycopeptides, which can then be used for identification of potential missing proteins having glycans. 27573070 9 78 gly N-glycopeptides 1789:1803 arg2 N-glycopeptides N-glycopeptides N-glycopeptides Thus, gFinder is a convenient, high-throughput analytical tool for interpreting the tandem mass spectra of N-glycopeptides, which can then be used for identification of potential missing proteins having glycans. 27573070 9 85 gly having 1878:1883 arg1 potential missing proteins AND glycans potential missing proteins glycans Fterm proteins Thus, gFinder is a convenient, high-throughput analytical tool for interpreting the tandem mass spectra of N-glycopeptides, which can then be used for identification of potential missing proteins having glycans. 29062024 4 64 gly Asn162 759:764 arg1 the N-glycan at Asn162 Asn162 the N-glycan at Asn162 Asn162 Our simulation highlights increased conformational fluctuation of the N-glycan at Asn162 of sFcγRIIIa upon fucosylation of IgG1-Fc, consistent with crystallographic data giving no interpretable electron density for this N-glycan, except for the innermost part. 29404022 6 51 gly contains 901:908 arg1 this database AND >8,700 N-glycans this database >8,700 N-glycans Fterm database In the initial version this database contains >8,700 N-glycans, and is compatible with MS instrument software and expandable. 24664808 3 26 gly glycopeptides 459:471 arg2 deprotonated glycopeptides deprotonated glycopeptides glycopeptides Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. 24664808 3 38 gly glycopeptide 540:551 arg2 glycopeptide signals glycopeptide signals glycopeptide Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. 24664808 3 51 gly glycopeptides 359:371 arg2 protonated glycopeptides protonated glycopeptides glycopeptides Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. 26925665 0 43 gly O-glycoprotein 27:40 arg1 O-glycoprotein Glycans O-glycoprotein Glycans Differential Expression of O-glycoprotein Glycans in Cholangiocarcinoma Cell Lines. 27333379 5 14 gly glycoproteins 812:824 arg1 recombinant glycoproteins recombinant glycoproteins Fterm glycoproteins Compared to other expression hosts, plants offer the opportunity for de novo synthesis of O-glycans on recombinant glycoproteins as they are lacking the mammalian O-glycosylation pathway. 28494147 3 38 gly O-glycosylated 568:581 arg1 the O-glycosylated carbohydrate-binding module the O-glycosylated carbohydrate-binding module By systematically comparing the structural features of the O-glycosylated carbohydrate-binding module of a Trichoderma reesei-derived Family 7 cellobiohydrolase, we were able to develop a better understanding of the influence of O-glycan structure on the molecule's physical stability. 28494147 3 43 gly cellobiohydrolase 652:668 arg1 the O-glycosylated carbohydrate-binding module cellobiohydrolase the O-glycosylated carbohydrate-binding module Fterm cellobiohydrolase By systematically comparing the structural features of the O-glycosylated carbohydrate-binding module of a Trichoderma reesei-derived Family 7 cellobiohydrolase, we were able to develop a better understanding of the influence of O-glycan structure on the molecule's physical stability. 27867116 5 67 gly glycosites 960:969 arg2 glycosites glycosites glycosites The method allows the straightforward and rapid obtention of a general glycosylated map of a given protein, including glycosites and their corresponding glycosylated structures. 29136858 6 13 gly glycopeptide 893:904 arg2 the glycopeptide level the glycopeptide level glycopeptide Here, we illustrate how the use of CE-ESI-MS method permits the comprehensive characterization of mAbs N-glycosylation at the glycopeptide level to perform relative quantitation of N-glycan species. 27873218 1 52 gly glycopeptides 232:244 arg2 glycopeptides glycopeptides glycopeptides Purification and liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of glycopeptides, originating from protease digests of glycoproteins, enables site-specific analysis of protein N- and O-glycosylations. 27873218 1 81 gly glycoproteins 284:296 arg1 glycoproteins glycoproteins Fterm glycoproteins Purification and liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of glycopeptides, originating from protease digests of glycoproteins, enables site-specific analysis of protein N- and O-glycosylations. 25142936 6 9 gly occupied 1058:1065 arg2 the glycosylation sites the glycosylation sites sites Whereas in brain s-eNPP6 all of the N-glycans were endo H-sensitive, in liver and kidney only one of the glycosylation sites was occupied by an endo H-sensitive glycan, likely N406, which is located within the cleft formed by the dimer interface. 25142936 6 11 gly glycosylation 1034:1046 arg2 the glycosylation sites the glycosylation sites sites Whereas in brain s-eNPP6 all of the N-glycans were endo H-sensitive, in liver and kidney only one of the glycosylation sites was occupied by an endo H-sensitive glycan, likely N406, which is located within the cleft formed by the dimer interface. 25142936 6 57 gly likely 1098:1103 arg1 N406 N406 N406 Whereas in brain s-eNPP6 all of the N-glycans were endo H-sensitive, in liver and kidney only one of the glycosylation sites was occupied by an endo H-sensitive glycan, likely N406, which is located within the cleft formed by the dimer interface. 26478188 3 28 part_of protein 714:720 arg1 the coiled-coil domain cartilage matrix protein the coiled-coil domain PUBTATOR Site cartilage matrix protein 4146 domain To overcome these limitations, we developed a simple and active dimeric CMP-Ang1 by replacing the N-terminal of native Ang1 with the coiled-coil domain of cartilage matrix protein (CMP) bearing mutations in its cysteine residues. 28079948 2 17 gly glycoproteins 444:456 arg1 glycoproteins glycoproteins Fterm glycoproteins Recent advances in glycoproteomics methodology and the "SimpleCell" strategy have enabled rapid identification of glycoproteins and specific glycosylation sites. 28079948 2 29 gly glycosylation 471:483 arg2 specific glycosylation sites specific glycosylation sites sites Recent advances in glycoproteomics methodology and the "SimpleCell" strategy have enabled rapid identification of glycoproteins and specific glycosylation sites. 24828077 7 44 gly glycosylation 1581:1593 arg2 glycosylation sites glycosylation sites sites Additionally, the ability of some bnmAbs to use other N-linked glycan sites can help counter neutralization escape mediated by shifting of glycosylation sites. 24352591 3 4 gly glycoprotein 695:706 arg1 the major carrier glycoprotein the major carrier glycoprotein Fterm glycoprotein Here, using mass spectrometric analyses, we identified the major carrier glycoprotein of the O-linked HNK-1 as phosphacan in developing mouse brains and determined the major O-glycan structures having the terminal HNK-1 epitope from partially purified phosphacan. 24803430 4 14 part_of EGF 805:807 arg1 EGF domains 11-13 EGF EGF domains 11-13 OGER Site EGF P01133 domains We have subsequently determined the crystal structures of EGF domains 11-13 of hN1 modified with either the O-fucose monosaccharide or the GlcNAc-fucose disaccharide at T466 of EGF12 and observed no change in backbone structure for each variant. 28935113 8 37 gly glycopeptide 1311:1322 arg2 glycopeptide mRNA display libraries glycopeptide mRNA display libraries glycopeptide Here, we provide an updated and optimized protocol for this method, which is designed to create glycopeptide mRNA display libraries containing ~1013 sequences and select them for target binding. 25210040 8 44 gly glycoproteins 1915:1927 arg1 extracellular matrix-related LacdiNAc-positive glycoproteins extracellular matrix-related LacdiNAc-positive glycoproteins The structural features of the LacdiNAc-inducing determinant on human TFF2 are discussed on the basis of crystal structures of porcine TFF2, and a series of extracellular matrix-related LacdiNAc-positive glycoproteins detected as novel candidate proteins in the secretome of HEK-293 cells. 28973586 7 6 part_of regions 931:937 arg1 ABP1 ABP1 regions PUBTATOR Site ABP1 P19801 regions The α-helix of C-terminal regions in ABP1 of both species unfolded during simulations, assuming a more extended structure in maize. 27412689 4 45 part_of proteins 839:846 arg1 tissue-specific regions proteins tissue-specific regions Fterm Site proteins regions A novel method for investigating tissue-specific N-linked glycans is using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) on formalin-fixed paraffin-embedded (FFPE) tissue sections that can spatially profile N-glycan compositions released from proteins in tissue-specific regions. 28729420 4 27 gly glycopeptides 946:958 arg2 glycopeptides glycopeptides glycopeptides Here, we revisited the substrate specificity of FUT8 by examining its in vitro activity toward an array of selected N-glycans, glycopeptides, and glycoproteins. 28729420 4 85 gly glycoproteins 965:977 arg1 glycoproteins glycoproteins Fterm glycoproteins Here, we revisited the substrate specificity of FUT8 by examining its in vitro activity toward an array of selected N-glycans, glycopeptides, and glycoproteins. 26383616 1 30 gly glycoprotein 160:171 arg1 other glycoprotein biopharmaceuticals other glycoprotein biopharmaceuticals Fterm glycoprotein Recent emergence in the use of monoclonal antibody therapeutics and other glycoprotein biopharmaceuticals requires high-throughput, robust, and automated techniques for their glycosylation analysis. 24279413 3 10 gly glycosylation 662:674 arg2 their corresponding glycosylation sites their corresponding glycosylation sites sites Although computational methods based on mass spectrometric data have proven to be effective in monitoring changes in the glycome, developing such methods for the glycoproteome are challenging, largely due to the inherent complexity in simultaneously studying glycan structures with their corresponding glycosylation sites. 24945257 2 16 gly glycoprotein 276:287 arg1 a 39 kDa glycoprotein a 39 kDa glycoprotein Fterm glycoprotein This defibrinogenating serine protease is a 39 kDa glycoprotein containing terminal disialyl-capped N-glycans. 24945257 2 36 gly containing 289:298 arg1 a 39 kDa glycoprotein AND terminal disialyl-capped N-glycans a 39 kDa glycoprotein terminal disialyl-capped N-glycans Fterm glycoprotein This defibrinogenating serine protease is a 39 kDa glycoprotein containing terminal disialyl-capped N-glycans. 25927005 8 58 gly glycosylation 1475:1487 arg2 glycosylation sites glycosylation sites sites Elimination of the single glycosylation sites of the E2 glycoprotein, except for the N6 site, did not affect its synthesis efficiency in Sf9 insect cells, while the electrophoretic mobility of mutant proteins increased in proportion to the decrease in the number of glycosylation sites. 25927005 8 135 gly glycoprotein 1265:1276 arg1 the E2 glycoprotein the E2 glycoprotein Fterm glycoprotein Elimination of the single glycosylation sites of the E2 glycoprotein, except for the N6 site, did not affect its synthesis efficiency in Sf9 insect cells, while the electrophoretic mobility of mutant proteins increased in proportion to the decrease in the number of glycosylation sites. 25927005 8 47 gly glycosylation 1235:1247 arg1 the E2 glycoprotein glycoprotein sites Fterm glycoprotein sites Elimination of the single glycosylation sites of the E2 glycoprotein, except for the N6 site, did not affect its synthesis efficiency in Sf9 insect cells, while the electrophoretic mobility of mutant proteins increased in proportion to the decrease in the number of glycosylation sites. 26439794 5 52 gly glycoproteins 821:833 arg1 the 44 glycoproteins the 44 glycoproteins Fterm glycoproteins The glycoproteomic approach to the human fetal lung fibroblasts membrane fraction resulted in the identification of over 272 glycoforms on 63 sites of the 44 glycoproteins. 26439794 5 64 gly glycoforms 788:797 arg2 63 sites 63 sites sites The glycoproteomic approach to the human fetal lung fibroblasts membrane fraction resulted in the identification of over 272 glycoforms on 63 sites of the 44 glycoproteins. 27439567 1 0 gly glycosites 210:219 arg2 core-fucosylated versus antennary-fucosylated glycosites core-fucosylated versus antennary-fucosylated glycosites glycosites A MS-based methodology has been developed for analysis of core-fucosylated versus antennary-fucosylated glycosites in glycoproteins. 27439567 1 5 gly antennary-fucosylated 188:208 arg1 core-fucosylated versus antennary-fucosylated glycosites core-fucosylated versus antennary-fucosylated glycosites glycosites A MS-based methodology has been developed for analysis of core-fucosylated versus antennary-fucosylated glycosites in glycoproteins. 27439567 1 10 gly glycoproteins 224:236 arg1 glycoproteins glycoproteins Fterm glycoproteins A MS-based methodology has been developed for analysis of core-fucosylated versus antennary-fucosylated glycosites in glycoproteins. 27439567 1 58 gly core-fucosylated 164:179 arg1 core-fucosylated versus antennary-fucosylated glycosites core-fucosylated versus antennary-fucosylated glycosites glycosites A MS-based methodology has been developed for analysis of core-fucosylated versus antennary-fucosylated glycosites in glycoproteins. 24780636 5 23 gly disialylated 732:743 arg1 disialylated biantennary glycans disialylated biantennary glycans Mass spectrometric analyses confirmed that Tf-2 is modified with disialylated biantennary glycans at both of the two N-glycosylation sites, which are similar to the N-glycans of sTf. 24780636 5 41 gly N-glycosylation 784:798 arg2 the two N-glycosylation sites the two N-glycosylation sites sites Mass spectrometric analyses confirmed that Tf-2 is modified with disialylated biantennary glycans at both of the two N-glycosylation sites, which are similar to the N-glycans of sTf. 26868756 4 8 gly glycoproteins 716:728 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins Therefore, this NbGNTI-RNAi would be a promising system for the production of therapeutic glycoproteins in plants. 29069609 2 8 gly glycopeptides 302:314 arg2 glycopeptides glycopeptides glycopeptides Identification of glycopeptides from data-dependent acquisition (DDA) relies on high quality MS/MS spectra of glycopeptide precursors and often requires manual validation to ensure confident assignments. 29069609 2 87 gly glycopeptide 394:405 arg2 glycopeptide glycopeptide glycopeptide Identification of glycopeptides from data-dependent acquisition (DDA) relies on high quality MS/MS spectra of glycopeptide precursors and often requires manual validation to ensure confident assignments. 26582203 2 68 gly N-glycosylation 324:338 arg2 its potential N-glycosylation site its potential N-glycosylation site site In order to decipher the function of its potential N-glycosylation site, we produced pro-KLK2 in Leishmania tarentolae cells and compared it with its non-glycosylated counterpart from Escherichia coli expression. 25820733 5 18 gly glycopeptide 1205:1216 arg2 glycopeptide glycopeptide glycopeptide Here, we describe protocols for the enrichment of bacterial glycopeptides using zwitterionic-hydrophilic interaction liquid chromatography (ZIC-HILIC) and their analysis using liquid chromatography coupled to electrospray ionization tandem mass spectrometry (LC-MS/MS) with collision-induced dissociation (CID) and higher energy collisional dissociation (HCD) fragmentation for glycan structure elucidation and glycopeptide identification. 25820733 5 47 gly glycopeptides 854:866 arg2 bacterial glycopeptides bacterial glycopeptides glycopeptides Here, we describe protocols for the enrichment of bacterial glycopeptides using zwitterionic-hydrophilic interaction liquid chromatography (ZIC-HILIC) and their analysis using liquid chromatography coupled to electrospray ionization tandem mass spectrometry (LC-MS/MS) with collision-induced dissociation (CID) and higher energy collisional dissociation (HCD) fragmentation for glycan structure elucidation and glycopeptide identification. 24798328 4 48 gly O-glycosylation 474:488 arg2 O-glycosylation sites O-glycosylation sites sites Recently we identified O-glycosylation sites in the linker regions between the characteristic LDLR class A repeats in several LDLR-related receptors using the "SimpleCell" O-glycoproteome shotgun strategy. 24798328 4 93 gly repeats 558:564 arg1 several LDLR-related receptors receptors repeats Fterm receptors Recently we identified O-glycosylation sites in the linker regions between the characteristic LDLR class A repeats in several LDLR-related receptors using the "SimpleCell" O-glycoproteome shotgun strategy. 25927005 7 21 part_of E2 1077:1078 arg1 the N-glycosylation sites E2 the N-glycosylation sites Cterm Site E2 sites In order to investigate these processes, point mutations of the N-glycosylation sites of HCV protein E2 (genotype 1b strain 274933RU) were generated and the mutant proteins were further analyzed in the baculovirus expression system. 27073020 3 1 gly glycoproteins 502:514 arg1 plasma glycoproteins plasma glycoproteins Fterm glycoproteins Since the majority of plasma glycoproteins originate from the liver, the HepG2 cells represent a good model for glycosylation changes in HCC that are detectable in blood, which is an easily accessible analytic material in a clinical setting. 24308717 11 24 gly N- 1608:1609 arg1 sites sites sites The determination of N- and O-glycans and O-glycosylation sites in etanercept provides a basis for future studies addressing the biological importance of specific protein glycosylations in the production of safe and efficacious biotherapeutics. 25818946 2 78 gly glycoprotein 534:545 arg1 the wild-type S-layer glycoprotein wtSgsE the wild-type S-layer glycoprotein wtSgsE Fterm glycoprotein Here, we show for the first time the recrystallization of the wild-type S-layer glycoprotein wtSgsE from Geobacillus stearothermophilus NRS 2004/3a and its recombinantly produced non-glycosylated form, rSgsE, on gold sensor surfaces. 27523326 7 29 gly glycosite 1113:1121 arg2 a particular glycosite a particular glycosite glycosite It is presented as a promising tool for assessing and refining the knowledge about the constraints that link a particular glycan structure to a particular glycosite, and in the long term, this application could help improve prediction tools. 27869200 7 71 gly glycopeptides 1232:1244 arg2 HILIC enriched glycopeptides HILIC enriched glycopeptides glycopeptides Finally, the performance of the developed predictive model was evaluated in HILIC enriched glycopeptides extracted from human serum. 29404022 1 26 gly glycosylation 124:136 arg1 proteins proteins Fterm proteins The glycosylation of proteins is responsible for their structural and functional roles in many cellular activities. 26482295 7 60 gly glycosylate 1332:1342 arg1 the Fc domain human immunoglobulin G domain Cterm human immunoglobulin G domain One notable example is D. gigas PglB, which was the only bacterial OST to glycosylate the Fc domain of human immunoglobulin G at its native 'QYNST' sequon. 26598643 6 36 gly O-glycopeptide 1110:1123 arg2 Enriched O-glycopeptide fractions Enriched O-glycopeptide fractions O-glycopeptide Enriched O-glycopeptide fractions were subjected to mass spectrometric analysis using reversed-phase liquid chromatography coupled online to an ion trap mass spectrometer operated in positive-ion mode. 24341799 2 35 part_of Cel7A 483:487 arg1 the catalytic domain Cel7A the catalytic domain Cterm Site Cel7A domain We present two new structures of the catalytic domain of Hypocrea jecorina GH Family 7 cellobiohydrolase Cel7A, namely a Michaelis complex with a full cellononaose ligand and a glycosyl-enzyme intermediate, that reveal details of the 'static' reaction coordinate. 25160934 2 22 part_of gp120-CD4 464:472 arg1 gp120-CD4(+) binding site CD4 gp120-CD4(+) binding site PUBTATOR Site CD4 920 site DESIGN: Monoclonal antibodies, derived from Chinese hamster ovary cells or Epstein-Barr virus-immortalized mouse heteromyelomas, with specificity to key regions of the HIV envelope including gp120-V2, gp120-V3 loop, gp120-CD4(+) binding site, and gp41-specific antibodies, were functionally profiled to determine the relative contribution of the variable and constant domain features of the antibodies in driving robust Fc-effector functions. 27798070 5 50 gly motifs 1050:1055 arg1 the well-recognized and important glycan motifs the well-recognized and important glycan motifs Data from radioisotope assays and detailed product analysis by sequential tandem mass spectrometry show that blood has the capacity to generate many of the well-recognized and important glycan motifs, including the Lewis, sialyl-Lewis, H- and Sialyl-T antigens. 27798070 5 50 gly motifs 1050:1055 arg1 the Lewis, sialyl-Lewis, H- and Sialyl-T antigens the Lewis, sialyl-Lewis, H- and Sialyl-T antigens Data from radioisotope assays and detailed product analysis by sequential tandem mass spectrometry show that blood has the capacity to generate many of the well-recognized and important glycan motifs, including the Lewis, sialyl-Lewis, H- and Sialyl-T antigens. 27798070 5 50 gly motifs 1050:1055 arg1 many many Data from radioisotope assays and detailed product analysis by sequential tandem mass spectrometry show that blood has the capacity to generate many of the well-recognized and important glycan motifs, including the Lewis, sialyl-Lewis, H- and Sialyl-T antigens. 29069609 5 4 gly N-glycosylation 922:936 arg2 all three N-glycosylation sites all three N-glycosylation sites sites The advantage of MRM-HR over DDA for N-glycopeptide detection was demonstrated from targeted analysis of bovine fetuin where all three N-glycosylation sites were detected, which was not the case with DDA. 29069609 5 75 gly N-glycopeptide 824:837 arg2 N-glycopeptide detection N-glycopeptide detection N-glycopeptide The advantage of MRM-HR over DDA for N-glycopeptide detection was demonstrated from targeted analysis of bovine fetuin where all three N-glycosylation sites were detected, which was not the case with DDA. 28539451 3 45 part_of gp120 460:464 arg1 the gp120 V3 region gp120 the gp120 V3 region PUBTATOR Site gp120 3700 region Among the latter are epitopes in the gp120 V3 region that are highly immunogenic when SOSIP trimers are evaluated in animal models. 28539451 3 48 part_of epitopes 444:451 arg1 the gp120 V3 region epitopes the gp120 V3 region region Among the latter are epitopes in the gp120 V3 region that are highly immunogenic when SOSIP trimers are evaluated in animal models. 29065342 5 14 gly glycopeptides 848:860 arg2 complex glycopeptides complex glycopeptides glycopeptides The described approach is broadly applicable to the synthesis of a variety of complex glycopeptides containing O-linked LeX or sialyl LewisX (sLeX). 29065342 5 23 gly containing 862:871 arg1 complex glycopeptides AND sialyl LewisX complex glycopeptides sialyl LewisX glycopeptides The described approach is broadly applicable to the synthesis of a variety of complex glycopeptides containing O-linked LeX or sialyl LewisX (sLeX). 26701617 5 74 gly O-glycosylation 846:860 arg2 putative O-glycosylation sites putative O-glycosylation sites sites We demonstrated that PDGF-BB was O-glycosylated during the secretion process and detected putative O-glycosylation sites using glycosylation staining and immunoblotting. 25095792 4 29 part_of c 712:712 arg1 Lys Cyt c Lys PUBTATOR AminoAcid Cyt c 54205 Lys RESULTS Three different molecular weight glycans (lactose and two dextrans with 1 kD and 10 kD) were chemically coupled to surface exposed Cyt c lysine (Lys) residues using succinimidyl chemistry via amide bonds. 25095792 4 29 part_of c 712:712 arg1 surface exposed Cyt c lysine Cyt c surface exposed Cyt c lysine PUBTATOR AminoAcid Cyt c 54205 lysine RESULTS Three different molecular weight glycans (lactose and two dextrans with 1 kD and 10 kD) were chemically coupled to surface exposed Cyt c lysine (Lys) residues using succinimidyl chemistry via amide bonds. 25095792 4 83 part_of Cyt 708:710 arg1 Lys Cyt c Lys PUBTATOR AminoAcid Cyt c 54205 Lys RESULTS Three different molecular weight glycans (lactose and two dextrans with 1 kD and 10 kD) were chemically coupled to surface exposed Cyt c lysine (Lys) residues using succinimidyl chemistry via amide bonds. 25095792 4 83 part_of Cyt 708:710 arg1 surface exposed Cyt c lysine Cyt c surface exposed Cyt c lysine PUBTATOR AminoAcid Cyt c 54205 lysine RESULTS Three different molecular weight glycans (lactose and two dextrans with 1 kD and 10 kD) were chemically coupled to surface exposed Cyt c lysine (Lys) residues using succinimidyl chemistry via amide bonds. 24797265 12 70 gly glycosylation 1686:1698 arg2 glycosylation sites glycosylation sites sites Electron transfer dissociation was used to assign glycosylation sites leading to the unambiguous identification of six serines and one threonine residues. 25359784 3 36 part_of N-glycosylated 416:429 arg1 an N-glycosylated residue N-glycosylated an N-glycosylated residue Cterm Site N-glycosylated residue To investigate the function of N-glycan in IPU, we focused on an N-glycosylated residue located in the vicinity of the active site, Asn448. 26812091 7 42 gly O-glycopeptides 1084:1098 arg2 The O-glycopeptides The O-glycopeptides O-glycopeptides The O-glycopeptides of both hFSHs, which have not been described previously, were characterized herein. 24467287 1 58 gly glycoproteins 228:240 arg1 viral envelope glycoproteins viral envelope glycoproteins Fterm glycoproteins Cross-species viral transmission subjects parent and progeny alphaviruses to differential post-translational processing of viral envelope glycoproteins. 28849661 3 11 gly glycopeptide 267:278 arg2 The glycopeptide The glycopeptide glycopeptide The glycopeptide was successfully assembled via a 2+ (3 + 3) glycosylation strategy followed by peptide chain elongation. 24981920 4 6 gly glycopeptides 849:861 arg2 glycopeptides glycopeptides glycopeptides A successful strategy was established by constructing the partially deprotected single glycan chain containing glycopeptides first, followed by union of the glycan-bearing fragments and cleavage of the ester-type protecting groups. 26231935 7 10 gly N-glycosylation 1277:1291 arg2 different N-glycosylation sites different N-glycosylation sites sites The binding affinity with lectins showed no significant difference between various N-glycosylation mutants, which suggested that similar glycan composition should be resulted from different N-glycosylation sites. 26840264 5 67 gly glycosylation 1041:1053 arg1 plasmatic β4 galactosyltransferase plasmatic β4 galactosyltransferase Fterm galactosyltransferase In cohorts of individuals ranging from infancy to centenarians we determined the activity of plasmatic β4 galactosyltransferase(s) (B4GALTs) and of α2,6-sialyltransferase ST6GAL1, the glycosylation of IgG, the GlycoAge test (a glycosylation-based marker of aging) and the plasma level of inflammatory and liver damage markers. 26565680 3 4 gly glycopeptide 513:524 arg2 a glycopeptide a glycopeptide glycopeptide In addition, a glycopeptide may contain multiple glycosylation sites, making the problem complex. 26565680 3 14 gly glycosylation 547:559 arg2 multiple glycosylation sites multiple glycosylation sites sites In addition, a glycopeptide may contain multiple glycosylation sites, making the problem complex. 25265424 5 23 part_of carry 847:851 arg1 all three proteins AND H epitopes all three proteins H epitopes Fterm Site proteins epitopes MSn analysis of permethylated detached glycans confirms the presence of LeY glycoforms on haptoglobin, which cannot be detected in hemopexin or complement factor H; all three proteins carry Lewis and H epitopes. 25883177 11 111 gly multifucosylated 2034:2049 arg1 multifucosylated GlcNAc repeats multifucosylated GlcNAc repeats Lipid glycans with multifucosylated GlcNAc repeats were present throughout egg development, but with the longer highly fucosylated stretches enriched in mature eggs and miracidia. 24327294 4 58 gly asparagine-linked 676:692 arg1 the asparagine-linked glycans asparagine the asparagine-linked glycans asparagine However, the asparagine-linked glycans on the surface of glycosylated BChE may interfere with the PEGylation modification. 26850169 4 59 gly attached 736:743 arg1 a conserved asparagine AND N-linked glycans a conserved asparagine N-linked glycans asparagine The affinity of IgG Fc for binding activating Fc receptors depends on IgG subclass and the composition of N-linked glycans attached to a conserved asparagine in the Fc CH2 domain. 25927005 11 136 gly glycosylation 1931:1943 arg2 single glycosylation sites HCV E2 sites Cterm HCV E2 sites In addition, elimination of single glycosylation sites of HCV E2 had no impact on the RNA synthesis of structural proteins and formation of virus-like particles in insect and mammalian cells. 25732693 0 115 gly alfa-acid-glycoprotein 46:67 arg1 human alfa-acid-glycoprotein alfa-acid-glycoprotein N-glycans Fterm alfa-acid-glycoprotein Quantitative analysis of N-glycans from human alfa-acid-glycoprotein using stable isotope labeling and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry as tool for pancreatic disease diagnosis. 27873218 2 15 gly glycopeptides 487:499 arg2 CS-glycopeptides CS-glycopeptides CS-glycopeptides We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive mode LC-MS/MS. 27873218 2 15 gly glycopeptides 487:499 arg2 chondroitin sulfate-containing glycopeptides chondroitin sulfate-containing glycopeptides glycopeptides We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive mode LC-MS/MS. 27873218 2 73 gly CS-glycopeptides 502:517 arg2 CS-glycopeptides CS-glycopeptides CS-glycopeptides We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive mode LC-MS/MS. 27873218 2 73 gly CS-glycopeptides 502:517 arg2 chondroitin sulfate-containing glycopeptides chondroitin sulfate-containing glycopeptides glycopeptides We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive mode LC-MS/MS. 26918373 5 12 gly glycoproteins 830:842 arg1 these glycoproteins these glycoproteins Fterm glycoproteins Lectin binding signals were analyzed to generate glycan profiles that were generally consistent with the known glycan patterns for these glycoproteins. 26083095 4 15 gly fucosylated 598:608 arg1 the fucosylated polysaccharides the fucosylated polysaccharides Further manipulations on the fucosylated polysaccharides, including multiple de-O-benzylation and sulfation, furnished for the first time nonanimal sourced fucosylated chondroitin sulfates (fCSs)-polysaccharides obtained so far exclusively from sea cucumbers (Echinoidea, Holothuroidea) and showing several very interesting biological activities. 26083095 4 36 gly fucosylated 725:735 arg1 sourced fucosylated chondroitin sulfates sourced fucosylated chondroitin sulfates Further manipulations on the fucosylated polysaccharides, including multiple de-O-benzylation and sulfation, furnished for the first time nonanimal sourced fucosylated chondroitin sulfates (fCSs)-polysaccharides obtained so far exclusively from sea cucumbers (Echinoidea, Holothuroidea) and showing several very interesting biological activities. 26083095 4 36 gly fucosylated 725:735 arg1 fCSs fCSs Further manipulations on the fucosylated polysaccharides, including multiple de-O-benzylation and sulfation, furnished for the first time nonanimal sourced fucosylated chondroitin sulfates (fCSs)-polysaccharides obtained so far exclusively from sea cucumbers (Echinoidea, Holothuroidea) and showing several very interesting biological activities. 25587188 8 44 part_of ACPA 1199:1202 arg1 the (hyper)variable domains ACPA the (hyper)variable domains PUBTATOR Site ACPA 5657 domains Structural analysis revealed that a high frequency of N-glycans in the (hyper)variable domains of ACPA is responsible for this observation. 28516782 7 59 gly N-glycosylation 1178:1192 arg2 the individual N-glycosylation sites the individual N-glycosylation sites sites The site-specific analysis revealed major differences between the individual N-glycosylation sites of each IgA subtype. 25300029 3 44 gly observed 678:685 arg1 α3 integrin AND Higher molecular weight glycan structures integrin sites Higher molecular weight glycan structures Fterm integrin sites Higher molecular weight glycan structures with a different monosaccharide composition were observed at two sites, namely, Asn-925 and Asn-928 sites in α3 integrin isolated from Pkd1(+/+) cells compared with Pkd1(-/-) cells. 25300029 3 44 gly observed 678:685 arg1 α3 integrin AND Higher molecular weight glycan structures integrin Asn-925 and Asn-928 sites Higher molecular weight glycan structures Fterm integrin Asn-925 and Asn-928 sites Higher molecular weight glycan structures with a different monosaccharide composition were observed at two sites, namely, Asn-925 and Asn-928 sites in α3 integrin isolated from Pkd1(+/+) cells compared with Pkd1(-/-) cells. 26098314 6 51 gly O-glycosylation 1143:1157 arg2 potential cancer-specific O-glycosylation sites potential cancer-specific O-glycosylation sites sites This article addresses the recent application of genetically engineered cancer cell models to produce simplified homogenous O-glycans allowing the characterization of cancer cells O-glycoproteomes, using advanced mass spectrometry methods and the identification of potential cancer-specific O-glycosylation sites. 25452312 14 79 gly N-glycopeptides 1611:1625 arg2 these N-glycopeptides these N-glycopeptides N-glycopeptides The peptide sequences of these N-glycopeptides were identified unambiguously and their glycan composition (for 125 N-glycopeptides) and structures (for 87 N-glycopeptides) were proposed. 25452312 14 81 gly N-glycopeptides 1695:1709 arg2 125 N-glycopeptides 125 N-glycopeptides N-glycopeptides The peptide sequences of these N-glycopeptides were identified unambiguously and their glycan composition (for 125 N-glycopeptides) and structures (for 87 N-glycopeptides) were proposed. 25452312 14 91 gly N-glycopeptides 1735:1749 arg2 87 N-glycopeptides 87 N-glycopeptides N-glycopeptides The peptide sequences of these N-glycopeptides were identified unambiguously and their glycan composition (for 125 N-glycopeptides) and structures (for 87 N-glycopeptides) were proposed. 28510654 0 30 gly Asn-linked 0:9 arg1 Asn-linked oligosaccharide chain Asn Asn-linked oligosaccharide chain Asn Asn-linked oligosaccharide chain of a crenarchaeon, Pyrobaculum calidifontis, is reminiscent of the eukaryotic high-mannose-type glycan. 28935113 2 88 gly glycoproteins 310:322 arg1 glycoproteins glycoproteins Fterm glycoproteins Because of the abundance and importance of glycosylation in nature, directed evolution of glycopeptides and glycoproteins is also highly desirable. 28935113 2 90 gly glycopeptides 292:304 arg2 glycopeptides glycopeptides glycopeptides Because of the abundance and importance of glycosylation in nature, directed evolution of glycopeptides and glycoproteins is also highly desirable. 29404022 0 45 gly glycoproteins 24:36 arg1 glycoproteins glycoproteins Fterm glycoproteins N-glycans released from glycoproteins using a commercial kit and comprehensively analyzed with a hypothetical database. 29224385 9 43 gly fucosylated 1528:1538 arg1 fucosylated N-glycans fucosylated N-glycans The increase of nonsialylated, nonfucosylated N-glycans and decrease of fucosylated N-glycans are associated with the development of osteonecrosis of the femoral head. 29224385 9 81 gly nonsialylated 1472:1484 arg1 nonsialylated, nonfucosylated N-glycans nonsialylated, nonfucosylated N-glycans The increase of nonsialylated, nonfucosylated N-glycans and decrease of fucosylated N-glycans are associated with the development of osteonecrosis of the femoral head. 25552259 3 60 gly glycophorin 566:576 arg1 oligosaccharide attachment sites glycophorin oligosaccharide attachment sites Fterm glycophorin Adv Exp Med Biol, 491:155-169; Tomita M and Marchesi VT. 1975, Amino-acid sequence and oligosaccharide attachment sites of human erythrocyte glycophorin. 26316330 4 45 gly glycoprotein 434:445 arg1 glycoprotein species" glycoprotein species" Fterm glycoprotein We therefore introduced a new term called "glycoprotein species" to join the two concepts from different fields of biology. 28938401 7 4 gly multifucosylated 1295:1310 arg1 multifucosylated glycans multifucosylated glycans Results Four groups of neutral N-glycan signals were more abundant in metastasized tumors than in nonmetastasized tumors: complex-type N-glycan signals of cancer-associated terminal N-acetylglucosamine, multifucosylated glycans (complex fucosylation), hybrid-type N-glycans, and fucosylated pauci-mannose-type N-glycans. 28938401 7 4 gly multifucosylated 1295:1310 arg1 complex fucosylation complex fucosylation Results Four groups of neutral N-glycan signals were more abundant in metastasized tumors than in nonmetastasized tumors: complex-type N-glycan signals of cancer-associated terminal N-acetylglucosamine, multifucosylated glycans (complex fucosylation), hybrid-type N-glycans, and fucosylated pauci-mannose-type N-glycans. 28938401 7 106 gly fucosylated 1371:1381 arg1 fucosylated pauci-mannose-type N-glycans fucosylated pauci-mannose-type N-glycans Results Four groups of neutral N-glycan signals were more abundant in metastasized tumors than in nonmetastasized tumors: complex-type N-glycan signals of cancer-associated terminal N-acetylglucosamine, multifucosylated glycans (complex fucosylation), hybrid-type N-glycans, and fucosylated pauci-mannose-type N-glycans. 25004930 1 64 part_of G 227:227 arg1 the constant fragment immunoglobulin G the constant fragment Cterm Site immunoglobulin G fragment The N-linked glycosylation of the constant fragment (Fc) of immunoglobulin G has been shown to change during pathological and physiological events and to strongly influence antibody inflammatory properties. 26067753 1 8 gly glycosite 201:209 arg2 a glycosite a glycosite glycosite We investigated N-glycan processing of immunoglobulin G1 using the monoclonal antibody cetuximab (CxMab), which has a glycosite in the Fab domain in addition to the conserved Fc glycosylation, as a reporter. 27523326 1 38 gly glycosylation 158:170 arg2 glycosylation sites glycosylation sites sites GlycoSiteAlign is a tool designed to align amino acid sequences of variable length surrounding glycosylation sites depending on the knowledge of glycan structure. 28534482 0 32 gly N-glycopeptides 101:115 arg2 N-glycopeptides N-glycopeptides N-glycopeptides An engineered high affinity Fbs1 carbohydrate binding protein for selective capture of N-glycans and N-glycopeptides. 27573070 3 13 gly N-glycopeptides 614:628 arg2 native N-glycopeptides native N-glycopeptides N-glycopeptides Here we report on the development of gFinder, a web-based bioinformatics tool that analyzes mixtures of native N-glycopeptides that have been profiled by tandem MS. gFinder not only enables the simultaneous integration of collision-induced dissociation (CID) and high-energy collisional dissociation (HCD) fragmentation but also merges the spectra for high-throughput analysis. 25450502 4 57 gly O-glycopeptides 724:738 arg2 28 O-glycopeptides 28 O-glycopeptides O-glycopeptides We detected 28 O-glycopeptides from 7 O-glycosylation regions of human OPN, occupied by highly heterogeneous O-glycans. 28060516 7 5 gly N193 1275:1278 arg1 the globular head the globular head the globular head Our major findings include (1) decreasing complexity of glycosylation from the stem to the globular head, (2) absence of glycosylation at N10 and N193, (3) complex glycans at N165 in HEK293T cell HA but high mannose glycans at this site in HEK293S and S2 cells, and (4) differences between the three-dimensional structures of H3 and H5 HAs that may explain glycan type preferences at selected sites. 28060516 7 18 gly N10 1267:1269 arg1 the globular head the globular head the globular head Our major findings include (1) decreasing complexity of glycosylation from the stem to the globular head, (2) absence of glycosylation at N10 and N193, (3) complex glycans at N165 in HEK293T cell HA but high mannose glycans at this site in HEK293S and S2 cells, and (4) differences between the three-dimensional structures of H3 and H5 HAs that may explain glycan type preferences at selected sites. 28060516 7 33 gly site 1361:1364 arg1 the globular head the globular head the globular head Our major findings include (1) decreasing complexity of glycosylation from the stem to the globular head, (2) absence of glycosylation at N10 and N193, (3) complex glycans at N165 in HEK293T cell HA but high mannose glycans at this site in HEK293S and S2 cells, and (4) differences between the three-dimensional structures of H3 and H5 HAs that may explain glycan type preferences at selected sites. 28060516 7 72 gly head 1229:1232 arg1 the globular head, (2) absence of glycosylation at N10 and N193, (3) complex glycans at N165 in HEK293T cell HA but high mannose glycans at this site in HEK293S and S2 cells, and (4) differences the globular head, (2) absence of glycosylation at N10 and N193, (3) complex glycans at N165 in HEK293T cell HA but high mannose glycans at this site in HEK293S and S2 cells, and (4) differences Our major findings include (1) decreasing complexity of glycosylation from the stem to the globular head, (2) absence of glycosylation at N10 and N193, (3) complex glycans at N165 in HEK293T cell HA but high mannose glycans at this site in HEK293S and S2 cells, and (4) differences between the three-dimensional structures of H3 and H5 HAs that may explain glycan type preferences at selected sites. 28060516 7 86 gly N165 1304:1307 arg1 the globular head the globular head the globular head Our major findings include (1) decreasing complexity of glycosylation from the stem to the globular head, (2) absence of glycosylation at N10 and N193, (3) complex glycans at N165 in HEK293T cell HA but high mannose glycans at this site in HEK293S and S2 cells, and (4) differences between the three-dimensional structures of H3 and H5 HAs that may explain glycan type preferences at selected sites. 25092234 7 60 gly glycopeptides 999:1011 arg2 hFXI glycopeptides hFXI glycopeptides glycopeptides Analysis of hFXI glycopeptides by LC-MS/MS enabled site-specific glycan profiling and occupancy. 26051934 6 3 gly glycans 883:889 arg1 uncleaved, non-native oligomeric gp140 proteins proteins glycans Fterm proteins The glycans on uncleaved, non-native oligomeric gp140 proteins are also highly processed. 27287011 0 26 gly glycoproteins 183:195 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins LC-MS analysis combined with principal component analysis and soft independent modelling by class analogy for a better detection of changes in N-glycosylation profiles of therapeutic glycoproteins. 27287011 0 81 gly N-glycosylation 143:157 arg1 therapeutic glycoproteins therapeutic glycoproteins Fterm glycoproteins LC-MS analysis combined with principal component analysis and soft independent modelling by class analogy for a better detection of changes in N-glycosylation profiles of therapeutic glycoproteins. 26869352 10 67 gly fucosylated 1724:1734 arg1 Lewis-type fucosylated N-glycan Lewis-type fucosylated N-glycan In metastatic prostate cancer, Lewis-type fucosylated N-glycan was also increased. 24821760 3 35 part_of sites 572:576 arg1 Family 7 cellobiohydrolase cellobiohydrolase sites Fterm Site cellobiohydrolase sites Here, the effects of O-mannosylation are examined on the Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase at three glycosylation sites. 28585084 4 29 gly glycoproteins 986:998 arg1 glycoproteins glycoproteins Fterm glycoproteins Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. 28486782 8 41 gly N-glycosylation 901:915 arg1 the EGFR extracellular domain the EGFR extracellular domain domain Here, atomistic MD simulations show that N-glycosylation of the EGFR extracellular domain plays critical roles in the binding of growth factors, monoclonal antibodies, and the dimeric partners to the monomeric EGFR extracellular domain. 26984886 3 38 gly glycoprotein 473:484 arg1 the predominant surface glycoprotein the predominant surface glycoprotein Fterm glycoprotein Hemagglutinin is the predominant surface glycoprotein and the primary determinant of antigenicity, virulence and zoonotic potential. 26984886 3 38 gly glycoprotein 473:484 arg1 Hemagglutinin Hemagglutinin Fterm Hemagglutinin Hemagglutinin is the predominant surface glycoprotein and the primary determinant of antigenicity, virulence and zoonotic potential. 27932460 0 31 gly Glycosylation 114:126 arg1 α-Dystroglycan α-Dystroglycan Protein O-Linked Mannose β-1,4-N-Acetylglucosaminyl-transferase 2 (POMGNT2) Is a Gatekeeper Enzyme for Functional Glycosylation of α-Dystroglycan. 25660649 3 90 gly glycosylation 515:527 arg1 these two residues these two residues residues Moreover, it appears that the glycosylation of these two residues can influence dramatically the virus production and the infection spreading in either mosquito or mammalian cells. 25406038 10 32 gly O-glycopeptides 1244:1258 arg2 14 O-glycopeptides 14 O-glycopeptides O-glycopeptides Fifty-six N-glycopeptides covering 10 N-glycan sites, and 14 O-glycopeptides were sequenced and characterized. 25406038 10 47 gly N-glycopeptides 1193:1207 arg2 Fifty-six N-glycopeptides Fifty-six N-glycopeptides N-glycopeptides Fifty-six N-glycopeptides covering 10 N-glycan sites, and 14 O-glycopeptides were sequenced and characterized. 28323417 1 2 gly glycoproteins 317:329 arg1 the well-characterized glycoproteins the well-characterized glycoproteins Fterm glycoproteins An ion mobility quadrupole time-of-flight mass spectrometer was used to examine the gas-phase structures of a set of glycopeptides resulting from proteolytic digestion of the well-characterized glycoproteins bovine ribonuclease B, human transferrin, bovine fetuin and human α1-acid glycoprotein, the corresponding deglycosylated peptides, and the glycans released by the endoglycosidase PNGase F. 28323417 1 2 gly glycoproteins 317:329 arg1 bovine fetuin bovine fetuin Fterm fetuin An ion mobility quadrupole time-of-flight mass spectrometer was used to examine the gas-phase structures of a set of glycopeptides resulting from proteolytic digestion of the well-characterized glycoproteins bovine ribonuclease B, human transferrin, bovine fetuin and human α1-acid glycoprotein, the corresponding deglycosylated peptides, and the glycans released by the endoglycosidase PNGase F. 28323417 1 9 gly deglycosylated 437:450 arg1 the corresponding deglycosylated peptides the corresponding deglycosylated peptides peptides An ion mobility quadrupole time-of-flight mass spectrometer was used to examine the gas-phase structures of a set of glycopeptides resulting from proteolytic digestion of the well-characterized glycoproteins bovine ribonuclease B, human transferrin, bovine fetuin and human α1-acid glycoprotein, the corresponding deglycosylated peptides, and the glycans released by the endoglycosidase PNGase F. 28323417 1 37 gly glycopeptides 240:252 arg2 glycopeptides glycopeptides glycopeptides An ion mobility quadrupole time-of-flight mass spectrometer was used to examine the gas-phase structures of a set of glycopeptides resulting from proteolytic digestion of the well-characterized glycoproteins bovine ribonuclease B, human transferrin, bovine fetuin and human α1-acid glycoprotein, the corresponding deglycosylated peptides, and the glycans released by the endoglycosidase PNGase F. 28323417 1 71 gly glycoprotein 405:416 arg1 the well-characterized glycoproteins the well-characterized glycoproteins Fterm glycoproteins An ion mobility quadrupole time-of-flight mass spectrometer was used to examine the gas-phase structures of a set of glycopeptides resulting from proteolytic digestion of the well-characterized glycoproteins bovine ribonuclease B, human transferrin, bovine fetuin and human α1-acid glycoprotein, the corresponding deglycosylated peptides, and the glycans released by the endoglycosidase PNGase F. 26599081 4 36 gly glycosylated 692:703 arg1 M. arthritidis glycosylated surface lipoproteins M. arthritidis glycosylated surface lipoproteins Fterm lipoproteins Previously, it was shown that M. arthritidis glycosylated surface lipoproteins through O-linkage. 26729457 4 7 gly disialylated 657:668 arg1 synthetic disialylated, biantennary N-glycopeptides synthetic disialylated, biantennary N-glycopeptides N-glycopeptides Here, we used a small set of synthetic disialylated, biantennary N-glycopeptides to systematically tune Q-TOF instrument parameters towards optimal energy stepping collision induced dissociation (CID) of glycopeptides. 26729457 4 49 gly glycopeptides 822:834 arg2 glycopeptides glycopeptides glycopeptides Here, we used a small set of synthetic disialylated, biantennary N-glycopeptides to systematically tune Q-TOF instrument parameters towards optimal energy stepping collision induced dissociation (CID) of glycopeptides. 26729457 4 50 gly N-glycopeptides 683:697 arg2 synthetic disialylated, biantennary N-glycopeptides synthetic disialylated, biantennary N-glycopeptides N-glycopeptides Here, we used a small set of synthetic disialylated, biantennary N-glycopeptides to systematically tune Q-TOF instrument parameters towards optimal energy stepping collision induced dissociation (CID) of glycopeptides. 25234305 2 22 gly desialylated 437:448 arg1 desialylated N-glycans desialylated N-glycans Capillary electrophoresis coupled with laser-induced fluorescence (CE-LIF) is a robust method to quantify desialylated N-glycans that are labeled with 8-aminopyrene-1,3,6-trisulfonic acid prior to analysis. 28928219 5 1 part_of Skp1 1203:1206 arg1 the intrinsically flexible F-box-binding domain Skp1 the intrinsically flexible F-box-binding domain PUBTATOR Site Skp1 6500 domain Here, NMR and MS approaches were used to determine the glycan structure, and then a combination of NMR and molecular dynamics simulations were employed to characterize the impact of the glycan on the conformation and motions of the intrinsically flexible F-box-binding domain of Skp1. 28729420 2 53 gly attachment 380:389 arg3 a GlcNAc AND the α1,3 mannose arm the α1,3 mannose arm a GlcNAc Previously, intensive in vitro studies with crude extract or purified enzyme concluded that the attachment of a GlcNAc on the α1,3 mannose arm of N-glycan is essential for FUT8-catalyzed core fucosylation. 25868116 6 23 gly glycosylated 1254:1265 arg1 the resulting disaccharide alcohol the resulting disaccharide alcohol Glycosidation of this thioglycoside donor with 5-methoxycarbonylpentanol gave the disaccharide tether glycoside and after catalytic removal of benzyl ether the resulting disaccharide alcohol was glycosylated by the thioglycoside in a 2+2 reaction to yield a tetrasaccharide. 25341402 4 30 part_of 321-amino-acid 486:499 arg1 a 321-amino-acid polypeptide 321-amino-acid a 321-amino-acid polypeptide Cterm Site 321-amino-acid polypeptide The full-length pelA encodes a 321-amino-acid polypeptide containing a putative 18-residue signal peptide and a pectate lyase family 1 catalytic domain. 26202417 7 25 gly glycopeptide 851:862 arg2 glycopeptide composition glycopeptide composition glycopeptide We have used: nano-LC-MS(E) for glycopeptide composition, sequence and site occupancy analysis, and MALDI-TOF MS permethylation profiling for characterization of released glycans. 28052259 1 37 part_of glycoprotein 186:197 arg1 a large modular ectodomain glycoprotein a large modular ectodomain Fterm Site glycoprotein ectodomain LDL-receptor-related protein 6 (LRP6) is a single-pass membrane glycoprotein with a large modular ectodomain and forms a higher order signaling platform upon binding Wnt ligands on the cell surface. 26993603 5 33 gly Removal 712:718 arg2 N-glycans AND Asn144 Asn144 N-glycans Asn144 Removal of N-glycans at Asn144 enhanced the motility and invasiveness of hepatocellular carcinoma cells, possibly due to inhibition of cell adhesion related to the changes of cell membrane glycosylation. 28975713 4 9 gly glycopeptide 626:637 arg2 The theoretical glycopeptide search space The theoretical glycopeptide search space glycopeptide The theoretical glycopeptide search space can be customized in an advanced query mode that specifies potential proteins/peptides, glycan compositions, and several experimental parameters. 28446609 1 80 gly glycosylation 221:233 arg2 ∼25 glycosylation sites ∼25 glycosylation sites sites The gp120 subunit of the HIV-1 envelope (Env) protein is heavily glycosylated at ∼25 glycosylation sites, of which ∼7-8 are located in the V1/V2 and V3 variable loops and the others in the remaining core gp120 region. 28446609 1 28 gly glycosylated 201:212 arg1 The gp120 subunit gp120 subunit sites PUBTATOR gp120 subunit 3700 sites The gp120 subunit of the HIV-1 envelope (Env) protein is heavily glycosylated at ∼25 glycosylation sites, of which ∼7-8 are located in the V1/V2 and V3 variable loops and the others in the remaining core gp120 region. 28370937 7 1 gly trisialylated 1000:1012 arg1 trisialylated triantennary structures trisialylated triantennary structures The cell-surface N-glycosylation of PHHs was more biologically processed than that of HLCs, with bisialylated biantennary and trisialylated triantennary structures predominant. 24803430 3 1 part_of Notch1 486:491 arg1 the ligand-binding region Notch1 the ligand-binding region PUBTATOR Site Notch1 4851 region We have modified the ligand-binding region (EGF domains 11-13) of human Notch1 (hN1) with O-fucose and O-glucose glycans and shown by flow cytometry and surface plasmon resonance that the Fringe-catalyzed addition of GlcNAc to the O-fucose at T466 in EGF12 substantially increases binding to Jagged1 and Delta-like 1 (DLL1) ligands. 24803430 3 1 part_of Notch1 486:491 arg1 EGF domains 11-13 Notch1 EGF domains 11-13 PUBTATOR Site Notch1 4851 domains We have modified the ligand-binding region (EGF domains 11-13) of human Notch1 (hN1) with O-fucose and O-glucose glycans and shown by flow cytometry and surface plasmon resonance that the Fringe-catalyzed addition of GlcNAc to the O-fucose at T466 in EGF12 substantially increases binding to Jagged1 and Delta-like 1 (DLL1) ligands. 24803430 3 55 part_of EGF 458:460 arg1 the ligand-binding region EGF the ligand-binding region OGER Site EGF P01133 region We have modified the ligand-binding region (EGF domains 11-13) of human Notch1 (hN1) with O-fucose and O-glucose glycans and shown by flow cytometry and surface plasmon resonance that the Fringe-catalyzed addition of GlcNAc to the O-fucose at T466 in EGF12 substantially increases binding to Jagged1 and Delta-like 1 (DLL1) ligands. 24803430 3 55 part_of EGF 458:460 arg1 EGF domains 11-13 EGF EGF domains 11-13 OGER Site EGF P01133 domains We have modified the ligand-binding region (EGF domains 11-13) of human Notch1 (hN1) with O-fucose and O-glucose glycans and shown by flow cytometry and surface plasmon resonance that the Fringe-catalyzed addition of GlcNAc to the O-fucose at T466 in EGF12 substantially increases binding to Jagged1 and Delta-like 1 (DLL1) ligands. 28091715 6 14 gly glycopeptide 1059:1070 arg2 glycopeptide mapping glycopeptide mapping glycopeptide Here we used the cytotoxic T lymphocyte associated protein 4-immunoglobulin G (Ig) fusion protein and fetuin as models for O-glycan analysis and compared the analytical methods glycopeptide mapping, 2-AB labelling and RapiFluor-MS labelling. 27616296 1 7 gly Glycosylation 103:115 arg1 many proteins many proteins Fterm proteins Glycosylation of many proteins has been revealed to be closely related with food allergies, and screening and structural analysis of related glycoproteins and glycoallergens are essential for studies in this field. 27616296 1 12 gly glycoproteins 244:256 arg1 related glycoproteins related glycoproteins Fterm glycoproteins Glycosylation of many proteins has been revealed to be closely related with food allergies, and screening and structural analysis of related glycoproteins and glycoallergens are essential for studies in this field. 27320861 11 44 gly modified 1754:1761 arg3 many photosynthesis-related proteins AND N-glycans many photosynthesis-related proteins N-glycans Fterm proteins Thus, we propose that the N-glycan synthetic system of the O. sativa shoot is almost unaffected by light conditions and that many photosynthesis-related proteins are not modified by N-glycans. 26507102 9 0 gly monosialylated 1217:1230 arg1 monosialylated Core 1 O-glycans monosialylated Core 1 O-glycans Synovial fluid from normal joints (49.5 ± 1.9%) contained significantly lower amounts of monosialylated Core 1 O-glycans compared with joints with osteoarthritis (53.8 ± 7.8%, P = 0.03) or joints with osteochondral fragments (57.3 ± 8.8%, P = 0.001). 28717478 5 35 part_of 9-mer 1147:1151 arg1 a 9-mer epitope mer a 9-mer epitope OGER Site mer Q12866 epitope These high-mannose containing glycopeptides were tested for enhanced targeting to human antigen presenting cells (APCs), putatively mediated via the mannose receptor, and for processing by the APCs for presentation to human CD8+ T cells specific for a 9-mer epitope within the peptide. 24820161 7 7 gly Trp¹³⁰ 1030:1035 arg1 C-mannosylation Trp¹³⁰ C-mannosylation Trp¹³⁰ Computer simulation demonstrated that C-mannosylation of HYAL1 at Trp¹³⁰ changed conformation of the catalytic active site, and faced Glu¹³¹ in the opposite direction toward its substrate, HA, indicating that C-mannosylation will negatively regulate its secretion, and will attenuate its enzymatic activity. 24820161 7 40 gly C-mannosylation 1002:1016 arg1 HYAL1 HYAL1 Trp¹³⁰ PUBTATOR HYAL1 3373 Trp¹³⁰ Computer simulation demonstrated that C-mannosylation of HYAL1 at Trp¹³⁰ changed conformation of the catalytic active site, and faced Glu¹³¹ in the opposite direction toward its substrate, HA, indicating that C-mannosylation will negatively regulate its secretion, and will attenuate its enzymatic activity. 26610891 5 31 gly possess 1222:1228 arg1 The enzymes AND relaxed glycan specificity The enzymes relaxed glycan specificity Fterm enzymes The enzymes were shown to possess relaxed glycan specificity, transferring diverse glycan structures and demonstrated different glycosylation sequon specificities. 28921966 7 64 gly attached 1334:1341 arg1 the peptides AND the glycan structures the peptides the glycan structures peptides Acquisition on a high resolution tandem-MSn system with fragmentation methodologies such as high-energy collision dissociation (HCD) and collision induced dissociation (CID), provided the complete sequence of the glycan structures attached to the peptides. 28816453 8 3 gly O-glycans 1178:1186 arg1 glycoproteins glycoproteins O-glycans Fterm glycoproteins This, finally, allows us to suggest several efficient approaches to construct complete N- and O-glycans on glycoproteins, as exemplified on two relevant examples. 28816453 8 40 gly glycoproteins 1191:1203 arg1 glycoproteins glycoproteins Fterm glycoproteins This, finally, allows us to suggest several efficient approaches to construct complete N- and O-glycans on glycoproteins, as exemplified on two relevant examples. 28816453 8 55 gly N- 1171:1172 arg1 glycoproteins glycoproteins N- Fterm glycoproteins This, finally, allows us to suggest several efficient approaches to construct complete N- and O-glycans on glycoproteins, as exemplified on two relevant examples. 24549892 3 61 gly glycopeptides 920:932 arg2 glycopeptides glycopeptides glycopeptides Here we report a novel strategy to reliably determine site-specific N-glycosylation mapping by combining collision-induced dissociation (CID)-only fragmentation with chromatographic retention times of glycopeptides. 24511137 5 0 gly attached 1136:1143 arg2 the Fc regions AND N-linked glycans the Fc regions N-linked glycans regions However, we observed no apparent heterogeneity in the structure of N-linked glycans attached to three different sites of the Fc regions of nephritogenic and non-nephritogenic 6-19 IgAs. 24511137 5 0 gly attached 1136:1143 arg2 three different sites AND N-linked glycans three different sites N-linked glycans sites However, we observed no apparent heterogeneity in the structure of N-linked glycans attached to three different sites of the Fc regions of nephritogenic and non-nephritogenic 6-19 IgAs. 28800497 1 35 gly core-fucosylated 183:198 arg1 a core-fucosylated N-glycan trisaccharide GlcNAcβ1,4(Fucα1,6)GlcNAc a core-fucosylated N-glycan trisaccharide GlcNAcβ1,4(Fucα1,6)GlcNAc Glyco-PAMAM dendrimers and glyco-agarose beads bearing a core-fucosylated N-glycan trisaccharide GlcNAcβ1,4(Fucα1,6)GlcNAc or a non-fucose disaccharide GlcNAcβ1,4GlcNAc were successfully synthesized and characterized by monosaccharide analysis with HPAEC-PAD technique. 26075387 10 84 gly glycoproteins 1511:1523 arg1 serum glycoproteins glycoproteins the decreased core fucosylation, bisecting and increased sialylation characters Fterm glycoproteins Moreover, the decreased core fucosylation, bisecting and increased sialylation characters of serum glycoproteins were observed in patients with LCMM. 29162910 3 51 gly glycoproteins 769:781 arg1 wild-type Saccharomyces cerevisiae glycoproteins wild-type Saccharomyces cerevisiae glycoproteins Fterm glycoproteins Unlike starting material obtained by chemical synthesis or direct isolation from natural sources, which can be time consuming and costly to generate, our approach involves precursors derived from renewable sources including wild-type Saccharomyces cerevisiae glycoproteins and lipid-linked oligosaccharides from glycoengineered Escherichia coli. 26773038 9 11 part_of VWF 1338:1340 arg1 the VWF A2 domain VWF the VWF A2 domain PUBTATOR Site VWF 7450 domain Glycan stabilization of the VWF A2 domain acts together with the Ca(2+)binding site and vicinal cysteine disulfide bond to control unfolding and ADAMTS13 proteolysis. 26773038 9 58 part_of Ca 1375:1376 arg1 the Ca(2+)binding site Ca(2 the Ca(2+)binding site OGER Site Ca(2 P00918 site Glycan stabilization of the VWF A2 domain acts together with the Ca(2+)binding site and vicinal cysteine disulfide bond to control unfolding and ADAMTS13 proteolysis. 27529638 1 28 gly glycosylation 158:170 arg1 peptide/protein peptide/protein peptide/protein Here we report a facile and efficient method for site-directed glycosylation of peptide/protein. 24702330 3 23 part_of IgG1 466:469 arg1 the crystallizable fragment IgG1 the crystallizable fragment OGER Site IgG1 P01857 fragment Here, we report the installation of a genetically encoded aldehyde tag at the internal glycosylation site of the crystallizable fragment (Fc) of IgG1. 26571101 1 18 gly glycoproteins 245:257 arg1 glycoproteins glycoproteins Fterm glycoproteins Comprehensive characterization of protein glycosylation is critical for understanding the structure and function of glycoproteins. 25230686 0 30 part_of -acetylglucosaminyltransferase 30:59 arg1 The transmembrane domain N -acetylglucosaminyltransferase I The transmembrane domain OGER Site N -acetylglucosaminyltransferase I Q8N0V5 domain The transmembrane domain of N -acetylglucosaminyltransferase I is the key determinant for its Golgi subcompartmentation. 24393138 0 13 gly glycoprotein 76:87 arg1 the intact glycoprotein the intact glycoprotein Fterm glycoprotein Glycan analysis of Prostate Specific Antigen (PSA) directly from the intact glycoprotein by HR-ESI/TOF-MS. 25746926 1 14 gly glycosylated 213:224 arg1 Trypanosoma brucei variant surface glycoproteins Trypanosoma brucei variant surface glycoproteins Fterm glycoproteins Trypanosoma brucei variant surface glycoproteins (VSG) are glycosylated by both paucimannose and oligomannose structures which are involved in the formation of a protective barrier against the immune system. 25746926 1 45 gly glycoproteins 189:201 arg1 Trypanosoma brucei variant surface glycoproteins Trypanosoma brucei variant surface glycoproteins Fterm glycoproteins Trypanosoma brucei variant surface glycoproteins (VSG) are glycosylated by both paucimannose and oligomannose structures which are involved in the formation of a protective barrier against the immune system. 27867116 3 1 gly glycoforms 671:680 arg1 glycopeptide glycoforms glycopeptide glycoforms glycopeptide Moreover, we evaluated several acquisition strategies in order to improve the detection and characterization of glycopeptide glycoforms with the maximum number of identification percentages. 27867116 3 53 gly glycopeptide 658:669 arg2 glycopeptide glycoforms glycopeptide glycoforms glycopeptide Moreover, we evaluated several acquisition strategies in order to improve the detection and characterization of glycopeptide glycoforms with the maximum number of identification percentages. 25477510 3 82 gly attached 537:544 arg1 cryptococcal mannoproteins AND the O-glycans cryptococcal mannoproteins the O-glycans Fterm mannoproteins In this study, we performed a detailed structural analysis of the O-glycans attached to cryptococcal mannoproteins using HPLC combined with exoglycosidase treatment and showed that the major C. neoformans O-glycans were short manno-oligosaccharides that were connected mostly by α1,2-linkages but connected by an α1,6-linkage at the third mannose residue. 29273683 2 27 gly N-glycosylation 182:196 arg2 six N-glycosylation sites six N-glycosylation sites sites Human and rat CBGs have six N-glycosylation sites. 24295789 3 21 gly N-glycopeptides 583:597 arg2 N-glycopeptides N-glycopeptides N-glycopeptides Peptide de novo sequencing and structural elucidation of N-glycopeptides obtained either directly from proteolytic digestion or after zwitterionic hydrophilic interaction liquid chromatography solid phase extraction-based separation were performed by use of nanoelectrospray ionization quadrupole time-of-flight mass spectrometry and low-energy collision-induced dissociation experiments. 27259834 9 23 gly strain 1376:1381 arg1 The yeast invertase invertase strain Fterm invertase The yeast invertase from the core 3-producing strain was less extensively N-glycosylated; however, it was partially restored by the addition of MnCl2 to the medium. 27259834 9 40 gly N-glycosylated 1404:1417 arg1 The yeast invertase The yeast invertase Fterm invertase The yeast invertase from the core 3-producing strain was less extensively N-glycosylated; however, it was partially restored by the addition of MnCl2 to the medium. 24632142 4 27 gly glycosylation 749:761 arg2 the putative glycosylation site the putative glycosylation site site However, the structure of this enzyme did not show the presence of any non-amino acid components at the putative glycosylation site. 26231935 1 1 gly glycosylation 187:199 arg2 three conserved N-linked glycosylation sites three conserved N-linked glycosylation sites sites Acetylcholinesterase (AChE; EC 3.1.1.7) is a glycoprotein possessing three conserved N-linked glycosylation sites in mammalian species, locating at 296, 381, and 495 residues of the human sequence. 26231935 1 30 gly glycoprotein 138:149 arg1 a glycoprotein a glycoprotein Fterm glycoprotein Acetylcholinesterase (AChE; EC 3.1.1.7) is a glycoprotein possessing three conserved N-linked glycosylation sites in mammalian species, locating at 296, 381, and 495 residues of the human sequence. 27641064 4 19 gly N-glycosylation 563:577 arg1 Asn712 Asn712 Asn712 Here, we characterize the S3-5,10-14 mutants in detail and found that the N-glycosylation of site-11 (Asn712) is key for cell growth. 27641064 4 19 gly N-glycosylation 563:577 arg1 site-11 site-11 site-11 Here, we characterize the S3-5,10-14 mutants in detail and found that the N-glycosylation of site-11 (Asn712) is key for cell growth. 27842516 1 15 gly attachment 178:187 arg2 target proteins AND sugar chains target proteins sugar chains Fterm proteins BACKGROUND Protein glycosylation involves the post-translational attachment of sugar chains to target proteins and has been observed in all three domains of life. 27842516 1 37 gly glycosylation 132:144 arg1 all three domains all three domains domains BACKGROUND Protein glycosylation involves the post-translational attachment of sugar chains to target proteins and has been observed in all three domains of life. 28661444 11 16 gly glycosylated 1871:1882 arg1 additional lysines additional lysines lysines Furthermore, additional lysines included in different epitopes (Lys103, -123 and -282) are also glycosylated. 26231935 3 32 gly sites 477:481 arg1 glycan composition sites glycan composition sites In order to determine the role of three N-glycosylation sites in AChE activity and glycan composition, the site-directed mutagenesis of N-glycosylation sites in wild-type human AChE(T) sequence was employed to generate the single-site mutants (i.e., AChE(T) (N296Q), AChET (N381Q), and AChE(T) (N495Q)) and all site mutant (i.e., AChE(T) (3N→3Q)). 26231935 3 46 gly N-glycosylation 557:571 arg2 N-glycosylation sites N-glycosylation sites sites In order to determine the role of three N-glycosylation sites in AChE activity and glycan composition, the site-directed mutagenesis of N-glycosylation sites in wild-type human AChE(T) sequence was employed to generate the single-site mutants (i.e., AChE(T) (N296Q), AChET (N381Q), and AChE(T) (N495Q)) and all site mutant (i.e., AChE(T) (3N→3Q)). 26231935 3 63 gly N-glycosylation 461:475 arg2 three N-glycosylation sites three N-glycosylation sites sites In order to determine the role of three N-glycosylation sites in AChE activity and glycan composition, the site-directed mutagenesis of N-glycosylation sites in wild-type human AChE(T) sequence was employed to generate the single-site mutants (i.e., AChE(T) (N296Q), AChET (N381Q), and AChE(T) (N495Q)) and all site mutant (i.e., AChE(T) (3N→3Q)). 28849661 0 4 part_of Bearing 35:41 arg1 A Bearing Syndecan-1 Glycopeptide Bearing Syndecan-1 A Bearing Syndecan-1 Glycopeptide PUBTATOR Site Bearing Syndecan-1 6382 Glycopeptide Synthesis of Chondroitin Sulfate A Bearing Syndecan-1 Glycopeptide. 28849661 0 16 part_of Syndecan-1 43:52 arg1 A Bearing Syndecan-1 Glycopeptide Bearing Syndecan-1 A Bearing Syndecan-1 Glycopeptide PUBTATOR Site Bearing Syndecan-1 6382 Glycopeptide Synthesis of Chondroitin Sulfate A Bearing Syndecan-1 Glycopeptide. 27616296 2 34 gly glycoprotein 375:386 arg1 all glycoprotein fractions all glycoprotein fractions Fterm glycoprotein Herein, we describe detailed N-glycoform analysis of all glycoprotein fractions of soybean protein isolate (SPI) separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) to disclose structural features of the glycan moieties of more soybean glycoproteins. 27616296 2 54 gly glycoproteins 584:596 arg1 the glycan moieties glycoproteins the glycan moieties Fterm glycoproteins Herein, we describe detailed N-glycoform analysis of all glycoprotein fractions of soybean protein isolate (SPI) separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) to disclose structural features of the glycan moieties of more soybean glycoproteins. 25358049 2 55 gly glycopeptide 364:375 arg2 glycopeptide glycopeptide glycopeptide However, characterization of glycan and glycopeptide structural isomers remains challenging and often relies on biosynthetic pathways being conserved. 24798328 9 82 gly glycosylation 1344:1356 arg1 the linker regions the linker regions regions Probing into which isoform(s) contributed to glycosylation of the linker regions of the LDLR class A repeats by in vitro enzyme assays suggested a major role of GalNAc-T11. 25422509 7 20 gly sialylated 1110:1119 arg1 sialylated N-glycans sialylated N-glycans The absence of sialic acid residues abolishes these inhibitory activities, showing a key role of sialylated N-glycans in inducing the IgM-mediated immune suppression. 24668806 0 43 part_of s 39:39 arg1 Fragments bacterial endoglycosidase s Fragments Cterm bacterial endoglycosidase s Fragments of bacterial endoglycosidase s and immunoglobulin g reveal subdomains of each that contribute to deglycosylation. 24668806 0 48 part_of g 60:60 arg1 Fragments immunoglobulin g Fragments Cterm immunoglobulin g Fragments of bacterial endoglycosidase s and immunoglobulin g reveal subdomains of each that contribute to deglycosylation. 28039139 12 20 gly N-glycosylation 2602:2616 arg1 a secreted reporter protein a secreted reporter protein Fterm protein Here, insight into the purpose of archaeal N-glycosylation was gained by addressing the surface layer (S-layer) surrounding cells of the halophilic species Haloferax volcanii Relying on mutant strains defective in N-glycosylation, such efforts revealed that compromised N-glycosylation affected S-layer integrity and the transfer of a secreted reporter protein across the S-layer into the growth medium, as well as the conformation of the S-layer glycoprotein, the sole component of the S-layer. 28039139 12 20 gly N-glycosylation 2602:2616 arg1 the S-layer glycoprotein the S-layer glycoprotein Fterm glycoprotein Here, insight into the purpose of archaeal N-glycosylation was gained by addressing the surface layer (S-layer) surrounding cells of the halophilic species Haloferax volcanii Relying on mutant strains defective in N-glycosylation, such efforts revealed that compromised N-glycosylation affected S-layer integrity and the transfer of a secreted reporter protein across the S-layer into the growth medium, as well as the conformation of the S-layer glycoprotein, the sole component of the S-layer. 28039139 12 26 gly glycoprotein 2779:2790 arg1 the S-layer glycoprotein the S-layer glycoprotein Fterm glycoprotein Here, insight into the purpose of archaeal N-glycosylation was gained by addressing the surface layer (S-layer) surrounding cells of the halophilic species Haloferax volcanii Relying on mutant strains defective in N-glycosylation, such efforts revealed that compromised N-glycosylation affected S-layer integrity and the transfer of a secreted reporter protein across the S-layer into the growth medium, as well as the conformation of the S-layer glycoprotein, the sole component of the S-layer. 27932460 6 60 gly glycopeptide 1167:1178 arg2 an acceptor glycopeptide an acceptor glycopeptide glycopeptide Additionally, an acceptor glycopeptide is a less efficient substrate for POMGNT2 when two of the conserved amino acids are replaced. 27249581 3 11 gly glycosylation 440:452 arg2 the glycosylation site the glycosylation site site Herein, we have determined the relative strengths of intramolecular interactions between a series of monosaccharides and an aromatic ring close to the glycosylation site in an N-glycoprotein host. 27249581 3 70 gly N-glycoprotein 465:478 arg1 N-glycoprotein N-glycoprotein Fterm N-glycoprotein Herein, we have determined the relative strengths of intramolecular interactions between a series of monosaccharides and an aromatic ring close to the glycosylation site in an N-glycoprotein host. 27439567 1 1 part_of glycosites 210:219 arg1 glycoproteins glycoproteins glycosites Fterm Site glycoproteins glycosites A MS-based methodology has been developed for analysis of core-fucosylated versus antennary-fucosylated glycosites in glycoproteins. 24947385 4 8 gly sialylated 556:565 arg1 GFP-tagged GLUT4 GFP-tagged GLUT4 sialylated glycoforms PUBTATOR GFP-tagged GLUT4 6517 We found that sialylated glycoforms of GFP-tagged GLUT4 appear to be internalized more slowly than non-sialylated GLUT4 upon insulin removal. 26231935 8 19 gly glycosylation 1319:1331 arg2 the three glycosylation sites the three glycosylation sites sites Although the three glycosylation sites within AChE sequence have different extent in affecting the enzymatic activity, their glycan compositions are very similar. 27151270 5 33 part_of sites 850:854 arg1 windmill palm tree peroxidase peroxidase sites Fterm Site peroxidase sites Mass spectrometry analysis provided a detailed glycosylation profile at the 13 sites of N-linked glycosylation on windmill palm tree peroxidase. 27151270 5 44 part_of peroxidase 904:913 arg1 the 13 sites peroxidase the 13 sites Fterm Site peroxidase sites Mass spectrometry analysis provided a detailed glycosylation profile at the 13 sites of N-linked glycosylation on windmill palm tree peroxidase. 25498018 5 69 gly fucosylated 1216:1226 arg1 bi-antennary, tri-antennary and tetra-antennary, N-linked, fucosylated glycans bi-antennary, tri-antennary and tetra-antennary, N-linked, fucosylated glycans The results reveal that a specific glycosylation site, Asn 134, is differently glycosylated in the two forms, with complex types of bi-antennary, tri-antennary and tetra-antennary, N-linked, fucosylated glycans identified at this site in the HMW form but not in the LMW form. 25498018 5 8 gly glycosylation 1060:1072 arg2 a specific glycosylation site site, Asn 134 site, Asn 134 The results reveal that a specific glycosylation site, Asn 134, is differently glycosylated in the two forms, with complex types of bi-antennary, tri-antennary and tetra-antennary, N-linked, fucosylated glycans identified at this site in the HMW form but not in the LMW form. 25498018 5 46 gly glycosylated 1104:1115 arg1 Asn 134 site, Asn 134 site, Asn 134 The results reveal that a specific glycosylation site, Asn 134, is differently glycosylated in the two forms, with complex types of bi-antennary, tri-antennary and tetra-antennary, N-linked, fucosylated glycans identified at this site in the HMW form but not in the LMW form. 25498018 5 46 gly glycosylated 1104:1115 arg2 a specific glycosylation site site, Asn 134 site, Asn 134 The results reveal that a specific glycosylation site, Asn 134, is differently glycosylated in the two forms, with complex types of bi-antennary, tri-antennary and tetra-antennary, N-linked, fucosylated glycans identified at this site in the HMW form but not in the LMW form. 25498018 5 46 gly glycosylated 1104:1115 arg1 a specific glycosylation site site, Asn 134 site, Asn 134 The results reveal that a specific glycosylation site, Asn 134, is differently glycosylated in the two forms, with complex types of bi-antennary, tri-antennary and tetra-antennary, N-linked, fucosylated glycans identified at this site in the HMW form but not in the LMW form. 25498018 5 46 gly glycosylated 1104:1115 arg2 a specific glycosylation site site, Asn 134 site, Asn 134 The results reveal that a specific glycosylation site, Asn 134, is differently glycosylated in the two forms, with complex types of bi-antennary, tri-antennary and tetra-antennary, N-linked, fucosylated glycans identified at this site in the HMW form but not in the LMW form. 25498018 5 46 gly glycosylated 1104:1115 arg1 a specific glycosylation site site, Asn 134 site, Asn 134 The results reveal that a specific glycosylation site, Asn 134, is differently glycosylated in the two forms, with complex types of bi-antennary, tri-antennary and tetra-antennary, N-linked, fucosylated glycans identified at this site in the HMW form but not in the LMW form. 25498018 5 46 gly glycosylated 1104:1115 arg1 a specific glycosylation site site, Asn 134 site, Asn 134 The results reveal that a specific glycosylation site, Asn 134, is differently glycosylated in the two forms, with complex types of bi-antennary, tri-antennary and tetra-antennary, N-linked, fucosylated glycans identified at this site in the HMW form but not in the LMW form. 28516782 1 72 gly glycosylated 264:275 arg1 these extensively glycosylated proteins these extensively glycosylated proteins Fterm proteins The full potential of recombinant Immunoglobulin A as therapeutic antibody is not fully explored, owing to the fact that structure-function relationships of these extensively glycosylated proteins are not well understood. 24663386 6 58 gly sialylated 1213:1222 arg1 the neutral glycan the neutral glycan Very minor glycans accounting for ∼0.01-0.1% of the total include (i) the neutral glycan, Galβ1-4GlcNAcβ1-6(Galβ1-3)GalNAc, (ii) sialylated glycans, having sialyl Tn antigen, agalacto and trisialylated structures, (iii) fucosylated glycans forming blood type H antigen, blood type A antigen, blood type B antigen, Lewis X antigen and sialyl Lewis X antigen and (iv) sulfated glycans, having 6-sulfo and 3'-sulfo structures. 24663386 6 58 gly sialylated 1213:1222 arg1 (ii) sialylated glycans (ii) sialylated glycans Very minor glycans accounting for ∼0.01-0.1% of the total include (i) the neutral glycan, Galβ1-4GlcNAcβ1-6(Galβ1-3)GalNAc, (ii) sialylated glycans, having sialyl Tn antigen, agalacto and trisialylated structures, (iii) fucosylated glycans forming blood type H antigen, blood type A antigen, blood type B antigen, Lewis X antigen and sialyl Lewis X antigen and (iv) sulfated glycans, having 6-sulfo and 3'-sulfo structures. 24663386 6 82 gly fucosylated 1304:1314 arg1 (i) the neutral glycan, Galβ1-4GlcNAcβ1-6(Galβ1-3)GalNAc, (ii) sialylated glycans, having sialyl Tn antigen, agalacto and trisialylated structures, (iii) fucosylated glycans (i) the neutral glycan, Galβ1-4GlcNAcβ1-6(Galβ1-3)GalNAc, (ii) sialylated glycans, having sialyl Tn antigen, agalacto and trisialylated structures, (iii) fucosylated glycans Very minor glycans accounting for ∼0.01-0.1% of the total include (i) the neutral glycan, Galβ1-4GlcNAcβ1-6(Galβ1-3)GalNAc, (ii) sialylated glycans, having sialyl Tn antigen, agalacto and trisialylated structures, (iii) fucosylated glycans forming blood type H antigen, blood type A antigen, blood type B antigen, Lewis X antigen and sialyl Lewis X antigen and (iv) sulfated glycans, having 6-sulfo and 3'-sulfo structures. 24663386 6 98 gly trisialylated 1272:1284 arg1 trisialylated structures trisialylated structures Very minor glycans accounting for ∼0.01-0.1% of the total include (i) the neutral glycan, Galβ1-4GlcNAcβ1-6(Galβ1-3)GalNAc, (ii) sialylated glycans, having sialyl Tn antigen, agalacto and trisialylated structures, (iii) fucosylated glycans forming blood type H antigen, blood type A antigen, blood type B antigen, Lewis X antigen and sialyl Lewis X antigen and (iv) sulfated glycans, having 6-sulfo and 3'-sulfo structures. 25552259 2 35 gly glycoprotein 337:348 arg1 the major erythrocyte glycoprotein the major erythrocyte glycoprotein Fterm glycoprotein The O- and N-glycosidic chains of the major erythrocyte glycoprotein (Lisowska E. 2001, Antigenic properties of human glycophorins - an update. 27506355 1 19 gly glycopeptide 190:201 arg2 Intact glycopeptide MS analysis Intact glycopeptide MS analysis glycopeptide Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. 25092234 9 39 gly glycosite 1266:1274 arg2 a new glycosite a new glycosite glycosite We also identified a new glycosite of the noncanonical format NXC at N145 , occupied at around 5%. 27638310 3 25 part_of sites 624:628 arg1 rrhGM-CSF CSF sites OGER Site CSF sites However, there are no previous reports of the O-glycosylation of rhGM-CSF from plant cells, and so this study investigated O-glycans, O-glycosylation sites, and their structural role in rrhGM-CSF. 27506355 7 0 gly glycopeptide 726:737 arg2 intact glycopeptide analysis intact glycopeptide analysis glycopeptide Chem.2010, 82, 10194-10202) for intact glycopeptide analysis has been developed. 27585995 11 72 part_of proteins 2567:2574 arg1 residues proteins residues Fterm Site proteins residues BIOLOGICAL SIGNIFICANCE O-Linked glycoproteins, generated via a widely existing glycosylation modification process on serine (Ser) or threonine (Thr) residues of nascent proteins, play essential roles in a series of biological processes. 28244757 6 14 gly O-glycopeptides 1016:1030 arg2 1375 N- and 2159 O-glycopeptides 1375 N- and 2159 O-glycopeptides N- and 2159 O-glycopeptides Application of the IsoTaG platform to 15 cell lines metabolically labeled with Ac4GalNAz or Ac4ManNAz revealed 1375 N- and 2159 O-glycopeptides, variously modified with 74 discrete glycan structures. 24941220 4 20 part_of gp120 658:662 arg1 low abundant glycopeptides gp120 low abundant glycopeptides PUBTATOR Site gp120 3700 glycopeptides This challenge promoted us to employ a Q-Exactive mass spectrometer to identify low abundant glycopeptides from virion-associated gp120. 25850302 12 26 part_of glucuronoxylan-xylanohydrolase 1689:1718 arg1 conserved active site residues glucuronoxylan-xylanohydrolase conserved active site residues Fterm Site glucuronoxylan-xylanohydrolase residues We report overall structural feature, conserved active site residues and enzymeligand docking of first glucuronoxylan-xylanohydrolase (Xyn30A) of family 30 glycosyl hydrolase (GH30) from Clostridium thermocellum. 26918528 7 29 gly peptide 1430:1436 arg1 peptide and glycan substrates peptide and glycan substrates Distance measurements between peptide and glycan substrates and the C. jejuni PglB offer new experimental information on substrate binding to the related, but structurally uncharacterized, eukaryotic OTase. 26306636 2 80 gly glycosites 531:540 arg2 all the five potential N-linked glycosites all the five potential N-linked glycosites glycosites Mass spectrometry-based site-specific N-glycoprofiling of Tr7 showed that heterogeneous high-mannose type N-glycans were present at all the five potential N-linked glycosites. 26306636 2 79 gly present 488:494 arg1 all the five potential N-linked glycosites AND heterogeneous high-mannose type N-glycans glycosites heterogeneous high-mannose type N-glycans glycosites Mass spectrometry-based site-specific N-glycoprofiling of Tr7 showed that heterogeneous high-mannose type N-glycans were present at all the five potential N-linked glycosites. 25462875 3 50 part_of B4GALT1 531:537 arg1 the cytoplasmic/transmembrane/stem (CTS) domains B4GALT1 the cytoplasmic/transmembrane/stem (CTS) domains PUBTATOR Site B4GALT1 2683 domains To test this hypothesis, we replaced the cytoplasmic/transmembrane/stem (CTS) domains of B4GALT1 with those from human α1,3-fucosyltransferase 7 (FUT7), which is not cleaved and secreted. 29029079 4 14 gly sialylated 622:631 arg1 sialylated biantennary structures sialylated biantennary structures Here we analyzed glycan structures on native EC-SOD purified from human sera, and identified sialylated biantennary structures. 28955811 1 60 gly glycoprotein 125:136 arg1 a glycoprotein a glycoprotein Fterm glycoprotein 8824 Human carboxylesterase 2 (hCES2) is a glycoprotein involved in the metabolism of drugs and several environmental xenobiotics, whose crystallization has been proved to be a challenging task. 28800704 3 30 gly glycoproteins 587:599 arg1 carbohydrate moieties glycoproteins carbohydrate moieties Fterm glycoproteins The aim of this study was to analyze carbohydrate moieties, especially N-linked glycans, of glycoproteins from Ginkgo seeds originating from different places for detailed structures, to enable further research on the role played by N-glycans in Ginkgo-caused allergy. 28800704 3 30 gly glycoproteins 587:599 arg1 N-linked glycans glycoproteins N-linked glycans Fterm glycoproteins The aim of this study was to analyze carbohydrate moieties, especially N-linked glycans, of glycoproteins from Ginkgo seeds originating from different places for detailed structures, to enable further research on the role played by N-glycans in Ginkgo-caused allergy. 24798328 6 35 gly O-glycosylation 901:915 arg2 position -1 position -1 position We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position -1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. 24798328 6 35 gly O-glycosylation 901:915 arg2 an evolutionarily conserved O-glycosylation site an evolutionarily conserved O-glycosylation site site We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position -1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. 24798328 6 51 gly sialylated 1046:1055 arg1 the typical sialylated core 1 structure the typical sialylated core 1 structure We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position -1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. 24798328 6 53 gly cysteine 950:957 arg1 most repeats cysteine residue most repeats cysteine residue We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position -1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. 24798328 6 44 gly glycosylated 1016:1027 arg1 an evolutionarily conserved O-glycosylation site site site We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position -1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. 27311011 6 16 gly glycopeptides 1131:1143 arg2 130 distinct glycopeptides 130 distinct glycopeptides glycopeptides This study demonstrates the utility of an MRM-based method to rapidly characterize over 130 distinct glycopeptides and determine the extent of site occupancy within minutes. 25636227 3 16 part_of proteins 526:533 arg1 the O-glycosylation sites proteins the O-glycosylation sites Fterm Site proteins sites In this work, we designed a rapid and convenient workflow for characterizing the O-glycosylation sites of individual proteins and the human-plasma proteome. 25793890 9 60 gly glycosylation 1885:1897 arg2 these glycosylation sites these glycosylation sites sites Our results suggest that vaccine immunogens based on recombinant envelope proteins from clade CRF01_AE viruses might be improved by inclusion of envelope proteins that lack these glycosylation sites. 26507102 1 16 gly glycoprotein 112:123 arg1 The glycoprotein lubricin The glycoprotein lubricin Fterm glycoprotein REASON FOR PERFORMING STUDY The glycoprotein lubricin contributes to the boundary lubrication of the articular cartilage surface. 24889612 7 33 gly receptors 993:1001 arg1 the binding motif the binding motif the binding motif Site motif These findings provide significant insight into the binding motif and molecular mechanism (which is distinct from sugar-recognition receptors) by which O-glycosylated mucin proteins with sTn modifications are recognized in the immune system as well as during viral entry. 24889612 7 50 gly O-glycosylated 1013:1026 arg1 O-glycosylated mucin proteins O-glycosylated mucin proteins Fterm proteins These findings provide significant insight into the binding motif and molecular mechanism (which is distinct from sugar-recognition receptors) by which O-glycosylated mucin proteins with sTn modifications are recognized in the immune system as well as during viral entry. 26908049 2 16 gly glycoprotein 284:295 arg1 the glycoprotein Artemin the glycoprotein Artemin Fterm glycoprotein Here, the glycoprotein Artemin (ART) was carefully assessed by multiple analytical methods that allow us to provide a comprehensive understanding of how N-linked glycosylation impact the structural and functional properties of ART. 28681696 7 7 gly fucosylated 1704:1714 arg1 10 fucosylated neutral complex N-glycans 10 fucosylated neutral complex N-glycans Furthermore, using a statistical analysis of variance assay, we found that different N-glycan patterns, including 2 high-mannose-type, 2 fucosylated and sialylated complex structures, and 10 fucosylated neutral complex N-glycans, exhibited specific changes in N-glycan abundance across epithelial ovarian cancer grades. 28681696 7 79 gly sialylated 1666:1675 arg1 2 fucosylated and sialylated complex structures 2 fucosylated and sialylated complex structures Furthermore, using a statistical analysis of variance assay, we found that different N-glycan patterns, including 2 high-mannose-type, 2 fucosylated and sialylated complex structures, and 10 fucosylated neutral complex N-glycans, exhibited specific changes in N-glycan abundance across epithelial ovarian cancer grades. 28681696 7 84 gly fucosylated 1650:1660 arg1 2 fucosylated and sialylated complex structures 2 fucosylated and sialylated complex structures Furthermore, using a statistical analysis of variance assay, we found that different N-glycan patterns, including 2 high-mannose-type, 2 fucosylated and sialylated complex structures, and 10 fucosylated neutral complex N-glycans, exhibited specific changes in N-glycan abundance across epithelial ovarian cancer grades. 25113421 2 49 gly glycosylated 283:294 arg1 more than 50% eukaryotic proteins more than 50% eukaryotic proteins Fterm proteins It is believed that more than 50% eukaryotic proteins are glycosylated. 29145098 7 40 gly MPDPZ-Boc-Asn-GlcNAc-labeled 1595:1622 arg1 MPDPZ-Boc-Asn-GlcNAc-labeled glycans Asn MPDPZ-Boc-Asn-GlcNAc-labeled glycans Asn Moreover, the QMERSIL using LC-MS/MS was evaluated with various molar ratios (1:1, 1:5, 5:1) of d0(d8)- MPDPZ-Boc-Asn-GlcNAc-labeled glycans from ribonuclease B, bovine fetuin, and ovalbumin. 29145098 7 61 gly fetuin 1660:1665 arg1 MPDPZ-Boc-Asn-GlcNAc-labeled glycans fetuin MPDPZ-Boc-Asn-GlcNAc-labeled glycans Fterm fetuin Moreover, the QMERSIL using LC-MS/MS was evaluated with various molar ratios (1:1, 1:5, 5:1) of d0(d8)- MPDPZ-Boc-Asn-GlcNAc-labeled glycans from ribonuclease B, bovine fetuin, and ovalbumin. 28729420 0 3 gly fucosylation 105:116 arg1 N-glycans N-glycans Revisiting the substrate specificity of mammalian α1,6-fucosyltransferase reveals that it catalyzes core fucosylation of N-glycans lacking α1,3-arm GlcNAc. 25837443 5 25 gly glycoproteins 690:702 arg1 glycoproteins glycoproteins Fterm glycoproteins Lectin affinity isolations are followed by chemical immobilization of the captured glycopeptides, allowing the identification of glycoproteins containing specific glycans by subsequent mass spectrometry. 25837443 5 39 gly glycopeptides 644:656 arg2 the captured glycopeptides the captured glycopeptides glycopeptides Lectin affinity isolations are followed by chemical immobilization of the captured glycopeptides, allowing the identification of glycoproteins containing specific glycans by subsequent mass spectrometry. 25837443 5 49 gly containing 704:713 arg1 glycoproteins AND specific glycans glycoproteins specific glycans Fterm glycoproteins Lectin affinity isolations are followed by chemical immobilization of the captured glycopeptides, allowing the identification of glycoproteins containing specific glycans by subsequent mass spectrometry. 26232512 3 27 gly α1,2-fucosylated 594:609 arg1 α1,2-fucosylated glycan structures α1,2-fucosylated glycan structures Down regulation of HIF-1α expression resulted in elevated FUT1 and FUT2 transcript levels and an increased expression of α1,2-fucosylated glycan structures on the surface of these cells. 24440233 9 17 gly sites 1598:1602 arg1 two O-linked sites two O-linked sites sites Overall, 38 unique intact glycopeptides corresponding to eight glycosylation sites (six N-linked and two O-linked sites) were confidently identified from a standard protein mixture. 24440233 9 76 gly glycopeptides 1547:1559 arg2 38 unique intact glycopeptides 38 unique intact glycopeptides glycopeptides Overall, 38 unique intact glycopeptides corresponding to eight glycosylation sites (six N-linked and two O-linked sites) were confidently identified from a standard protein mixture. 24440233 9 80 gly glycosylation 1584:1596 arg2 eight glycosylation sites eight glycosylation sites sites Overall, 38 unique intact glycopeptides corresponding to eight glycosylation sites (six N-linked and two O-linked sites) were confidently identified from a standard protein mixture. 24664808 0 50 gly glycopeptides 55:67 arg2 deprotonated N-linked glycopeptides deprotonated N-linked glycopeptides glycopeptides Fragmentation characteristics of deprotonated N-linked glycopeptides: influences of amino acid composition and sequence. 27957769 5 122 gly glycopeptides 883:895 arg2 mucin 1 glycopeptides mucin 1 glycopeptides glycopeptides For assessment of the influence of the immune stimulant on antibody recognition, a comprehensive library of mucin 1 glycopeptides (>100 entries) is synthesized and employed in antibody microarray profiling; these range from small tumor-associated glycans (TN , STN , and T-antigen structures) to heavily extended O-glycan core structures (type-1 and type-2 elongated core 1-3 tri-, tetra-, and hexasaccharides) glycosylated in variable density at the five different sites of the MUC1 tandem repeat. 27957769 5 82 gly glycosylated 1178:1189 arg1 heavily extended O-glycan core structures sites heavily extended O-glycan core structures sites For assessment of the influence of the immune stimulant on antibody recognition, a comprehensive library of mucin 1 glycopeptides (>100 entries) is synthesized and employed in antibody microarray profiling; these range from small tumor-associated glycans (TN , STN , and T-antigen structures) to heavily extended O-glycan core structures (type-1 and type-2 elongated core 1-3 tri-, tetra-, and hexasaccharides) glycosylated in variable density at the five different sites of the MUC1 tandem repeat. 27957769 5 82 gly glycosylated 1178:1189 arg1 type-2 elongated core 1-3 tri- sites type-2 elongated core 1-3 tri- sites For assessment of the influence of the immune stimulant on antibody recognition, a comprehensive library of mucin 1 glycopeptides (>100 entries) is synthesized and employed in antibody microarray profiling; these range from small tumor-associated glycans (TN , STN , and T-antigen structures) to heavily extended O-glycan core structures (type-1 and type-2 elongated core 1-3 tri-, tetra-, and hexasaccharides) glycosylated in variable density at the five different sites of the MUC1 tandem repeat. 25499076 0 42 gly glycoprotein 38:49 arg1 a simple glycoprotein model a simple glycoprotein model Fterm glycoprotein N-glycoprofiling analysis in a simple glycoprotein model: a comparison between recombinant and pituitary glycosylated human prolactin. 25187161 7 66 gly sialylated 1236:1245 arg1 the sialylated Tn antigen the sialylated Tn antigen There were significant differences in the sialylated species between the TCRδ(-/-) and WT mice with the sialylated Tn antigen found exclusively in the TCRδ(-/-)small intestine, whereas the sulfation pattern remained mostly unchanged. 24308486 6 48 gly contained 1056:1064 arg1 sites Asn21, Asn49, Asn99, Asn146, and Asn252 AND complex-type glycans sites Asn21, Asn49, Asn99, Asn146, and Asn252 complex-type glycans sites Asn21, Asn49, Asn99, Asn146, and Asn252 In all three samples, site Asn275 contained exclusively oligomannosidic structures with between 2 and 9 mannoses, whereas sites Asn21, Asn49, Asn99, Asn146, and Asn252 contained exclusively complex-type glycans. 28052259 3 35 part_of LRP6 630:633 arg1 the entire ectodomain LRP6 the entire ectodomain PUBTATOR Site LRP6 4040 ectodomain Here, we used negative-stain electron microscopy to probe conformational states of the entire ectodomain of LRP6 in solution and found that the four-module ectodomain undergoes a large bending motion hinged at the junction between the second and the third modules. 28692416 2 55 part_of G 379:379 arg1 immunoglobulin G (IgG) glycome composition immunoglobulin G immunoglobulin G (IgG) glycome composition Cterm Site immunoglobulin G position, Our previous work has shown an association between hypertension and immunoglobulin G (IgG) glycome composition, suggesting that individual variation in N-glycosylation of IgG might contribute to hypertension pathogenesis. 25305020 1 44 part_of CaSR 218:221 arg1 the dimeric extracellular domain CaSR the dimeric extracellular domain PUBTATOR Site CaSR 846 domain Numerous in vivo functional studies have indicated that the dimeric extracellular domain (ECD) of the CaSR plays a crucial role in regulating Ca(2+) homeostasis by sensing Ca(2+) and l-Phe. 26663535 1 34 gly glycosylation 141:153 arg1 proteins proteins Fterm proteins Post-translational glycosylation of proteins play key roles in cellular processes and the site-specific characterisation of glycan structures is critical to understanding these events. 24417605 6 0 gly found 840:844 arg1 multiple glycoproteins AND a biantennary complex type glycan multiple glycoproteins a biantennary complex type glycan Fterm glycoproteins The most abundant N-glycan was a biantennary complex type glycan with two sialic acids (Hexose5HexNAc4Neu5Ac2) and was found in multiple glycoproteins using site-specific glycosylation analysis. 24417605 6 0 gly found 840:844 arg2 multiple glycoproteins AND The most abundant N-glycan multiple glycoproteins The most abundant N-glycan Fterm glycoproteins The most abundant N-glycan was a biantennary complex type glycan with two sialic acids (Hexose5HexNAc4Neu5Ac2) and was found in multiple glycoproteins using site-specific glycosylation analysis. 24417605 6 65 gly glycoproteins 858:870 arg1 multiple glycoproteins multiple glycoproteins Fterm glycoproteins The most abundant N-glycan was a biantennary complex type glycan with two sialic acids (Hexose5HexNAc4Neu5Ac2) and was found in multiple glycoproteins using site-specific glycosylation analysis. 26863921 0 60 gly glycoproteins 71:83 arg1 glycoproteins glycoproteins Fterm glycoproteins Structural characterization of the N-linked pentasaccharide decorating glycoproteins of the halophilic archaeon Haloferax volcanii. 27506354 3 86 gly sites 509:513 arg1 glycan sites glycan sites The relatively low abundance of glycan in complex biological mixtures, lack of basic sites for protonation, and suppression by other highly abundant proteins/peptides lead to the particularly poor detection sensitivity of N-glycans in the MS analysis. 27145274 3 49 gly attached 664:671 arg1 asparagine (Asn) 297 AND N- linked oligosaccharide asparagine (Asn) 297 N- linked oligosaccharide Asn) 297 In contrast, N- linked oligosaccharide attached to asparagine (Asn) 297 of IgG Fc was located in the inside of the natural protein and was inaccessible by ConA. 29065342 1 3 gly glycoproteins 195:207 arg1 many cell surface glycoproteins many cell surface glycoproteins Fterm glycoproteins LewisX (LeX) is a branched trisaccharide Galβ1→4(Fucα1→3)GlcNAc that is expressed on many cell surface glycoproteins and plays critical roles in innate and adaptive immune responses. 27020775 6 8 gly glycosylated 1076:1087 arg1 the glycosylated protein the glycosylated protein Fterm protein Analysis of the glycosylated protein showed that glycans in donkey lactoferrin are linked to the protein backbone via an amide bond to asparagine residues located at the positions 137, 281 and 476. 27020775 6 32 gly positions 1230:1238 arg1 476 positions 137, 281 and 476 positions 137, 281 and 476 Analysis of the glycosylated protein showed that glycans in donkey lactoferrin are linked to the protein backbone via an amide bond to asparagine residues located at the positions 137, 281 and 476. 27020775 6 32 gly positions 1230:1238 arg1 281 positions 137, 281 and 476 positions 137, 281 and 476 Analysis of the glycosylated protein showed that glycans in donkey lactoferrin are linked to the protein backbone via an amide bond to asparagine residues located at the positions 137, 281 and 476. 27020775 6 32 gly positions 1230:1238 arg1 281 positions 137, 281 and 476 positions 137, 281 and 476 Analysis of the glycosylated protein showed that glycans in donkey lactoferrin are linked to the protein backbone via an amide bond to asparagine residues located at the positions 137, 281 and 476. 27223297 0 5 gly N-Glycans 0:8 arg1 the Rift Valley Fever Virus Envelope Glycoproteins Glycoproteins N-Glycans Fterm Glycoproteins N-Glycans on the Rift Valley Fever Virus Envelope Glycoproteins Gn and Gc Redundantly Support Viral Infection via DC-SIGN. 27808502 2 70 gly glycopeptides 384:396 arg2 glycopeptides glycopeptides glycopeptides This approach is based on our discovery that the fragmentation of glycopeptides is glycan-structure dependent and glycans with core mannose structures overwhelmingly lead to the generation of Y1 ions when subjected to MS/MS in mass spectrometry. 24575722 0 45 gly glycoproteins 32:44 arg1 glycoproteins glycoproteins Fterm glycoproteins Analysis of glycan variation on glycoproteins from serum by the reverse lectin-based ELISA assay. 24575722 0 66 gly variation 19:27 arg1 glycoproteins glycoproteins variation Fterm glycoproteins Analysis of glycan variation on glycoproteins from serum by the reverse lectin-based ELISA assay. 26567221 4 46 gly N-glycosylated 645:658 arg1 two consensus (N37 and N134) and one non-consensus (N135) residues HMGB1 residues PUBTATOR HMGB1 3146 residues We found two consensus (N37 and N134) and one non-consensus (N135) residues that were N-glycosylated in HMGB1 by performing liquid chromatography tandem mass spectrometry (LC-MS/MS) and analyzing for N-glycan composition and structure. 26567221 4 46 gly N-glycosylated 645:658 arg2 two consensus (N37 and N134) and one non-consensus (N135) residues HMGB1 residues PUBTATOR HMGB1 3146 residues We found two consensus (N37 and N134) and one non-consensus (N135) residues that were N-glycosylated in HMGB1 by performing liquid chromatography tandem mass spectrometry (LC-MS/MS) and analyzing for N-glycan composition and structure. 26567221 4 46 gly N-glycosylated 645:658 arg2 two consensus (N37 and N134) and one non-consensus (N135) residues residues residues We found two consensus (N37 and N134) and one non-consensus (N135) residues that were N-glycosylated in HMGB1 by performing liquid chromatography tandem mass spectrometry (LC-MS/MS) and analyzing for N-glycan composition and structure. 27873218 7 80 gly CS-glycopeptides 1488:1503 arg2 CS-glycopeptides CS-glycopeptides CS-glycopeptides The intensities of protonated and sodiated saccharide oxonium ions were very prominent in the HCD-MS2 spectra, which provided complementary structural analysis of sulfate substituents of CS-glycopeptides. 26823463 5 74 part_of dimer 857:861 arg1 The two active sites dimer The two active sites Fterm Site dimer sites The two active sites of the dimer are connected by a long crevice, which might indicate its potential ability to accommodate branched fructans. 25110774 1 77 gly glycoproteins 275:287 arg1 glycoproteins glycoproteins Fterm glycoproteins Selective enrichment of glycopeptides from complicated biological samples is critical for glycoproteomics to obtain the structure and glycosylation information of glycoproteins using mass spectrometry (MS), which still remains a great challenge. 25110774 1 78 gly glycopeptides 136:148 arg2 glycopeptides glycopeptides glycopeptides Selective enrichment of glycopeptides from complicated biological samples is critical for glycoproteomics to obtain the structure and glycosylation information of glycoproteins using mass spectrometry (MS), which still remains a great challenge. 29076618 6 23 gly glycosylated 999:1010 arg1 the flagellin the flagellin Fterm flagellin Deletion of the gene amb0685 coding for Maf produced a nonflagellated bacterium where the flagellin was still produced but no longer glycosylated. 26304114 7 5 part_of acid/base 1163:1171 arg1 the proposed catalytic acid/base residue acid/base residue Fterm Site acid/base residue In all of the bound forms of the enzyme, however, the proposed catalytic acid/base residue was found to be too distant from the glycosidic oxygen (>4.3 Å) to serve directly as a general catalytic acid/base residue and thereby facilitate cleavage of the glycosidic bond. 26304114 7 10 part_of acid/base 1286:1294 arg1 the proposed catalytic acid/base residue acid/base residue Fterm Site acid/base residue In all of the bound forms of the enzyme, however, the proposed catalytic acid/base residue was found to be too distant from the glycosidic oxygen (>4.3 Å) to serve directly as a general catalytic acid/base residue and thereby facilitate cleavage of the glycosidic bond. 25660649 2 103 gly glycosylated 471:482 arg1 two potential glycosylation residues two potential glycosylation residues residues Glycosylation characterization of the envelope proteins in both insect and mammalian cell-derived dengue virus (DENV) has established that two potential glycosylation residues, the asparagine 67 and 153 can potentially be glycosylated. 25660649 2 103 gly glycosylated 471:482 arg1 the asparagine the asparagine asparagine 67 and 153 Glycosylation characterization of the envelope proteins in both insect and mammalian cell-derived dengue virus (DENV) has established that two potential glycosylation residues, the asparagine 67 and 153 can potentially be glycosylated. 25636227 4 68 gly attached 691:698 arg2 the Ser or Thr residues AND an N-acetylgalacosamine (GalNAc) residue the Ser or Thr residues an N-acetylgalacosamine (GalNAc) residue Thr residues A mixture of exoglycosidases was used to partially remove O-glycan chains and leave an N-acetylgalacosamine (GalNAc) residue attached to the Ser or Thr residues. 27439567 8 12 gly glycosites 1281:1290 arg2 various glycosites various glycosites glycosites Both core and antennary fucosylation are shown to be present on various glycosites in A1AT. 27439567 8 36 gly present 1262:1268 arg1 various glycosites AND antennary fucosylation glycosites antennary fucosylation glycosites Both core and antennary fucosylation are shown to be present on various glycosites in A1AT. 26483525 9 104 gly glycosylated 1606:1617 arg1 the major pilin subunit the major pilin subunit Fterm subunit Despite clear evidence for a substantial number of glycoprotein substrates, the major pilin subunit of the endogenous type IV pilus was not glycosylated. 26483525 9 136 gly glycoprotein 1517:1528 arg1 glycoprotein substrates glycoprotein substrates Fterm glycoprotein Despite clear evidence for a substantial number of glycoprotein substrates, the major pilin subunit of the endogenous type IV pilus was not glycosylated. 25016576 9 4 part_of gp120 1750:1754 arg1 the V1/V2 domain gp120 the V1/V2 domain PUBTATOR Site gp120 Q14624 domain Our results demonstrate that, in addition to natural HIV-1 infection, immunization with recombinant proteins can elicit antibodies to the GDEs in the V1/V2 domain of gp120. 29048990 1 83 gly glycoproteins 237:249 arg1 the viral glycoproteins the viral glycoproteins Fterm glycoproteins The study of influenza virus evolution in humans has revealed a significant role of glycosylation profile alterations in the viral glycoproteins - hemagglutinin (HA) and neuraminidase (NA), in the emergence of both seasonal and pandemic strains. 29273683 7 54 gly N238 785:788 arg1 only one N-glycan N238 only one N-glycan N238 Deglycosylation of fully glycosylated human CBG or human CBG with only one N-glycan at N238 with Endo H-reduced steroid-binding affinity, while PNGase F-mediated deglycosylation does not, indicating that steroid binding is preserved by deamidation of N238 when its N-glycan is removed. 24910992 5 56 gly carrying 784:791 arg1 a soluble protein AND a single N-glycan a soluble protein a single N-glycan Fterm protein In this study, we systematically study the function and substrate specificity of known mammalian ER lectins, including EDEM1/2/3, OS-9 and XTP-3B using the recently identified ERAD substrate sonic hedgehog (SHH), a soluble protein carrying a single N-glycan, as well as its nonglycosylated mutant N278A. 28922740 4 59 gly glycoproteins 827:839 arg1 N-linked glycoproteins N-linked glycoproteins Fterm glycoproteins Similarly, complementation of a C. jejuni pglB knock-out strain with mutated pglB alleles results in reduced levels of N-linked glycoproteins and fOS in the native host. 24664808 6 37 gly glycopeptides 1118:1130 arg2 glycopeptides glycopeptides glycopeptides The CID spectra of glycopeptides having a short peptide sequence were dominated by type (i) glycan fragments (e.g., (2,4)AR, (2,4)AR-1, D, and E ions). 24945257 10 40 gly acutobin 1565:1572 arg1 the conjugated glycans acutobin the conjugated glycans Fterm acutobin Taken together, our results suggest that the conjugated glycans of acutobin are involved in its interaction with fibrinogen, and that the selection of cells optimally expressing efficient glycoforms and further glycosylation engineering are desirable before a recombinant product can replace the native enzyme for clinical use. 26959529 10 35 gly fucosylated 1322:1332 arg1 N-glycans N-glycans Goat and human milk free oligosaccharides and N-glycans from whey proteins were both highly fucosylated. 26959529 10 35 gly fucosylated 1322:1332 arg1 Goat and human milk free oligosaccharides Goat and human milk free oligosaccharides Goat and human milk free oligosaccharides and N-glycans from whey proteins were both highly fucosylated. 26959529 10 39 gly proteins 1296:1303 arg1 N-glycans proteins N-glycans Fterm proteins Goat and human milk free oligosaccharides and N-glycans from whey proteins were both highly fucosylated. 26959529 10 39 gly proteins 1296:1303 arg1 Goat and human milk free oligosaccharides proteins Goat and human milk free oligosaccharides Fterm proteins Goat and human milk free oligosaccharides and N-glycans from whey proteins were both highly fucosylated. 28052259 5 29 part_of LRP6 937:940 arg1 the LRP6 ectodomain LRP6 the LRP6 ectodomain PUBTATOR Site LRP6 4040 ectodomain We also found that the LRP6 ectodomain becomes highly compact upon complexation with the Wnt antagonist Dkk1, suggesting a potential role for the ectodomain conformational change in the regulation of receptor oligomerization and signaling. 28434712 6 2 gly fragment 1332:1339 arg1 high resolution mass fragment ions high resolution mass fragment ions Model studies were carried out using A2G0F standard and N-acetyllactosamine to identify the impurity as an imidazoline ring structure located at the reducing end of the glycan as confirmed by high resolution mass fragment ions. 28510654 12 4 gly α-Man- 1782:1787 arg1 α-Man-(1-4)-β-GlcANAc3NAc-(1-4)-β-GlcNAc3NAc-Asn α-Man-(1-4)-β-GlcANAc3NAc-(1-4)-β-GlcNAc3NAc-Asn Asn As a result, the core structure of the P. calidifontisN-glycan is α-Man-(1-3)-(α-Man-(1-6)-)α-Man-(1-4)-β-GlcANAc3NAc-(1-4)-β-GlcNAc3NAc-Asn, in which the unique features of the P. calidifontisN-glycan are underlined. 27235585 5 16 gly glycoprotein 857:868 arg1 a glycoprotein a glycoprotein Fterm glycoprotein In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. 29076618 7 46 part_of Maf 1078:1080 arg1 the central domain Maf the central domain OGER Site Maf O75444 domain Our X-ray structure analysis revealed that the central domain of Maf exhibits similarity to sialyltransferases from Campylobacter jejuni. 25895110 2 17 gly attached 296:303 arg2 the immunoglobulin G (IgG) Fc fragment AND N-glycans the immunoglobulin G (IgG) Fc fragment N-glycans fragment Alterations in N-glycans attached to the immunoglobulin G (IgG) Fc fragment can affect molecular structure and immunological function. 28452462 2 74 gly N-glycoproteins 452:466 arg1 N-glycoproteins N-glycoproteins Fterm N-glycoproteins We have previously reported a chemoenzymatic glycan remodeling method for producing homogeneous glycoforms of N-glycoproteins including intact antibodies, which consist of endoglycosidase-catalyzed deglycosylation and novel glycosynthase-catalyzed transglycosylation, but its application to complex glycoproteins carrying multiple N-glycans remains to be examined. 28452462 2 76 gly glycoforms 438:447 arg1 N-glycoproteins N-glycoproteins Fterm N-glycoproteins We have previously reported a chemoenzymatic glycan remodeling method for producing homogeneous glycoforms of N-glycoproteins including intact antibodies, which consist of endoglycosidase-catalyzed deglycosylation and novel glycosynthase-catalyzed transglycosylation, but its application to complex glycoproteins carrying multiple N-glycans remains to be examined. 28452462 2 85 gly glycoproteins 641:653 arg1 complex glycoproteins complex glycoproteins Fterm glycoproteins We have previously reported a chemoenzymatic glycan remodeling method for producing homogeneous glycoforms of N-glycoproteins including intact antibodies, which consist of endoglycosidase-catalyzed deglycosylation and novel glycosynthase-catalyzed transglycosylation, but its application to complex glycoproteins carrying multiple N-glycans remains to be examined. 28452462 2 88 gly carrying 655:662 arg1 complex glycoproteins AND multiple N-glycans complex glycoproteins multiple N-glycans Fterm glycoproteins We have previously reported a chemoenzymatic glycan remodeling method for producing homogeneous glycoforms of N-glycoproteins including intact antibodies, which consist of endoglycosidase-catalyzed deglycosylation and novel glycosynthase-catalyzed transglycosylation, but its application to complex glycoproteins carrying multiple N-glycans remains to be examined. 27223297 12 59 gly N-glycans 1434:1442 arg1 the Gc and Gn surface glycoproteins glycoproteins N-glycans Fterm glycoproteins Our study showed that N-glycans on the Gc and Gn surface glycoproteins redundantly support RVFV infection via DC-SIGN. 27223297 12 71 gly glycoproteins 1469:1481 arg1 the Gc and Gn surface glycoproteins the Gc and Gn surface glycoproteins Fterm glycoproteins Our study showed that N-glycans on the Gc and Gn surface glycoproteins redundantly support RVFV infection via DC-SIGN. 24233973 7 59 gly sialylated 1411:1420 arg1 sialylated core 1 sialylated core 1 The H5 hemagglutinin binds with similar strength to PSGL-1/mIgG(2b) carrying mostly sialylated core 1 (clone C-P55), a mix of sialylated core 1 and sialylated lactosamine (clone 293-P) or mainly sialylated lactosamine (clone C-PSLex) O-glycans, indicating that this hemagglutinin is unable to discriminate between these structures.The potential use of the large, flexible PSGL-1/mIgG(2b) mucin-type fusion protein carrying Siaα2-3Gal as a multivalent inhibitor of influenza virus is discussed. 24233973 7 77 gly sialylated 1480:1489 arg1 mainly sialylated lactosamine mainly sialylated lactosamine The H5 hemagglutinin binds with similar strength to PSGL-1/mIgG(2b) carrying mostly sialylated core 1 (clone C-P55), a mix of sialylated core 1 and sialylated lactosamine (clone 293-P) or mainly sialylated lactosamine (clone C-PSLex) O-glycans, indicating that this hemagglutinin is unable to discriminate between these structures.The potential use of the large, flexible PSGL-1/mIgG(2b) mucin-type fusion protein carrying Siaα2-3Gal as a multivalent inhibitor of influenza virus is discussed. 24233973 7 77 gly sialylated 1480:1489 arg1 clone C-PSLex clone C-PSLex The H5 hemagglutinin binds with similar strength to PSGL-1/mIgG(2b) carrying mostly sialylated core 1 (clone C-P55), a mix of sialylated core 1 and sialylated lactosamine (clone 293-P) or mainly sialylated lactosamine (clone C-PSLex) O-glycans, indicating that this hemagglutinin is unable to discriminate between these structures.The potential use of the large, flexible PSGL-1/mIgG(2b) mucin-type fusion protein carrying Siaα2-3Gal as a multivalent inhibitor of influenza virus is discussed. 24233973 7 88 gly sialylated 1433:1442 arg1 sialylated lactosamine (clone 293-P) or mainly sialylated lactosamine (clone C-PSLex) O-glycans sialylated lactosamine (clone 293-P) or mainly sialylated lactosamine (clone C-PSLex) O-glycans The H5 hemagglutinin binds with similar strength to PSGL-1/mIgG(2b) carrying mostly sialylated core 1 (clone C-P55), a mix of sialylated core 1 and sialylated lactosamine (clone 293-P) or mainly sialylated lactosamine (clone C-PSLex) O-glycans, indicating that this hemagglutinin is unable to discriminate between these structures.The potential use of the large, flexible PSGL-1/mIgG(2b) mucin-type fusion protein carrying Siaα2-3Gal as a multivalent inhibitor of influenza virus is discussed. 24233973 7 0 gly carrying 1699:1706 arg1 the large, flexible PSGL-1/mIgG(2b) mucin-type fusion protein AND Siaα2-3Gal the large, flexible PSGL-1/mIgG(2b) mucin-type fusion protein Siaα2-3Gal Fterm protein The H5 hemagglutinin binds with similar strength to PSGL-1/mIgG(2b) carrying mostly sialylated core 1 (clone C-P55), a mix of sialylated core 1 and sialylated lactosamine (clone 293-P) or mainly sialylated lactosamine (clone C-PSLex) O-glycans, indicating that this hemagglutinin is unable to discriminate between these structures.The potential use of the large, flexible PSGL-1/mIgG(2b) mucin-type fusion protein carrying Siaα2-3Gal as a multivalent inhibitor of influenza virus is discussed. 24233973 7 12 gly sialylated 1369:1378 arg1 clone C-P55 P55 mostly sialylated core 1 OGER P55 P19438 The H5 hemagglutinin binds with similar strength to PSGL-1/mIgG(2b) carrying mostly sialylated core 1 (clone C-P55), a mix of sialylated core 1 and sialylated lactosamine (clone 293-P) or mainly sialylated lactosamine (clone C-PSLex) O-glycans, indicating that this hemagglutinin is unable to discriminate between these structures.The potential use of the large, flexible PSGL-1/mIgG(2b) mucin-type fusion protein carrying Siaα2-3Gal as a multivalent inhibitor of influenza virus is discussed. 25361541 8 23 gly O-mannosylated 1548:1561 arg1 responsible responsible We also showed that the Lewis X epitope almost disappeared due to the knockout of protein O-mannose β1,2-N-acetylglucosaminyltransferase 1, an N-acetylglucosaminyltransferase essential for the synthesis of O-mannosylated glycans, which indicated that the O-mannosylated glycan is responsible for presenting the Lewis X epitope. 25361541 8 23 gly O-mannosylated 1548:1561 arg1 the O-mannosylated glycan the O-mannosylated glycan We also showed that the Lewis X epitope almost disappeared due to the knockout of protein O-mannose β1,2-N-acetylglucosaminyltransferase 1, an N-acetylglucosaminyltransferase essential for the synthesis of O-mannosylated glycans, which indicated that the O-mannosylated glycan is responsible for presenting the Lewis X epitope. 25361541 8 62 gly O-mannosylated 1499:1512 arg1 O-mannosylated glycans O-mannosylated glycans We also showed that the Lewis X epitope almost disappeared due to the knockout of protein O-mannose β1,2-N-acetylglucosaminyltransferase 1, an N-acetylglucosaminyltransferase essential for the synthesis of O-mannosylated glycans, which indicated that the O-mannosylated glycan is responsible for presenting the Lewis X epitope. 27249581 10 28 gly attached 1878:1885 arg1 glycoproteins AND N-linked glycans glycoproteins N-linked glycans Fterm glycoproteins Finally, we discuss our results in light of recent literature regarding the contribution of electrostatics to CH-π interactions and speculate on what our observations imply about the absolute conservation of GlcNAc as the monosaccharide through which N-linked glycans are attached to glycoproteins in eukaryotes. 27249581 10 34 gly glycoproteins 1890:1902 arg1 glycoproteins glycoproteins Fterm glycoproteins Finally, we discuss our results in light of recent literature regarding the contribution of electrostatics to CH-π interactions and speculate on what our observations imply about the absolute conservation of GlcNAc as the monosaccharide through which N-linked glycans are attached to glycoproteins in eukaryotes. 27439567 2 37 part_of contains 319:326 arg1 the glycoprotein alpha-1-antitrypsin AND antennary-fucosylated glycosites the glycoprotein alpha-1-antitrypsin antennary-fucosylated glycosites Fterm Site glycoprotein glycosites This procedure is applied to the glycoprotein alpha-1-antitrypsin (A1AT), which contains both core- and antennary-fucosylated glycosites. 27439567 2 37 part_of contains 319:326 arg1 A1AT AND antennary-fucosylated glycosites A1AT antennary-fucosylated glycosites Cterm Site A1AT P01009 glycosites This procedure is applied to the glycoprotein alpha-1-antitrypsin (A1AT), which contains both core- and antennary-fucosylated glycosites. 25545631 6 35 gly structures 940:949 arg1 the mAb constant region the mAb constant region the mAb constant region Site region The specific antibody productivity increased by 25% at 32°C and was accompanied by a reduction in intracellular nucleotide sugar donor (NSD) concentrations and a decreased proportion of the more processed glycan structures on the mAb constant region. 25545631 6 37 gly region 971:976 arg1 intracellular nucleotide sugar donor (NSD) concentrations region intracellular nucleotide sugar donor (NSD) concentrations region The specific antibody productivity increased by 25% at 32°C and was accompanied by a reduction in intracellular nucleotide sugar donor (NSD) concentrations and a decreased proportion of the more processed glycan structures on the mAb constant region. 25545631 6 53 gly concentrations 869:882 arg1 the mAb constant region the mAb constant region the mAb constant region Site region The specific antibody productivity increased by 25% at 32°C and was accompanied by a reduction in intracellular nucleotide sugar donor (NSD) concentrations and a decreased proportion of the more processed glycan structures on the mAb constant region. 26248080 6 37 gly glycoproteins 807:819 arg1 glycoproteins glycoproteins Fterm glycoproteins Furthermore, the presence of glycoproteins bearing complex N-glycans with α2,3-linked sialic acid, fucose, bisecting-GlcNAc and LacdiNAc structures, and O-glycans with the T-antigen were detected. 28193043 5 46 gly peptides 971:978 arg1 a large diversity a large diversity HDX information can typically not be obtained from regions of the glycoprotein that contain the actual N-linked glycan as glycan heterogeneity combined with pepsin digestion yields a large diversity of peptic N-glycosylated peptides that can be difficult to detect. 28193043 5 51 gly N-glycosylated 956:969 arg1 peptic N-glycosylated peptides peptic N-glycosylated peptides HDX information can typically not be obtained from regions of the glycoprotein that contain the actual N-linked glycan as glycan heterogeneity combined with pepsin digestion yields a large diversity of peptic N-glycosylated peptides that can be difficult to detect. 28193043 5 91 gly glycoprotein 813:824 arg1 the glycoprotein the glycoprotein Fterm glycoprotein HDX information can typically not be obtained from regions of the glycoprotein that contain the actual N-linked glycan as glycan heterogeneity combined with pepsin digestion yields a large diversity of peptic N-glycosylated peptides that can be difficult to detect. 28193043 5 88 gly contain 831:837 arg1 the glycoprotein AND the actual N-linked glycan as glycan heterogeneity combined with pepsin digestion yields a large diversity of peptic N-glycosylated peptides that can be difficult to detect the glycoprotein the actual N-linked glycan as glycan heterogeneity combined with pepsin digestion yields a large diversity of peptic N-glycosylated peptides that can be difficult to detect Fterm glycoprotein HDX information can typically not be obtained from regions of the glycoprotein that contain the actual N-linked glycan as glycan heterogeneity combined with pepsin digestion yields a large diversity of peptic N-glycosylated peptides that can be difficult to detect. 27581986 5 46 part_of CD4 1005:1007 arg1 the early CD4 binding site CD4 the early CD4 binding site PUBTATOR Site CD4 920 site Here we report the isolation and structural characterization of CAP257-RH1, an N276 glycan-dependent CD4 binding site antibody representative of the early CD4 binding site plasma response in donor CAP257. 27993676 5 28 gly asparagine-linked 743:759 arg1 asparagine-linked N-acetyl-β-d-glucosamine asparagine asparagine-linked N-acetyl-β-d-glucosamine asparagine Both fucosyltransferases showed l-galactosylation activity from GDP-l-Gal to asparagine-linked N-acetyl-β-d-glucosamine of asialo-agalacto-bi-antennary N-glycan instead of l-fucosylation. 25927005 10 82 part_of N10 1724:1726 arg1 the N1, N2, and N10 sites N10 the N1, N2, and N10 sites PUBTATOR Site N10 3164 sites At the same time, elimination of glycans at the N1, N2, and N10 sites led to the accumulation of unproductive E1E2 dimers as aggregates and productive assembly suppression of virus-like particles both in insect and mammalian cells. 28575723 2 18 part_of o 251:251 arg1 The deduced amino acid sequence Cha o 3 The deduced amino acid sequence OGER Site Cha o 3 Q9UL49 sequence The deduced amino acid sequence of Cha o 3 indicates that this glycoallergen contains a cellulase domain and a number of putative N-glycosylation sites. 25895110 5 64 part_of IgG 605:607 arg1 METHODS IgG glycome composition |METHODS Ig| METHODS IgG glycome composition Cterm Site |METHODS Ig| position METHODS IgG glycome composition in patients with UC (n = 507), CD (n = 287), and controls (n = 320) was analyzed by ultra performance liquid chromatography. 25895110 5 96 part_of METHODS 597:603 arg1 METHODS IgG glycome composition |METHODS Ig| METHODS IgG glycome composition Cterm Site |METHODS Ig| position METHODS IgG glycome composition in patients with UC (n = 507), CD (n = 287), and controls (n = 320) was analyzed by ultra performance liquid chromatography. 25113421 10 0 gly glycopeptides 1330:1342 arg2 intact N-linked glycopeptides intact N-linked glycopeptides glycopeptides To address this need, we developed a novel software tool, GlycoMaster DB, to assist the automated and high-throughput identification of intact N-linked glycopeptides from MS/MS spectra. 27073020 7 15 gly Core-fucosylated 1243:1258 arg1 Core-fucosylated tetra-antennary structures Core-fucosylated tetra-antennary structures Core-fucosylated tetra-antennary structures were decreased in quantity likely as a result of hypomethylated MGAT3 gene promoter followed by increased expression of this gene. 25759508 9 83 gly occupancy 1302:1310 arg2 the three O-glycosylation sites the three O-glycosylation sites sites The occupancy of each of the three O-glycosylation sites was found to be ∼10% in six serum-derived IgG3 samples and ∼13% in two monoclonal IgG3 allotypes. 25759508 9 90 gly O-glycosylation 1333:1347 arg2 the three O-glycosylation sites the three O-glycosylation sites sites The occupancy of each of the three O-glycosylation sites was found to be ∼10% in six serum-derived IgG3 samples and ∼13% in two monoclonal IgG3 allotypes. 28489325 1 48 part_of contains 243:250 arg1 L-Selectin AND seven N-glycosylation sites L-Selectin seven N-glycosylation sites PUBTATOR Site L-Selectin 6402 sites L-Selectin, a cell-adhesion receptor on the surface of most leukocytes, contains seven N-glycosylation sites. 28489325 1 48 part_of contains 243:250 arg1 a cell-adhesion receptor AND seven N-glycosylation sites a cell-adhesion receptor seven N-glycosylation sites Fterm Site receptor sites L-Selectin, a cell-adhesion receptor on the surface of most leukocytes, contains seven N-glycosylation sites. 27956708 9 15 gly hyper-sialylated 1499:1514 arg1 hyper-sialylated Fab-glycans hyper-sialylated Fab-glycans These observations provide the first evidence pointing to the ability of ACPA-IgG to mediate novel immunological activities, for example through binding specific lectins via hyper-sialylated Fab-glycans. 28696719 7 74 gly O-glycosites 868:879 arg2 O-glycosites O-glycosites O-glycosites Out of 257 HCD spectra, 181 characterized glycoforms were specified as either N- or O-glycosites. 25359784 2 5 gly N-glycosylated 261:274 arg1 a highly N-glycosylated protein a highly N-glycosylated protein Fterm protein Isopullulanase (IPU), a polysaccharide-hydrolyzing enzyme, is a highly N-glycosylated protein, and IPU deglycosylation results in a decrease in thermostability. 25359784 2 5 gly N-glycosylated 261:274 arg1 Isopullulanase Isopullulanase Fterm Isopullulanase Isopullulanase (IPU), a polysaccharide-hydrolyzing enzyme, is a highly N-glycosylated protein, and IPU deglycosylation results in a decrease in thermostability. 29069609 0 28 gly glycopeptide 83:94 arg2 glycopeptide analysis glycopeptide analysis glycopeptide Development of a data independent acquisition mass spectrometry workflow to enable glycopeptide analysis without predefined glycan compositional knowledge. 24234447 4 61 gly glycoprotein 820:831 arg1 published glycoprotein information published glycoprotein information Fterm glycoprotein UniCarbKB provides comprehensive information concerning glycan structures, and published glycoprotein information including global and site-specific attachment information. 25528754 8 56 gly glycosylation 715:727 arg2 the glycosylation sites the glycosylation sites sites Among the five repeat units of DII, most of the glycosylation sites are from the second unit, which is highly divergent and rich in serine and threonine, but has no cysteine residues. 26439794 9 57 gly glycoproteins 1366:1378 arg1 glycoproteins glycoproteins Fterm glycoproteins Our method provides new insights into transport, biosynthesis, and degradation of glycoproteins. 27485625 4 46 gly proteins 763:770 arg1 the N-linked glycans proteins the N-linked glycans Fterm proteins Due to the strong interactions between carbon and glycans as well as the size-exclusion effect of pore against protein, the N-linked glycans from standard glycoprotein or complex human serum proteins could be identified with high efficiency. 27485625 4 35 gly glycoprotein 727:738 arg1 standard glycoprotein glycoprotein the N-linked glycans Fterm glycoprotein Due to the strong interactions between carbon and glycans as well as the size-exclusion effect of pore against protein, the N-linked glycans from standard glycoprotein or complex human serum proteins could be identified with high efficiency. 27705835 0 23 gly linked 33:38 arg2 glycoproteins AND N-glycans glycoproteins N-glycans Fterm glycoproteins Structural features of N-glycans linked to glycoproteins expressed in three kinds of water plants: Predominant occurrence of the plant complex type N-glycans bearing Lewis a epitope. 27705835 0 67 gly glycoproteins 43:55 arg1 glycoproteins glycoproteins Fterm glycoproteins Structural features of N-glycans linked to glycoproteins expressed in three kinds of water plants: Predominant occurrence of the plant complex type N-glycans bearing Lewis a epitope. 28258464 5 61 gly glycopeptides 652:664 arg2 the Endo H-treated glycopeptides the Endo H-treated glycopeptides glycopeptides Thirdly, a fraction of the Endo H-treated glycopeptides was further subjected to PNGase F treatment in 18O water to remove the remaining complex glycans. 25113421 6 72 gly glycopeptides 780:792 arg2 glycopeptides glycopeptides glycans glycopeptides One consists of isolating glycans from glycopeptides and generating MS/MS spectra of the glycans and peptides separately. 27145274 1 13 gly attached 279:286 arg1 the two F(ab')2 arms AND oligosaccharide the two F(ab')2 arms oligosaccharide arms Concanavalin A (ConA) chromatography has been extensively used to separate asymmetric Immunoglobulin G (IgG), which possesses oligosaccharide attached to one of the two F(ab')2 arms, from symmetric IgG with no glycan attached to Fab fragments. 27145274 1 34 gly attached 354:361 arg1 Fab fragments AND no glycan Fab fragments no glycan fragments Concanavalin A (ConA) chromatography has been extensively used to separate asymmetric Immunoglobulin G (IgG), which possesses oligosaccharide attached to one of the two F(ab')2 arms, from symmetric IgG with no glycan attached to Fab fragments. 25753708 1 11 part_of http 241:244 arg1 website http website OGER Site http Q9P0V3 website This chapter describes the Glycan Pathway Predictor Tool, which is available as a part of the RINGS (Resource for INformatics of Glycomes at Soka) website at http://www.rings.t.soka.ac.jp/. 27732771 3 115 gly asialoglycoprotein 364:381 arg1 asialoglycoprotein receptor asialoglycoprotein receptor Fterm asialoglycoprotein Reduction in sialylation resulted in enhanced VWF clearance through asialoglycoprotein receptor. 24308486 0 29 gly glycoprotein 108:119 arg1 a heterodimeric glycoprotein a heterodimeric glycoprotein Fterm glycoprotein Site-specific N-glycosylation analysis of human immunoglobulin e. Immunoglobulin E (IgE) is a heterodimeric glycoprotein involved in antiparasitic and allergic immune reactions. 29233911 2 45 gly glycoprotein 321:332 arg1 a highly glycosylated plasma glycoprotein a highly glycosylated plasma glycoprotein Fterm glycoprotein It is known to be a highly glycosylated plasma glycoprotein. 29233911 2 53 gly glycosylated 301:312 arg1 a highly glycosylated plasma glycoprotein a highly glycosylated plasma glycoprotein Fterm glycoprotein It is known to be a highly glycosylated plasma glycoprotein. 27601469 1 20 gly glycosylation 137:149 arg1 specific carbohydrate epitopes specific carbohydrate epitopes Aberrant glycosylation and the overexpression of specific carbohydrate epitopes is a hallmark of many cancers, and tumor-associated oligosaccharides are actively investigated as targets for immunotherapy and diagnostics. 25227423 0 5 gly glycans 9:15 arg1 influenza A H3N2 hemagglutinin hemagglutinin glycans Fterm hemagglutinin N-linked glycans on influenza A H3N2 hemagglutinin constrain binding of host antibodies, but shielding is limited. 29085933 2 67 gly attached 270:277 arg2 asparagine residues AND N-Glycans proteins asparagine residues N-Glycans Fterm proteins asparagine residues N-Glycans, which are attached to asparagine residues of proteins, are studied most often due to their compatibility with enzymatic release. 25636227 8 0 gly O-glycosylation 1247:1261 arg2 most previously known O-glycosylation sites most previously known O-glycosylation sites sites The workflow indicated superior sensitivity by not only covering most previously known O-glycosylation sites but also discovering several novel sites. 28955811 7 7 gly N-glycosylation 1200:1214 arg2 N-glycosylation sites N-glycosylation sites sites In agreement, mutation of each and both N-glycosylation sites led to decreased levels of secreted active hCES2. 28955811 7 13 gly each 1186:1189 arg1 N-glycosylation sites N-glycosylation sites sites In agreement, mutation of each and both N-glycosylation sites led to decreased levels of secreted active hCES2. 27356208 6 49 gly N-glycosylation 1109:1123 arg2 new N-glycosylation site new N-glycosylation site site With this aim, the first 45 residues of mature hFIX were explored to find out suitable positions for introducing either Asn or Ser/Thr residues, to create new N-glycosylation site(s). 25305020 0 76 part_of receptor 106:113 arg1 the extracellular domain calcium-sensing receptor the extracellular domain PUBTATOR Site calcium-sensing receptor 846 domain Direct determination of multiple ligand interactions with the extracellular domain of the calcium-sensing receptor. 29016103 8 19 gly glycopeptides 1214:1226 arg2 O-linked glycopeptides O-linked glycopeptides glycopeptides The enrichment of O-linked glycopeptides was further improved when a Retain AX cartridge (RAX) was used. 28328971 3 7 gly glycosites 355:364 arg2 the first N-linked glycosites mapping the first N-linked glycosites mapping glycosites Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. 28328971 3 17 gly glycopeptides 467:479 arg2 a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy glycopeptides Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. 25629924 5 27 gly glycosites 768:777 arg2 Multiple glycosites Multiple glycosites glycosites Multiple glycosites were identified with nearly 30 glycan compositions located at seven sites on the secretory component, six compositions at a single site on the J chain, and 16 compositions at five sites on the IgA heavy (H) chain. 25629924 5 37 gly site 910:913 arg1 nearly 30 glycan compositions site nearly 30 glycan compositions site Multiple glycosites were identified with nearly 30 glycan compositions located at seven sites on the secretory component, six compositions at a single site on the J chain, and 16 compositions at five sites on the IgA heavy (H) chain. 28258464 6 66 gly deglycosylated 793:806 arg1 deglycosylated peptides deglycosylated peptides peptides The intact glycopeptides and deglycosylated peptides were analyzed by nano-RPLC-MS/MS, and the glycan structures and the peptide sequences were identified by using the Byonic or pFind tools. 28258464 6 69 gly glycopeptides 775:787 arg2 The intact glycopeptides The intact glycopeptides glycopeptides The intact glycopeptides and deglycosylated peptides were analyzed by nano-RPLC-MS/MS, and the glycan structures and the peptide sequences were identified by using the Byonic or pFind tools. 27493216 0 36 gly region 48:53 arg1 Carbohydrate-binding domain region Carbohydrate-binding domain region Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of α-dystroglycan. 27439567 8 51 part_of glycosites 1281:1290 arg1 A1AT A1AT glycosites Cterm Site A1AT P01009 glycosites Both core and antennary fucosylation are shown to be present on various glycosites in A1AT. 25533529 1 22 gly N-glycosylation 210:224 arg2 four N-glycosylation sites four N-glycosylation sites sites Acutobin, the α-fibrinogenase from Deinagkistrodon acutus venom, contains four N-glycosylation sites with disialylated complex-typed glycans. 25533529 1 26 gly disialylated 237:248 arg1 disialylated complex-typed glycans disialylated complex-typed glycans Acutobin, the α-fibrinogenase from Deinagkistrodon acutus venom, contains four N-glycosylation sites with disialylated complex-typed glycans. 25533529 1 55 gly sites 226:230 arg1 disialylated complex-typed glycans sites disialylated complex-typed glycans sites Acutobin, the α-fibrinogenase from Deinagkistrodon acutus venom, contains four N-glycosylation sites with disialylated complex-typed glycans. 26959529 9 52 gly proteins 1162:1169 arg1 N-glycans proteins N-glycans Fterm proteins Bovine milk free oligosaccharides and N-glycans from whey proteins were highly sialylated and to a lesser extend fucosylated. 26959529 9 52 gly proteins 1162:1169 arg1 Bovine milk free oligosaccharides proteins Bovine milk free oligosaccharides Fterm proteins Bovine milk free oligosaccharides and N-glycans from whey proteins were highly sialylated and to a lesser extend fucosylated. 26959529 9 57 gly sialylated 1183:1192 arg1 N-glycans N-glycans Bovine milk free oligosaccharides and N-glycans from whey proteins were highly sialylated and to a lesser extend fucosylated. 26959529 9 57 gly sialylated 1183:1192 arg1 Bovine milk free oligosaccharides Bovine milk free oligosaccharides Bovine milk free oligosaccharides and N-glycans from whey proteins were highly sialylated and to a lesser extend fucosylated. 26067753 2 24 gly glycoforms 334:343 arg1 CxMab CxMab Three GlcNAc (Gn) terminating bi-antennary glycoforms of CxMab differing in core fucosylation (α1,3- and α1,6-linkage) were generated in a plant-based expression platform. 25501957 1 14 gly enzymes 228:234 arg1 β-Fructosidases enzymes β-Fructosidases Fterm enzymes β-Fructosidases are a widespread group of enzymes that catalyze the hydrolysis of terminal fructosyl units from various substrates. 26059692 4 24 part_of c/MAM 575:579 arg1 the c/MAM domain MAM the c/MAM domain PUBTATOR Site MAM 6445 domain We found that the c/MAM domain was heavily O-glycosylated with up to 24 monosaccharide units in the form of disialylated core 1 and core 2 O-glycans. 25279697 5 17 gly O-mannosylated 1022:1035 arg1 the functional O-mannosylated glycan structure the functional O-mannosylated glycan structure Our results further define the functional O-mannosylated glycan structure and indicate that B4GAT1 is involved in the initiation of the LARGE-dependent repeating disaccharide that is necessary for extracellular matrix protein binding to O-mannosylated α-dystroglycan that is lacking in secondary dystroglycanopathies. 25279697 5 39 gly O-mannosylated 1217:1230 arg1 O-mannosylated α-dystroglycan O-mannosylated α-dystroglycan Our results further define the functional O-mannosylated glycan structure and indicate that B4GAT1 is involved in the initiation of the LARGE-dependent repeating disaccharide that is necessary for extracellular matrix protein binding to O-mannosylated α-dystroglycan that is lacking in secondary dystroglycanopathies. 26940363 10 84 gly glycoproteins 1974:1986 arg1 glycoproteins glycoproteins Fterm glycoproteins The integration of site-specific glycosylation data obtained from large-scale glycoproteomics and introduction of cell line studies will improve the analysis of glycoproteins and entire glycomes. 25124522 3 47 gly sialylglycopeptide 496:513 arg2 sialylglycopeptide sialylglycopeptide sialylglycopeptide We report here an optimized procedure for gram-scale production of sialylglycopeptide (SGP) containing a disialyl biantennary complex-type N-glycan from egg yolks. 25124522 3 35 gly containing 521:530 arg1 sialylglycopeptide AND a disialyl biantennary complex-type N-glycan sialylglycopeptide a disialyl biantennary complex-type N-glycan sialylglycopeptide We report here an optimized procedure for gram-scale production of sialylglycopeptide (SGP) containing a disialyl biantennary complex-type N-glycan from egg yolks. 25118826 0 92 gly Polysialylated 0:13 arg1 Polysialylated N-glycans Polysialylated N-glycans Polysialylated N-glycans identified in human serum through combined developments in sample preparation, separations, and electrospray ionization-mass spectrometry. 25820733 4 25 gly glycopeptide 771:782 arg2 intact glycopeptide analysis intact glycopeptide analysis glycopeptide In many cases however, unique bacterial sugars preclude enzymatic removal, therefore ultimately requiring a site-specific approach for intact glycopeptide analysis. 28938401 2 74 gly asparagine-linked 280:296 arg1 specific asparagine-linked glycan (N-glycan) structures asparagine specific asparagine-linked glycan (N-glycan) structures asparagine The identification of specific asparagine-linked glycan (N-glycan) structures, which are associated with metastasized pheochromocytomas and paragangliomas, may serve as a diagnostic tool. 26603318 7 36 gly N-glycosylation 1659:1673 arg1 turmeric lectin turmeric lectin Fterm lectin These results suggest that N-glycosylation in turmeric lectin is important for the maintenance of its proper folding upon changes in pH, and that the oligosaccharides help in maintaining the active conformation and prevent aggregation in unfolded or partially folded molecules. 25155433 6 71 gly O-glycosylation 1205:1219 arg2 actual O-glycosylation sites actual O-glycosylation sites sites In vitro analysis of acceptor peptide substrate specificities using recombinant expressed GalNAc-Ts has been the method of choice for probing activities of individual isoforms, but these studies have been hampered by biological validation of actual O-glycosylation sites in proteins and number of substrate testable. 28955811 4 20 gly approaches 787:796 arg1 both N-glycosylation sites both N-glycosylation sites sites Partial or non-glycosylated forms of a secreted form of hCES2 have been obtained by three approaches: (i) enzymatic deglycosylation with peptide N-glycosidase F; (ii) incubation with the inhibitor tunicamycin; ii) site directed mutagenesis of each or both N-glycosylation sites. 28955811 4 20 gly approaches 787:796 arg1 ii) site directed mutagenesis of each or both N-glycosylation sites ii) site directed mutagenesis of each or both N-glycosylation sites site Partial or non-glycosylated forms of a secreted form of hCES2 have been obtained by three approaches: (i) enzymatic deglycosylation with peptide N-glycosidase F; (ii) incubation with the inhibitor tunicamycin; ii) site directed mutagenesis of each or both N-glycosylation sites. 28955811 4 51 gly N-glycosylation 953:967 arg2 both N-glycosylation sites both N-glycosylation sites sites Partial or non-glycosylated forms of a secreted form of hCES2 have been obtained by three approaches: (i) enzymatic deglycosylation with peptide N-glycosidase F; (ii) incubation with the inhibitor tunicamycin; ii) site directed mutagenesis of each or both N-glycosylation sites. 29187599 2 97 part_of has 225:227 arg1 Human diamine oxidase AND multiple N-glycosylation sites Human diamine oxidase multiple N-glycosylation sites PUBTATOR Site diamine oxidase 26 sites Human diamine oxidase (hDAO), required for histamine catabolism, has multiple N-glycosylation sites, but their roles, for example in DAO secretion, are unclear. 29187599 2 97 part_of has 225:227 arg1 hDAO AND multiple N-glycosylation sites hDAO multiple N-glycosylation sites PUBTATOR Site hDAO 1610 sites Human diamine oxidase (hDAO), required for histamine catabolism, has multiple N-glycosylation sites, but their roles, for example in DAO secretion, are unclear. 28681696 1 36 gly modifications 143:155 arg1 proteins proteins modifications Fterm proteins Aberrant changes of N-glycan modifications on proteins have been linked to various diseases including different cancers, suggesting possible avenue for exploring their etiologies based on N-glycomic analysis. 24945257 0 32 gly glycoforms 107:116 arg1 acutobin acutobin Fterm acutobin Correlation between the glycan variations and defibrinogenating activities of acutobin and its recombinant glycoforms. 24945257 0 70 gly acutobin 78:85 arg1 glycan variations acutobin glycan variations Fterm acutobin Correlation between the glycan variations and defibrinogenating activities of acutobin and its recombinant glycoforms. 27423877 2 59 gly heterogeneity 332:344 arg1 the capsular polysaccharide the capsular polysaccharide The development of a vaccine based on the capsular polysaccharide of C. neoformans is still an open challenge due to the heterogeneity of the capsular polysaccharide and the difficulty of identifying protective epitopes. 26869352 4 105 part_of has 980:982 arg1 Haptoglobin AND four potential glycosylation sites Haptoglobin four potential glycosylation sites PUBTATOR Site Haptoglobin 3240 sites To ascertain if characteristic fucosylation is observed in each cancer type, we undertook site-specific analyses of N-glycans on haptoglobin in the sera of patients with five types of operable gastroenterological cancer (esophageal, gastric, colon, gallbladder, pancreatic), a non-gastroenterological cancer (prostate cancer) and normal controls using ODS column LC-ESI MS. Haptoglobin has four potential glycosylation sites (Asn184, Asn207, Asn211, Asn241). 25673493 2 35 gly glycoproteins 330:342 arg1 other recombinant glycoproteins other recombinant glycoproteins Fterm glycoproteins Over half of these new generation drugs are glycoproteins, such as monoclonal antibodies or other recombinant glycoproteins, which are mostly produced in mammalian cell lines. 25673493 2 4 gly glycoproteins 264:276 arg1 glycoproteins glycoproteins Fterm glycoproteins Over half of these new generation drugs are glycoproteins, such as monoclonal antibodies or other recombinant glycoproteins, which are mostly produced in mammalian cell lines. 26488311 1 70 part_of clusterin 133:141 arg1 Specific glycosylated peptides clusterin Specific glycosylated peptides OGER Site clusterin P10909 peptides Specific glycosylated peptides of clusterin are found associated with hippocampal atrophy. 24910992 11 82 gly glycoproteins 1656:1668 arg1 misfolded glycoproteins misfolded glycoproteins Fterm glycoproteins EDEM2 also interacts with calnexin and SEL1L, suggesting a potential avenue by which misfolded glycoproteins may be shunted towards SEL1L and ERAD rather than being released into the secretory pathway. 26598643 4 23 gly O-glycosylation 579:593 arg1 human blood plasma glycoproteins human blood plasma glycoproteins Fterm glycoproteins Here, we report on the site-specific O-glycosylation analysis of human blood plasma glycoproteins. 26598643 4 31 gly glycoproteins 626:638 arg1 human blood plasma glycoproteins human blood plasma glycoproteins Fterm glycoproteins Here, we report on the site-specific O-glycosylation analysis of human blood plasma glycoproteins. 29217182 2 41 gly glycoprotein 184:195 arg1 a glycoprotein a glycoprotein Fterm glycoprotein It is a glycoprotein, not much is known about its N-glycan structures, site occupancy and site-specific N-glycosylation. 29237727 5 13 gly N-glycopeptides 837:851 arg2 1110 N-glycopeptides 1110 N-glycopeptides N-glycopeptides A total of 492 N-glycosites were identified from 324 Arabidopsis proteins with extensive N-glycan structural heterogeneity revealed through 1110 N-glycopeptides. 29237727 5 17 gly N-glycosites 707:718 arg2 492 N-glycosites 492 N-glycosites N-glycosites A total of 492 N-glycosites were identified from 324 Arabidopsis proteins with extensive N-glycan structural heterogeneity revealed through 1110 N-glycopeptides. 29237727 5 63 gly proteins 757:764 arg1 extensive N-glycan structural heterogeneity proteins extensive N-glycan structural heterogeneity Fterm proteins A total of 492 N-glycosites were identified from 324 Arabidopsis proteins with extensive N-glycan structural heterogeneity revealed through 1110 N-glycopeptides. 24327294 0 31 gly glycosylated 11:22 arg1 glycosylated human butyrylcholinesterase glycosylated human butyrylcholinesterase Fterm butyrylcholinesterase A model of glycosylated human butyrylcholinesterase. 24549892 7 2 gly glycoproteins 1699:1711 arg1 complex relatively pure glycoproteins complex relatively pure glycoproteins Fterm glycoproteins The challenges provided by this example provide guidance in analyzing complex relatively pure glycoproteins and potentially even more complex glycoprotein mixtures. 24549892 7 94 gly glycoprotein 1747:1758 arg1 more complex glycoprotein mixtures more complex glycoprotein mixtures Fterm glycoprotein The challenges provided by this example provide guidance in analyzing complex relatively pure glycoproteins and potentially even more complex glycoprotein mixtures. 26729457 9 88 gly N-glycopeptides 1622:1636 arg2 Twenty-six out of 30 N-glycopeptides Twenty-six out of 30 N-glycopeptides N-glycopeptides Twenty-six out of 30 N-glycopeptides and four out of five O-glycopeptides carrying >110 different glycoforms could be identified by this optimized LC-ESI tandem MS method with minimal user input. 26729457 9 98 gly O-glycopeptides 1659:1673 arg2 four out of five O-glycopeptides four out of five O-glycopeptides O-glycopeptides Twenty-six out of 30 N-glycopeptides and four out of five O-glycopeptides carrying >110 different glycoforms could be identified by this optimized LC-ESI tandem MS method with minimal user input. 25793407 5 94 gly glycoproteins 940:952 arg1 serum glycoproteins serum glycoproteins Fterm glycoproteins N-glycome was evaluated in serum glycoproteins. 27928741 12 83 part_of protein 1897:1903 arg1 the stalk domain protein the stalk domain Fterm Site protein domain In addition, a previously undocumented O-linked glycopeptide was identified from the stalk domain of the haemagglutinin-neuraminidase protein. 25359784 3 45 gly N-glycosylated 416:429 arg1 an N-glycosylated residue an N-glycosylated residue residue To investigate the function of N-glycan in IPU, we focused on an N-glycosylated residue located in the vicinity of the active site, Asn448. 28630087 10 54 gly glycosylation 1662:1674 arg2 The three glycosylation sites HNE sites PUBTATOR HNE 1991 sites The three glycosylation sites of HNE were located distal to the active site indicating glycan functions other than interference with HNE enzyme activity. 25182382 0 115 gly N-glycopeptides 39:53 arg2 intact N-glycopeptides intact N-glycopeptides N-glycopeptides Large-scale characterization of intact N-glycopeptides using an automated glycoproteomic method. 24912705 4 38 gly glycosylated 671:682 arg1 the modified protein the modified protein Fterm protein Electrophoresis and infrared spectroscopy analysis confirmed the modified protein to be crosslinked and glycosylated. 28661444 10 73 gly glycosylation 1587:1599 arg2 the main glycosylation site the main glycosylation site site Lys30 of Ag85B, identified as the main glycosylation site, proved to be the most important site involved in the formation of T-cell epitopes, reasonably explaining why its glycosylation strongly influenced the T-cell activity. 27249581 4 54 gly N-glycoproteins 582:596 arg1 some N-glycoproteins some N-glycoproteins Fterm N-glycoproteins We employed the enhanced aromatic sequon, a structural motif found in the reverse turns of some N-glycoproteins, to facilitate face-to-face monosaccharide-aromatic interactions. 27932460 5 4 part_of POMGNT1-only 1043:1054 arg1 a POMGNT1-only site POMGNT1 a POMGNT1-only site OGER Site POMGNT1 Q8WZA1 site We define a POMGNT2 acceptor motif, conserved among 59 vertebrate species, in α-dystroglycan that when engineered into a POMGNT1-only site is sufficient to convert the O-mannosylated peptide to a substrate for POMGNT2. 27932460 5 47 part_of POMGNT2 934:940 arg1 a POMGNT2 acceptor motif POMGNT2 a POMGNT2 acceptor motif OGER Site POMGNT2 Q8NAT1 motif We define a POMGNT2 acceptor motif, conserved among 59 vertebrate species, in α-dystroglycan that when engineered into a POMGNT1-only site is sufficient to convert the O-mannosylated peptide to a substrate for POMGNT2. 26160412 0 82 gly glycoproteins 87:99 arg1 the major glycoproteins the major glycoproteins Fterm glycoproteins Evaluation of a combined glycomics and glycoproteomics approach for studying the major glycoproteins present in biofluids: Application to cerebrospinal fluid. 29031045 0 36 gly glycoform 40:48 arg1 the Man5 glycoform the Man5 glycoform Structural characterization of the Man5 glycoform of human IgG3 Fc. 27810711 2 11 gly glycopeptides 261:273 arg2 glycopeptides glycopeptides glycopeptides Due to their structural complexities, strategies towards synthesis of this class of glycopeptides bearing well-defined glycan chains are urgently needed. 25212784 5 28 gly sialylated 1462:1471 arg1 sialylated structures sialylated structures Overall, as the follicle develops from Selection, Differentiation and Luteinisation in both cows and heifers, there is an overall decrease in sialylated structures on FF N-glycans. 24575722 4 1 gly removed 754:760 arg1 the glycoproteins AND sialic acid the glycoproteins sialic acid Fterm glycoproteins In the presence of competing sugars of lectin AAL or with sialic acid removed from the glycoproteins, we confirmed that this method specifically detects glycosylation changes of proteins rather than protein abundance variation. 24575722 4 69 gly glycoproteins 771:783 arg1 the glycoproteins the glycoproteins Fterm glycoproteins In the presence of competing sugars of lectin AAL or with sialic acid removed from the glycoproteins, we confirmed that this method specifically detects glycosylation changes of proteins rather than protein abundance variation. 27311011 4 38 gly N-glycopeptide 827:840 arg2 N-glycopeptide N-glycopeptide N-glycopeptide Our results showed that irrespective of the IgG subclass expressed in the drugs, the N-glycopeptide profiles are nearly the same but differ in abundances. 26563299 7 0 gly N-glycosylation 1091:1105 arg2 The two potential IL-15 N-glycosylation sites The two potential IL-15 N-glycosylation sites sites The two potential IL-15 N-glycosylation sites (Asn71 and Asn112) located at the IL-2 receptor interface were unoccupied. 26563299 7 82 gly sites 1107:1111 arg1 The two potential IL-15 N-glycosylation sites The two potential IL-15 N-glycosylation sites sites The two potential IL-15 N-glycosylation sites (Asn71 and Asn112) located at the IL-2 receptor interface were unoccupied. 26563299 7 0 gly N-glycosylation 1091:1105 arg2 Asn71 Asn71 and Asn112 Asn71 and Asn112 The two potential IL-15 N-glycosylation sites (Asn71 and Asn112) located at the IL-2 receptor interface were unoccupied. 26563299 7 82 gly sites 1107:1111 arg1 Asn112 Asn71 and Asn112 Asn71 and Asn112 The two potential IL-15 N-glycosylation sites (Asn71 and Asn112) located at the IL-2 receptor interface were unoccupied. 28060516 2 20 gly glycoform 559:567 arg1 predominantly the canonical Man5GlcNAc2 glycoform predominantly the canonical Man5GlcNAc2 glycoform The proteins were expressed in (i) HEK293T cells to produce complex glycoforms, (ii) HEK293T cells treated with Vibrio cholera neuraminidase to provide asialo-complex glycoforms, (iii) HEK293S GnTI(-) cells with predominantly the canonical Man5GlcNAc2 glycoform, and (iv) Drosophila S2 insect cells producing primarily paucimannose glycoforms. 28060516 2 68 gly glycoforms 474:483 arg1 asialo-complex glycoforms asialo-complex glycoforms The proteins were expressed in (i) HEK293T cells to produce complex glycoforms, (ii) HEK293T cells treated with Vibrio cholera neuraminidase to provide asialo-complex glycoforms, (iii) HEK293S GnTI(-) cells with predominantly the canonical Man5GlcNAc2 glycoform, and (iv) Drosophila S2 insect cells producing primarily paucimannose glycoforms. 26554003 1 63 part_of proteins 158:165 arg1 the ectodomain proteins the ectodomain Fterm Site proteins ectodomain Regulated shedding of the ectodomain of cell membrane proteins by proteases is a common process that releases the extracellular domain from the cell and activates cell signaling. 25212784 4 3 gly nonsialylated 1227:1239 arg1 nonsialylated glycans nonsialylated glycans A comparison of FF N-glycans from cows and heifers indicated higher levels of nonsialylated glycans with a lower proportion of sialylated glycans in cows than in heifers. 25212784 4 67 gly sialylated 1276:1285 arg1 sialylated glycans sialylated glycans A comparison of FF N-glycans from cows and heifers indicated higher levels of nonsialylated glycans with a lower proportion of sialylated glycans in cows than in heifers. 27145274 2 14 gly attached 512:519 arg1 Fab fragment AND N- linked oligosaccharide Fab fragment N- linked oligosaccharide fragment In this study, applying affinity chromatography, silver stain, Western blot and lectin stain techniques, N- linked oligosaccharide attached to Fab fragment was demonstrated to be exposed on the surface of the protein and be accessible by ConA. 24467287 7 97 gly glycoprotein 1266:1277 arg1 the protruding E2 attachment glycoprotein the protruding E2 attachment glycoprotein Fterm glycoprotein In contrast, the protruding E2 attachment glycoprotein primarily contained conserved under-processed oligomannose-type structures when produced in both rodent and mosquito cell lines. 24467287 7 66 gly contained 1289:1297 arg1 the protruding E2 attachment glycoprotein AND conserved under-processed oligomannose-type structures the protruding E2 attachment glycoprotein conserved under-processed oligomannose-type structures Fterm glycoprotein In contrast, the protruding E2 attachment glycoprotein primarily contained conserved under-processed oligomannose-type structures when produced in both rodent and mosquito cell lines. 25636227 5 10 gly O-glycosylated 732:745 arg1 The O-glycosylated peptides The O-glycosylated peptides peptides The O-glycosylated peptides could then be identified by using liquid chromatography-tandem mass spectrometry (LC-MS-MS) to detect the 203 Da mass increase. 25212784 1 23 gly glycosylated 210:221 arg1 many proteins many proteins Fterm proteins Follicular fluid (FF), an important microenvironment for the development of oocytes, contains many proteins that are glycosylated with N-linked glycans. 28988842 1 63 gly glycoproteins 194:206 arg1 the glycoproteins the glycoproteins Fterm glycoproteins Mucin-type O-glycans are involved in biological functions on the cell surface as well as the glycoproteins and can also be used as specific carbohydrate biomarkers of many diseases. 26648038 4 28 gly carries 562:568 arg1 Each domain AND a carbohydrate binding site Each domain a carbohydrate binding site domain Each domain carries a carbohydrate binding site in type II RIPs of known structure. 28978918 3 38 gly glycoforms 645:654 arg1 sequentially truncated high-mannose IgG1 Fc glycoforms sequentially truncated high-mannose IgG1 Fc glycoforms Through atomistic molecular dynamics simulations of a series of sequentially truncated high-mannose IgG1 Fc glycoforms, we found that the C'E loop and the Cγ2-Cγ3 orientation are highly dynamic, and changes in N-glycan composition alter their conformational ensembles. 28978918 3 38 gly glycoforms 645:654 arg1 sequentially truncated high-mannose IgG1 Fc glycoforms sequentially truncated high-mannose IgG1 Fc glycoforms Through atomistic molecular dynamics simulations of a series of sequentially truncated high-mannose IgG1 Fc glycoforms, we found that the C'E loop and the Cγ2-Cγ3 orientation are highly dynamic, and changes in N-glycan composition alter their conformational ensembles. 28978918 3 38 gly glycoforms 645:654 arg1 sequentially truncated high-mannose IgG1 Fc glycoforms sequentially truncated high-mannose IgG1 Fc glycoforms Through atomistic molecular dynamics simulations of a series of sequentially truncated high-mannose IgG1 Fc glycoforms, we found that the C'E loop and the Cγ2-Cγ3 orientation are highly dynamic, and changes in N-glycan composition alter their conformational ensembles. 26940433 1 74 gly glycoproteins 303:315 arg1 glycoproteins glycoproteins Fterm glycoproteins Congenital disorders of glycosylation (CDGs) constitute a rapidly growing family of human diseases resulting from heritable mutations in genes driving the production and modification of glycoproteins. 27151270 4 7 gly glycopeptide 666:677 arg2 glycopeptide fragmentation spectra glycopeptide fragmentation spectra glycopeptide The workflow developed in this study includes novel tools, written in R, to aid plant glycan identification, pGlycoFilter, for annotation of glycopeptide fragmentation spectra, gPSMvalidator, and for relative quantitation of glycoforms, glycoRQ. 28630087 10 83 part_of HNE 1685:1687 arg1 The three glycosylation sites HNE The three glycosylation sites PUBTATOR Site HNE 1991 sites The three glycosylation sites of HNE were located distal to the active site indicating glycan functions other than interference with HNE enzyme activity. 27984785 0 12 gly glycoproteins 67:79 arg1 ebolavirus glycoproteins ebolavirus glycoproteins Fterm glycoproteins Comparison of N- and O-linked glycosylation patterns of ebolavirus glycoproteins. 27984785 0 49 gly glycosylation 30:42 arg1 ebolavirus glycoproteins ebolavirus glycoproteins Fterm glycoproteins Comparison of N- and O-linked glycosylation patterns of ebolavirus glycoproteins. 25451932 0 77 part_of corin 56:60 arg1 different sites corin different sites PUBTATOR Site corin 10699 sites Distinct roles of N-glycosylation at different sites of corin in cell membrane targeting and ectodomain shedding. 27869200 9 44 gly glycopeptides 1522:1534 arg2 glycopeptides glycopeptides glycopeptides The developed model facilitates interpretation of tandem mass spectrometry data for assignment of glycopeptides. 25029371 3 0 gly glycopeptide 601:612 arg2 a type I transmembrane glycopeptide scaffold a type I transmembrane glycopeptide scaffold glycopeptide Here, we examined the effect of the consensus site X and hydroxyl residue on the distributions of co- and post-translational N-glycosylation of a type I transmembrane glycopeptide scaffold. 28186137 5 24 gly glycoproteins 547:559 arg1 myelin glycoproteins myelin glycoproteins Fterm glycoproteins However, the roles of glycans on myelin glycoproteins remain poorly understood. 28397166 6 68 gly sialylation 1168:1178 arg1 IgG N-glycans IgG N-glycans Further accurate quantitation indicated that galactosylation and sialylation of IgG N-glycans in RA cases were significantly lower than in healthy subjects. 28079948 6 33 gly glycopeptide 1053:1064 arg2 a glycopeptide vaccine construct a glycopeptide vaccine construct glycopeptide In this work, a glycopeptide vaccine construct was synthesized and used to generate antibodies against branched O-mannosyl glycans. 28888681 2 11 gly glycopeptide 400:411 arg2 glycopeptide analysis glycopeptide analysis glycopeptide A combination of reversed phase chromatography with tandem mass spectrometry (RP-LC-MS/MS) is one of the most powerful tools for glycopeptide analysis. 29275050 4 54 part_of has 638:640 arg1 the enzyme AND the large positively numbered subsites the enzyme the large positively numbered subsites Fterm Site enzyme subsites This result strongly implies that the enzyme has the large positively numbered subsites. 26306636 1 18 gly sialylated 327:336 arg1 sialylated human milk oligosaccharides sialylated human milk oligosaccharides A mutant Trypanosoma rangeli sialidase, Tr7, expressed in Pichia pastoris, exhibits significant trans-sialidase activity, and has been used for analytical-scale production of sialylated human milk oligosaccharides. 25355867 8 28 gly sialylated 1330:1339 arg1 sialylated N-glycan structures sialylated N-glycan structures Notwithstanding, an intensive glycoengineering approach led to secreted A1AT carrying sialylated N-glycan structures largely resembling its serum-derived counterpart. 25118826 6 83 gly sialylated 1503:1512 arg1 both large and heavily sialylated glycans both large and heavily sialylated glycans Online separations were improved by using extended length graphitized carbon columns and adding TFA as an acid modifier to a formic acid/reversed phase gradient, providing additional resolving power and significantly improved desorption of both large and heavily sialylated glycans. 29042829 3 76 part_of IgG 758:760 arg1 IgG glycopeptides IgG IgG glycopeptides Cterm Site IgG glycopeptides The importance of obtaining complete glycan release for accurate quantitation led us to investigate the kinetics of this de-glycosylation reaction for IgG glycopeptides and to determine the effect of glycan structure and amino acid sequence on the rate of glycan release from glycopeptides of IgGs. 26295743 1 6 gly glycosylated 120:131 arg1 heavily glycosylated proteoglycans proteins heavily glycosylated proteoglycans Fterm proteins Arabinogalactan proteins are heavily glycosylated proteoglycans in plants. 29042829 2 77 gly asparagine 436:445 arg1 all N-glycans asparagine residue all N-glycans asparagine residue A standard approach to analyze glycosylation of IgGs involves the release of the N-glycans by the enzyme peptide N-glycosidase F, which cleaves the linkage between the asparagine residue and innermost N-acetylglucosamine (GlcNAc) of all N-glycans except those containing a 3-linked fucose attached to the reducing terminal GlcNAc residue. 28681696 6 76 gly fucosylated 1392:1402 arg1 four high-mannose and three fucosylated neutral complex N-glycans four high-mannose and three fucosylated neutral complex N-glycans By applying receiver operating characteristic analysis, we show that a combined panel composed of four high-mannose and three fucosylated neutral complex N-glycans allows for good discrimination of epithelial ovarian cancer from healthy controls. 26202417 5 38 gly glycosylation 636:648 arg2 glycosylation sites glycosylation sites sites Here we examine HA N-glycosylation of H3N2 virus strains that we have engineered to closely mimic glycosylation sites gained between 1968 through 2002 starting with pandemic A/Hong Kong/1/68 (H3N2: HK68). 26921321 0 37 gly Glycosylation 0:12 arg1 BclA Glycoprotein BclA Glycoprotein Fterm Glycoprotein Glycosylation of BclA Glycoprotein from Bacillus cereus and Bacillus anthracis Exosporium Is Domain-specific. 25265424 3 25 gly glycoforms 356:365 arg1 four proteins four proteins Fterm proteins We present a case study that compares site specific glycoforms of four proteins including haptoglobin, complement factor H, kininogen-1, and hemopexin isolated from the same patient. 26929048 0 38 gly Disialylated 27:38 arg1 the Disialylated Tetrasaccharide Motif the Disialylated Tetrasaccharide Motif Efficient Synthesis of the Disialylated Tetrasaccharide Motif in N-Glycans through an Amide-Protection Strategy. 27249581 8 35 gly N-glycoproteins 1298:1312 arg1 the monosaccharide-containing N-glycoproteins the monosaccharide-containing N-glycoproteins The NMR solution structures of several of the monosaccharide-containing N-glycoproteins were solved to further understand the origins of the similarities and differences between the monosaccharide-aromatic interaction energies. 29187599 5 33 gly Asn-168 761:767 arg1 Glycans Asn-168 Glycans Asn-168 Glycans at Asn-168 were predominantly sialylated with bi- to tetra-antennary branches, and Asn-538 and Asn-745 had similar complex-type glycans with some tissue- and cell line-specific variations. 29187599 5 47 gly sialylated 788:797 arg1 Glycans Glycans Glycans at Asn-168 were predominantly sialylated with bi- to tetra-antennary branches, and Asn-538 and Asn-745 had similar complex-type glycans with some tissue- and cell line-specific variations. 29187599 5 19 gly had 861:863 arg1 Asn-538 AND similar complex-type glycans Asn-538 and Asn-745 similar complex-type glycans Asn-538 and Asn-745 Glycans at Asn-168 were predominantly sialylated with bi- to tetra-antennary branches, and Asn-538 and Asn-745 had similar complex-type glycans with some tissue- and cell line-specific variations. 28539451 6 28 gly positions 969:977 arg1 inserting glycans positions 306 and 314 inserting glycans positions 306 and 314 We found that inserting glycans at positions 306 and 314 (termed M1 and M7) markedly reduced V3 antigenicity while improving the presentation of trimer apex bNAb epitopes. 27957769 2 84 gly glycopeptide 305:316 arg2 tumor-associated glycopeptide structures tumor-associated glycopeptide structures glycopeptide Many successful methodologies for reliably increasing the antigenicity toward tumor-associated glycopeptide structures have been reported. 29019687 3 47 gly glycans 440:446 arg1 the ligand binding domain the ligand binding domain the ligand binding domain Site domain We recently demonstrated that certain glycans on the ligand binding domain (LBD) of NMDA receptors (NMDARs) can serve as intramolecular potentiators, changing EC50 of NMDAR coagonists. 29019687 3 47 gly glycans 440:446 arg1 NMDA receptors receptors glycans Fterm receptors We recently demonstrated that certain glycans on the ligand binding domain (LBD) of NMDA receptors (NMDARs) can serve as intramolecular potentiators, changing EC50 of NMDAR coagonists. 27547921 1 30 gly N-glycosylated 124:137 arg1 Glucose transporter 4 protein Glucose transporter 4 Fterm protein Glucose transporter 4 (GLUT4) is an N-glycosylated protein that maintains glucose homeostasis by regulating the protein translocation. 28336547 2 46 gly residues 392:399 arg1 N50 N50 N50, N406, N439, N510, N515, and N532 We recently demonstrated that the proton-coupled oligopeptide transporter 1 (PEPT1) in the intestine is glycosylated at six asparagine residues (N50, N406, N439, N510, N515, and N532). 28336547 2 36 gly N50 402:404 arg1 N532 N50, N406, N439, N510, N515, and N532 N50, N406, N439, N510, N515, and N532 We recently demonstrated that the proton-coupled oligopeptide transporter 1 (PEPT1) in the intestine is glycosylated at six asparagine residues (N50, N406, N439, N510, N515, and N532). 28336547 2 36 gly N50 402:404 arg1 N510 N50, N406, N439, N510, N515, and N532 N50, N406, N439, N510, N515, and N532 We recently demonstrated that the proton-coupled oligopeptide transporter 1 (PEPT1) in the intestine is glycosylated at six asparagine residues (N50, N406, N439, N510, N515, and N532). 28336547 2 36 gly N50 402:404 arg1 N439 N50, N406, N439, N510, N515, and N532 N50, N406, N439, N510, N515, and N532 We recently demonstrated that the proton-coupled oligopeptide transporter 1 (PEPT1) in the intestine is glycosylated at six asparagine residues (N50, N406, N439, N510, N515, and N532). 28336547 2 36 gly N50 402:404 arg1 N510 N50, N406, N439, N510, N515, and N532 N50, N406, N439, N510, N515, and N532 We recently demonstrated that the proton-coupled oligopeptide transporter 1 (PEPT1) in the intestine is glycosylated at six asparagine residues (N50, N406, N439, N510, N515, and N532). 28336547 2 36 gly N50 402:404 arg1 N439 N50, N406, N439, N510, N515, and N532 N50, N406, N439, N510, N515, and N532 We recently demonstrated that the proton-coupled oligopeptide transporter 1 (PEPT1) in the intestine is glycosylated at six asparagine residues (N50, N406, N439, N510, N515, and N532). 28336547 2 36 gly N50 402:404 arg1 N439 N50, N406, N439, N510, N515, and N532 N50, N406, N439, N510, N515, and N532 We recently demonstrated that the proton-coupled oligopeptide transporter 1 (PEPT1) in the intestine is glycosylated at six asparagine residues (N50, N406, N439, N510, N515, and N532). 28336547 2 90 gly glycosylated 361:372 arg1 the proton-coupled oligopeptide transporter 1 proton-coupled oligopeptide transporter 1 asparagine residues PUBTATOR proton-coupled oligopeptide transporter 1 56643 asparagine residues We recently demonstrated that the proton-coupled oligopeptide transporter 1 (PEPT1) in the intestine is glycosylated at six asparagine residues (N50, N406, N439, N510, N515, and N532). 28336547 2 90 gly glycosylated 361:372 arg1 PEPT1 PEPT1 asparagine residues PUBTATOR PEPT1 56643 asparagine residues We recently demonstrated that the proton-coupled oligopeptide transporter 1 (PEPT1) in the intestine is glycosylated at six asparagine residues (N50, N406, N439, N510, N515, and N532). 25851037 4 52 gly immunoglobulin 1007:1020 arg1 in vitro and in-cell glycan-engineered Fc proteins immunoglobulin in vitro and in-cell glycan-engineered Fc proteins Fterm immunoglobulin Herein, we describe a lectin-based microtiter assay (lectin-enzyme-linked immunosorbent assay [ELISA]) to quantify terminal glycan moieties, applicable to in vitro and in-cell glycan-engineered Fc proteins as well as intact IgGs from intravenous immunoglobulin (IVIG), a blood product containing pooled polyvalent IgG antibodies extracted from plasma from healthy human donors. 25030939 3 18 gly N-glycosylated 628:641 arg1 N-glycosylated variants N-glycosylated variants Fterm variants A highly efficient convergent synthetic route, involving a combination of solid phase peptide synthesis and enzymatic glycosylation, delivered a library of N-glycosylated variants of pramlintide bearing either GlcNAc, the core N-glycan pentasaccharide [Man3(GlcNAc)2] or a complex biantennary glycan [(NeuAcGalGlcNAcMan)2Man(GlcNAc)2] at each of its six asparagine residues. 28052259 1 14 gly glycoprotein 186:197 arg1 a single-pass membrane glycoprotein a single-pass membrane glycoprotein Fterm glycoprotein LDL-receptor-related protein 6 (LRP6) is a single-pass membrane glycoprotein with a large modular ectodomain and forms a higher order signaling platform upon binding Wnt ligands on the cell surface. 29237727 3 58 gly N-glycopeptides 457:471 arg2 profile intact plant N-glycopeptides profile intact plant N-glycopeptides N-glycopeptides However, few studies have applied advanced mass spectrometry to profile intact plant N-glycopeptides. 27933952 4 15 part_of enoxaparin 650:659 arg1 the end-site enoxaparin the end-site Fterm Site enoxaparin end-site Focusing on this end-site-specific activity of LMWHs, we conjugated the tetraoligomer of deoxycholic acid (TetraDOCA; TD) at the end-site of enoxaparin via nonenzymatic glycosylation reaction. 24664808 8 44 gly glycopeptides 1347:1359 arg2 glycopeptides glycopeptides glycopeptides For glycopeptides with medium or long peptide sequences, the major fragments were type (ii) ions (e.g., [peptide + (0,2)X0-H](-) and [peptide-NH3-H](-)). 24855066 4 31 gly glycosylation 702:714 arg1 A2780 A2780 A2780 To address this effect, we analyzed the membrane glycosylation of non-cancerous ovarian surface epithelial (HOSE 6.3 and HOSE 17.1) and serous ovarian cancer cell lines (SKOV 3, IGROV1, A2780, and OVCAR 3), the most common histotype among epithelial ovarian cancers. 24855066 4 78 gly lines 816:820 arg1 A2780 A2780 A2780 To address this effect, we analyzed the membrane glycosylation of non-cancerous ovarian surface epithelial (HOSE 6.3 and HOSE 17.1) and serous ovarian cancer cell lines (SKOV 3, IGROV1, A2780, and OVCAR 3), the most common histotype among epithelial ovarian cancers. 28334636 1 21 gly transglycosylated 234:250 arg1 α-glucosyl rhoifolin α-glucosyl rhoifolin Fterm rhoifolin We report the full assignment of 1H and 13C NMR signals belonging to α-glucosyl rhoifolin (Rhf-G), a novel transglycosylated compound synthesized from a flavone glycoside, rhoifolin, as well as its chemical structure. 25155433 6 14 part_of sites 1221:1225 arg1 proteins proteins sites Fterm Site proteins sites In vitro analysis of acceptor peptide substrate specificities using recombinant expressed GalNAc-Ts has been the method of choice for probing activities of individual isoforms, but these studies have been hampered by biological validation of actual O-glycosylation sites in proteins and number of substrate testable. 25416425 10 51 gly sialylated 1445:1454 arg1 a sialylated complex-type N-glycan a sialylated complex-type N-glycan Our data suggest that composition of the N-glycan plays an important role in protein stability and trafficking, and a sialylated complex-type N-glycan promoted high cell surface expression of Kv1.4. 25916169 8 6 gly Asn 1115:1117 arg1 the N-glycan position Asn(211) the N-glycan position Asn(211) Whereas the N-glycan at position Asn(211) seems to negatively influence the activity of the enzyme using both glycolipid and glycoprotein as acceptor substrates, the single N-glycan mutant at Asn(92) had only a moderate effect. 25916169 8 39 gly Asn 1274:1276 arg1 the single N-glycan mutant Asn(92) the single N-glycan mutant Asn(92) Whereas the N-glycan at position Asn(211) seems to negatively influence the activity of the enzyme using both glycolipid and glycoprotein as acceptor substrates, the single N-glycan mutant at Asn(92) had only a moderate effect. 25916169 8 63 gly glycoprotein 1207:1218 arg1 glycoprotein glycoprotein Fterm glycoprotein Whereas the N-glycan at position Asn(211) seems to negatively influence the activity of the enzyme using both glycolipid and glycoprotein as acceptor substrates, the single N-glycan mutant at Asn(92) had only a moderate effect. 28905148 3 26 gly released 579:586 arg2 ovalbumin AND previously reported N-glycan structures ovalbumin previously reported N-glycan structures Fterm ovalbumin We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. 28905148 3 26 gly released 579:586 arg2 α1-acid glycoprotein AND previously reported N-glycan structures α1-acid glycoprotein previously reported N-glycan structures Fterm glycoprotein We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. 28905148 3 26 gly released 579:586 arg1 fetuin AND previously reported N-glycan structures fetuin previously reported N-glycan structures Fterm fetuin We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. 28905148 3 26 gly released 579:586 arg1 the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin AND previously reported N-glycan structures the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin previously reported N-glycan structures Fterm glycoproteins We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. 28905148 3 45 gly glycoproteins 606:618 arg1 ovalbumin ovalbumin Fterm ovalbumin We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. 28905148 3 45 gly glycoproteins 606:618 arg1 α1-acid glycoprotein α1-acid glycoprotein Fterm glycoprotein We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. 28905148 3 45 gly glycoproteins 606:618 arg1 fetuin fetuin Fterm fetuin We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. 28905148 3 45 gly glycoproteins 606:618 arg1 the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin Fterm glycoproteins We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. 28905148 3 59 gly glycoprotein 689:700 arg1 α1-acid glycoprotein α1-acid glycoprotein Fterm glycoprotein We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. 28905148 3 59 gly glycoprotein 689:700 arg1 the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin Fterm glycoproteins We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. 25451932 9 7 part_of protease 1214:1221 arg1 the protease domain protease the protease domain Fterm Site protease domain We also found that the location of the N-glycosylation site in the protease domain was not critical. 25883177 7 0 gly multifucosylated 1459:1474 arg1 multifucosylated antennae multifucosylated antennae During egg development, a rich diversity of N-glycans with fucosylated motifs was expressed, but with α3-core fucose and a high degree of multifucosylated antennae only in mature eggs and miracidia. 25883177 7 96 gly fucosylated 1380:1390 arg1 fucosylated motifs fucosylated motifs motifs During egg development, a rich diversity of N-glycans with fucosylated motifs was expressed, but with α3-core fucose and a high degree of multifucosylated antennae only in mature eggs and miracidia. 28299519 1 20 gly N-glycosylation 188:202 arg2 two N-glycosylation sites two N-glycosylation sites sites CrataBL is a glycoprotein isolated from Crataeva tapia bark, containing two N-glycosylation sites. 28299519 1 38 gly glycoprotein 125:136 arg1 a glycoprotein a glycoprotein Fterm glycoprotein CrataBL is a glycoprotein isolated from Crataeva tapia bark, containing two N-glycosylation sites. 28328971 4 4 gly glycosites 580:589 arg2 242 glycosites 242 glycosites glycosites A total of 242 glycosites from 191 unique proteins was discovered. 27356208 1 54 gly attaches 145:152 arg2 the asparagine residue AND a glycan moiety the asparagine residue a glycan moiety asparagine residue N-glycosylation is a process during which a glycan moiety attaches to the asparagine residue in the N-glycosylation consensus sequence (Asn-Xxx-Ser/Thr), where Xxx can be any amino acid except proline. 28860626 6 12 part_of proteins 1461:1468 arg1 the specific glycosylation sites proteins the specific glycosylation sites Fterm Site proteins sites Interestingly, sulfation, fucosylation and bisecting N-acetylglucosamine of N-glycans were also reliably identified at the specific glycosylation sites of the two influenza proteins that may serve a crucial role in regulating the protein structure and increasing the protein abundance of the influenza virus reassortants. 25927005 8 45 part_of glycoprotein 1265:1276 arg1 the single glycosylation sites glycoprotein the single glycosylation sites Fterm Site glycoprotein sites Elimination of the single glycosylation sites of the E2 glycoprotein, except for the N6 site, did not affect its synthesis efficiency in Sf9 insect cells, while the electrophoretic mobility of mutant proteins increased in proportion to the decrease in the number of glycosylation sites. 23581857 5 76 gly glycosylated 1206:1217 arg1 the glycosylated enzyme the glycosylated enzyme Fterm enzyme In addition, at acidic pH, the glycosylated enzyme presented a higher secondary conformational stability when compared to its nonglycosylated counterpart, supporting experimental findings on triple glycosylation as the essential state of ARSA. 24085030 6 94 gly glycoprotein 1040:1051 arg1 ten glycoprotein bands ten glycoprotein bands Fterm glycoprotein In lectin blotting ten glycoprotein bands were analyzed. 25282312 0 47 gly glycoproteins 75:87 arg1 neo glycoproteins neo glycoproteins Fterm glycoproteins Liquid chromatography-mass spectrometry structural characterization of neo glycoproteins aiding the rational design and synthesis of a novel glycovaccine for protection against tuberculosis. 25482815 7 61 gly flagellin 1298:1306 arg1 the immature glycan flagellin the immature glycan Fterm flagellin The data indicate that the immature glycan of flagellin from KΔ3FG cannot prevent the epitope recognition in rice. 28818784 3 23 gly glycoproteins 378:390 arg1 glycoproteins glycoproteins Fterm glycoproteins The eluted imprinted cavities showed good affinity for template glycosyls and glycoproteins carrying template glycosyl. 24549892 5 0 part_of protein 1097:1103 arg1 16 predicted sites protein 16 predicted sites Fterm Site protein sites As the test case we chose ABCA4, a large integral membrane protein with 16 predicted sites for N-glycosylation. 24326091 7 7 gly glycosylated 1442:1453 arg1 the glycosylated asparagine the glycosylated asparagine asparagine In this way, useful functional handles are introduced onto the glycosylated asparagine while maintaining the structural integrity of the reducing end of the oligosaccharide. 28445724 3 31 part_of CD4 450:452 arg1 the CD4 supersite CD4 the CD4 supersite PUBTATOR Site CD4 P01730 supersite We engineered diverse Env trimers with select glycans removed proximal to the CD4 supersite, characterized their structures and glycosylation, and immunized guinea pigs and rhesus macaques. 28737213 6 20 gly N-glycopeptides 886:900 arg2 intact N-glycopeptides intact N-glycopeptides N-glycopeptides In total, 517 unique N-glycosylated peptides have been identified, including intact N-glycopeptides that harbored N-acetylhexosamine (HexNAc) at the nonreducing end. 28737213 6 37 gly N-glycosylated 823:836 arg1 517 unique N-glycosylated peptides 517 unique N-glycosylated peptides peptides In total, 517 unique N-glycosylated peptides have been identified, including intact N-glycopeptides that harbored N-acetylhexosamine (HexNAc) at the nonreducing end. 26773038 2 38 part_of Ca 351:352 arg1 a Ca(2+)binding site Ca(2 a Ca(2+)binding site OGER Site Ca(2 P00918 site The conformational transition depends upon a Ca(2+)binding site and a vicinal cysteine disulfide bond. 28902916 0 33 gly site 51:54 arg1 Targeted N-glycan deletion site Targeted N-glycan deletion site Targeted N-glycan deletion at the receptor-binding site retains HIV Env NFL trimer integrity and accelerates the elicited antibody response. 25451932 6 59 gly N-glycosylation 790:804 arg1 Asn-80 Asn-80 Asn-80 By Western analysis of corin proteins in cell lysate and conditioned medium from transfected HEK293 cells and HL-1 cardiomyocytes, we found that N-glycosylation at Asn-80 inhibited corin shedding in the juxtamembrane domain. 26075384 10 103 gly fucosylated 1583:1593 arg1 fucosylated structures fucosylated structures In contrast, this type of fucosylated structures were low abundant in the high-grade mucinous carcinomas or in serous carcinomas. 26244886 5 15 gly alpha2-3-sialylated 778:796 arg1 high mannose high mannose As a result, a strong preferential digestion of high mannose, hybrid, alpha2-3-sialylated and bisected glycoforms was observed over the most abundant neutral, fucosylated glycoforms. 26244886 5 15 gly alpha2-3-sialylated 778:796 arg1 alpha2-3-sialylated and bisected glycoforms alpha2-3-sialylated and bisected glycoforms As a result, a strong preferential digestion of high mannose, hybrid, alpha2-3-sialylated and bisected glycoforms was observed over the most abundant neutral, fucosylated glycoforms. 25064132 2 2 gly α-galactosidase 127:141 arg1 gal36A4 α-galactosidase gal36A4 Fterm α-galactosidase An α-galactosidase gene (gal36A4) of glycosyl hydrolase family 36 was identified in the genome of Alicyclobacillus sp. 27351377 4 28 gly multifucosylated 830:845 arg1 multifucosylated N-glycans multifucosylated N-glycans Moreover, we observed a slight decrease in the proportion of multifucosylated N-glycans and α2,6-sialylation. 29069609 10 63 gly glycopeptides 1694:1706 arg2 specific glycopeptides specific glycopeptides glycopeptides SIGNIFICANCE: We developed a data-independent mass spectrometry workflow to identify specific glycopeptides from complex biological mixtures. 26512079 3 35 gly residue 550:556 arg1 a highly conserved potential N-linked glycan (PNLG) site residue a highly conserved potential N-linked glycan (PNLG) site residue Previous work has shown that removal of a highly conserved potential N-linked glycan (PNLG) site at amino acid residue 197 (N7) on the surface antigen gp120 of HIV-1 increases neutralization sensitivity of the mutant virus to CD4 binding site (CD4bs)-directed antibodies compared to its wild-type (WT) counterpart. 26512079 3 110 gly -directed 689:697 arg1 CD4 binding site CD4 binding site site Previous work has shown that removal of a highly conserved potential N-linked glycan (PNLG) site at amino acid residue 197 (N7) on the surface antigen gp120 of HIV-1 increases neutralization sensitivity of the mutant virus to CD4 binding site (CD4bs)-directed antibodies compared to its wild-type (WT) counterpart. 28510654 4 53 gly N-glycosylation 522:536 arg2 at least one potential N-glycosylation site at least one potential N-glycosylation site site The MASCOT search identified proteins with at least one potential N-glycosylation site. 28888681 8 26 gly glycoform 1185:1193 arg1 SWPAVGDCSSALR glycopeptide SWPAVGDCSSALR glycopeptide glycopeptide The nanoHILIC method was able to partially separate linkage isomers of fucose (core and outer arm) on bi-antennary glycoform of SWPAVGDCSSALR glycopeptide, which is beneficial in the elucidation of the structure of the fucosylated glycoforms. 28888681 8 46 gly fucosylated 1289:1299 arg1 the fucosylated glycoforms the fucosylated glycoforms The nanoHILIC method was able to partially separate linkage isomers of fucose (core and outer arm) on bi-antennary glycoform of SWPAVGDCSSALR glycopeptide, which is beneficial in the elucidation of the structure of the fucosylated glycoforms. 28888681 8 27 gly glycopeptide 1212:1223 arg2 SWPAVGDCSSALR glycopeptide glycopeptide bi-antennary glycoform glycopeptide The nanoHILIC method was able to partially separate linkage isomers of fucose (core and outer arm) on bi-antennary glycoform of SWPAVGDCSSALR glycopeptide, which is beneficial in the elucidation of the structure of the fucosylated glycoforms. 28714086 11 65 part_of subunit 2097:2103 arg1 the subunit composition subunit the subunit composition Fterm Site subunit position In the present study, we show that altering glycan content on kainate receptors (KARs) changes the functional properties of the receptors in a manner dependent on the identity of both the modified sugars and the subunit composition of the receptor to which they are attached. 28714086 11 70 part_of receptor 2124:2131 arg1 the subunit composition receptor the subunit composition Fterm Site receptor position In the present study, we show that altering glycan content on kainate receptors (KARs) changes the functional properties of the receptors in a manner dependent on the identity of both the modified sugars and the subunit composition of the receptor to which they are attached. 28452462 5 64 gly sialylated 1148:1157 arg1 homogeneous sialylated glycoform homogeneous sialylated glycoform With this acceptor, homogeneous sialylated glycoform or azide-tagged glycoform were produced using the glycosynthase (EndoF3-D165A) catalyzed transglycosylation. 26316330 8 1 gly glycoprotein 1158:1169 arg1 glycoprotein species glycoprotein species Fterm glycoprotein This study extends the sight of protein species by the following contributions: 1) The new term "glycoprotein species" was defined to introduce the concept of glycoforms into the field. 26208004 3 58 gly glycoprotein 436:447 arg1 The N-glycans glycoprotein The N-glycans Fterm glycoprotein The N-glycans of E glycoprotein have been shown to influence the proper folding of the protein, its cellular localization, its interactions with receptors and its immunogenicity. 26501333 5 2 gly fucosylated 932:942 arg1 singly fucosylated N-glycans singly fucosylated N-glycans In addition, the distribution of singly fucosylated N-glycans detected in tumor tissue microarray cores were compared to the histochemistry staining pattern of a core fucose binding lectin. 28258464 7 75 gly glycopeptide 1078:1089 arg2 each glycopeptide each glycopeptide glycopeptide Sequential digestion by endoglycosidase provided candidate glycosites information and indication of the glycoforms on each glycopeptide, thus helping to confine the database search space and improve the confidence regarding intact glycopeptide identification. 28258464 7 96 gly glycosites 1014:1023 arg2 candidate glycosites information candidate glycosites information glycosites Sequential digestion by endoglycosidase provided candidate glycosites information and indication of the glycoforms on each glycopeptide, thus helping to confine the database search space and improve the confidence regarding intact glycopeptide identification. 28258464 7 101 gly glycopeptide 1186:1197 arg2 intact glycopeptide identification intact glycopeptide identification glycopeptide Sequential digestion by endoglycosidase provided candidate glycosites information and indication of the glycoforms on each glycopeptide, thus helping to confine the database search space and improve the confidence regarding intact glycopeptide identification. 28295836 5 14 gly N-glycans 1022:1030 arg1 the egg jelly coat glycoproteins glycoproteins N-glycans Fterm glycoproteins N-glycans in the egg jelly coat glycoproteins were indicated by sodiated molecules at m/z 1579.8, 1783.9, 1988.0, 2192.0, and 2397.1 for permethylated oligosaccharides on MALDI-TOF MS. Fragmentation and structural characterization of these oligosaccharides were performed by ESI-Ion trap MS/MS. 28295836 5 58 gly glycoproteins 1054:1066 arg1 the egg jelly coat glycoproteins the egg jelly coat glycoproteins Fterm glycoproteins N-glycans in the egg jelly coat glycoproteins were indicated by sodiated molecules at m/z 1579.8, 1783.9, 1988.0, 2192.0, and 2397.1 for permethylated oligosaccharides on MALDI-TOF MS. Fragmentation and structural characterization of these oligosaccharides were performed by ESI-Ion trap MS/MS. 26760037 4 60 gly sialylation 1227:1237 arg1 glycans glycans Using inhibitors of glycosylation we found that both, binding of Gal-3 to the RPE cell surface and Gal-3-mediated inhibition of RPE attachment and spreading, strongly depend on the interaction of Gal-3 with tri- or tetra-antennary complex type N-glycans and sialylation of glycans but not on complex-type O-glycans. 27780868 3 11 gly glycosylated 541:552 arg1 the glycosylated linker peptide the glycosylated linker peptide peptide TrCel7A consists of a catalytic domain (CD) and a smaller carbohydrate-binding module (CBM) connected through the glycosylated linker peptide. 26156869 7 15 part_of Fc-glycosylation 1644:1659 arg1 the Fc-glycosylation site Fc the Fc-glycosylation site Cterm Site Fc site We conclude that EndoS and EndoS2 hydrolyze different glycoforms from the Fc-glycosylation site on therapeutic mAbs and that this can be used for rapid quantification of high mannose content. 26156869 7 47 part_of site 1661:1664 arg1 therapeutic mAbs mAbs site PUBTATOR Site mAbs 72935 site We conclude that EndoS and EndoS2 hydrolyze different glycoforms from the Fc-glycosylation site on therapeutic mAbs and that this can be used for rapid quantification of high mannose content. 26101185 5 38 gly glycoproteins 864:876 arg1 bovine colostrum whey glycoproteins bovine colostrum whey glycoproteins Fterm glycoproteins The effects of different processing conditions (pH, temperature, reaction time, and enzyme/protein ratio) were evaluated for their ability to change EndoBI-1 activity on bovine colostrum whey glycoproteins using advanced mass spectrometry. 26598643 14 93 gly disialylated 2049:2060 arg1 core-1 mucin-type O-glycans core-1 mucin-type O-glycans The identified O-glycan compositions most probably correspond to mono- and disialylated core-1 mucin-type O-glycans (T-antigen). 25202310 4 17 gly glycoproteins 877:889 arg1 secreted glycoproteins secreted glycoproteins Fterm glycoproteins Detailed subcellular glycome profiling of proteins derived from three breast cell lines (MCF7/MDA468/MCF10A) demonstrated that secreted glycoproteins displayed significantly more α-sialylation and α1,6-fucosylation, but less α-mannosylation, than both the intermediately glycan-processed cell-surface glycoproteomes and the under-processed microsomal glycoproteomes. 28975713 3 18 gly glycopeptide 568:579 arg1 the correct peptide and glycan composition glycopeptide the correct peptide and glycan composition glycopeptide PepSweetener simplifies the determination of the correct peptide and glycan composition of a glycopeptide based on its precursor mass. 28975713 3 21 gly glycopeptide 568:579 arg2 a glycopeptide glycopeptide the correct peptide and glycan composition glycopeptide PepSweetener simplifies the determination of the correct peptide and glycan composition of a glycopeptide based on its precursor mass. 28975713 3 21 gly glycopeptide 568:579 arg2 a glycopeptide glycopeptide the correct peptide and glycan composition glycopeptide PepSweetener simplifies the determination of the correct peptide and glycan composition of a glycopeptide based on its precursor mass. 29190644 5 3 gly glycosylation 840:852 arg2 ASN241 site ASN241 site ASN241 To investigate the effects of populating glycosylation site ASN241, monomeric human BChE glycoforms were simulated with and without site ASN241 glycosylated. 27439567 7 13 gly glycosylation 1065:1077 arg2 glycosylation sites glycosylation sites sites This procedure provided site-specific identification of glycosylation sites and the ability to distinguish core fucosylation and antennary fucosylation via a double digestion and a mass profile scan. 25820733 1 31 gly glycosylated 302:313 arg1 their formerly glycosylated peptides their formerly glycosylated peptides peptides Large-scale analysis of protein N- and O-linked glycosylation by mass spectrometry has traditionally been performed in eukaryotes by parallel approaches aimed at elucidating glycan structures (glycomics) and their formerly glycosylated peptides (glycoproteomics) without reference to their intact state. 28516782 8 6 part_of IgA1 1289:1292 arg1 the proline-rich hinge region IgA1 the proline-rich hinge region PUBTATOR Site IgA1 P01876 region Moreover, the proline-rich hinge region from HEK293-6E cell-derived IgA1 was occupied with mucin-type O-glycans, whereas IgA1 from N. benthamiana displayed numerous plant-specific modifications. 28104755 9 22 gly N-glycosylation 1363:1377 arg2 individual N-glycosylation sites individual N-glycosylation sites sites Site-directed mutagenesis of individual N-glycosylation sites in SMPDL3A identified glycosylation of Asn69 and Asn222 as affecting maturation of its N-glycans and secretion. 28104755 9 62 gly glycosylation 1407:1419 arg1 Asn69 Asn69 and Asn222 Asn69 and Asn222 Site-directed mutagenesis of individual N-glycosylation sites in SMPDL3A identified glycosylation of Asn69 and Asn222 as affecting maturation of its N-glycans and secretion. 27718394 8 9 gly glycosylation 1510:1522 arg1 two different proteins two different proteins Fterm proteins The developed method was evaluated concerning its specificity, and thereafter implemented for studying the glycosylation pattern of two different proteins, alpha-1-antitrypsin and transferrin, in human serum and cerebrospinal fluid. 28277614 9 109 gly glycopeptide 1768:1779 arg2 glycopeptide analysis glycopeptide analysis glycopeptide Using glycopeptide analysis, this novel O-glycan composition was found to be present on the catalytic domain of cellobiohydrolase I, the most abundant secreted protein by T. reesei. 28277614 9 52 gly present 1839:1845 arg2 cellobiohydrolase I AND this novel O-glycan composition cellobiohydrolase I domain this novel O-glycan composition Cterm cellobiohydrolase I domain Using glycopeptide analysis, this novel O-glycan composition was found to be present on the catalytic domain of cellobiohydrolase I, the most abundant secreted protein by T. reesei. 28277614 9 123 gly present 1839:1845 arg2 the catalytic domain AND this novel O-glycan composition domain this novel O-glycan composition domain Using glycopeptide analysis, this novel O-glycan composition was found to be present on the catalytic domain of cellobiohydrolase I, the most abundant secreted protein by T. reesei. 28277614 9 123 gly present 1839:1845 arg2 the catalytic domain AND this novel O-glycan composition cellobiohydrolase I domain this novel O-glycan composition Cterm cellobiohydrolase I domain Using glycopeptide analysis, this novel O-glycan composition was found to be present on the catalytic domain of cellobiohydrolase I, the most abundant secreted protein by T. reesei. 26307003 6 75 gly attached 1443:1450 arg2 Ser14 AND the mannose Ser14 the mannose Ser14 Additionally, detailed analysis of the NMR structures and molecular simulations indicates that the protein backbone of the CBM is not significantly altered by attachment of monosaccharides, and that the mannose attached to Ser14 may be more flexible than the mannose at Ser3. 26307003 6 103 gly Ser3 1502:1505 arg1 the mannose Ser3 the mannose Ser3 Additionally, detailed analysis of the NMR structures and molecular simulations indicates that the protein backbone of the CBM is not significantly altered by attachment of monosaccharides, and that the mannose attached to Ser14 may be more flexible than the mannose at Ser3. 25995273 2 4 gly glycopeptide 437:448 arg2 glycopeptide analysis glycopeptide analysis glycopeptide Incorporation of different sialic acid variants in both N- and O-linked glycans was observed, and the importance of using both collisional activation and electron transfer dissociation for glycopeptide analysis was illustrated. 28433761 2 126 gly glycosylation 301:313 arg1 the S-layer protein the S-layer protein Fterm protein The aim of this work was to characterize in detail the glycosylation of the S-layer protein of Lactobacillus kefiri CIDCA 83111. 27873218 3 5 gly ΔHexAGalNAcGlcAGalGalXyl-O-Ser 642:671 arg1 ΔHexAGalNAcGlcAGalGalXyl-O-Ser hexasaccharide structure Ser ΔHexAGalNAcGlcAGalGalXyl-O-Ser hexasaccharide structure Ser The CS-glycopeptides, originating from the Bikunin proteoglycan of human urine samples, had ΔHexAGalNAcGlcAGalGalXyl-O-Ser hexasaccharide structure and were further substituted with 0-3 sulfate and 0-1 phosphate groups. 27873218 3 87 gly CS-glycopeptides 554:569 arg2 The CS-glycopeptides The CS-glycopeptides CS-glycopeptides The CS-glycopeptides, originating from the Bikunin proteoglycan of human urine samples, had ΔHexAGalNAcGlcAGalGalXyl-O-Ser hexasaccharide structure and were further substituted with 0-3 sulfate and 0-1 phosphate groups. 27873218 3 27 gly had 638:640 arg1 The CS-glycopeptides AND ΔHexAGalNAcGlcAGalGalXyl-O-Ser hexasaccharide structure The CS-glycopeptides ΔHexAGalNAcGlcAGalGalXyl-O-Ser hexasaccharide structure CS-glycopeptides The CS-glycopeptides, originating from the Bikunin proteoglycan of human urine samples, had ΔHexAGalNAcGlcAGalGalXyl-O-Ser hexasaccharide structure and were further substituted with 0-3 sulfate and 0-1 phosphate groups. 27867116 6 36 part_of proteins 1150:1157 arg1 136 unique peptides proteins 136 unique peptides Fterm Site proteins peptides The MS strategy selected in this work, based on a gas phase fractionation approach, led to 136 unique peptides from four standard proteins, which represented 78% of the total number of peptides identified. 27216994 8 13 gly N-glycosylation 1551:1565 arg2 7 out of 7 N-glycosylation sites 7 out of 7 N-glycosylation sites sites Finally, using mutant recombinant GluN subunits expressed in HEK293 cells, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 27216994 8 57 gly N-glycosylation 1505:1519 arg2 11 out of 12 predicted N-glycosylation sites 11 out of 12 predicted N-glycosylation sites sites Finally, using mutant recombinant GluN subunits expressed in HEK293 cells, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 27216994 8 20 gly occupied 1587:1594 arg2 7 out of 7 N-glycosylation sites sites sites Finally, using mutant recombinant GluN subunits expressed in HEK293 cells, we found that 11 out of 12 predicted N-glycosylation sites in GluN1 and 7 out of 7 N-glycosylation sites in GluN2B are occupied by N-glycans. 25799047 8 59 gly glycosylation 1761:1773 arg1 protein export protein export Fterm protein Analysis of protein in culture supernatants revealed that the extracellular CelA protein is glycosylated whereas the intracellular CelA is not, suggesting that either protein transport is required for this post-translational modification or that glycosylation is required for protein export. 26791533 7 2 part_of sites 1017:1021 arg1 50 glycoproteins glycoproteins sites Fterm Site glycoproteins sites We have elucidated glycan compositions and proposed structures for 243 glycopeptides belonging to 73 N-glycosylation sites on 50 glycoproteins. 27616296 5 55 gly α1,3-fucosylated 1214:1229 arg1 core α1,3-fucosylated N-glycans glycoproteins core α1,3-fucosylated N-glycans Fterm glycoproteins This study is the first report that discovers core α1,3-fucosylated N-glycans in bands 1, 2, and 6 and discloses bands 3, 4, 5, and 7 as glycoproteins and their N-glycoforms. 27616296 5 67 gly glycoproteins 1300:1312 arg1 core α1,3-fucosylated N-glycans glycoproteins core α1,3-fucosylated N-glycans Fterm glycoproteins This study is the first report that discovers core α1,3-fucosylated N-glycans in bands 1, 2, and 6 and discloses bands 3, 4, 5, and 7 as glycoproteins and their N-glycoforms. 27743372 6 5 gly glycoprotein 1002:1013 arg1 the magnetic bead based glycoprotein sample preparation the magnetic bead based glycoprotein sample preparation Fterm glycoprotein One of the newest exciting developments of the field is the magnetic bead based glycoprotein sample preparation technique. 28482115 7 57 part_of Fas1 1424:1427 arg1 its carboxy-proximal Fas1 domain Fas1 its carboxy-proximal Fas1 domain OGER Site Fas1 P25445 domain FLA4 functions as a soluble glycoprotein via its carboxy-proximal Fas1 domain and its normal cellular trafficking depends on N- and O-glycosylation. 24511137 5 13 part_of IgAs 1232:1235 arg1 the Fc regions 6-19 IgAs the Fc regions Cterm Site 6-19 IgAs regions However, we observed no apparent heterogeneity in the structure of N-linked glycans attached to three different sites of the Fc regions of nephritogenic and non-nephritogenic 6-19 IgAs. 28575723 2 1 gly N-glycosylation 342:356 arg2 putative N-glycosylation sites putative N-glycosylation sites sites The deduced amino acid sequence of Cha o 3 indicates that this glycoallergen contains a cellulase domain and a number of putative N-glycosylation sites. 24927272 3 49 part_of IgG 618:620 arg1 an IgG Fc domain IgG an IgG Fc domain Cterm Site IgG domain In this paper, a portion of an unrelated protein was fused to the C-terminus of an IgG Fc domain using the common (G4S) 4 linker repeat. 28322444 2 3 gly N-glycosylation 284:298 arg2 specific asparagine residues asparagine residues asparagine residues In the present study, we demonstrate the impact of N-glycosylation at specific asparagine residues on the trafficking of the Kv3.1b protein. 26929048 2 16 gly sialylated 418:427 arg1 a sialylated disaccharide a sialylated disaccharide Compound 1 was obtained through an α-sialylation reaction between a sialic acid donor and a trisaccharide that was synthesized from the glycosylation of a sialylated disaccharide with a glucosaminyl donor. 26929048 2 33 gly glycosylation 399:411 arg1 a sialylated disaccharide a sialylated disaccharide Compound 1 was obtained through an α-sialylation reaction between a sialic acid donor and a trisaccharide that was synthesized from the glycosylation of a sialylated disaccharide with a glucosaminyl donor. 26784534 11 61 gly distribution 1569:1580 arg1 all 10 O-glycosylation sites all 10 O-glycosylation sites all 10 O-glycosylation sites Site sites CONCLUSIONS: This is the first study to describe the qualitative and semi-quantitative distribution of O-glycan structures on all 10 O-glycosylation sites, which will provide a valuable starting point for further studies exploring the functional and structural implications of O-glycosylation in VWF. 26784534 11 85 gly O-glycosylation 1615:1629 arg2 all 10 O-glycosylation sites all 10 O-glycosylation sites sites CONCLUSIONS: This is the first study to describe the qualitative and semi-quantitative distribution of O-glycan structures on all 10 O-glycosylation sites, which will provide a valuable starting point for further studies exploring the functional and structural implications of O-glycosylation in VWF. 28680094 2 61 gly N-glycosylation 217:231 arg2 N-glycosylation sites N-glycosylation sites sites Great variations in both the number and distribution of N-glycosylation sites are found in the 18 α and 8 β integrin subunits. 25369125 7 49 part_of Galectin-3 986:995 arg1 the N-terminal domain Galectin-3 the N-terminal domain PUBTATOR Site Galectin-3 3958 domain Moreover, from Nuclear Magnetic Resonance (NMR) and Surface Plasmon Resonance experiments, we observed no significant specificity or affinity variations for carbohydrates related to the presence of the N-terminal domain of Galectin-3. 25936869 6 119 gly defectively-glycosylated 1335:1358 arg1 BGN (D-BGN) protein BGN (D-BGN) protein Fterm protein These smaller-sized ones were reduced by transfection of BGN siRNA, and shifted to the core protein size by treatment with ChABC, suggesting that they are defectively-glycosylated forms of BGN (D-BGN) protein. 27295180 6 13 gly glycoforms 771:780 arg1 serum α1-acid glycoprotein serum α1-acid glycoprotein Fterm glycoprotein Recently, we have looked at glycoforms of serum α1-acid glycoprotein (AGP) by using a crossed affinoimmunoelectrophoresis with two lectins and an anti-AGP antibody. 27295180 6 44 gly glycoprotein 799:810 arg1 serum α1-acid glycoprotein serum α1-acid glycoprotein Fterm glycoprotein Recently, we have looked at glycoforms of serum α1-acid glycoprotein (AGP) by using a crossed affinoimmunoelectrophoresis with two lectins and an anti-AGP antibody. 26812091 4 1 gly N-glycosylation 609:623 arg2 N-glycosylation sites N-glycosylation sites sites Intact and subunit masses, N-glycans, N-glycosylation sites, and intact N- and O-glycopeptides were analyzed and compared by mass spectrometry. 26812091 4 54 gly O-glycopeptides 650:664 arg2 O-glycopeptides O-glycopeptides O-glycopeptides Intact and subunit masses, N-glycans, N-glycosylation sites, and intact N- and O-glycopeptides were analyzed and compared by mass spectrometry. 26598643 2 52 gly O-glycosylated 323:336 arg1 O-glycosylated proteins O-glycosylated proteins Fterm proteins The analysis, though, is quite challenging and time consuming, in particular for O-glycosylated proteins. 25348702 5 64 gly glycopeptides 734:746 arg2 glycopeptides glycopeptides glycopeptides We directly released glycopeptides from cell surfaces through tryptic digestion of freshly harvested and vital cells, thereby improving the detection and quantification of complex-type N-glycans by increasing their relative amount from 14 to 85%. 26701617 6 55 gly O-glycosylation 1071:1085 arg2 the major O-glycosylation sites the major O-glycosylation sites sites By site-directed mutagenesis and high-resolution LC/MS analysis, we, for the first time, identified two threonine residues at the C-terminus as the major O-glycosylation sites on rhPDGF-BB produced in P. pastoris. 26701617 6 55 gly O-glycosylation 1071:1085 arg2 two threonine residues two threonine residues threonine residues By site-directed mutagenesis and high-resolution LC/MS analysis, we, for the first time, identified two threonine residues at the C-terminus as the major O-glycosylation sites on rhPDGF-BB produced in P. pastoris. 25451932 2 40 gly N-glycosylation 255:269 arg2 19 predicted N-glycosylation sites 19 predicted N-glycosylation sites sites Human corin has 19 predicted N-glycosylation sites in its extracellular domains. 29069609 7 32 gly N-glycopeptides 1298:1312 arg2 N-glycopeptides N-glycopeptides N-glycopeptides This allowed development of a targeted DIA method to identify N-glycopeptides without pre-defined knowledge of the glycan composition, thus providing the potential to identify N-glycopeptides with unexpected structures. 29069609 7 77 gly N-glycopeptides 1184:1198 arg2 N-glycopeptides N-glycopeptides N-glycopeptides This allowed development of a targeted DIA method to identify N-glycopeptides without pre-defined knowledge of the glycan composition, thus providing the potential to identify N-glycopeptides with unexpected structures. 27957769 6 35 gly glycopeptide 1300:1311 arg2 the most extensive glycopeptide libraries the most extensive glycopeptide libraries glycopeptide This is one of the most extensive glycopeptide libraries ever made through total synthesis. 24325898 1 14 gly N-glycosylation 129:143 arg2 the conserved N-glycosylation site the conserved N-glycosylation site site Fine structural details of glycans attached to the conserved N-glycosylation site significantly not only affect function of individual immunoglobulin G (IgG) molecules but also mediate inflammation at the systemic level. 24325898 1 49 gly attached 103:110 arg1 the conserved N-glycosylation site AND glycans the conserved N-glycosylation site glycans site Fine structural details of glycans attached to the conserved N-glycosylation site significantly not only affect function of individual immunoglobulin G (IgG) molecules but also mediate inflammation at the systemic level. 28323417 5 50 gly glycopeptide 1028:1039 arg1 derivatized glycans glycopeptide derivatized glycans glycopeptide For the glycoforms of a given glycopeptide or set of derivatized glycans, the slope of the line connecting CCS values remained similar for the [M+3H]3+ ions observed as the glycan antennae were shortened by stepwise exoglycosidase treatments; this trend was consistent regardless of the peptide length or the saccharide removed. 28323417 5 57 gly glycoforms 1006:1015 arg1 a given glycopeptide or set glycopeptide derivatized glycans glycopeptide For the glycoforms of a given glycopeptide or set of derivatized glycans, the slope of the line connecting CCS values remained similar for the [M+3H]3+ ions observed as the glycan antennae were shortened by stepwise exoglycosidase treatments; this trend was consistent regardless of the peptide length or the saccharide removed. 25737449 9 66 gly glycosylation 1470:1482 arg1 Asn-415 Asn-415 Asn-415 Whereas Asn-415 is buried by HCV1 and AP33, it is solvent-exposed in the HC33.1-E2(412-423) complex, such that glycosylation of Asn-415 would not prevent antibody binding. 26918373 0 47 gly glycosylation 43:55 arg1 therapeutic proteins therapeutic proteins Fterm proteins The use of lectin microarray for assessing glycosylation of therapeutic proteins. 25927005 11 11 part_of E2 1958:1959 arg1 single glycosylation sites HCV E2 single glycosylation sites Cterm Site HCV E2 sites In addition, elimination of single glycosylation sites of HCV E2 had no impact on the RNA synthesis of structural proteins and formation of virus-like particles in insect and mammalian cells. 28975713 5 28 gly glycopeptide 891:902 arg2 theoretical glycopeptide theoretical glycopeptide glycopeptide RESULTS PepSweetener displays the results on an interactive heat-map chart where theoretical glycopeptide tile colors correspond to ppm deviations from the query precursor mass. 25868252 1 9 part_of containing 134:143 arg1 Recombinant protein SMB AND two Somatomedin B domains Recombinant protein SMB two Somatomedin B domains Fterm Site protein domains Recombinant protein SMB(PRG4) containing two Somatomedin B domains and a small amount of glycosylation of repetitive sequences of proteoglycan 4 was cloned according to PGR4 gene polymorphism. 25868252 1 9 part_of containing 134:143 arg1 PRG4 AND two Somatomedin B domains PRG4 two Somatomedin B domains PUBTATOR Site PRG4 10216 domains Recombinant protein SMB(PRG4) containing two Somatomedin B domains and a small amount of glycosylation of repetitive sequences of proteoglycan 4 was cloned according to PGR4 gene polymorphism. 27581986 3 107 gly epitope 629:635 arg1 the CD4 binding site the CD4 binding site the CD4 binding site Site site We previously described an HIV-1 clade C-infected donor, CAP257, who developed broadly neutralizing plasma antibodies targeting an N276 glycan-dependent epitope in the CD4 binding site. 26304114 2 11 gly serine 364:369 arg1 residues residues threonine residues Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is α-linked to serine or threonine residues. 26304114 2 20 gly α-linked 352:359 arg1 threonine AND an N-acetylgalactosamine residue threonine an N-acetylgalactosamine residue threonine residues Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is α-linked to serine or threonine residues. 26304114 2 20 gly α-linked 352:359 arg1 serine AND an N-acetylgalactosamine residue serine an N-acetylgalactosamine residue serine Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is α-linked to serine or threonine residues. 26924641 5 17 gly disialylated 1220:1231 arg1 "branching sialylation" "branching sialylation" Moreover, MS/MS structural analysis, assisted by linkage-specific derivatization of sialic acids, revealed the presence of O-acetylated sialic acids as well as disialylated antennae ("branching sialylation") characterized by the presence of α2-6-linked NeuGc on the GlcNAc of the NeuGcα2-3-Galβ1-3-GlcNAc terminal motif. 26924641 5 17 gly disialylated 1220:1231 arg1 disialylated antennae disialylated antennae Moreover, MS/MS structural analysis, assisted by linkage-specific derivatization of sialic acids, revealed the presence of O-acetylated sialic acids as well as disialylated antennae ("branching sialylation") characterized by the presence of α2-6-linked NeuGc on the GlcNAc of the NeuGcα2-3-Galβ1-3-GlcNAc terminal motif. 26924641 5 79 gly motif 1374:1378 arg1 the GlcNAc the GlcNAc Moreover, MS/MS structural analysis, assisted by linkage-specific derivatization of sialic acids, revealed the presence of O-acetylated sialic acids as well as disialylated antennae ("branching sialylation") characterized by the presence of α2-6-linked NeuGc on the GlcNAc of the NeuGcα2-3-Galβ1-3-GlcNAc terminal motif. 28328971 5 31 gly glycosites 713:722 arg2 all the glycosites all the glycosites glycosites Inspection of the motifs and sequence structures involved suggested that all the glycosites were concentrated within [NxS/T] motif, while 82.3% of them were in a coil structure. 27493216 0 33 part_of POMGnT1 35:41 arg1 the POMGnT1 stem region POMGnT1 the POMGnT1 stem region PUBTATOR Site POMGnT1 55624 region Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of α-dystroglycan. 28921966 1 36 gly glycopeptides 252:264 arg2 glycopeptides glycopeptides glycopeptides To overcome the challenges in the analysis of protein glycosylation, we have developed a comprehensive and universal tool through permethylation of glycopeptides and their tandem mass spectrometric analysis. 26316330 6 67 gly glycoprotein 896:907 arg1 glycoprotein species glycoprotein species Fterm glycoprotein Moreover, we showed that variations in the used cell lines and their cultivation conditions strongly influence the number of glycoprotein species in case of recombinant A1AT production. 24279413 1 50 gly attachment 162:171 arg2 amino acid residues AND sugars amino acid residues sugars residues Glycosylation is an important protein modification that involves enzymatic attachment of sugars to amino acid residues. 26582281 2 24 gly linked 385:390 arg2 an asparagine residue AND a β-glucose an asparagine residue a β-glucose asparagine residue This N-glycan core structure, common to all chloroviruses, is a pentasaccharide with a β-glucose linked to an asparagine residue which is not located in the typical sequon N-X-T/S. 28510654 8 76 gly glycopeptides 1020:1032 arg1 isotopically labeled oligosaccharide moieties glycopeptides isotopically labeled oligosaccharide moieties glycopeptides An incubation with a synthetic peptide substrate produced glycopeptides with isotopically labeled oligosaccharide moieties. 26202417 3 11 gly N-glycosylation 396:410 arg2 N-glycosylation sequons N-glycosylation sequons After a leap to humans from a zoonotic host, influenza can gain N-glycosylation sequons over time as part of its fitness strategy. 28956227 7 98 part_of NTPDase3/CD39L3 1407:1421 arg1 the non-glycosylated NTPDase3/CD39L3 ecto-enzymatic domain NTPDase3 the non-glycosylated NTPDase3/CD39L3 ecto-enzymatic domain PUBTATOR Site NTPDase3 956 domain Our functional data indicate that the non-glycosylated NTPDase3/CD39L3 ecto-enzymatic domain retains activity, but that N-glycan attachments, such as the GlcNAc-Asn, substantially upregulate specific NTPDase activity by 2-20 fold. 28104755 10 28 part_of N-linked 1536:1543 arg1 an N-linked site N-linked an N-linked site Cterm Site N-linked site Glycosylation of Asn356 in SMPDL3A, an N-linked site conserved throughout the aSMase-like family, was critical for protection against proteasomal degradation and preservation of enzymatic activity. 26488311 3 51 gly N-glycosylation 361:375 arg2 All six known N-glycosylation sites All six known N-glycosylation sites sites All six known N-glycosylation sites are covered, three in the alpha subunit (α64N, α81N and α123N) and three in the beta subunit (β64N, β127N, and β147N). 28381551 0 43 gly glycoprotein 26:37 arg1 homogeneous glycoprotein homogeneous glycoprotein Fterm glycoprotein Production of homogeneous glycoprotein with multisite modifications by an engineered N-glycosyltransferase mutant. 24308717 7 82 gly O-glycopeptides 1158:1172 arg2 O-glycopeptides O-glycopeptides O-glycopeptides The removal of the N-glycans from etanercept facilitated the selective characterization of O-glycopeptides and enabled the O-glycans to be identified. 30023556 3 23 gly glycopeptide 390:401 arg2 an MUC1 glycopeptide library an MUC1 glycopeptide library glycopeptide In this study, using an MUC1 glycopeptide library, we established two novel anti-MUC1 monoclonal antibodies (1B2 and 12D10) with designed carbohydrate specificities. 28258464 8 86 gly glycopeptides 1361:1373 arg2 glycopeptides glycopeptides glycopeptides We demonstrated the effectiveness of this approach using RNase B and IgG and applied this sequential digestion strategy for the identification of glycopeptides from the HepG2 cell line. 24632452 9 55 gly glycosylated 1603:1614 arg1 client proteins client proteins Fterm proteins Improving the glycosylation efficiency ensures that not only homogeneous N-glycan structures are generated, but also client proteins are fully glycosylated. 24475074 0 48 gly glycoprotein 60:71 arg1 glycoprotein evolution glycoprotein evolution Fterm glycoprotein Encoding asymmetry of the N-glycosylation motif facilitates glycoprotein evolution. 24475074 0 97 gly N-glycosylation 26:40 arg2 the N-glycosylation motif the N-glycosylation motif motif Encoding asymmetry of the N-glycosylation motif facilitates glycoprotein evolution. 25113421 0 32 gly glycopeptides 76:88 arg2 N-linked glycopeptides N-linked glycopeptides glycopeptides GlycoMaster DB: software to assist the automated identification of N-linked glycopeptides by tandem mass spectrometry. 25628020 3 15 gly N-glycosylation 540:554 arg2 112 novel N-glycosylation sites 112 novel N-glycosylation sites sites RESULTS: We analyzed the human glycoproteome data set (2,534 N-glycosylation sites in 1,027 proteins) and identified 112 novel N-glycosylation sites in 91 proteins that arose in the human lineage since the last common ancestor of Euarchonta (primates and treeshrews). 25628020 3 26 gly N-glycosylation 474:488 arg2 2,534 N-glycosylation sites 2,534 N-glycosylation sites sites RESULTS: We analyzed the human glycoproteome data set (2,534 N-glycosylation sites in 1,027 proteins) and identified 112 novel N-glycosylation sites in 91 proteins that arose in the human lineage since the last common ancestor of Euarchonta (primates and treeshrews). 25628020 3 56 gly set 463:465 arg1 2,534 N-glycosylation sites 2,534 N-glycosylation sites sites RESULTS: We analyzed the human glycoproteome data set (2,534 N-glycosylation sites in 1,027 proteins) and identified 112 novel N-glycosylation sites in 91 proteins that arose in the human lineage since the last common ancestor of Euarchonta (primates and treeshrews). 26160412 5 61 gly glycopeptides 981:993 arg2 intact enriched glycopeptides intact enriched glycopeptides glycopeptides A first aliquot was enzymatically deglycosylated and analyzed by nano-liquid chromatography/tandem mass spectrometry while the second one, containing intact enriched glycopeptides, was directly analyzed. 26918373 7 43 gly glycoproteins 1123:1135 arg1 therapeutic glycoproteins glycoproteins glycan patterns Fterm glycoproteins These data suggest that lectin microarray could be used for screening glycan patterns of therapeutic glycoproteins. 29197583 5 22 gly glycoprotein 1047:1058 arg1 the intact glycoprotein the intact glycoprotein Fterm glycoprotein Particularly, we aim to assess the performance of this platform for the separation of isomeric glycoconjugates due to the type of sialic acid linkage, at the intact glycoprotein, glycopeptide and glycan level. 29197583 5 25 gly glycopeptide 1061:1072 arg2 glycopeptide glycopeptide glycopeptide Particularly, we aim to assess the performance of this platform for the separation of isomeric glycoconjugates due to the type of sialic acid linkage, at the intact glycoprotein, glycopeptide and glycan level. 24766575 1 13 gly N-glycopeptides 333:347 arg2 N-glycopeptides N-glycopeptides N-glycopeptides Study of site-specific N-glycosylation in complex sample remains a huge analytical challenge because protein glycosylation is structurally diverse in post-translational modifications, resulting in an intricacy of N-glycopeptides. 27012207 0 0 gly neuraminidase 75:87 arg1 Core-6 fucose neuraminidase Core-6 fucose Fterm neuraminidase 4758 Core-6 fucose and the oligomerization of the 1918 pandemic influenza viral neuraminidase. 24467287 5 4 gly glycoprotein 894:905 arg1 the protruding E2 attachment glycoprotein the protruding E2 attachment glycoprotein Fterm glycoprotein We observe that both the membrane-proximal E1 fusion glycoprotein and the protruding E2 attachment glycoprotein display heterogeneous glycosylation that contains N-linked glycans exhibiting both limited and extensive processing. 24467287 5 51 gly glycoprotein 848:859 arg1 the membrane-proximal E1 fusion glycoprotein the membrane-proximal E1 fusion glycoprotein Fterm glycoprotein We observe that both the membrane-proximal E1 fusion glycoprotein and the protruding E2 attachment glycoprotein display heterogeneous glycosylation that contains N-linked glycans exhibiting both limited and extensive processing. 26791533 4 16 gly glycopeptides 595:607 arg2 glycopeptides glycopeptides glycopeptides We have devised a strategy to analyze glycopeptides from a complex, unknown mixture of protease-digested proteins. 24664808 4 27 gly glycopeptides 726:738 arg2 deprotonated N-linked glycopeptides deprotonated N-linked glycopeptides glycopeptides Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. 24664808 4 65 gly glycopeptides 582:594 arg2 glycopeptides glycopeptides glycopeptides Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. 24664808 4 80 gly glycoproteins 628:640 arg1 well-characterized glycoproteins well-characterized glycoproteins Fterm glycoproteins Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. 26515403 7 47 part_of domain 1072:1077 arg1 B. cenocepacia ArnT ArnT domain OGER Site ArnT P27540 domain Deletion of the C-terminal domain in B. cenocepacia ArnT resulted in a protein with significantly reduced in vitro binding to a lipid A fluorescent substrate and unable to catalyze lipid A modification with l-Ara4N. 25452312 3 0 gly glycoproteins 284:296 arg1 vesicle surface glycoproteins vesicle surface glycoproteins Fterm glycoproteins One potential targeting mechanism is adhesion between vesicle surface glycoproteins and target cells. 24417605 2 28 gly glycoprotein 355:366 arg1 glycoprotein glycoprotein Fterm glycoprotein In this study, HDL was isolated from plasma by sequential micro-ultracentrifugation, followed by glycoprotein and glycolipid analysis. 27810711 0 15 gly glycopeptides 69:81 arg2 syndecan-3 (53-62) glycopeptides syndecan-3 (53-62) glycopeptides glycopeptides Obstacles and solutions for chemical synthesis of syndecan-3 (53-62) glycopeptides with two heparan sulfate chains. 28452462 1 2 gly glycoproteins 193:205 arg1 glycoproteins glycoproteins Fterm glycoproteins The tremendous structural heterogeneity of N-glycosylation of glycoproteins poses a great challenge for deciphering the biological functions of specific glycoforms and for developing protein-based therapeutics. 28452462 1 14 gly N-glycosylation 174:188 arg1 glycoproteins glycoproteins Fterm glycoproteins The tremendous structural heterogeneity of N-glycosylation of glycoproteins poses a great challenge for deciphering the biological functions of specific glycoforms and for developing protein-based therapeutics. 28109443 6 116 gly O-glycoprotein 1462:1475 arg1 the O-glycoprotein IgA1 molecules the O-glycoprotein IgA1 molecules Fterm O-glycoprotein Unexpectedly, we found that a variable minor fraction of IgA1 from both IgAN patients and healthy controls had Tn/STn antigens, and that the O-glycoprotein IgA1 molecules from most samples had only two distinct O-glycoforms: one major glycoform with homogeneous normal core 1-based O-glycans and one minor glycoform with homogeneous Tn/STn antigens. 24475074 7 29 gly N-glycosylation 1426:1440 arg2 N-glycosylation site number N-glycosylation site number site Furthermore, secretory proteins have evolved at rates proportional to N-glycosylation site number, indicating adaptive interactions between the N-glycans and underlying protein. 29285644 9 40 gly glycopeptides 1505:1517 arg2 Three glycopeptides Three glycopeptides glycopeptides Three glycopeptides exhibited exceptionally high control-to-cancer fold changes along with receiver operating characteristic curve areas of 1.0, indicating perfect discrimination between the two groups. 28097217 5 40 gly transglycosylation 519:536 arg1 a bound sugar chain a bound sugar chain They are able to catalyze an intramolecular transglycosylation of a bound sugar chain yielding polymeric sugar rings, the cycloamyloses (CAs), consisting of 20 to 100 glucose units. 28433761 0 67 gly glycoprotein 51:62 arg1 the S-layer glycoprotein the S-layer glycoprotein Fterm glycoprotein A glycoproteomic approach reveals that the S-layer glycoprotein of Lactobacillus kefiri CIDCA 83111 is O- and N-glycosylated. 26082231 6 2 gly glycoproteins 1228:1240 arg1 glycoproteins glycoproteins Fterm glycoproteins Both approaches have the capacity for controlled, radical alteration of oligosaccharide processing in eukaryotic cells used for heterologous protein expression, and have great utility in the structural analysis of glycoproteins. 28371718 7 45 gly N-glycosylation 1049:1063 arg2 The N-glycosylation site The N-glycosylation site site The N-glycosylation site was confirmed for both, the originator and the biosimilar. 28860626 1 49 gly glycosylation 337:349 arg2 a glycosylation site a glycosylation site site The outbreak of a pandemic influenza H1N1 in 2009 required the rapid generation of high-yielding vaccines against the A/California/7/2009 virus, which were achieved by either addition or deletion of a glycosylation site in the influenza proteins hemagglutinin and neuraminidase. 25282312 3 29 part_of protein 1091:1097 arg1 protein residues protein protein residues Fterm Site protein residues Intact protein analysis was carried out to quantify the glycosylation degree and profile the glycoform composition of all the prepared neo glycoconjugates, while pronase and chymotriptic digests were analyzed to map and rank the reactivity of protein residues. 28935113 9 45 gly glycoprotein 1569:1580 arg1 the HIV envelope glycoprotein gp120 the HIV envelope glycoprotein gp120 Fterm glycoprotein The target described here is the HIV broadly neutralizing monoclonal antibody 2G12; 2G12 binds to cluster of high-mannose oligosaccharides on the HIV envelope glycoprotein gp120; and glycopeptides that mimic this epitope may be useful in HIV vaccine applications. 28935113 9 48 gly glycopeptides 1593:1605 arg2 glycopeptides glycopeptides glycopeptides The target described here is the HIV broadly neutralizing monoclonal antibody 2G12; 2G12 binds to cluster of high-mannose oligosaccharides on the HIV envelope glycoprotein gp120; and glycopeptides that mimic this epitope may be useful in HIV vaccine applications. 28888681 3 24 gly glycoforms 591:600 arg1 two peptides two peptides peptides In this work, we developed and compared RP-LC and hydrophilic interaction liquid chromatography (HILIC) in nanoscale on a chip combined with MS/MS in order to separate glycoforms of two peptides obtained from the tryptic digest of hemopexin. 25628020 3 27 part_of sites 556:560 arg1 91 proteins proteins sites Fterm Site proteins sites RESULTS: We analyzed the human glycoproteome data set (2,534 N-glycosylation sites in 1,027 proteins) and identified 112 novel N-glycosylation sites in 91 proteins that arose in the human lineage since the last common ancestor of Euarchonta (primates and treeshrews). 25628020 3 30 part_of sites 490:494 arg1 1,027 proteins proteins sites Fterm Site proteins sites RESULTS: We analyzed the human glycoproteome data set (2,534 N-glycosylation sites in 1,027 proteins) and identified 112 novel N-glycosylation sites in 91 proteins that arose in the human lineage since the last common ancestor of Euarchonta (primates and treeshrews). 27928741 5 91 gly attached 718:725 arg2 haemagglutinin-neuraminidase AND the glycan compositions haemagglutinin-neuraminidase the glycan compositions Fterm haemagglutinin-neuraminidase This study concerns characterisation of the glycan compositions attached to haemagglutinin-neuraminidase of the Avulavirus Newcastle disease virus, which causes Newcastle disease in a range of avian species. 26959529 3 63 gly glycosylated 400:411 arg1 the proteins the proteins Fterm proteins Since the proteins in milk are highly glycosylated, N-glycans in milk also play an import role. 25253346 15 45 part_of sites 2390:2394 arg1 the exposed envelope protein surface protein sites Fterm Site protein sites HIV-1 does harbor highly conserved sites on the exposed envelope protein surface of gp120, one of which is the virus receptor (CD4) binding site. 25253346 15 53 part_of binding 2487:2493 arg1 the virus receptor (CD4) binding site CD4 the virus receptor (CD4) binding site PUBTATOR Site CD4 920 site HIV-1 does harbor highly conserved sites on the exposed envelope protein surface of gp120, one of which is the virus receptor (CD4) binding site. 25253346 15 53 part_of binding 2487:2493 arg1 highly conserved sites CD4 highly conserved sites PUBTATOR Site CD4 920 sites HIV-1 does harbor highly conserved sites on the exposed envelope protein surface of gp120, one of which is the virus receptor (CD4) binding site. 29065342 2 38 gly glycopeptides 307:319 arg2 glycopeptides glycopeptides glycopeptides However, efficient synthesis of glycopeptides bearing LeX remains a major limitation for structure-function studies of the LeX determinant. 28890404 4 13 part_of asparagine 787:796 arg1 the enzyme enzyme asparagine Fterm SpecificSite enzyme asparagine 83 The gene AN7908 was cloned and transformed in A. nidulans for homologous production of AnAbf62Awt, and we confirmed that the enzyme is N-glycosylated at asparagine 83 by mass spectrometry analysis. 24941220 5 66 gly glycopeptides 695:707 arg2 glycopeptides glycopeptides glycopeptides To search the HCD-MS data for glycopeptides, a novel spectral-aligning strategy was developed. 28255882 1 16 gly glycoprotein 222:233 arg1 glycoprotein receptors glycoprotein receptors Fterm glycoprotein Glycoprofiling recombinant proteins expressed and secreted from mammalian cells is key to understanding their interactions with glycoprotein receptors in vivo. 26773038 6 9 gly site 971:974 arg1 GlcNAc site GlcNAc site The essential component of the glycan structure is the first sugar residue (GlcNAc) at the N1574 attachment site. 26773038 6 9 gly site 971:974 arg1 the first sugar residue site the first sugar residue site The essential component of the glycan structure is the first sugar residue (GlcNAc) at the N1574 attachment site. 27111718 7 32 gly glycopeptides 1400:1412 arg2 N-linked glycopeptides cell lines N-linked glycopeptides cell lines glycopeptides We tested the tool on two sets of tandem mass spectra of N-linked glycopeptides cell lines acquired from breast cancer patients. 24308457 1 21 gly glycosylation 339:351 arg1 a specific protein a specific protein Fterm protein Metabolic labeling of glycans with chemical reproters (e.g., alkyne or azide) in conjunction with bioorthogonal chemistry is a powerful tool for imaging glycome; however, this method lacks protein-specificity and therefore is not applicable to imaging glycosylation of a specific protein of interest (POI). 26208004 2 6 gly glycosylation 376:388 arg2 two potential N-linked glycosylation sites two potential N-linked glycosylation sites sites It is well known that DENV E glycoprotein has two potential N-linked glycosylation sites at Asn67 and Asn153. 26208004 2 17 gly glycoprotein 336:347 arg1 DENV E glycoprotein DENV E glycoprotein Fterm glycoprotein It is well known that DENV E glycoprotein has two potential N-linked glycosylation sites at Asn67 and Asn153. 29048990 2 52 gly glycosylation 412:424 arg2 glycosylation sites glycosylation sites sites Viral antigenic drift can modify the number and location of glycosylation sites, altering a wide range of biological activities and the antigenic properties of the strain. 25793890 8 85 gly glycosylation 1632:1644 arg2 fewer glycosylation sites fewer glycosylation sites sites Previous studies have reported that the length of the V1/V2 domain in transmitted founder viruses is shorter and possesses fewer glycosylation sites compared to viruses isolated from chronic infections. 28620050 6 85 part_of terminus 1230:1237 arg1 an additional fully occupied N-linked glycosylation site terminus an additional fully occupied N-linked glycosylation site site We also found that introduction of an additional fully occupied N-linked glycosylation site at the N terminus at position 1 (equivalent to Asp-221 in the Fc of IgG1) dramatically enhances overall sialic acid content of the Fc multimers. 25416425 1 69 gly glycosylated 155:166 arg1 Kv1.4 potassium channels Kv1.4 potassium channels Fterm channels Kv1.4 potassium channels are heavily glycosylated proteins involved in shaping action potentials and in neuronal excitability and plasticity. 25416425 1 69 gly glycosylated 155:166 arg1 heavily glycosylated proteins heavily glycosylated proteins Fterm proteins Kv1.4 potassium channels are heavily glycosylated proteins involved in shaping action potentials and in neuronal excitability and plasticity. 26784534 3 67 gly VWF-O-glycopeptides 363:381 arg2 Tryptic VWF-O-glycopeptides Tryptic VWF-O-glycopeptides VWF-O-glycopeptides METHODS: Tryptic VWF-O-glycopeptides were isolated by lectin affinity chromatography and/or by reverse-phase high-performance liquid chromatography. 28529241 4 4 gly glycoproteins 648:660 arg1 glycoproteins glycoproteins Fterm glycoproteins Herein, we investigated whether or not Sp1-downregulation affects to N-glycosylation of glycoproteins and malignant properties of A549 human lung cancer cell line. 28529241 4 68 gly N-glycosylation 629:643 arg1 glycoproteins glycoproteins Fterm glycoproteins Herein, we investigated whether or not Sp1-downregulation affects to N-glycosylation of glycoproteins and malignant properties of A549 human lung cancer cell line. 24417605 7 39 gly sialylated 948:957 arg1 The observed O-glycans The observed O-glycans The observed O-glycans were all sialylated, and most contained a core 1 structure with two Neu5Acs, including those that were associated with apolipoprotein CIII (ApoC-III) and fetuin A. GM3 (monosialoganglioside, NeuAc2-3Gal1-4Glc-Cer) and GD3 (disialoganglioside, NeuAc2-8NeuAc2-3Gal1-4Glc-Cer) were the major gangliosides in HDL. 25358049 5 0 gly glycopeptides 1112:1124 arg2 such glycopeptides such glycopeptides glycopeptides The difference in the oxonium ion fragmentation profiles of such glycopeptides may thus be used to distinguish among these glycan structures and could be of importance in LC-MS/MS-based glycoproteomic studies. 25501957 3 15 gly glycoprotein 626:637 arg1 a monomeric glycoprotein a monomeric glycoprotein Fterm glycoprotein A β-fructosidase (BfrA) with high transglycosylation activity was purified from Aspergillus oryzae FS4 as a monomeric glycoprotein. 28921955 5 68 gly glycopeptide 910:921 arg1 The glycan structure glycopeptide The glycan structure glycopeptide The glycan structure of a given glycopeptide was determined by collision-induced dissociation MS/MS fragmentation, and the peptide backbone information was provided by collision-induced dissociation (CID)-MS3 fragmentation. 25279697 1 34 gly hypoglycosylation 275:291 arg1 α-dystroglycan α-dystroglycan Recent studies demonstrated that mutations in B3GNT1, an enzyme proposed to be involved in poly-N-acetyllactosamine synthesis, were causal for congenital muscular dystrophy with hypoglycosylation of α-dystroglycan (secondary dystroglycanopathies). 24308717 10 21 gly O-glycosylation 1564:1578 arg2 the 12 occupied O-glycosylation sites the 12 occupied O-glycosylation sites sites Electron-transfer dissociation (ETD) was then used to pinpoint the 12 occupied O-glycosylation sites. 28381551 1 3 gly sequon 208:213 arg1 N-glycan sequon occupancy N-glycan sequon occupancy Naturally occurring N-glycoproteins exhibit glycoform heterogeneity with respect to N-glycan sequon occupancy (macroheterogeneity) and glycan structure (microheterogeneity). 28381551 1 42 gly N-glycoproteins 135:149 arg1 Naturally occurring N-glycoproteins Naturally occurring N-glycoproteins Fterm N-glycoproteins Naturally occurring N-glycoproteins exhibit glycoform heterogeneity with respect to N-glycan sequon occupancy (macroheterogeneity) and glycan structure (microheterogeneity). 24275651 5 44 part_of containing 770:779 arg1 A synthetic peptide AND the conserved motif A synthetic peptide the conserved motif motif A synthetic peptide containing the conserved motif can partially but specifically rescue in vitro activity of mutated PglB lacking Tyr293. 24451126 0 82 part_of IgG1-insights 64:76 arg1 the crystallizable fragment IgG1 the crystallizable fragment PUBTATOR Site IgG1 P01857 fragment Molecular dynamics simulation of the crystallizable fragment of IgG1-insights for the design of Fcabs. 25614628 3 27 part_of PNGase 459:464 arg1 a predicted PNGase domain PNGase a predicted PNGase domain OGER Site PNGase Q96IV0 domain Recently, a novel gene encoding a protein with a predicted PNGase domain was identified from a clinical isolate of Elizabethkingia meningoseptica. 25614628 3 46 part_of protein 434:440 arg1 a predicted PNGase domain protein a predicted PNGase domain Fterm Site protein domain Recently, a novel gene encoding a protein with a predicted PNGase domain was identified from a clinical isolate of Elizabethkingia meningoseptica. 24715520 1 36 gly glycoproteins 181:193 arg1 glycoproteins glycoproteins Fterm glycoproteins Oligosaccharide conjugates, such as glycoproteins and glycolipids, are potential chemotherapeutics and also serve as useful tools for understanding the biological roles of carbohydrates. 26489654 4 37 gly attached 564:571 arg2 the termini AND saccharides the termini saccharides termini We have discovered an intrinsic mechanism of secreted protein aging and turnover linked to the stepwise elimination of saccharides attached to the termini of N-glycans. 28534482 2 53 gly glycoproteins 482:494 arg1 N-linked glycoproteins glycoproteins Man3GlcNAc2 Fterm glycoproteins The method takes advantage of the inherent properties of Fbs1, which functions within the ubiquitin-mediated degradation system to recognize the common core pentasaccharide motif (Man3GlcNAc2) of N-linked glycoproteins. 28534482 2 53 gly glycoproteins 482:494 arg1 N-linked glycoproteins glycoproteins the common core pentasaccharide motif Fterm glycoproteins The method takes advantage of the inherent properties of Fbs1, which functions within the ubiquitin-mediated degradation system to recognize the common core pentasaccharide motif (Man3GlcNAc2) of N-linked glycoproteins. 26749838 5 12 gly glycosylated 952:963 arg1 a glycosylated rhamnose a glycosylated rhamnose Whilst acylation of rhamnose moieties in position 4 is quite common, the occurrence in anthocyanins of a glycosylated rhamnose is a unique trait. 26956484 6 49 gly glycosylation 879:891 arg2 the only glycosylation site Orai1N223A site PUBTATOR Orai1N223A 84876 site Ca(2+) imaging experiments and patch-clamp experiments revealed that mutation of the only glycosylation site of Orai1 (Orai1N223A) enhanced SOCE in Jurkat T cells. 26956484 6 49 gly glycosylation 879:891 arg2 the only glycosylation site Orai1 site PUBTATOR Orai1 84876 site Ca(2+) imaging experiments and patch-clamp experiments revealed that mutation of the only glycosylation site of Orai1 (Orai1N223A) enhanced SOCE in Jurkat T cells. 25210040 5 39 gly fucosylated 1243:1253 arg1 fucosylated LacdiNAc fucosylated LacdiNAc In agreement with natural gastric TFF2, the recombinant full-length and single domain probes expressed nearly exclusively fucosylated LacdiNAc on bi-antennary complex-type chains indicating that a single TFF domain was sufficient to induce transfer of this modification. 25029371 6 57 part_of NXT 1164:1166 arg1 NXT consensus sites NXT NXT consensus sites PUBTATOR Site NXT 29107 sites In contrast, NXT consensus sites (barring NWT) were efficiently modified by the cotranslational machinery, reducing STT3B's role in modifying consensus sites skipped during protein translation. 27500750 8 49 gly glycosites 1377:1386 arg2 glycosites glycosites glycosites These features provide a solid foundation to analyze the complex glycan structures and glycosites simultaneously, which will benefit future development of glycoproteomics and glycobiology. 27957769 10 108 gly glycosylation 2058:2070 arg2 very high glycosylation site specificity very high glycosylation site specificity site It is observed that the induced antibodies recognize MUC1 peptides with very high glycosylation site specificity. 25636227 0 15 gly O-glycosylation 67:81 arg2 O-glycosylation sites O-glycosylation sites sites From individual proteins to proteomic samples: characterization of O-glycosylation sites in human chorionic gonadotropin and human-plasma proteins.