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 PMC7124471-1-10 5 85 gly glycosites 476:485 arg1 serotransferrin serotransferrin OGER serotransferrin P02787 There were four N-linked glycosites of serotransferrin identified, i.e. N432, N630, N637, and N523 (Fig. 6B, supplemental Table S26). PMC6934601-1-fig6 11 43 gly SPN 1298:1300 arg1 sialic acid SPN sialic acid OGER SPN P16150 (F) The sialic acid and O-glycan content of SPN in MV-4-11 and THP-1 cells was assessed following treatment with neuraminidase, to remove sialic acids, and O-glycosidase, to cleave core 1 O-glycans. PMC5643531-1-9 0 372 gly Glycosylation 0:12 arg1 Fz8 Fz8 OGER Fz8 Q9H461 Glycosylation of Fz8 is required for Wnt/β-catenin signaling. PMC5795011-1-fig2 2 26 gly glycoprotein 325:336 arg1 Standard bovine alpha-1-acid glycoprotein 1 Standard bovine alpha-1-acid glycoprotein 1 OGER alpha-1-acid glycoprotein 1 P02763 Standard bovine alpha-1-acid glycoprotein 1 was digested with trypsin, the glycopeptides were analyzed by LC-MS and the data were searched against the custom glycoprotein database using the Mascot search engine. PMC6243375-1-4 28 174 gly glycoproteins 5221:5233 arg1 heavily O‐linked glycoproteins heavily O‐linked glycoproteins Cterm O‐linked Analysis of the site distribution on glycoproteins demonstrated advantage of EXoO to study heavily O‐linked glycoproteins that is difficult to be analyzed by current analytical approach due to structural complexity and resistance to enzymatic digestion. PMC5643531-1-9 45 179 gly Glycosylation 5802:5814 arg1 Fz8 Fz8 OGER Fz8 Q9H461 Glycosylation of Fz8 is critical for the onset of Wnt signaling by facilitating cell surface localization of Fz8. PMC5643531-1-8 0 60 gly glycosylation 19:31 arg1 Fz8 Fz8 OGER Fz8 Q9H461 OTG is involved in glycosylation of Fz8. PMC5098438-1-5 68 534 gly glycoforms 12620:12629 arg1 IgG1 Fc glycoforms IgG1 Fc glycoforms Cterm IgG1 We can rationalize these properties by the analysis of known crystal structures of IgG1 Fc glycoforms. PMC5098438-1-5 68 534 gly glycoforms 12620:12629 arg1 IgG1 Fc glycoforms IgG1 Fc glycoforms Cterm Fc We can rationalize these properties by the analysis of known crystal structures of IgG1 Fc glycoforms. PMC5643531-1-9 10 102 gly glycosylation 1318:1330 arg1 Fz8 Fz8 OGER Fz8 Q9H461 Taken together, these results suggest that N-linked glycosylation of Fz8 may be critical for its cell surface localization and subsequently for Wnt/β-catenin signaling during early embryogenesis. PMC7124471-1-11 21 58 part_of N-linked 2530:2537 arg1 all other N-linked intact glycopeptide carrying N630 N-linked all other N-linked intact glycopeptide carrying N630 Cterm SpecificSite N-linked N630 For all other N-linked intact glycopeptide carrying N630, a spectrum sequence list (. PMC5098438-1-5 52 116 gly glycoforms 9179:9188 arg1 homogeneous IgG-Fc glycoforms homogeneous IgG-Fc glycoforms Cterm IgG SPR binding studies with homogeneous IgG-Fc glycoforms with defined core N-linked glycan transferred to the GlcNAc moiety by the transglycosylation activity of an Arthrobacter endoglycosidase (EndoA) showed that the presence of a bisecting GlcNAc or even a bisecting mannose residue could significantly enhance the binding of the Fc to FcγRIIIA. PMC7124471-1-6 9 96 gly glycoproteins 1309:1321 arg1 QSOX1 QSOX1 OGER QSOX1 O00391 The plant glycoprotein HRP and the four chicken glycoproteins including IOVO, OVAL, Ogchi and QSOX1 were used to validate the setting of database search parameters. PMC6243375-1-4 26 151 gly glycoproteins 4772:4784 arg1 these heavily O‐linked glycoproteins these heavily O‐linked glycoproteins Cterm O‐linked Among these heavily O‐linked glycoproteins, VCAN contained the highest number of sites reaching 165 sites with distinct peptide sequences surrounding the sites, whereas MUC1 contained 161 sites, the second highest, but composited from only six distinct sequence repeats. PMC7124471-1-11 4 352 part_of serotransferrin 684:698 arg1 the glycosite N630 serotransferrin the glycosite N630 OGER SpecificSite serotransferrin P02787 glycosite N630 To obtain the quantitative information of these glycans identified on the glycosite N630 of serotransferrin, the peak area of each precursor ion was integrated by Skyline (35). PMC3942810-2-1 7 218 gly RJ 1124:1125 arg1 all RJ all Cterm RJ This method suggested that all of the 13 novel proteins predicted to be secretory proteins are real protein components of RJ. PMC5098438-1-5 11 256 gly glycoproteins 1964:1976 arg1 CD152 CD152 OGER CD152 P16410 Furthermore, this series of ions is prominent in the corresponding spectrum of Glc3Man7GlcNAc2 obtained from recombinant glycoproteins, such as CD152 expressed in CHO cells in the presence of the glucosidase inhibitor NB-DNJ, further confirming the structure of the 3-antenna. PMC5643531-1-8 13 72 gly glycosylation 1737:1749 arg1 Fz8 Fz8 OGER Fz8 Q9H461 These results suggest the possibility that OTG inhibits cell surface localization of Fz8 by interfering with N-linked glycosylation of Fz8. PMC7124471-1-fig5 2 30 gly glycosites 281:290 arg1 serotransferrin serotransferrin OGER serotransferrin P02787 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 47 gly glycosites 347:356 arg1 complement factor H complement factor H OGER complement factor H P08603 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-11 66 281 part_of albumin 9333:9339 arg1 N68 albumin N68 Cterm SpecificSite albumin N68 They included the previously reported glycosite N63 of alpha-1B-glycoprotein and N68 of albumin (7), suggesting that our method was reliable. PMC5976746-1-5 38 201 gly glycosylation 6114:6126 arg1 BG505 NFL trimers BG505 NFL trimers OGER BG505 NFL trimers P07196 The minor increase in thermo stability may be due to less variation in the glycosylation profiles of BG505 NFL trimers produced in CHO-M cells. PMC7124471-1-11 23 437 part_of serotransferrin 2934:2948 arg1 N630 serotransferrin N630 OGER SpecificSite serotransferrin P02787 N630 For quantitative study of site-specific glycosylation in human serum using peak areas on LC-MS/MS, it needs to consider the numerous variants of N-linked intact glycopeptides containing the same N-glycosite, such as N630 of serotransferrin. PMC7143757-1-1 8 67 gly glycosylated 1129:1140 arg1 rCTB rCTB OGER CTB The MW of rCTB increased when PglL was co-expressed, indicating that rCTB might have been glycosylated. PMC4595782-1-7 56 83 gly SAC 11186:11188 arg1 Par-4 SAC Par-4 OGER SAC Q96PN6 The cytotoxic effect of this protein on both human (PC3) and rat prostate cancer cell lines (MAT-LyLu) further suggests its efficacy on cancer cells of different origin, and this might be due to the highly conserved SAC domain of Par-4 (El-Guendy and Rangnekar, 2003). PMC7124471-1-10 8 18 gly glycosites 935:944 arg1 serotransferrin serotransferrin OGER serotransferrin P02787 Among the mentioned glycosites of serotransferrin, N523 and N637 are not reported in Uniprot. PMC3938046-1-3 22 165 gly glycoprotein 3816:3827 arg1 lysosome-associated membrane glycoprotein 1 lysosome-associated membrane glycoprotein 1 OGER lysosome-associated membrane glycoprotein 1 P11279 Other glycoproteins with 10 or more N-glycosites included receptor-type tyrosine-protein phosphatase eta isoform 1, plexin B2, nicastrin, toll-like receptor 13, and lysosome-associated membrane glycoprotein 1. PMC7124471-1-11 7 443 part_of serotransferrin 1032:1046 arg1 N630 serotransferrin N630 OGER SpecificSite serotransferrin P02787 N630 In total, 363 N-glycan masses were identified on N630 of serotransferrin from UGP and FGP data sets. PMC5098438-1-1 13 38 gly aglycosylated 2067:2079 arg1 aglycosylated HCs aglycosylated HCs OGER HCs O75390 Treatment with PNGase F (peptide N-glycosidase F) led to aglycosylated HCs with similar apparent molecular weights for the commercial MabThera® and for Tt/C2B8. PMC7124471-1-10 23 89 gly N-glycosites 2439:2450 arg1 transferrin receptor 1 transferrin receptor 1 OGER transferrin receptor 1 P02787 S4, the two N-glycosites of serotransferrin and the two N-glycosites of transferrin receptor 1 identified in our work don't approach to each other in their protein complex's structure. PMC7124471-1-10 23 89 gly N-glycosites 2439:2450 arg1 serotransferrin serotransferrin OGER serotransferrin P02787 S4, the two N-glycosites of serotransferrin and the two N-glycosites of transferrin receptor 1 identified in our work don't approach to each other in their protein complex's structure. PMC7124471-1-10 23 96 gly N-glycosites 2483:2494 arg1 transferrin receptor 1 transferrin receptor 1 OGER transferrin receptor 1 P02787 S4, the two N-glycosites of serotransferrin and the two N-glycosites of transferrin receptor 1 identified in our work don't approach to each other in their protein complex's structure. PMC7124471-1-10 23 96 gly N-glycosites 2483:2494 arg1 serotransferrin serotransferrin OGER serotransferrin P02787 S4, the two N-glycosites of serotransferrin and the two N-glycosites of transferrin receptor 1 identified in our work don't approach to each other in their protein complex's structure. PMC7124471-1-8 4 56 part_of CD44 618:621 arg1 The N-glycosite N25 CD44 The N-glycosite N25 OGER SpecificSite CD44 P16070 N-glycosite N25 The N-glycosite N25 of CD44 locates at its extracellular part. PMC5795011-1-fig1 0 22 gly glycoprotein 113:124 arg1 bovine alpha-1-acid glycoprotein 1 bovine alpha-1-acid glycoprotein 1 OGER alpha-1-acid glycoprotein 1 P02763 HCD-MS2 spectrum of a di-sialylated bi-antennary glycopeptide (m/z 1177.81373+) derived from bovine alpha-1-acid glycoprotein 1. PMC5643531-1-9 13 191 gly glycosylation 1935:1947 arg1 Fz8 Fz8 OGER Fz8 Q9H461 OTG interacted with Wnt receptor Fz8 and inhibited its cell surface targeting possibly by preventing N-linked glycosylation of Fz8. PMC5098438-1-3 7 9 gly glycosylated 1127:1138 arg1 fully glycosylated full IgG fully glycosylated full IgG Cterm IgG As mentioned above, T. thermophila produces a population of aglycosylated HCs (Fig. 1D) leading to the formation of a-, hemi- and fully glycosylated full IgG. PMC5098438-1-3 7 48 gly aglycosylated 1051:1063 arg1 aglycosylated HCs aglycosylated HCs OGER HCs O75390 As mentioned above, T. thermophila produces a population of aglycosylated HCs (Fig. 1D) leading to the formation of a-, hemi- and fully glycosylated full IgG. PMC7124471-1-11 73 505 gly glycoform 10395:10403 arg1 serotransferrin glycoform serotransferrin glycoform OGER serotransferrin P02787 Compared with the established methods based on immuno-capture and MS, our method avoids immuno-capture and provides more details of serotransferrin glycoform in a site-specific manner. PMC5795011-1-4 64 407 part_of glycoprotein 11184:11195 arg1 Asn 93 alpha-1-acid glycoprotein 1 Asn 93 OGER SpecificSite alpha-1-acid glycoprotein 1 P02763 Asn 93 For example, Mascot annotated a total of nine different mono-, di-, tri- and tetra-sialylated N-glycan structures on a single glycosylation site (Asn 93) of serum alpha-1-acid glycoprotein 1 (Fig. 5). PMC7124471-1-fig5 2 46 part_of glycosites 347:356 arg1 commercial transferrin transferrin glycosites OGER SpecificSite transferrin P02787 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 13 part_of H 406:406 arg1 N529 complement factor H glycosites N529, N822, N882 and N1029 OGER SpecificSite complement factor H P08603 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 13 part_of H 406:406 arg1 N1029 complement factor H glycosites N529, N822, N882 and N1029 OGER SpecificSite complement factor H P08603 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 13 part_of H 406:406 arg1 N822 complement factor H glycosites N529, N822, N882 and N1029 OGER SpecificSite complement factor H P08603 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 13 part_of H 406:406 arg1 N882 complement factor H glycosites N529, N822, N882 and N1029 OGER SpecificSite complement factor H P08603 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 13 part_of H 406:406 arg1 N1029 complement factor H glycosites N529, N822, N882 and N1029 OGER SpecificSite complement factor H P08603 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 13 part_of H 406:406 arg1 N822 complement factor H glycosites N529, N822, N882 and N1029 OGER SpecificSite complement factor H P08603 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 13 part_of H 406:406 arg1 N882 complement factor H glycosites N529, N822, N882 and N1029 OGER SpecificSite complement factor H P08603 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 13 part_of H 406:406 arg1 N822 complement factor H glycosites N529, N822, N882 and N1029 OGER SpecificSite complement factor H P08603 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 13 part_of H 406:406 arg1 N882 complement factor H glycosites N529, N822, N882 and N1029 OGER SpecificSite complement factor H P08603 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 13 part_of H 406:406 arg1 N882 complement factor H glycosites N529, N822, N882 and N1029 OGER SpecificSite complement factor H P08603 glycosites N529, N822, N882 and N1029 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 33 part_of serotransferrin 315:329 arg1 the four glycosites serotransferrin glycosites N432, N630 and N637 OGER SpecificSite serotransferrin P02787 glycosites N432, N630 and N637 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 33 part_of serotransferrin 315:329 arg1 N630 serotransferrin glycosites N432, N630 and N637 OGER SpecificSite serotransferrin P02787 glycosites N432, N630 and N637 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 33 part_of serotransferrin 315:329 arg1 N432 serotransferrin glycosites N432, N630 and N637 OGER SpecificSite serotransferrin P02787 glycosites N432, N630 and N637 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 33 part_of serotransferrin 315:329 arg1 N630 serotransferrin glycosites N432, N630 and N637 OGER SpecificSite serotransferrin P02787 glycosites N432, N630 and N637 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 33 part_of serotransferrin 315:329 arg1 N432 serotransferrin glycosites N432, N630 and N637 OGER SpecificSite serotransferrin P02787 glycosites N432, N630 and N637 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC7124471-1-fig5 2 33 part_of serotransferrin 315:329 arg1 N432 serotransferrin glycosites N432, N630 and N637 OGER SpecificSite serotransferrin P02787 glycosites N432, N630 and N637 C, D, The overlap of N-glycan masses identified on the four glycosites N432, N630 and N637 of serotransferrin and on the four glycosites N529, N822, N882 and N1029 of complement factor H in different samples including commercial transferrin, serum spiked with HRP and ovalbumin, UGP and FGP data set. PMC6243375-1-4 27 60 gly glycosylated 5056:5067 arg1 LPA LPA OGER LPA P08519 ACAN, LPA, and TNXB were heavily O‐linked glycosylated to have 82, 73, and 44 sites, respectively. PMC6243375-1-4 27 60 gly glycosylated 5056:5067 arg1 TNXB TNXB OGER TNXB P22105 ACAN, LPA, and TNXB were heavily O‐linked glycosylated to have 82, 73, and 44 sites, respectively. PMC6243375-1-4 27 60 gly glycosylated 5056:5067 arg1 ACAN ACAN OGER ACAN P16112 ACAN, LPA, and TNXB were heavily O‐linked glycosylated to have 82, 73, and 44 sites, respectively. PMC7124471-1-fig5 1 17 gly glycosites 176:185 arg1 B B Cterm B P02787 The number of identified N-glycan masses on each of the eight glycosites of complement factor H (A) and on each of the four glycosites of serotransferrin (B) are shown. PMC7124471-1-fig5 1 17 gly glycosites 176:185 arg1 serotransferrin serotransferrin OGER serotransferrin P02787 The number of identified N-glycan masses on each of the eight glycosites of complement factor H (A) and on each of the four glycosites of serotransferrin (B) are shown. PMC7124471-1-fig5 1 22 gly glycosites 114:123 arg1 complement factor H complement factor H OGER complement factor H P08603 The number of identified N-glycan masses on each of the eight glycosites of complement factor H (A) and on each of the four glycosites of serotransferrin (B) are shown. PMC7124471-1-fig5 1 22 gly glycosites 114:123 arg1 A A Cterm A P08603 The number of identified N-glycan masses on each of the eight glycosites of complement factor H (A) and on each of the four glycosites of serotransferrin (B) are shown. PMC6243375-1-4 8 154 gly glycosylation 1731:1743 arg1 VCAN VCAN OGER VCAN P13611 Interestingly, immunoglobulin heavy constant alpha 1 (IGHA1) has the highest PSM number in the normal tissue and serum but had the second highest PSM number in the tumor tissue where versican core protein (VCAN) scored the highest PSM number suggesting their relatively high abundance for detection and aberrant O‐linked glycosylation of VCAN in tumor tissue. PMC7081908-1-1 1 34 gly glycoproteins 95:107 arg1 The four gp120 glycoproteins The four gp120 glycoproteins OGER gp120 glycoproteins Q14624 The four gp120 glycoproteins included in the current study were selected on the basis of the immunogenicity analysis of a large panel of HIV-1 Env variants (16) and were included in a polyvalent DNA prime-protein boost HIV vaccine formulation currently going through a phase I clinical study at HVTN (HVTN124). PMC5643531-1-9 5 109 gly glycosylation 744:756 arg1 Fz8 Fz8 OGER Fz8 Q9H461 These results demonstrate that glycosylation of Fz8 could be an essential factor in its membrane targeting. PMC5643531-1-fig7 0 35 gly N-glycosylation 9:23 arg1 Fz8 receptor Fz8 receptor OGER Fz8 receptor Q9H461 Putative N-glycosylation sites of Fz8 receptor are important for Wnt8 signaling. PMC5457524-1-1 3 207 gly SNAP 417:420 arg1 the SNAP tag SNAP the SNAP tag OGER SNAP P60880 The human Fbs1 sugar-binding domain (residues 92–296, hereafter referred as Fbs1) was expressed as a fusion to the C-terminus of the SNAP tag to facilitate its immobilization to beads35. PMC5643531-1-8 3 62 gly glycosylation 465:477 arg1 Fz8 Fz8 OGER Fz8 Q9H461 Since OTG interacts and co-localizes with Fz8 in the ER, we speculated that OTG may influence glycosylation and maturation of Fz8. PMC5457524-1-3 7 5 gly Fbs1–glycoprotein 1340:1356 arg1 high- and low-affinity Fbs1–glycoprotein interactions high- and low-affinity Fbs1–glycoprotein interactions OGER Fbs1 Q9HAH7 Much higher levels of plasmid were captured with RNase B beads, indicating that the plasmid display system can differentiate between high- and low-affinity Fbs1–glycoprotein interactions. PMC5795011-1-4 64 181 gly glycosylation 11134:11146 arg1 serum alpha-1-acid glycoprotein 1 serum alpha-1-acid glycoprotein 1 OGER alpha-1-acid glycoprotein 1 P02763 For example, Mascot annotated a total of nine different mono-, di-, tri- and tetra-sialylated N-glycan structures on a single glycosylation site (Asn 93) of serum alpha-1-acid glycoprotein 1 (Fig. 5). PMC5795011-1-4 64 295 gly glycoprotein 11184:11195 arg1 serum alpha-1-acid glycoprotein 1 serum alpha-1-acid glycoprotein 1 OGER alpha-1-acid glycoprotein 1 P02763 For example, Mascot annotated a total of nine different mono-, di-, tri- and tetra-sialylated N-glycan structures on a single glycosylation site (Asn 93) of serum alpha-1-acid glycoprotein 1 (Fig. 5). PMC5643531-1-8 8 2 gly glycosylation 987:999 arg1 Fz8 Fz8 OGER Fz8 Q9H461 We also tested whether OTG affected glycosylation of Fz8. PMC7124471-1-11 72 22 gly serotransferrin 10121:10135 arg1 Hex5HexNAc4NANA2 serotransferrin Hex5HexNAc4NANA2 OGER serotransferrin P02787 In the serum of patient with CDG-1a, the loss of an entire oligosaccharide moiety, i.e. Hex5HexNAc4NANA2 from serotransferrin was identified by MS. In our result, this glycan is identified on all the five glycosites of serotransferrin. PMC7124471-1-11 72 236 gly glycosites 10216:10225 arg1 serotransferrin serotransferrin OGER serotransferrin P02787 In the serum of patient with CDG-1a, the loss of an entire oligosaccharide moiety, i.e. Hex5HexNAc4NANA2 from serotransferrin was identified by MS. In our result, this glycan is identified on all the five glycosites of serotransferrin. PMC6243375-1-5 9 75 gly glycoprotein 1740:1751 arg1 fibulin‐2 fibulin‐2 OGER fibulin‐2 P98095 In addition to VCAN and ACAN, an average of 4.3‐fold increase was detected in 14 sites across fibulin‐2 (FBLN2), a glycoprotein known to be involved in stabilizing the VCAN and ACAN network for growth and metastasis of tumor (Olin et al, 2001; Baird et al, 2013; Fig 3D and Appendix Table S1). PMC5457524-1-3 19 64 gly B 3217:3217 arg1 IV RNase B IV OGER RNase B P07998 Mizushima et al.3738 previously reported that Man(IV) of RNase B forms a hydrogen bond with the sidechain Nδ atom of Asn-159 of mouse Fbs1. PMC5457524-1-3 19 64 gly B 3217:3217 arg1 Man RNase B Man OGER RNase B P07998 Mizushima et al.3738 previously reported that Man(IV) of RNase B forms a hydrogen bond with the sidechain Nδ atom of Asn-159 of mouse Fbs1. PMC5795011-1-fig5 0 6 part_of glycoprotein 162:173 arg1 Asn 93 alpha-1-acid glycoprotein 1 Asn 93 OGER SpecificSite alpha-1-acid glycoprotein 1 P02763 Asn 93 Annotation of nine different glycan structures with varied degree of complexity and sialylation by Mascot on a single glycosylation site (Asn 93) of alpha-1-acid glycoprotein 1 in serum. PMC5643531-1-fig6 0 2 gly glycosylation 14:26 arg1 Fz8 receptor Fz8 receptor OGER Fz8 receptor Q9H461 OTG regulates glycosylation of Fz8 receptor. PMC7124471-1-10 7 49 part_of H 830:830 arg1 N882 complement factor H N529, N822, N882, and N1029 OGER SpecificSite complement factor H P08603 N529, N822, N882, and N1029 The number of N-glycans on N529, N822, N882, and N1029 of complement factor H also varied among serum spiked with glycoproteins, UGP and FGP data set (Fig. 6D). PMC7124471-1-10 7 49 part_of H 830:830 arg1 N1029 complement factor H N529, N822, N882, and N1029 OGER SpecificSite complement factor H P08603 N529, N822, N882, and N1029 The number of N-glycans on N529, N822, N882, and N1029 of complement factor H also varied among serum spiked with glycoproteins, UGP and FGP data set (Fig. 6D). PMC7124471-1-10 7 49 part_of H 830:830 arg1 N822 complement factor H N529, N822, N882, and N1029 OGER SpecificSite complement factor H P08603 N529, N822, N882, and N1029 The number of N-glycans on N529, N822, N882, and N1029 of complement factor H also varied among serum spiked with glycoproteins, UGP and FGP data set (Fig. 6D). PMC7124471-1-10 7 49 part_of H 830:830 arg1 N1029 complement factor H N529, N822, N882, and N1029 OGER SpecificSite complement factor H P08603 N529, N822, N882, and N1029 The number of N-glycans on N529, N822, N882, and N1029 of complement factor H also varied among serum spiked with glycoproteins, UGP and FGP data set (Fig. 6D). PMC7124471-1-10 7 49 part_of H 830:830 arg1 N822 complement factor H N529, N822, N882, and N1029 OGER SpecificSite complement factor H P08603 N529, N822, N882, and N1029 The number of N-glycans on N529, N822, N882, and N1029 of complement factor H also varied among serum spiked with glycoproteins, UGP and FGP data set (Fig. 6D). PMC7124471-1-10 7 49 part_of H 830:830 arg1 N822 complement factor H N529, N822, N882, and N1029 OGER SpecificSite complement factor H P08603 N529, N822, N882, and N1029 The number of N-glycans on N529, N822, N882, and N1029 of complement factor H also varied among serum spiked with glycoproteins, UGP and FGP data set (Fig. 6D). PMC7143757-1-1 17 59 gly glycosylated 1907:1918 arg1 glycosylated CTB4573H CTB4573H (CTB OGER CTB4573H (CTB Q01459 The higher MW band of glycosylated CTB4573H (CTB-OPSBa) was detected by both antibodies, while the lower band was not observed because of the poor immunogenicity of short-chain OPS (Figure 1B). PMC5976746-1-5 41 215 gly glycosylation 6491:6503 arg1 BG505 NFL BG505 NFL OGER BG505 NFL P07196 A comparison of glycosylation profiles of BG505 NFL and BG505 SOSIP both expressed from CHO cells, but purified differently, was also performed (35). PMC5976746-1-5 41 215 gly glycosylation 6491:6503 arg1 BG505 SOSIP BG505 SOSIP Cterm BG505 SOSIP A comparison of glycosylation profiles of BG505 NFL and BG505 SOSIP both expressed from CHO cells, but purified differently, was also performed (35). PMC3938046-1-9 3 8 gly N-glycosylated 478:491 arg1 Prkar1a/b Prkar1a/b OGER Prkar1a P10644 Further, several membrane proteins and N-glycosylated proteins (Ctnnb1, Abcc8, Stat3, Basp1, Acadvl, Prkar1a/b, and Flnb) were detected in the crude membrane-enriched fractions. PMC3938046-1-9 3 8 gly N-glycosylated 478:491 arg1 Stat3 Stat3 OGER Stat3 P40763 Further, several membrane proteins and N-glycosylated proteins (Ctnnb1, Abcc8, Stat3, Basp1, Acadvl, Prkar1a/b, and Flnb) were detected in the crude membrane-enriched fractions. PMC3938046-1-9 3 8 gly N-glycosylated 478:491 arg1 Basp1 Basp1 OGER Basp1 P80723 Further, several membrane proteins and N-glycosylated proteins (Ctnnb1, Abcc8, Stat3, Basp1, Acadvl, Prkar1a/b, and Flnb) were detected in the crude membrane-enriched fractions. PMC3938046-1-9 3 8 gly N-glycosylated 478:491 arg1 Flnb Flnb OGER Flnb O75369 Further, several membrane proteins and N-glycosylated proteins (Ctnnb1, Abcc8, Stat3, Basp1, Acadvl, Prkar1a/b, and Flnb) were detected in the crude membrane-enriched fractions. PMC3938046-1-9 3 8 gly N-glycosylated 478:491 arg1 Ctnnb1 Ctnnb1 OGER Ctnnb1 P35222 Further, several membrane proteins and N-glycosylated proteins (Ctnnb1, Abcc8, Stat3, Basp1, Acadvl, Prkar1a/b, and Flnb) were detected in the crude membrane-enriched fractions. PMC3938046-1-9 3 8 gly N-glycosylated 478:491 arg1 Abcc8 Abcc8 OGER Abcc8 Q09428 Further, several membrane proteins and N-glycosylated proteins (Ctnnb1, Abcc8, Stat3, Basp1, Acadvl, Prkar1a/b, and Flnb) were detected in the crude membrane-enriched fractions. PMC3938046-1-9 3 8 gly N-glycosylated 478:491 arg1 Acadvl Acadvl OGER Acadvl P49748 Further, several membrane proteins and N-glycosylated proteins (Ctnnb1, Abcc8, Stat3, Basp1, Acadvl, Prkar1a/b, and Flnb) were detected in the crude membrane-enriched fractions. PMC7124471-1-7 13 20 gly N-glycosylation 1603:1617 arg1 CFH CFH OGER CFH P08603 This suggested that N-glycosylation of CFH was site-specific. PMC3942810-2-2 3 57 gly N-glycosylated 460:473 arg1 RJ RJ Cterm RJ To the best of our knowledge, this is the most comprehensive assignment of the N-glycosylated sites of RJ. PMC7124471-1-10 6 59 gly glycosites 618:627 arg1 serotransferrin serotransferrin OGER serotransferrin P02787 The number of N-glycans on those glycosites of serotransferrin varied among commercial serotransferrin, serum spiked with glycoproteins, UGP and FGP data set (Fig. 6C). PMC7107550-1-4 19 241 gly SMs 4138:4140 arg1 all SMs all OGER SMs P52788 Because all of the sequences obtained from the database were the result of one or several accidental transmissions from SMs to RMs of a single SIVsm subtype (8) only recently described (Apetrei et al. 2005, 2006), we cannot rule out the alternative hypotheses that this site is not polymorphic in the SIVsm subtype-8 envelope or that this polymorphism was fixed in RMs due to an extreme bottleneck upon transmission. PMC2762462-1-1 2 73 gly glycoprotein 406:417 arg1 ST6 ST6 OGER ST6 P27701 Like other sialyltransferases, ST6 is a type II transmembrane glycoprotein, comprised of a short N-terminal cytosolic tail, a hydrophobic signal-anchor sequence that is embedded in the membrane, a so-called "stem" region, and a long C-terminal catalytic domain that is exposed to the lumen of the Golgi apparatus. PMC7124471-1-10 20 27 gly N-glycosylation 2237:2251 arg1 serotransferrin serotransferrin OGER serotransferrin P02787 From the site-specific glycoform result of serotransferrin, it is easy to obtain a structure-function perspective of N-glycosylation of serotransferrin in pathogen-host interaction. PMC7124471-1-6 7 18 gly glycoproteins 1016:1028 arg1 QSOX1 QSOX1 OGER QSOX1 O00391 Among the 16 proteins, there are four glycoproteins including IOVO, Ogchi, OVAL and QSOX1, and most of the GPSMs identified from this sample were from IOVO instead of OVAL (supplemental Table S19). PMC5795011-1-4 4 303 gly glycoprotein 927:938 arg1 serum alpha-1-acid glycoprotein 1 serum alpha-1-acid glycoprotein 1 OGER alpha-1-acid glycoprotein 1 P02763 The result of the described strategy for large scale automated glycopeptide analysis of LC-MS datasets was demonstrated by serum alpha-1-acid glycoprotein 1 (A1AG1) as an example. PMC5795011-1-4 4 303 gly glycoprotein 927:938 arg1 A1AG1 A1AG1 Cterm A1AG1 P02763 The result of the described strategy for large scale automated glycopeptide analysis of LC-MS datasets was demonstrated by serum alpha-1-acid glycoprotein 1 (A1AG1) as an example. PMC5457524-1-3 19 124 part_of Fbs1 3288:3291 arg1 Asn-159 Fbs1 Asn-159 OGER SpecificSite Fbs1 Q9HAH7 Asn-159 Mizushima et al.3738 previously reported that Man(IV) of RNase B forms a hydrogen bond with the sidechain Nδ atom of Asn-159 of mouse Fbs1. PMC7081908-1-5 7 101 gly glycosylation 1555:1567 arg1 recombinant gp120 proteins recombinant gp120 proteins OGER gp120 proteins Q14624 This report presents the first extensive comparison of glycosylation patterns of recombinant gp120 proteins from four clades of HIV-1 in two different cell lines, grown either at laboratory scale or under 50-liter GMP conditions, purified using different methods, and in two GMP lots prepared under identical conditions. PMC6934601-1-7 12 104 gly highly-glycosylated 1816:1834 arg1 SPN SPN OGER SPN P16150 In particular, our findings uncover a role for highly-glycosylated cell surface molecules (SPN and MUC1) in hindering CD3 bsAb-induced T cell-tumor cell clustering and consequent tumor cell lysis. PMC7124471-1-11 81 111 gly glycoform 11348:11356 arg1 serotransferrin glycoform serotransferrin glycoform OGER serotransferrin P02787 This can be achieved by in-depth analysis of serotransferrin glycoform and the binding affinity of each glycan to TbpA. PMC5976746-1-5 80 53 gly homogeneity 13916:13926 arg1 the CHO-M-derived BG505 NFL the CHO-M-derived BG505 NFL OGER BG505 NFL trimers P07196 High homogeneity, low V3 exposure, and low F105 binding of the CHO-M-derived BG505 NFL trimers contributed to elicitation of robust tier 2 and low tier 1 neutralization when formulated in ISCOMATRIX and inoculated into rabbits. PMC5795011-1-fig5 0 8 gly glycoprotein 162:173 arg1 alpha-1-acid glycoprotein 1 alpha-1-acid glycoprotein 1 OGER alpha-1-acid glycoprotein 1 P02763 Annotation of nine different glycan structures with varied degree of complexity and sialylation by Mascot on a single glycosylation site (Asn 93) of alpha-1-acid glycoprotein 1 in serum. PMC5795011-1-fig5 0 26 gly glycosylation 118:130 arg1 alpha-1-acid glycoprotein 1 alpha-1-acid glycoprotein 1 OGER alpha-1-acid glycoprotein 1 P02763 Annotation of nine different glycan structures with varied degree of complexity and sialylation by Mascot on a single glycosylation site (Asn 93) of alpha-1-acid glycoprotein 1 in serum. PMC5795011-1-fig5 0 34 gly varied 52:57 arg1 alpha-1-acid glycoprotein 1 alpha-1-acid glycoprotein 1 OGER alpha-1-acid glycoprotein 1 P02763 Annotation of nine different glycan structures with varied degree of complexity and sialylation by Mascot on a single glycosylation site (Asn 93) of alpha-1-acid glycoprotein 1 in serum. PMC7124471-1-10 19 60 gly N-glycosites 2001:2012 arg1 serotransferrin serotransferrin OGER serotransferrin P02787 In this regard, the number of N-glycan mass identified on the four N-glycosites of serotransferrin might indicate the accessibility of each site to OSTs and their functional importance. PMC5795011-1-4 19 760 gly glycopeptide 3264:3275 arg1 alpha-2-macroglobulin alpha-2-macroglobulin OGER alpha-2-macroglobulin P01023 As opposed to the above examples, Mascot annotated the fucose residue to the core HexNAc of a di-sialylated bi-antennary glycopeptide of alpha-2-macroglobulin.