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
PMC5795011-1-fig3	0	15	gly	O-glycopeptide	17:30	arg2	O-glycopeptide MS2 spectra			O-glycopeptide MS2 spectra						O-glycopeptide	Mascot annotated O-glycopeptide MS2 spectra of fetuin using stepped NCE values.
PMC5795011-1-4	19	1063	gly	di-sialylated	3237:3249	arg1	a di-sialylated bi-antennary glycopeptide			a di-sialylated bi-antennary glycopeptide						glycopeptide	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.
PMC5795011-1-4	19	760	gly	glycopeptide	3264:3275	arg1	alpha-2-macroglobulin	alpha-2-macroglobulin		glycopeptide	the core HexNAc	OGER		alpha-2-macroglobulin	P01023	glycopeptide	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.
PMC5795011-1-4	19	760	gly	glycopeptide	3264:3275	arg2	a di-sialylated bi-antennary glycopeptide			glycopeptide	the core HexNAc					glycopeptide	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.
PMC5795011-1-4	19	760	gly	glycopeptide	3264:3275	arg2	a di-sialylated bi-antennary glycopeptide	alpha-2-macroglobulin		glycopeptide		OGER		alpha-2-macroglobulin	P01023	glycopeptide	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.
PMC5457524-1-5	1	8	gly	glycopeptides	157:169	arg2	the N-linked glycopeptides			the N-linked glycopeptides						glycopeptides	The selectivity of wt Fbs1 and the GYR mutant was tested by isolating and identifying the N-linked glycopeptides from a defined ‘complex' sample.
PMC5643531-1-8	0	60	gly	glycosylation	19:31	arg1	Fz8	Fz8				OGER		Fz8	Q9H461		OTG is involved in glycosylation of Fz8.
PMC6731604-1-3	14	13	gly	glycoproteins	1981:1993	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			The abundance glycoprotein content in urine and the high percentage of glycoproteins that overlap with tissue-derived glycoproteins suggests the high potential of urine in clinical detection and biomarker discovery.
PMC6731604-1-3	14	55	gly	glycoprotein	1924:1935	arg1	The abundance glycoprotein content	The abundance glycoprotein content				Fterm		glycoprotein			The abundance glycoprotein content in urine and the high percentage of glycoproteins that overlap with tissue-derived glycoproteins suggests the high potential of urine in clinical detection and biomarker discovery.
PMC6731604-1-3	14	64	gly	glycoproteins	2028:2040	arg1	tissue-derived glycoproteins	tissue-derived glycoproteins				Fterm		glycoproteins			The abundance glycoprotein content in urine and the high percentage of glycoproteins that overlap with tissue-derived glycoproteins suggests the high potential of urine in clinical detection and biomarker discovery.
PMC3942810-1-2	18	154	gly	glycoproteins	3194:3206	arg1	known glycoproteins	known glycoproteins				Fterm		glycoproteins			Thirty-three novel sites were identified in known glycoproteins, and nine novel sites in novel glycoproteins.
PMC3942810-1-2	18	230	gly	glycoproteins	3239:3251	arg1	novel glycoproteins	novel glycoproteins				Fterm		glycoproteins			Thirty-three novel sites were identified in known glycoproteins, and nine novel sites in novel glycoproteins.
PMC2538527-1-4	14	113	gly	disialylated	1970:1981	arg1	Hex1HexNAc1SA2				Hex1HexNAc1SA2						The most intense peak at 20 213 Da appears to be composed of the mature peptide chain plus a single core type-1 disialylated glycan (Hex1HexNAc1SA2).
PMC6731604-1-1	16	83	gly	glycosites	3057:3066	arg2	these identified glycosites			glycosites						glycosites	The confidence of these identified glycosites, especially the glycosites that were only identified once, can be further estimated based on their original mass spectrometry data and subsequent analytical methods.
PMC6731604-1-1	16	202	gly	glycosites	3030:3039	arg2	these identified glycosites			glycosites						glycosites	The confidence of these identified glycosites, especially the glycosites that were only identified once, can be further estimated based on their original mass spectrometry data and subsequent analytical methods.
PMC6731604-1-2	1	24	gly	glycoprotein	117:128	arg1	glycoprotein analysis	glycoprotein analysis				Fterm		glycoprotein			Determining the current status of glycoprotein analysis in each human tissue and body fluid will benefit future human glycoproteomic studies.
PMC5457524-1-1	23	128	gly	glycopeptide	3776:3787	arg2	the derivative glycopeptide			the derivative glycopeptide						glycopeptide	Removal of sialic acid clearly improves recovery of the derivative glycopeptide.
PMC7124471-1-4	31	126	gly	glycopeptide	5432:5443	arg2	the glycoprotein, glycosite and glycopeptide levels			the glycoprotein, glycosite and glycopeptide levels						glycosite and glycopeptide	Compared to the result obtained using the 701 N-glycan masses, the number of identifications increased by 2.3% (12/521), 2.9% (30/1,030), and 5% (1109/22,194) at the glycoprotein, glycosite and glycopeptide levels when using the combined glycan mass database (supplemental Table S7 and supplemental Table S13).
PMC7124471-1-4	31	224	gly	glycosite	5418:5426	arg2	the glycoprotein, glycosite and glycopeptide levels			the glycoprotein, glycosite and glycopeptide levels						glycosite and glycopeptide	Compared to the result obtained using the 701 N-glycan masses, the number of identifications increased by 2.3% (12/521), 2.9% (30/1,030), and 5% (1109/22,194) at the glycoprotein, glycosite and glycopeptide levels when using the combined glycan mass database (supplemental Table S7 and supplemental Table S13).
PMC7124471-1-4	31	285	gly	glycoprotein	5404:5415	arg1	the glycoprotein, glycosite and glycopeptide levels	the glycoprotein, glycosite and glycopeptide levels				Fterm		glycoprotein			Compared to the result obtained using the 701 N-glycan masses, the number of identifications increased by 2.3% (12/521), 2.9% (30/1,030), and 5% (1109/22,194) at the glycoprotein, glycosite and glycopeptide levels when using the combined glycan mass database (supplemental Table S7 and supplemental Table S13).
PMC5457524-1-1	17	153	gly	fucose	2728:2733	arg1	the innermost GlcNAc residue			the innermost GlcNAc residue	the innermost GlcNAc residue		Site			residue	In mammals, N-glycan structures may also include the heterogeneous presence of α1,6-linked fucose on the innermost GlcNAc residue of the N-glycan pentasaccharide core.
PMC7124471-1-11	37	277	gly	deglycopeptide	5148:5161	arg2	serum N-linked deglycopeptide spectral library			serum N-linked deglycopeptide spectral library						deglycopeptide	The combined results were filtered with 1% FDR at peptide level based on the peptides identified as having an Asn deamidation modification, and the remaining peptides were used to construct serum N-linked deglycopeptide spectral library.
PMC7124471-1-11	37	359	gly	used	5115:5118	arg2	the remaining peptides			the remaining peptides						peptides	The combined results were filtered with 1% FDR at peptide level based on the peptides identified as having an Asn deamidation modification, and the remaining peptides were used to construct serum N-linked deglycopeptide spectral library.
PMC5795011-1-fig6	2	14	gly	mono-sialylated	371:385	arg1	The three most frequent glycopeptide variants	The three most frequent glycopeptide variants				Fterm		variants			The three most frequent glycopeptide variants were the mono-sialylated bi-antennary, di-sialylated bi-antennary without and with one fucose residue.
PMC5795011-1-fig6	2	25	gly	glycopeptide	340:351	arg2	The three most frequent glycopeptide variants			The three most frequent glycopeptide variants						glycopeptide	The three most frequent glycopeptide variants were the mono-sialylated bi-antennary, di-sialylated bi-antennary without and with one fucose residue.
PMC5795011-1-4	33	152	gly	glycopeptide	5397:5408	arg2	glycopeptide			glycopeptide						glycopeptide	Figure 6 displays the glycopeptide ratios of the three most abundant glycan structures and most of them have peptide ratios near to 1.0, indicating no significant changes between the analyzed indolent and aggressive cancer samples.
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).
PMC7124471-1-11	45	259	gly	deglycopeptide	6299:6312	arg2	deglycopeptide identification			deglycopeptide identification						deglycopeptide	Target-decoy method was used to perform FDR control at the peptide level for deglycopeptide identification.
PMC6243375-1-3	17	128	gly	glycopeptide	3145:3156	arg2	a glycopeptide			a glycopeptide						glycopeptide	In addition, the possibility of multiple glycans on a glycopeptide demands caution in the data interpretation to define site‐specific glycan composition.
PMC3942810-2-2	23	319	gly	glycosylated	3467:3478	arg1	glycosylated proteins	glycosylated proteins				Fterm		proteins			The high number of glycosylated proteins related to metabolic processes indicates the production of enough energy through the metabolism of carbohydrates and proteins for queen spawning and larval growth, which may be achieved by modulating the enzymatic efficiency[64].
PMC6731604-1-1	18	4	gly	glycosites	3876:3885	arg2	the glycosites			the glycosites						glycosites	As most of the glycosite-containing peptides in N-GlycositeAtlas were identified as their de-glycosylation form with deamidation (+ 0.98 Da) at the former glycosites (after PNGase F treatment), the high resolution and accuracy of the mass spectrometers that were used to conduct these studies in recent years greatly increased the identification confidence of the glycosites and glycoproteins as well as increased the numbers of identified glycosite-containing peptides at pre-determined false discovery rates (FDR).
PMC6731604-1-1	18	156	gly	glycosites	3667:3676	arg2	the former glycosites			the former glycosites						glycosites	As most of the glycosite-containing peptides in N-GlycositeAtlas were identified as their de-glycosylation form with deamidation (+ 0.98 Da) at the former glycosites (after PNGase F treatment), the high resolution and accuracy of the mass spectrometers that were used to conduct these studies in recent years greatly increased the identification confidence of the glycosites and glycoproteins as well as increased the numbers of identified glycosite-containing peptides at pre-determined false discovery rates (FDR).
PMC6731604-1-1	18	211	gly	glycoproteins	3891:3903	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			As most of the glycosite-containing peptides in N-GlycositeAtlas were identified as their de-glycosylation form with deamidation (+ 0.98 Da) at the former glycosites (after PNGase F treatment), the high resolution and accuracy of the mass spectrometers that were used to conduct these studies in recent years greatly increased the identification confidence of the glycosites and glycoproteins as well as increased the numbers of identified glycosite-containing peptides at pre-determined false discovery rates (FDR).
PMC7124471-1-10	5	85	gly	glycosites	476:485	arg2	four N-linked glycosites	serotransferrin		glycosites		OGER		serotransferrin	P02787	glycosites	There were four N-linked glycosites of serotransferrin identified, i.e. N432, N630, N637, and N523 (Fig. 6B, supplemental Table S26).
PMC5098438-1-fig6	1	3	gly	glycoforms	51:60	arg1	the IgG Fc Cγ2 domain			the IgG Fc Cγ2 domain						domain	Human and T. thermophila glycoforms of the IgG Fc Cγ2 domain with the protein depicted in gray and the glycan residues shown as colored sticks with surface representation (red, fucose; blue, GlcNAc; green, mannose; cyan, glucose; magenta, sialic acid).
PMC5098438-1-fig6	1	38	gly	shown	145:149	arg1	the glycan residues			the glycan residues						residues	Human and T. thermophila glycoforms of the IgG Fc Cγ2 domain with the protein depicted in gray and the glycan residues shown as colored sticks with surface representation (red, fucose; blue, GlcNAc; green, mannose; cyan, glucose; magenta, sialic acid).
PMC3938046-1-5	30	2	gly	glycoproteins	4485:4497	arg1	the 474 glycoproteins	the 474 glycoproteins				Fterm		glycoproteins			Based on these data, microglia-specific N-glycosylation sites, particularly those that correspond to the 474 glycoproteins, are attractive candidate biomarkers and drug targets.
PMC3938046-1-5	30	160	gly	N-glycosylation	4416:4430	arg2	microglia-specific N-glycosylation sites			microglia-specific N-glycosylation sites						sites	Based on these data, microglia-specific N-glycosylation sites, particularly those that correspond to the 474 glycoproteins, are attractive candidate biomarkers and drug targets.
PMC6243375-1-5	15	121	gly	glycosylation	3358:3370	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	A novel tool (EXoO) has been developed for the combined mapping of O‐linked glycosylation sites in proteins and the definition of the O‐linked glycans at those sites.
PMC7124471-1-8	5	42	gly	glycopeptide	662:673	arg2	One glycopeptide			One glycopeptide						glycopeptide	One glycopeptide containing this site were identified using the 739 N-glycan masses.
PMC5795011-1-4	55	610	gly	glycopeptide	9889:9900	arg2	intact glycopeptide analysis			intact glycopeptide analysis						glycopeptide	Data driven acquisition strategies, for example HCD-product dependent CID-and ETD fragmentation strategies have also been shown to be effective in intact glycopeptide analysis.
PMC5795011-1-4	125	1090	gly	glycopeptide	21308:21319	arg2	automated glycopeptide analysis			automated glycopeptide analysis						glycopeptide	However, one of the major advantages of using Mascot for automated glycopeptide analysis is its wide distribution and easy to use nature compared to many of the available software tools for glycoproteomics analysis.
PMC6731604-1-fig1	3	0	gly	glycoprotein	374:385	arg1	glycoprotein database development	glycoprotein database development				Fterm		glycoprotein			The relevant information for each glycosite was then extracted for glycosite and glycoprotein database development
PMC6731604-1-fig1	3	6	gly	glycosite	360:368	arg2	glycosite			glycosite						glycosite	The relevant information for each glycosite was then extracted for glycosite and glycoprotein database development
PMC6731604-1-fig1	3	9	gly	glycosite	327:335	arg2	each glycosite			each glycosite						glycosite	The relevant information for each glycosite was then extracted for glycosite and glycoprotein database development
PMC6243375-1-2	9	4	gly	glycosylation	1680:1692	arg2	732 O‐linked glycosylation sites			732 O‐linked glycosylation sites						sites	With 1% FDR, 6,157 PSMs were assigned to 1,060 O‐linked glycopeptides with 732 O‐linked glycosylation sites from 306 glycoproteins being identified (Dataset EV4).
PMC6243375-1-2	9	71	gly	glycopeptides	1648:1660	arg2	1,060 O‐linked glycopeptides			1,060 O‐linked glycopeptides						glycopeptides	With 1% FDR, 6,157 PSMs were assigned to 1,060 O‐linked glycopeptides with 732 O‐linked glycosylation sites from 306 glycoproteins being identified (Dataset EV4).
PMC6243375-1-2	9	81	gly	glycoproteins	1709:1721	arg1	306 glycoproteins	306 glycoproteins				Fterm		glycoproteins			With 1% FDR, 6,157 PSMs were assigned to 1,060 O‐linked glycopeptides with 732 O‐linked glycosylation sites from 306 glycoproteins being identified (Dataset EV4).
PMC6731604-1-3	2	63	gly	glycoprotein	272:283	arg1	disease-related glycoprotein changes	disease-related glycoprotein changes				Fterm		glycoprotein			The detection of disease-related glycoprotein changes in serum is an important strategy for disease biomarker discovery [105].
PMC7107550-1-fig1	4	24	gly	glycosylation	531:543	arg2	Putative N-linked glycosylation motifs			Putative N-linked glycosylation motifs						motifs	Putative N-linked glycosylation motifs (NXS/T) are represented in gray.
PMC5795011-1-4	122	671	gly	glycopeptides	20874:20886	arg2	Fragmentated glycopeptides			Fragmentated glycopeptides						glycopeptides	Fragmentated glycopeptides are searched against this database and scored based on the peptide type b- and y-ions using the standard Mascot scoring algorithm.
PMC7124471-1-3	17	45	gly	deglycopeptide	2796:2809	arg2	N-linked deglycopeptide fractionation			N-linked deglycopeptide fractionation						deglycopeptide	These results revealed that the low and high abundant protein fractionation and N-linked deglycopeptide fractionation together significantly increased the depth of serum N-glycoproteome.
PMC3942810-1-fig4	1	1	gly	glycosylation	175:187	arg2	1, 2 and 3 N-linked glycosylation sites			1, 2 and 3 N-linked glycosylation sites						sites	“1, 2 and 3” are the N-glycosylated protein carrying 1, 2 and 3 N-linked glycosylation sites, respectvely.
PMC3942810-1-fig4	1	14	gly	N-glycosylated	123:136	arg1	the N-glycosylated protein	the N-glycosylated protein				Fterm		protein			“1, 2 and 3” are the N-glycosylated protein carrying 1, 2 and 3 N-linked glycosylation sites, respectvely.
PMC5795011-1-4	104	549	gly	glycopeptide	17679:17690	arg2	glycopeptide sequences			glycopeptide sequences						glycopeptide sequences	Fragmentation methods that generate glycan and peptide fragments, irrespective of glycopeptide sequences, will open up the possibility of using general proteome databases.
PMC3942810-1-2	22	53	gly	RJ	3939:3940	arg1	N = asparagine			N = asparagine						asparagine	In other words, the N-linked sequence motif was X-X-N-X-S/T-X in N-glycoproteins of RJ (N = asparagine, X = any amino acid except proline, S/T = serine or threonine).
PMC3942810-1-2	22	206	gly	N-glycoproteins	3920:3934	arg1	N-glycoproteins	N-glycoproteins				Fterm		N-glycoproteins			In other words, the N-linked sequence motif was X-X-N-X-S/T-X in N-glycoproteins of RJ (N = asparagine, X = any amino acid except proline, S/T = serine or threonine).
PMC6243375-1-fig2	5	33	gly	glycoproteins	571:583	arg1	O‐linked glycoproteins	O‐linked glycoproteins				Fterm		glycoproteins			Cellular component analysis of O‐linked glycoproteins.
PMC5457524-1-7	14	7	gly	glycosite	2895:2903	arg2	glycosite			glycosite						glycosite	Our data demonstrate that Fbs1 GYR enrichment can greatly improve identification of micro-heterogeneity of N-glycosylation, which can be indexed as the average number of glycan types per glycosite (number of unique N-glycopeptides/number of unique N-glycosites) and the average number of spectral counts per glycosite (number of spectral counts/number of unique N-glycosites).
PMC5457524-1-7	14	20	gly	N-glycosites	2956:2967	arg2	unique N-glycosites			unique N-glycosites						N-glycosites	Our data demonstrate that Fbs1 GYR enrichment can greatly improve identification of micro-heterogeneity of N-glycosylation, which can be indexed as the average number of glycan types per glycosite (number of unique N-glycopeptides/number of unique N-glycosites) and the average number of spectral counts per glycosite (number of spectral counts/number of unique N-glycosites).
PMC5457524-1-7	14	415	gly	glycosite	3016:3024	arg2	glycosite			glycosite						glycosite	Our data demonstrate that Fbs1 GYR enrichment can greatly improve identification of micro-heterogeneity of N-glycosylation, which can be indexed as the average number of glycan types per glycosite (number of unique N-glycopeptides/number of unique N-glycosites) and the average number of spectral counts per glycosite (number of spectral counts/number of unique N-glycosites).
PMC5457524-1-7	14	438	gly	N-glycosites	3070:3081	arg2	unique N-glycosites			unique N-glycosites						N-glycosites	Our data demonstrate that Fbs1 GYR enrichment can greatly improve identification of micro-heterogeneity of N-glycosylation, which can be indexed as the average number of glycan types per glycosite (number of unique N-glycopeptides/number of unique N-glycosites) and the average number of spectral counts per glycosite (number of spectral counts/number of unique N-glycosites).
PMC3938046-1-3	15	6	gly	occupied	2610:2617	arg2	The third position			The third position						position	The third position of the canonical motif was occupied by Thr (612; 58.2%) or Ser (431; 41%) and Thr (830; 58.7%) or Ser (511; 36%) in biological replicates 1 and 2, respectively.
PMC3938046-1-3	16	26	gly	glycosylation	2807:2819	arg2	mouse glycosylation sites			mouse glycosylation sites						sites	Threonine occurs 1.4-fold more frequently than serine in mouse glycosylation sites [18], which is consistent with our data (1.53 = 1442/942).
PMC7124471-1-6	20	82	gly	deglycopeptide	3780:3793	arg2	N-linked deglycopeptide library			N-linked deglycopeptide library						deglycopeptide	Compared to the 2041 GPSMs obtained using the N-linked deglycopeptide library and N-glycan masses database derived from Gallus gallus, it suggested the FDR of the proposed workflow was 0.59%.
PMC3938046-1-5	27	144	gly	glycoproteins	4006:4018	arg1	glycoproteins	glycoproteins		met		Fterm		glycoproteins		met	A total of 474 (67%) of 704 genes that encoded glycoproteins met the filtering criteria; 219 genes (31%) were constitutively expressed in other mouse tissues and cells.
PMC7124471-1-6	23	76	gly	glycopeptides	4168:4180	arg2	the N-linked intact glycopeptides			the N-linked intact glycopeptides						glycopeptides	Therefore, the N-linked intact glycopeptides carrying this major N-glycan in HRP may be identified using the N-linked deglycopeptides carrying other N-glycans that can be processed by PNGase F.
PMC7124471-1-6	23	145	gly	deglycopeptides	4255:4269	arg2	the N-linked deglycopeptides			the N-linked deglycopeptides						deglycopeptides	Therefore, the N-linked intact glycopeptides carrying this major N-glycan in HRP may be identified using the N-linked deglycopeptides carrying other N-glycans that can be processed by PNGase F.
PMC7124471-1-3	0	71	gly	Deglycopeptides	27:41	arg2	N-linked Deglycopeptides			N-linked Deglycopeptides						Deglycopeptides	Identification of N-linked Deglycopeptides.
PMC5795011-1-1	6	68	gly	glycopeptide	1055:1066	arg2	automated glycopeptide analysis			automated glycopeptide analysis						glycopeptide	In order to use the Mascot search engine for automated glycopeptide analysis, the basic requirements include that (i) the sugar residues must be defined with unique one-letter codes in a Mascot readable format, (ii) each glycan structure must be defined in a linear format and (iii) a customized database must be prepared which consists of combined protein and glycan sequences.
PMC5795011-1-3	28	115	gly	glycopeptide	4598:4609	arg2	automated glycopeptide annotation			automated glycopeptide annotation						glycopeptide	Taken together all these results clearly indicates the potential of the described approach i.e. using stepped NCE values, a custom linearized glycoprotein database and the Mascot search engine for automated glycopeptide annotation.
PMC5795011-1-3	28	144	gly	glycoprotein	4533:4544	arg1	a custom linearized glycoprotein database	a custom linearized glycoprotein database				Fterm		glycoprotein			Taken together all these results clearly indicates the potential of the described approach i.e. using stepped NCE values, a custom linearized glycoprotein database and the Mascot search engine for automated glycopeptide annotation.
PMC3938046-1-3	9	131	gly	N-glycosites	1780:1791	arg2	N-glycosites			N-glycosites						N-glycosites	As shown in Figure 3B, CMC identified significantly more N-glycosites and glycoproteins than WCC.
PMC3938046-1-3	9	137	gly	glycoproteins	1797:1809	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			As shown in Figure 3B, CMC identified significantly more N-glycosites and glycoproteins than WCC.
PMC3938046-1-7	8	61	gly	N-glycoproteins	1431:1445	arg1	N-glycoproteins	N-glycoproteins				Fterm		N-glycoproteins			We also detected N-glycoproteins that are associated with microglia-associated immune responses.
PMC6731604-1-3	6	74	gly	glycoprotein	917:928	arg1	glycoprotein changes	glycoprotein changes				Fterm		glycoprotein			The data confirmed the high value of serum tests in the detection of glycoprotein changes associated with various diseases.
PMC3938046-1-3	8	37	gly	glycosylation	1491:1503	arg2	glycosylation sites			glycosylation sites						sites	However, in combining all replicates, the difference in the number of glycosylation sites that were identified in each replicate reflects an important advantage with regard to the number of unique identifications; thus, our experiments enhanced the coverage of the N-glycoproteome as much as possible.
PMC3938046-1-fig4	1	18	gly	glycoproteins	126:138	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			(A) Analysis of transmembrane domains, GPI-anchors, and secretion of glycoproteins by multiple programs.
PMC5795011-1-4	114	477	gly	N-glycopeptides	19577:19591	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	For the database search of N-glycopeptides using Mascot, the glycan variable modification was defined as 5Hex + 4HexNAc attached for asparagine residues and loss of 5Hex + 4HexNAc or 5Hex + 3HexNAc from b- and y-ions including the N-glycosylation site was included.
PMC5795011-1-4	114	1125	gly	N-glycosylation	19781:19795	arg2	the N-glycosylation site			the N-glycosylation site						site	For the database search of N-glycopeptides using Mascot, the glycan variable modification was defined as 5Hex + 4HexNAc attached for asparagine residues and loss of 5Hex + 4HexNAc or 5Hex + 3HexNAc from b- and y-ions including the N-glycosylation site was included.
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).
PMC3942810-2-1	7	9	gly	protein	1102:1108	arg1	all	protein			all	Fterm		protein			This method suggested that all of the 13 novel proteins predicted to be secretory proteins are real protein components of RJ.
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.
PMC5457524-1-7	4	261	gly	N-glycosite	618:628	arg2	each respective N-glycosite			each respective N-glycosite						N-glycosite	Since Fbs1 GYR enrichment maintains the linkage of each N-glycan to each respective N-glycosite, and enrichment levels are >65%, our protocol allows simultaneous identification of the N-glycan diversity at a given N-glycosite.
PMC5457524-1-7	4	562	gly	N-glycosite	748:758	arg2	a given N-glycosite			a given N-glycosite						N-glycosite	Since Fbs1 GYR enrichment maintains the linkage of each N-glycan to each respective N-glycosite, and enrichment levels are >65%, our protocol allows simultaneous identification of the N-glycan diversity at a given N-glycosite.
PMC3938046-1-6	0	56	gly	glycoproteins	48:60	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Characterization of TMD-containing proteins and glycoproteins related to microglial physiology.
PMC5795011-1-4	50	697	gly	glycopeptide	8957:8968	arg2	glycopeptide			glycopeptide						glycopeptide	The enrichment strategy employed in this study worked well to enrich sialylated glycopeptides and the LC-MS data sets contained mainly glycopeptide spectra.
PMC5795011-1-4	50	939	gly	glycopeptides	8902:8914	arg2	sialylated glycopeptides			sialylated glycopeptides						glycopeptides	The enrichment strategy employed in this study worked well to enrich sialylated glycopeptides and the LC-MS data sets contained mainly glycopeptide spectra.
PMC5795011-1-4	50	1055	gly	sialylated	8891:8900	arg1	sialylated glycopeptides			sialylated glycopeptides						glycopeptides	The enrichment strategy employed in this study worked well to enrich sialylated glycopeptides and the LC-MS data sets contained mainly glycopeptide spectra.
PMC5457524-1-7	20	370	gly	N-glycopeptide	3936:3949	arg2	more effective intact N-glycopeptide analysis			more effective intact N-glycopeptide analysis						N-glycopeptide	Overall, this experiment demonstrates that Fbs1 GYR enrichment enables more effective intact N-glycopeptide analysis with greatly expanded coverage and reveals a deeper analysis of micro-heterogeneity of N-glycosylation.
PMC4595782-1-7	38	161	gly	Non-glycosylated	7537:7552	arg1	Non-glycosylated plant-derived SAC-Par-4-GFP				Non-glycosylated plant-derived SAC-Par-4-GFP						Non-glycosylated plant-derived SAC-Par-4-GFP had almost similar molecular mass (∼32 kDa) to that of deglycosylated SAC-Par-4-GFP-SEKDEL (∼32 kDa) and had lower molecular weight to that of the glycosylated SAC-Par-4-GFP-SEKDEL (∼34 kDa).
PMC4595782-1-7	38	487	gly	deglycosylated	7637:7650	arg1	deglycosylated SAC-Par-4-GFP-SEKDEL				deglycosylated SAC-Par-4-GFP-SEKDEL						Non-glycosylated plant-derived SAC-Par-4-GFP had almost similar molecular mass (∼32 kDa) to that of deglycosylated SAC-Par-4-GFP-SEKDEL (∼32 kDa) and had lower molecular weight to that of the glycosylated SAC-Par-4-GFP-SEKDEL (∼34 kDa).
PMC4595782-1-7	38	530	gly	glycosylated	7729:7740	arg1	the glycosylated SAC-Par-4-GFP-SEKDEL				the glycosylated SAC-Par-4-GFP-SEKDEL						Non-glycosylated plant-derived SAC-Par-4-GFP had almost similar molecular mass (∼32 kDa) to that of deglycosylated SAC-Par-4-GFP-SEKDEL (∼32 kDa) and had lower molecular weight to that of the glycosylated SAC-Par-4-GFP-SEKDEL (∼34 kDa).
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.
PMC7124471-1-11	26	30	gly	glycopeptide	3398:3409	arg2	glycopeptide			glycopeptide						glycopeptide	This, however, needs a high-throughput software tool to recognize all glycopeptide variants and sum their peak areas, which is not achieved in this study.
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.
PMC5795011-1-4	4	409	gly	glycopeptide	848:859	arg2	large scale automated glycopeptide analysis			large scale automated glycopeptide analysis						glycopeptide	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.
PMC6243375-1-4	16	181	gly	glycoproteins	2996:3008	arg1	EXoO identified glycoproteins	EXoO identified glycoproteins				Fterm		glycoproteins			Gene ontology (GO) analysis of EXoO identified glycoproteins was carried out, and this showed that extracellular space, the cell surface, the ER lumen, and the Golgi membrane were the major cellular components for O‐linked glycoproteins (Fig 2E).
PMC6243375-1-4	16	193	gly	glycoproteins	3172:3184	arg1	O‐linked glycoproteins	O‐linked glycoproteins				Fterm		glycoproteins			Gene ontology (GO) analysis of EXoO identified glycoproteins was carried out, and this showed that extracellular space, the cell surface, the ER lumen, and the Golgi membrane were the major cellular components for O‐linked glycoproteins (Fig 2E).
PMC5098438-1-fig2	1	5	gly	aglycosylated	100:112	arg1	variants	variants				Fterm		variants			Intact mass spectrum reveals aglycosylated, mono-glycosylated and di-glycosylated variants (top).
PMC5098438-1-fig2	1	24	gly	di-glycosylated	137:151	arg1	variants	variants				Fterm		variants			Intact mass spectrum reveals aglycosylated, mono-glycosylated and di-glycosylated variants (top).
PMC5098438-1-fig2	1	30	gly	mono-glycosylated	115:131	arg1	variants	variants				Fterm		variants			Intact mass spectrum reveals aglycosylated, mono-glycosylated and di-glycosylated variants (top).
PMC6731604-1-2	16	35	gly	glycoprotein	2268:2279	arg1	glycoprotein	glycoprotein				Fterm		glycoprotein			The glycoprotein and glycosite databases associated with individual tissues or body fluids can be downloaded from the N-GlycositeAtlas website.
PMC6731604-1-2	16	74	gly	glycosite	2285:2293	arg2	glycosite			glycosite						glycosite	The glycoprotein and glycosite databases associated with individual tissues or body fluids can be downloaded from the N-GlycositeAtlas website.
PMC3942810-2-2	37	129	gly	glycoprotein	5919:5930	arg1	a functional N-linked glycoprotein	a functional N-linked glycoprotein				Fterm		glycoprotein			This is possible because N-glycosylation is a conserved process of post-translational modification in a diversity of proteins in eukaryotic organisms[18], and the established N-linked glycosylation system in the Campylobacter system could transfer a functional N-linked glycoprotein into Escherichia coli[84].
PMC5457524-1-7	5	503	gly	N-glycopeptides	832:846	arg2	intact N-glycopeptides			intact N-glycopeptides						N-glycopeptides	To demonstrate this, we applied Fbs1 GYR to enrich and identify intact N-glycopeptides from IgG-depleted human serum, which contains fewer glycomolecules compared to HSA-depleted human serum.
PMC4804330-1-3	22	141	gly	glycoproteins	4148:4160	arg1	mucin-type glycoproteins	mucin-type glycoproteins				Fterm		glycoproteins			In fact, Core 3 O-glycans are primarily expressed in gastrointestinal mucosa, and are the major core structures of mucin-type glycoproteins in colonic tissue36373839.
PMC3938046-1-5	9	120	gly	glycosylation	1130:1142	arg2	5531 glycosylation sites			5531 glycosylation sites						sites	The list of 5531 glycosylation sites from the PHOSIDA database [45] was compared directly with our N-glycoproteome (1450 sites), based on mouse IPI accession numbers (IPI_IDs).
PMC5457524-1-7	75	576	gly	N-glycopeptide	11833:11846	arg2	N-glycopeptide abundance			N-glycopeptide abundance						N-glycopeptide	Fbs1 enrichment improves N-glycopeptide abundance to 66% in a specific and non-destructive manner.
PMC6243375-1-1	0	104	gly	glycopeptides	37:49	arg2	site‐specific O‐linked glycopeptides			site‐specific O‐linked glycopeptides						glycopeptides	Extraction of site‐specific O‐linked glycopeptides.
PMC5457524-1-6	0	172	gly	N-glycosites	36:47	arg2	N-glycosites			N-glycosites						N-glycosites	Application of Fbs1 GYR to identify N-glycosites in serum.
PMC5795011-1-4	46	260	gly	glycopeptides	8218:8230	arg2	glycopeptides			glycopeptides						glycopeptides	However, recent reviews summarizing the glycoproteomics field in terms of available software tools suggested the need of a single software tool which could address the following concerns: (i) elucidation of both N- and O-linked glycopeptide spectra, (ii) matching glycopeptides to known protein sequences, (iii) scoring/ranking of potential glycopeptides, (iv) usage of product ion spectra, and (v) high-throughput and batch-wise analysis.
PMC5795011-1-4	46	983	gly	glycopeptide	8182:8193	arg2	O-linked glycopeptide spectra			O-linked glycopeptide spectra						glycopeptide	However, recent reviews summarizing the glycoproteomics field in terms of available software tools suggested the need of a single software tool which could address the following concerns: (i) elucidation of both N- and O-linked glycopeptide spectra, (ii) matching glycopeptides to known protein sequences, (iii) scoring/ranking of potential glycopeptides, (iv) usage of product ion spectra, and (v) high-throughput and batch-wise analysis.
PMC5795011-1-4	46	1023	gly	glycopeptides	8295:8307	arg2	potential glycopeptides			potential glycopeptides						glycopeptides	However, recent reviews summarizing the glycoproteomics field in terms of available software tools suggested the need of a single software tool which could address the following concerns: (i) elucidation of both N- and O-linked glycopeptide spectra, (ii) matching glycopeptides to known protein sequences, (iii) scoring/ranking of potential glycopeptides, (iv) usage of product ion spectra, and (v) high-throughput and batch-wise analysis.
PMC7124471-1-3	19	23	gly	glycoproteins	3046:3058	arg1	764 N-linked glycoproteins	764 N-linked glycoproteins				Fterm		glycoproteins			They were from 764 N-linked glycoproteins carrying 1699 N-linked glycosites.
PMC7124471-1-3	19	143	gly	glycosites	3083:3092	arg2	1699 N-linked glycosites			1699 N-linked glycosites						glycosites	They were from 764 N-linked glycoproteins carrying 1699 N-linked glycosites.
PMC6243375-1-4	18	305	gly	glycoproteins	3572:3584	arg1	the glycoproteins	the glycoproteins				Fterm		glycoproteins			Specifically, extracellular matrix organization, cell adhesion, and platelet degranulation were the biological processes most represented in the glycoproteins identified (Appendix Fig S3), whereas heparin binding, calcium ion binding, and integrin binding were the top molecular functions identified (Appendix Fig S3).
PMC6243375-1-3	4	72	gly	glycosylation	694:706	arg2	glycosylation sites			glycosylation sites						sites	Among the 113 PSMs from ETD‐MS2 analysis, 105 PSMs were assigned to have core 1 O‐linked glycans conjugated at glycosylation sites localized at the first amino acid position of glycopeptides with ptmRS site probabilities of over 99% (Dataset EV5).
PMC6243375-1-3	4	77	gly	glycopeptides	760:772	arg2	glycopeptides			glycopeptides						glycopeptides	Among the 113 PSMs from ETD‐MS2 analysis, 105 PSMs were assigned to have core 1 O‐linked glycans conjugated at glycosylation sites localized at the first amino acid position of glycopeptides with ptmRS site probabilities of over 99% (Dataset EV5).
PMC3938046-1-3	10	32	gly	glycoproteins	1947:1959	arg1	176 glycoproteins	176 glycoproteins				Fterm		glycoproteins			By WCC, the quadruplicate of 2 biological replicates identified approximately 300 N-glycosylation sites, corresponding to 176 glycoproteins.
PMC3938046-1-3	10	45	gly	300 N-glycosylation	1899:1917	arg2	approximately 300 N-glycosylation sites			approximately 300 N-glycosylation sites						sites	By WCC, the quadruplicate of 2 biological replicates identified approximately 300 N-glycosylation sites, corresponding to 176 glycoproteins.
PMC5795011-1-4	56	85	gly	glycopeptide	10057:10068	arg2	intact glycopeptide analysis			intact glycopeptide analysis						glycopeptide	The recently introduced electron transfer and higher-energy collision induced dissociation (EThcD) technique seems to work quite well for intact glycopeptide analysis.
PMC6731604-1-fig2	1	8	gly	glycosite	100:108	arg2	glycosite			glycosite						glycosite	a The identification frequencies of each glycosite in the database.
PMC5795011-1-fig1	1	25	gly	glycopeptide	133:144	arg2	The glycopeptide			The glycopeptide						glycopeptide	The glycopeptide was fragmented at an NCE value of 15.
PMC5795011-1-fig5	3	22	gly	glycosylation	496:508	arg2	the same glycosylation site			the same glycosylation site						site	Tri- (G,H) and tetra-sialylated (I) glycan structures on the same glycosylation site were also annotated by Mascot.
PMC5457524-1-7	26	307	gly	glycopeptides	4872:4884	arg2	N-linked glycopeptides			N-linked glycopeptides						glycopeptides	In the present study, we developed a novel strategy for selective isolation of N-linked glycopeptides en masse from complex peptide mixtures or biological samples.
PMC6243375-1-5	13	339	gly	glycosylation	2989:3001	arg2	seven O‐linked glycosylation sites			seven O‐linked glycosylation sites						sites	Finally, EGF‐containing fibulin‐like extracellular matrix protein 1 (EFEMP1), which binds to epidermal growth factor receptor (EGFR) to promote tumor growth, invasion, and metastasis (Yin et al, 2016), showed a threefold increase across seven O‐linked glycosylation sites in tumor tissue (Fig 3D and Appendix Table S1).
PMC6731604-1-1	13	209	gly	glycosite	2383:2391	arg2	glycosite			glycosite						glycosite	Nevertheless, the confidence of a given glycosite or glycosite-containing peptide could still be estimated according to its identification frequency.
PMC5643531-1-8	1	7	gly	glycosylation	86:98	arg2	several potential glycosylation sites			several potential glycosylation sites						sites	Frizzled receptors contain several potential glycosylation sites which are critical for the onset of Wnt signaling by facilitating cell surface localization of Fz8.
PMC4876326-1-4	6	92	gly	glycosylation	752:764	arg2	four glycosylation sites			four glycosylation sites						sites	Genotype BA.1 has four glycosylation sites, three of which are consistent with the majority of circulating RSV-B BA.1 genomes.
PMC6243375-1-fig3	0	66	gly	glycoproteins	170:182	arg1	differential glycoproteins	differential glycoproteins				Fterm		glycoproteins			Comparative analysis of the O‐linked glycoproteome of normal and tumor‐derived kidney tissue  Data processing steps in label‐free quantification to identify differential glycoproteins between tumor and normal kidney tissues.
PMC2538527-1-fig7	5	31	gly	glycopeptide	685:696	arg2	the monosialylated glycopeptide			the monosialylated glycopeptide						glycopeptide	B) CID-MS/MS spectrum of the triply protonated ion at m/z 1340.8 corresponding to the monosialylated glycopeptide of T84-112.
PMC2538527-1-fig7	5	35	gly	monosialylated	670:683	arg1	the monosialylated glycopeptide			the monosialylated glycopeptide						glycopeptide	B) CID-MS/MS spectrum of the triply protonated ion at m/z 1340.8 corresponding to the monosialylated glycopeptide of T84-112.
PMC3938046-1-3	18	35	gly	occupied	3059:3066	arg2	The third position			The third position						position	The third position of the canonical motif was occupied by Thr (4477; 47%) or Ser (2826; 30%), and Thr (3329; 46%) or Ser (2120; 29%) in biological replicates 1 and 2, respectively (Additional file 7: Table S8).
PMC6243375-1-4	15	265	gly	glycosylation	2729:2741	arg2	Thirteen O‐linked glycosylation sites			Thirteen O‐linked glycosylation sites						sites	Thirteen O‐linked glycosylation sites were not used in the motif analysis because they were located close to the termini of proteins concerned and consequently did not have enough surrounding amino acids to allow for full motif analysis.
PMC6243375-1-4	15	268	gly	used	2758:2761	arg2	Thirteen O‐linked glycosylation sites			Thirteen O‐linked glycosylation sites						sites	Thirteen O‐linked glycosylation sites were not used in the motif analysis because they were located close to the termini of proteins concerned and consequently did not have enough surrounding amino acids to allow for full motif analysis.
PMC6731604-1-1	7	77	gly	glycosites	1387:1396	arg2	8818 unique glycosites			8818 unique glycosites						glycosites	Using the same strategy as above, we eventually collected 22,618 glycosite-containing peptides that belong to 8818 unique glycosites from 70 papers published by other laboratories [7, 14, 15, 17, 18, 33, 41–104].
PMC7124471-1-9	10	77	gly	glycopeptide	1211:1222	arg2	the two serum N-linked intact glycopeptide data sets			the two serum N-linked intact glycopeptide data sets						glycopeptide	The two glycan mass databases were thus combined and used to analyze the two serum N-linked intact glycopeptide data sets.
PMC5795011-1-2	12	75	gly	glycopeptide	1927:1938	arg2	41,727 potential glycopeptide sequences			41,727 potential glycopeptide sequences						glycopeptide sequences	After adding 21 unique linear sialylated glycan sequences (Supplementary Table 1), the database contained 41,727 potential glycopeptide sequences and a total of 1,195,485 residues.
PMC5795011-1-2	12	102	gly	sialylated	1834:1843	arg1	linear sialylated glycan sequences			linear sialylated glycan sequences						sequences	After adding 21 unique linear sialylated glycan sequences (Supplementary Table 1), the database contained 41,727 potential glycopeptide sequences and a total of 1,195,485 residues.
PMC5457524-1-7	15	306	gly	N-glycosite	3213:3223	arg2	N-glycosite			N-glycosite						N-glycosite	Figure 7c shows that Fbs1 GYR enrichment results in an average of 5.4 glycan types per N-glycosite and 13.4 spectral counts per N-glycosite, a 3.3-fold improvement over the values before enrichment.
PMC5457524-1-7	15	401	gly	N-glycosite	3172:3182	arg2	N-glycosite			N-glycosite						N-glycosite	Figure 7c shows that Fbs1 GYR enrichment results in an average of 5.4 glycan types per N-glycosite and 13.4 spectral counts per N-glycosite, a 3.3-fold improvement over the values before enrichment.
PMC6731604-1-3	15	1	gly	glycoproteins	2200:2212	arg1	these urinary glycoproteins	these urinary glycoproteins				Fterm		glycoproteins			However, additional studies are required to confirm whether these urinary glycoproteins change with disease and reflect different pathological states within different parts of the human body.
PMC6731604-1-fig5	7	6	gly	glycoprotein	761:772	arg1	each glycoprotein	each glycoprotein				Fterm		glycoprotein			The detailed information for each glycoprotein can be accessed in the second display page by clicking the glycoprotein accession number.
PMC6731604-1-fig5	7	62	gly	glycoprotein	833:844	arg1	the glycoprotein accession number	the glycoprotein accession number				Fterm		glycoprotein			The detailed information for each glycoprotein can be accessed in the second display page by clicking the glycoprotein accession number.
PMC7124471-1-6	8	185	gly	glycoprotein	1221:1232	arg1	a glycoprotein	a glycoprotein				Fterm		glycoprotein			This reflected the difficulty in obtaining a glycoprotein standard with high purity.
PMC3942810-2-2	34	287	gly	glycoproteins	5039:5051	arg1	Most glycosylated RJ glycoproteins	Most glycosylated RJ glycoproteins				Fterm		glycoproteins			Most glycosylated RJ glycoproteins (~ 50%) carried a single N-glycosylation site, ~ 20% carried two or three sites, and only a few carried four or five sites.
PMC3942810-2-2	34	356	gly	N-glycosylation	5078:5092	arg2	a single N-glycosylation site			a single N-glycosylation site						site	Most glycosylated RJ glycoproteins (~ 50%) carried a single N-glycosylation site, ~ 20% carried two or three sites, and only a few carried four or five sites.
PMC3942810-2-2	34	446	gly	glycosylated	5023:5034	arg1	Most glycosylated RJ glycoproteins	Most glycosylated RJ glycoproteins				Fterm		glycoproteins			Most glycosylated RJ glycoproteins (~ 50%) carried a single N-glycosylation site, ~ 20% carried two or three sites, and only a few carried four or five sites.
PMC3938046-1-3	20	65	gly	glycoproteins	3409:3421	arg1	50 glycoproteins	50 glycoproteins				Fterm		glycoproteins			Notably, there were 50 glycoproteins that contained 5 or more N-glycosylation sites and 6 with at least 10 sites.
PMC3938046-1-3	20	115	gly	N-glycosylation	3448:3462	arg2	5 or more N-glycosylation sites			5 or more N-glycosylation sites						sites	Notably, there were 50 glycoproteins that contained 5 or more N-glycosylation sites and 6 with at least 10 sites.
PMC7124471-1-fig6	5	17	gly	glycopeptide	463:474	arg2	the glycopeptide precursor ion			the glycopeptide precursor ion						glycopeptide	D, Experimentally observed isotopic distribution of the glycopeptide precursor ion in Run_01.
PMC6243375-1-5	23	313	gly	glycoproteins	5053:5065	arg1	mucin‐type glycoproteins	mucin‐type glycoproteins				Fterm		glycoproteins			Many of those identified were mucin‐type glycoproteins whose mucin domain contains clusters of dense O‐linked glycans that protect the underlying peptide backbone from normal proteolytic digestion, and consequently, typical proteomic analysis would not contain detailed information on many of these domains.
PMC3942810-1-fig4	2	5	gly	N-glycosylated	268:281	arg1	four or more N-glycosylated sites			four or more N-glycosylated sites						sites	“> = 4” is the N-glycosylated protein carried four or more N-glycosylated sites.
PMC3942810-1-fig4	2	9	gly	N-glycosylated	224:237	arg1	the N-glycosylated protein	the N-glycosylated protein				Fterm		protein			“> = 4” is the N-glycosylated protein carried four or more N-glycosylated sites.
PMC5643531-1-8	8	2	gly	glycosylation	987:999	arg1	Fz8	Fz8				OGER		Fz8	Q9H461		We also tested whether OTG affected glycosylation of Fz8.
PMC6731604-1-2	9	71	gly	glycoprotein	1342:1353	arg1	the glycoprotein components	the glycoprotein components				Fterm		glycoprotein			As N-linked glycoproteins account for a large portion of the protein content in serum and other body fluids, identifying the glycoprotein components in these body fluids is essential for their clinical utility.
PMC6731604-1-2	9	108	gly	glycoproteins	1229:1241	arg1	N-linked glycoproteins	N-linked glycoproteins				Fterm		glycoproteins			As N-linked glycoproteins account for a large portion of the protein content in serum and other body fluids, identifying the glycoprotein components in these body fluids is essential for their clinical utility.
PMC4595782-1-4	4	28	gly	glycosylated	1126:1137	arg1	plant-derived apoplast-targeted SAC-Par-4-GFP				plant-derived apoplast-targeted SAC-Par-4-GFP						Taken together, these results indicate plant-derived apoplast-targeted SAC-Par-4-GFP is not glycosylated.
PMC3938046-1-5	13	117	gly	glycoproteins	1734:1746	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			First, of 3739 mouse proteins that were annotated as glycoproteins by UniProtKB, 520 overlapped and 240 were identified as new glycoproteins in our study.
PMC3938046-1-5	13	117	gly	glycoproteins	1734:1746	arg1	3739 mouse proteins	3739 mouse proteins				Fterm		proteins			First, of 3739 mouse proteins that were annotated as glycoproteins by UniProtKB, 520 overlapped and 240 were identified as new glycoproteins in our study.
PMC3938046-1-5	13	148	gly	glycoproteins	1808:1820	arg1	new glycoproteins	new glycoproteins				Fterm		glycoproteins			First, of 3739 mouse proteins that were annotated as glycoproteins by UniProtKB, 520 overlapped and 240 were identified as new glycoproteins in our study.
PMC5457524-1-7	13	135	gly	N-glycosites	2655:2666	arg2	224 unique N-glycosites			224 unique N-glycosites						N-glycosites	Fbs1 GYR enrichment also identified 478 unique N-glycosites, compared to 343 following lectin enrichment, and 224 unique N-glycosites in the pre-enrichment sample (Fig. 7b).
PMC5457524-1-7	13	456	gly	N-glycosites	2581:2592	arg2	478 unique N-glycosites			478 unique N-glycosites						N-glycosites	Fbs1 GYR enrichment also identified 478 unique N-glycosites, compared to 343 following lectin enrichment, and 224 unique N-glycosites in the pre-enrichment sample (Fig. 7b).
PMC6243375-1-4	11	134	gly	glycosylation	2141:2153	arg2	possible O‐linked glycosylation motifs			possible O‐linked glycosylation motifs						motifs	To identify possible O‐linked glycosylation motifs, the amino acids (±7 amino acids) at and surrounding 3,042 of the sites mapped in this study were analyzed.
PMC5457524-1-7	25	510	gly	glycopeptide	4743:4754	arg2	the glycopeptide profile			the glycopeptide profile						glycopeptide	Effective enrichment procedures are critically important to permit accurate, comprehensive analysis of the glycopeptide profile of patient samples.
PMC6731604-1-4	2	46	gly	glycosylation	473:485	arg2	glycosylation site location			glycosylation site location						site	By using the web interface, users can easily search the database either using the general search function for basic search or advanced search by restricting the search based on protein accession number, gene name, protein name, glycosylation site location, glycosite-containing peptide, N-glycosylation motif (N-X-S/T), the name of tissue/liquid/cell line, year of publication, and/or reference for specific searches (Fig. 5a).
PMC6731604-1-4	2	98	gly	N-glycosylation	532:546	arg2	N-glycosylation motif			N-glycosylation motif						motif	By using the web interface, users can easily search the database either using the general search function for basic search or advanced search by restricting the search based on protein accession number, gene name, protein name, glycosylation site location, glycosite-containing peptide, N-glycosylation motif (N-X-S/T), the name of tissue/liquid/cell line, year of publication, and/or reference for specific searches (Fig. 5a).
PMC6731604-1-1	10	102	gly	N-glycosylation	1840:1854	arg2	the typical N-X-S/T N-glycosylation motif			the typical N-X-S/T N-glycosylation motif						motif	In N-GlycositeAtlas, only peptides containing the typical N-X-S/T N-glycosylation motif were included in the database to ensure the high confidence of the data, even though recent studies indicated that N-glycans can also be attached to other atypical motifs [19, 40].
PMC5457524-1-5	0	44	gly	N-glycopeptide	0:13	arg2	N-glycopeptide			N-glycopeptide						N-glycopeptide	N-glycopeptide enrichment by wt Fbs1 and the GYR variant.
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.
PMC7124471-1-3	14	49	gly	deglycopeptides	2269:2283	arg2	serum N-linked deglycopeptides			serum N-linked deglycopeptides						deglycopeptides	It is necessary to consider semi-tryptic digestion in database search for the identification of serum N-linked deglycopeptides.
PMC3938046-1-3	4	13	gly	glycoproteins	826:838	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			In addition, approximately 44% of N-glycosites and 48% of glycoproteins overlapped between biological replicates by WCC.
PMC3938046-1-3	4	20	gly	N-glycosites	802:813	arg2	N-glycosites			N-glycosites						N-glycosites	In addition, approximately 44% of N-glycosites and 48% of glycoproteins overlapped between biological replicates by WCC.
PMC5795011-1-2	11	68	gly	glycoproteins	1710:1722	arg1	406 potential glycoproteins	406 potential glycoproteins				Fterm		glycoproteins			The custom database used in the manuscript, if not otherwise described, consists of a total of 406 potential glycoproteins which were known to be glycosylated in serum (PeptideAtlas N-Glyco build 2010).
PMC5795011-1-2	11	97	gly	glycosylated	1747:1758	arg1	406 potential glycoproteins	406 potential glycoproteins				Fterm		glycoproteins			The custom database used in the manuscript, if not otherwise described, consists of a total of 406 potential glycoproteins which were known to be glycosylated in serum (PeptideAtlas N-Glyco build 2010).
PMC5795011-1-4	121	115	gly	glycoprotein	20838:20849	arg1	a single glycoprotein database	a single glycoprotein database				Fterm		glycoprotein			The linear glycans and the protein sequences are then curated into a single glycoprotein database.
PMC5098438-1-5	36	164	gly	deglycosylated	6209:6222	arg1	a commonly observed variant	a commonly observed variant				Fterm		variant			We observed a small proportion of potentially C-terminal lysine-clipped HCs in the native mass spectrometry analysis of the deglycosylated Tt/C2B8 antibody, which is a commonly observed variant of biopharmaceutical mAbs.
PMC6243375-1-5	31	122	gly	glycosylation	6557:6569	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	Compared to other O‐linked glycoproteomic methods (Nilsson et al, 2009; Steentoft et al, 2011; Woo et al, 2015; Darula et al, 2016; Hoffmann et al, 2016; King et al, 2017; Qin et al, 2017), EXoO identified a large number of O‐linked glycosylation sites and glycoproteins with 2,580 novel O‐linked glycosylation sites that are not reported in three major database including O‐GalNAc human SimpleCell glycoproteome DB (Steentoft et al, 2011, 2013), PhosphoSitePlus (Hornbeck et al, 2015), and UniProt database (UniProt Consortium T, 2018).
PMC6243375-1-5	31	137	gly	glycosylation	6621:6633	arg2	2,580 novel O‐linked glycosylation sites			2,580 novel O‐linked glycosylation sites						sites	Compared to other O‐linked glycoproteomic methods (Nilsson et al, 2009; Steentoft et al, 2011; Woo et al, 2015; Darula et al, 2016; Hoffmann et al, 2016; King et al, 2017; Qin et al, 2017), EXoO identified a large number of O‐linked glycosylation sites and glycoproteins with 2,580 novel O‐linked glycosylation sites that are not reported in three major database including O‐GalNAc human SimpleCell glycoproteome DB (Steentoft et al, 2011, 2013), PhosphoSitePlus (Hornbeck et al, 2015), and UniProt database (UniProt Consortium T, 2018).
PMC6243375-1-5	31	361	gly	glycoproteins	6581:6593	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Compared to other O‐linked glycoproteomic methods (Nilsson et al, 2009; Steentoft et al, 2011; Woo et al, 2015; Darula et al, 2016; Hoffmann et al, 2016; King et al, 2017; Qin et al, 2017), EXoO identified a large number of O‐linked glycosylation sites and glycoproteins with 2,580 novel O‐linked glycosylation sites that are not reported in three major database including O‐GalNAc human SimpleCell glycoproteome DB (Steentoft et al, 2011, 2013), PhosphoSitePlus (Hornbeck et al, 2015), and UniProt database (UniProt Consortium T, 2018).
PMC6243375-1-fig1	1	18	gly	glycopeptide	221:232	arg2	glycopeptide			glycopeptide						glycopeptide	MS/MS spectrum of the site‐specific O‐linked glycopeptide at Ser‐296 in bovine fetuin.
PMC6731604-1-3	8	38	gly	glycoproteins	1118:1130	arg1	urine-derived glycoproteins	urine-derived glycoproteins				Fterm		glycoproteins			In this study, we also analyzed urine-derived glycoproteins based on the clinical utility of urine.
PMC5457524-1-1	22	6	gly	glycopeptides	3689:3701	arg2	glycopeptides 1–4			glycopeptides 1–4						glycopeptides	Then the glycan residues in SGP-TMR (sialic acid, galactose and GlcNAc) were sequentially removed from the non-reducing end to produce a diverse set of N-glycopeptides (Fig. 1d, glycopeptides 1–4).
PMC5457524-1-1	22	160	gly	N-glycopeptides	3663:3677	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	Then the glycan residues in SGP-TMR (sialic acid, galactose and GlcNAc) were sequentially removed from the non-reducing end to produce a diverse set of N-glycopeptides (Fig. 1d, glycopeptides 1–4).
PMC5457524-1-7	10	49	gly	N-glycopeptide	1755:1768	arg2	2,142 N-glycopeptide spectra			2,142 N-glycopeptide spectra						N-glycopeptide	With the same input of tryptic peptides (1 μg peptides per MS run), an average of 2,142 N-glycopeptide spectra were identified after Fbs1 GYR enrichment, which is 2.2-fold more than the number (965) of N-glycopeptide spectra identified using lectin enrichment, and 7-fold more than the number (304) identified without enrichment (Fig. 7a and Supplementary Data 3–5).
PMC5457524-1-7	10	364	gly	N-glycopeptide	1869:1882	arg2	N-glycopeptide spectra			N-glycopeptide spectra						N-glycopeptide	With the same input of tryptic peptides (1 μg peptides per MS run), an average of 2,142 N-glycopeptide spectra were identified after Fbs1 GYR enrichment, which is 2.2-fold more than the number (965) of N-glycopeptide spectra identified using lectin enrichment, and 7-fold more than the number (304) identified without enrichment (Fig. 7a and Supplementary Data 3–5).
PMC5643531-1-9	6	283	gly	glycosylation	870:882	arg2	putative Fz8 glycosylation site mutants			putative Fz8 glycosylation site mutants						site	Finally, we examined the effects of putative Fz8 glycosylation site mutants on Wnt signaling.
PMC5457524-1-4	11	22	gly	glycopeptide	1550:1561	arg2	all four glycopeptide species			all four glycopeptide species						glycopeptide	The affinity of the GYR variant for all four glycopeptide species is very similar (recovery percentage ranged from 47% to 60%, Fig. 4b, black columns), whereas wt Fbs1 displays an obvious bias in capture of the different glycopeptides (Fig. 1d or Fig. 4b, white columns).
PMC5457524-1-4	11	44	gly	glycopeptides	1726:1738	arg2	the different glycopeptides			the different glycopeptides						glycopeptides	The affinity of the GYR variant for all four glycopeptide species is very similar (recovery percentage ranged from 47% to 60%, Fig. 4b, black columns), whereas wt Fbs1 displays an obvious bias in capture of the different glycopeptides (Fig. 1d or Fig. 4b, white columns).
PMC6243375-1-4	34	121	gly	glycoproteins	6291:6303	arg1	O‐linked glycoproteins	O‐linked glycoproteins				Fterm		glycoproteins			The structural correlation of the sites to extracellular, lumen, and Ser/Thr/Pro‐rich regions coincided with the location of O‐linked glycoproteins to present on extracellular space, the cell surface, the ER, and the Golgi lumen for various functionality.
PMC5457524-1-1	12	248	gly	N-glycopeptides	1790:1804	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	The interaction of Fbs1 with N-glycopeptides and free N-glycans was evaluated by isothermal calorimetric measurement (ITC).
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.
PMC3942810-1-2	3	70	gly	N-glycopeptide	489:502	arg2	N-glycopeptide			N-glycopeptide						N-glycopeptide	An example spectrum of N-glycopeptide is shown in Figure 1 (for all other spectra see Additional file2: Figure S1).
PMC6731604-1-1	1	66	gly	glycoprotein	87:98	arg1	a mass spectrometry-identified N-linked glycoprotein	a mass spectrometry-identified N-linked glycoprotein				Fterm		glycoprotein			Here, we present a mass spectrometry-identified N-linked glycoprotein and glycosite database, named N-GlycositeAtlas, to facilitate human protein glycosylation studies.
PMC6731604-1-1	1	71	gly	glycosite	104:112	arg2	glycosite database			glycosite database						glycosite	Here, we present a mass spectrometry-identified N-linked glycoprotein and glycosite database, named N-GlycositeAtlas, to facilitate human protein glycosylation studies.
PMC5795011-1-4	3	225	gly	glycopeptides	559:571	arg2	The N-linked sialylated glycopeptides			The N-linked sialylated glycopeptides						glycopeptides	The N-linked sialylated glycopeptides were analyzed by LC-MS using HCD with stepped NCE and the acquired MS2 spectra were submitted to the Mascot search engine for automated identification and relative quantification using Mascot Distiller (Fig. 4).
PMC5795011-1-4	3	959	gly	sialylated	548:557	arg1	The N-linked sialylated glycopeptides			The N-linked sialylated glycopeptides						glycopeptides	The N-linked sialylated glycopeptides were analyzed by LC-MS using HCD with stepped NCE and the acquired MS2 spectra were submitted to the Mascot search engine for automated identification and relative quantification using Mascot Distiller (Fig. 4).
PMC6243375-1-3	1	61	gly	glycopeptides	227:239	arg2	serum O‐linked glycopeptides			serum O‐linked glycopeptides						glycopeptides	To define cleavage specificities of peptides and O‐linked glycans of OpeRATOR in the complex samples, sequential ETD/HCD‐MS2 analysis was conducted on serum O‐linked glycopeptides generated using the EXoO method.
PMC7124471-1-4	30	55	gly	glycosites	4978:4987	arg2	1036 N-linked glycosites			1036 N-linked glycosites						glycosites	In total, 526 N-linked glycoproteins, 1036 N-linked glycosites, 22,677 N-linked intact glycopeptides and 738 N-glycan masses were identified, which represent the most in-depth N-glycoproteome in serum identified by LC-MS/MS at N-linked intact glycopeptide level (Table IV, supplemental Table S11, S12, and S13).
PMC7124471-1-4	30	56	gly	glycopeptides	5013:5025	arg2	22,677 N-linked intact glycopeptides			22,677 N-linked intact glycopeptides						glycopeptides	In total, 526 N-linked glycoproteins, 1036 N-linked glycosites, 22,677 N-linked intact glycopeptides and 738 N-glycan masses were identified, which represent the most in-depth N-glycoproteome in serum identified by LC-MS/MS at N-linked intact glycopeptide level (Table IV, supplemental Table S11, S12, and S13).
PMC7124471-1-4	30	115	gly	glycopeptide	5169:5180	arg2	N-linked intact glycopeptide level			N-linked intact glycopeptide level						glycopeptide	In total, 526 N-linked glycoproteins, 1036 N-linked glycosites, 22,677 N-linked intact glycopeptides and 738 N-glycan masses were identified, which represent the most in-depth N-glycoproteome in serum identified by LC-MS/MS at N-linked intact glycopeptide level (Table IV, supplemental Table S11, S12, and S13).
PMC7124471-1-4	30	312	gly	glycoproteins	4949:4961	arg1	526 N-linked glycoproteins	526 N-linked glycoproteins				Fterm		glycoproteins			In total, 526 N-linked glycoproteins, 1036 N-linked glycosites, 22,677 N-linked intact glycopeptides and 738 N-glycan masses were identified, which represent the most in-depth N-glycoproteome in serum identified by LC-MS/MS at N-linked intact glycopeptide level (Table IV, supplemental Table S11, S12, and S13).
PMC5457524-1-6	3	147	gly	N-glycosite	432:442	arg2	N-glycosite identification/deglycoproteomics10			N-glycosite identification/deglycoproteomics10						N-glycosite	Tryptic peptides prepared from human serum albumin (HSA)-depleted human serum without enrichment (pre-enrichment) or with Fbs1 GYR enrichment were subjected to direct LC-MS analysis (Fig. 6a), N-glycan profiling analysis (Fig. 6b) and N-glycosite identification/deglycoproteomics10 using the PNGase F/18O water method2439 (Fig. 6c,d).
PMC5098438-1-5	73	148	gly	glycoform	13305:13313	arg1	the Man9GlcNAc2 glycoform				the Man9GlcNAc2 glycoform						The absence of resolvable density for the D1 mannose in the crystal structure of the Man9GlcNAc2 glycoform would lead us to predict that both the D1 mannose and glucose cap in the T. thermophila glycoforms are very highly solvated and flexible (Fig. 6).
PMC3938046-1-3	7	136	gly	glycopeptide	1294:1305	arg2	individual glycopeptide preparation methods			individual glycopeptide preparation methods						glycopeptide	The variability between types of mass spectrometers, differences in LC-gradient between technical replicates, and differences in individual glycopeptide preparation methods might have resulted in imperfect reproducibility between technical and biological replicates.
PMC7124471-1-10	10	23	gly	occupied	1106:1113	arg2	N523			N523 and N637						N523 and N637	A recent study showed that N523 and N637 were both occupied by N-glycans (31).
PMC7124471-1-5	8	73	gly	glycoproteins	1325:1337	arg1	human serum glycoproteins	human serum glycoproteins				Fterm		glycoproteins			Moreover, the N-glycan composites Hex5HexNAc4NANA2 and Hex5HexNAc4NANA1 are reported to be the most abundant ones carried by human serum glycoproteins.
PMC7124471-1-5	8	91	gly	composites	1211:1220	arg1	the N-glycan composites			the N-glycan composites						composites	Moreover, the N-glycan composites Hex5HexNAc4NANA2 and Hex5HexNAc4NANA1 are reported to be the most abundant ones carried by human serum glycoproteins.
PMC5457524-1-1	30	196	gly	glycopeptide	4825:4836	arg2	glycopeptide analysis			glycopeptide analysis						glycopeptide	However, this feature does not affect the application of Fbs1 for glycopeptide analysis since the enrichment step would be upstream of the optional 2-AB labelling step.
PMC6243375-1-4	1	235	gly	glycosylation	90:102	arg2	3,055 O‐linked glycosylation sites			3,055 O‐linked glycosylation sites						sites	Our large‐scale analysis mapped 3,055 O‐linked glycosylation sites from 1,060 glycoproteins in kidney tissues, T cells, and serum (Dataset EV6).
PMC6243375-1-4	1	256	gly	glycoproteins	121:133	arg1	1,060 glycoproteins	1,060 glycoproteins				Fterm		glycoproteins			Our large‐scale analysis mapped 3,055 O‐linked glycosylation sites from 1,060 glycoproteins in kidney tissues, T cells, and serum (Dataset EV6).
PMC4876326-1-4	7	80	gly	glycosylation	926:938	arg2	just one glycosylation site			just one glycosylation site						site	Genotype BA.2 shows a novel RSV-B glycosylation pattern with just one glycosylation site present toward the C-terminal end of the G protein after the G duplication.
PMC7124471-1-11	69	50	gly	glycoproteins	9773:9785	arg1	Many serum glycoproteins	Many serum glycoproteins				Fterm		glycoproteins			Many serum glycoproteins are affected in CDG.
PMC7143757-1-4	21	1	gly	glycoprotein	2700:2711	arg1	The glycoprotein	The glycoprotein				Fterm		glycoprotein			The glycoprotein generated in YeO9_52212 was able to induce antibodies against B. abortus as a result of the similarity in OPS between these two bacterial species [37].
PMC3942810-2-2	6	163	gly	N-glycopeptide	968:981	arg2	N-glycopeptide			N-glycopeptide						N-glycopeptide	“Filter aided sample preparation” (FASP) is an N-glycopeptide enrichment protocol that uses a combination of different lectins to efficiently capture glycopeptides[55].
PMC3594191-1-4	9	23	gly	glycosylation	1366:1378	arg2	the major O-linked glycosylation site			the major O-linked glycosylation site						site	Serine at position 167 (Ser167) was identified via peptide mapping as the major O-linked glycosylation site and was subjected to site-specific mutagenesis.
PMC3594191-1-4	9	23	gly	glycosylation	1366:1378	arg2	Serine			Serine						Serine at position 167	Serine at position 167 (Ser167) was identified via peptide mapping as the major O-linked glycosylation site and was subjected to site-specific mutagenesis.
PMC6243375-1-3	11	63	gly	glycosylation	1914:1926	arg2	efficient O‐linked glycosylation site localization			efficient O‐linked glycosylation site localization						site	Therefore, one of the advantages of EXoO method for O‐linked glycoproteomics analysis empowered efficient O‐linked glycosylation site localization by high cleavage specificity of OpeRATOR that was confirmed by ETD‐MS2.
PMC7124471-1-4	9	112	gly	N-glycosylation	1862:1876	arg2	their N-glycosylation motifs			their N-glycosylation motifs						motifs	To increase the sensitivity of 1% FDR filtering, all GPSMs were grouped according to their N-glycosylation motifs observed on their peptide backbones.
PMC7124471-1-6	16	151	gly	increased	3234:3242	arg1	glycosite			glycosite						glycosite	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	160	gly	glycosite	3088:3096	arg2	glycosite			glycosite						glycosite	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	50	gly	glycosites	2849:2858	arg1	N99			glycosites N99, N93,N77, N34, N199						glycosites N99, N93,N77, N34, N199	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	143	gly	glycosites	2727:2736	arg2	the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22)			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	143	gly	glycosites	2727:2736	arg2	N312			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22)			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	N312			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	N293			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	143	gly	glycosites	2727:2736	arg2	N312			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22)			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	N312			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	N293			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22)			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	N312			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	N293			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	N312			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	N293			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	165	gly	glycosites	2727:2736	arg1	N293			glycosites N293 and N312						glycosites N293 and N312	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	16	221	gly	glycosites	2976:2985	arg1	N36			glycosites N36, N90 and N82						glycosites N36, N90 and N82	After spiking them into serum, the number of identified N-glycan masses increased by 8 and 1 on the N-linked glycosites N293 and N312 of OVAL, the number of identified N-glycan masses increased by 2, 5, 5, 5, and 6 on the N-linked glycosites N99, N93,N77, N34, N199, of IOVO, the number of identified N-glycan masses increased by 5, 3, and 2 on the N-linked glycosites N36, N90 and N82 of Ogchi, the number of identified N-glycan masses didn't increased in QSOX1 though glycosite of N371 was identified after spiking it into serum (supplemental Table S21), and the number of identified N-glycan masses in HRP didn't increased (supplemental TableS 22).
PMC7124471-1-6	1	61	gly	glycoprotein	79:90	arg1	commercial glycoprotein standards	commercial glycoprotein standards				Fterm		glycoprotein			We then used commercial glycoprotein standards (HRP, ovalbumin, serotransferrin) as well as the serum spiked with these proteins (HRP and ovalbumin) to validate our identification strategy.
PMC5795011-1-4	49	866	gly	glycopeptide	8710:8721	arg2	the software-assisted intact glycopeptide analysis			the software-assisted intact glycopeptide analysis						glycopeptide	The success of the software-assisted intact glycopeptide analysis also depends on the enrichment strategy and the information available in the MS2 spectra.
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.
PMC7124471-1-11	12	430	gly	glycopeptide	1697:1708	arg2	this glycopeptide			this glycopeptide						glycopeptide	For example, the spectrum in Fig. 7A was collected at 65.05 min in UGP_01, whereas the retention time of this glycopeptide shifted in other three LC-MS/MS runs (supplemental Fig.
PMC3942810-1-2	10	37	gly	N-glycosylated	1739:1752	arg1	a single N-glycosylated site			a single N-glycosylated site						site	Finally, two identified N-glycoproteins with unknown functions each had one unique peptide harboring a single N-glycosylated site (Table 2).
PMC3942810-1-2	10	38	gly	N-glycoproteins	1653:1667	arg1	N-glycoproteins	N-glycoproteins				Fterm		N-glycoproteins			Finally, two identified N-glycoproteins with unknown functions each had one unique peptide harboring a single N-glycosylated site (Table 2).
PMC2538527-1-4	45	72	gly	O-glycosylation	7195:7209	arg1	proteins	proteins				Fterm		proteins			Although O-glycosylation is less critical for structure and function of proteins, it has been shown for example to increase the serum half-life of IGFBP6 by 2,3 folds over the non-glycosylated protein [47] and to protect against proteolysis [48].
PMC3942810-1-2	8	26	gly	N-glycosylated	1363:1376	arg1	a single N-glycosylated site			a single N-glycosylated site						site	Of the proteins related to health improvement, seven were found N-glycosylated on 18 unique peptides, and each peptide had a single N-glycosylated site (Table 2).
PMC3942810-1-2	8	229	gly	N-glycosylated	1295:1308	arg2	18 unique peptides			18 unique peptides						peptides	Of the proteins related to health improvement, seven were found N-glycosylated on 18 unique peptides, and each peptide had a single N-glycosylated site (Table 2).
PMC3938046-1-5	23	131	gly	N-glycosylation	3192:3206	arg1	Toll-like receptors	receptors		sites		Fterm		receptors		sites	As shown in Additional file 7: Table S8, many N-glycosylation sites of Toll-like receptors in our N-glycoproteome have not been reported.
PMC6243375-1-5	20	204	gly	glycosylation	4685:4697	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	As stated by the manufacturer, the use of sialidase in the procedure facilitated efficient cleavage by OpeRATOR that was used to improve mapping of O‐linked glycosylation sites.
PMC6731604-1-4	6	5	gly	glycoprotein	1130:1141	arg1	each glycoprotein	each glycoprotein				Fterm		glycoprotein			The additional information for each glycoprotein can be gained in the second display page by clicking the related glycoprotein accession number.
PMC6731604-1-4	6	92	gly	glycoprotein	1208:1219	arg1	the related glycoprotein accession number	the related glycoprotein accession number				Fterm		glycoprotein			The additional information for each glycoprotein can be gained in the second display page by clicking the related glycoprotein accession number.
PMC6731604-1-4	5	28	gly	glycosylation	1063:1075	arg2	identified glycosylation sites			identified glycosylation sites						sites	The first layer of the display page only exhibits general information of the glycoproteins, including glycoprotein accession numbers (UniProt), gene names, protein names and identified glycosylation sites (Fig. 5b).
PMC6731604-1-4	5	141	gly	glycoprotein	980:991	arg1	glycoprotein accession numbers	glycoprotein accession numbers				Fterm		glycoprotein			The first layer of the display page only exhibits general information of the glycoproteins, including glycoprotein accession numbers (UniProt), gene names, protein names and identified glycosylation sites (Fig. 5b).
PMC6731604-1-4	5	77	gly	glycoproteins	955:967	arg1	the glycoproteins	glycoproteins		sites		Fterm		glycoproteins		sites	The first layer of the display page only exhibits general information of the glycoproteins, including glycoprotein accession numbers (UniProt), gene names, protein names and identified glycosylation sites (Fig. 5b).
PMC6731604-1-1	14	101	gly	glycosites	2504:2513	arg2	glycosites			glycosites						glycosites	Generally, glycosites that were identified more frequently from different samples or studies (based on either the same glycosite-containing peptide or a glycosite-containing peptide with a different length resulting from missed cleavages or different enzyme digestion) had a higher confidence.
PMC2538527-1-fig6	0	26	gly	glycoprotein	37:48	arg1	the intact IFNα2b glycoprotein	the intact IFNα2b glycoprotein				Fterm		glycoprotein			ESI-MS analysis of the intact IFNα2b glycoprotein.
PMC5795011-1-4	116	1135	gly	glycopeptide	19990:20001	arg2	glycopeptide data analysis			glycopeptide data analysis						glycopeptide	Byonic is one of the most frequently used software package for glycopeptide data analysis and successfully reported in several different glycoproteomics studies.
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.
PMC6243375-1-3	18	107	gly	glycopeptide	3283:3294	arg2	a glycopeptide			a glycopeptide						glycopeptide	For example, two Hex(1)HexNAc(1) on a glycopeptide could yield a glycan composition of Hex(2)HexNAc(2) in the result.
PMC6243375-1-3	18	176	gly	Hex	3262:3264	arg1	a glycopeptide			a glycopeptide	a glycopeptide		Site			glycopeptide	For example, two Hex(1)HexNAc(1) on a glycopeptide could yield a glycan composition of Hex(2)HexNAc(2) in the result.
PMC7124471-1-9	15	106	gly	glycopeptides	1836:1848	arg2	serum N-linked intact glycopeptides			serum N-linked intact glycopeptides						glycopeptides	It is thus critical to include modified N-glycans when identifying serum N-linked intact glycopeptides.
PMC6731604-1-2	2	13	gly	glycoproteins	296:308	arg1	identified glycoproteins	identified glycoproteins				Fterm		glycoproteins			Using N-GlycositeAtlas, we investigated the distribution of identified glycoproteins across different human tissues and body fluids.
PMC3938046-1-9	5	4	gly	N-glycosylated	864:877	arg1	N-glycosylated proteins	N-glycosylated proteins				Fterm		proteins			Collectively, these data suggest that our crude membrane fractionation strategies are useful methods for studying membrane proteins and N-glycosylated proteins in microglia.
PMC3938046-1-8	7	11	gly	N-glycosylated	1118:1131	arg1	N-glycosylated peptides			N-glycosylated peptides						peptides	Sixty-two CDs were identified with greater than 3 unique peptides per CD in at least 1 biological set, whereas 16 proteins were identified by N-glycosylated peptides.
PMC3942810-1-2	15	0	gly	53 N-glycosylated	2724:2740	arg1	the 53 N-glycosylated sites			the 53 N-glycosylated sites						sites	As shown in Figure 3 and Table 2, the distribution of the 53 N-glycosylated sites was subdivided into known and novel proteins.
PMC6731604-1-1	11	148	gly	glycosylation	2190:2202	arg2	the former glycosylation sites			the former glycosylation sites						sites	In addition, all glycosite-containing peptides identified from studies conducted in our laboratory must contain ≥ 1 deamidation site at the former glycosylation sites (after PNGase F treatment).
PMC5795011-1-1	2	14	gly	glycoprotein	465:476	arg1	bovine alpha-1-acid glycoprotein	bovine alpha-1-acid glycoprotein				Fterm		glycoprotein			A typical example of an HCD (NCE = 15) MS2 spectrum of a glycopeptide derived from bovine alpha-1-acid glycoprotein is presented in Fig. 1A.
PMC5795011-1-1	2	70	gly	glycopeptide	419:430	arg2	a glycopeptide			a glycopeptide						glycopeptide	A typical example of an HCD (NCE = 15) MS2 spectrum of a glycopeptide derived from bovine alpha-1-acid glycoprotein is presented in Fig. 1A.
PMC7124471-1-11	53	419	gly	glycopeptides	7318:7330	arg2	N-linked intact glycopeptides			N-linked intact glycopeptides						glycopeptides	However, we have detected 16 abundant PTMs and included them into database search, the proportion of N-linked intact glycopeptides with unusual PTMs is expected to be small, and the incorrect glycan identification caused by this way is neglectable.
PMC7124471-1-10	7	61	gly	glycoproteins	868:880	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			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).
PMC7124471-1-11	62	529	gly	glycopeptide	8797:8808	arg2	N-linked intact glycopeptide identification			N-linked intact glycopeptide identification						glycopeptide	However, stringent FDR estimation is needed in order to decrease false positives caused by including this newly identified motif, which is not addressed by employing database search strategy in N-linked intact glycopeptide identification to date.
PMC3938046-1-fig5	0	7	gly	N-glycoproteins	101:115	arg1	N-glycoproteins	N-glycoproteins				Fterm		N-glycoproteins			Pathway enrichment analysis for identified membrane proteins, transmembrane-containing proteins, and N-glycoproteins.
PMC5795011-1-3	22	175	gly	O-glycopeptides	3347:3361	arg2	two other O-glycopeptides	protein		O-glycopeptides		Fterm		protein		O-glycopeptides	A similar fragmentation behavior was observed for two other O-glycopeptides of the same protein (Fig. 3C,D).
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.
PMC7081908-1-2	10	111	gly	glycosylation	1693:1705	arg2	the site			the site						site	Treatment with PNGase F removes all glycans that have not been affected by endo H treatment and leaves an aspartic acid residue at the site of N-linked glycosylation, which can be distinguished from the original asparagine by MS analysis of the peptides.
PMC5795011-1-4	107	718	gly	glycopeptides	18203:18215	arg2	glycopeptides			glycopeptides						glycopeptides	As mentioned above, several computational tools have been developed for automated identification of glycopeptides and the following reviews provide a detailed overview.
PMC7124471-1-11	25	47	gly	glycopeptide	3119:3130	arg2	glycopeptide			glycopeptide						glycopeptide	If the peak area of all glycopeptide variants carrying the same glycosite and glycan is summed and compared among samples, it will reflect the site-specific abundance change of this glycan composite among samples in an unbiased way.
PMC7124471-1-11	25	265	gly	glycosite	3159:3167	arg2	the same glycosite			the same glycosite						glycosite	If the peak area of all glycopeptide variants carrying the same glycosite and glycan is summed and compared among samples, it will reflect the site-specific abundance change of this glycan composite among samples in an unbiased way.
PMC3594191-1-4	11	47	gly	glycosylation	1797:1809	arg2	Ser167			Ser167				FGF21	Q9NSA1	Ser167	Protein characterization of the FGF21 variant produced in Pichia pastoris displayed low levels of O-linked glycosylation (<3%), confirming Ser167 as the primary glycosylation site in yeast.
PMC3594191-1-4	11	47	gly	glycosylation	1797:1809	arg2	the primary glycosylation site			the primary glycosylation site						site	Protein characterization of the FGF21 variant produced in Pichia pastoris displayed low levels of O-linked glycosylation (<3%), confirming Ser167 as the primary glycosylation site in yeast.
PMC3938046-1-3	2	43	gly	glycoproteins	425:437	arg1	671 unique glycoproteins	671 unique glycoproteins				Fterm		glycoproteins			We also identified 605 distinct N-glycosites for 330 unique glycoproteins by WCC and 1267 distinct N-glycosites for 671 unique glycoproteins by CMC; 422 N-glycosites from 241 glycoproteins were common in both approaches (Figure 3A and Additional file 4: Figure S4).
PMC3938046-1-3	2	53	gly	N-glycosites	397:408	arg2	1267 distinct N-glycosites			1267 distinct N-glycosites						N-glycosites	We also identified 605 distinct N-glycosites for 330 unique glycoproteins by WCC and 1267 distinct N-glycosites for 671 unique glycoproteins by CMC; 422 N-glycosites from 241 glycoproteins were common in both approaches (Figure 3A and Additional file 4: Figure S4).
PMC3938046-1-3	2	66	gly	glycoproteins	358:370	arg1	330 unique glycoproteins	330 unique glycoproteins				Fterm		glycoproteins			We also identified 605 distinct N-glycosites for 330 unique glycoproteins by WCC and 1267 distinct N-glycosites for 671 unique glycoproteins by CMC; 422 N-glycosites from 241 glycoproteins were common in both approaches (Figure 3A and Additional file 4: Figure S4).
PMC3938046-1-3	2	76	gly	glycoproteins	473:485	arg1	241 glycoproteins	241 glycoproteins				Fterm		glycoproteins			We also identified 605 distinct N-glycosites for 330 unique glycoproteins by WCC and 1267 distinct N-glycosites for 671 unique glycoproteins by CMC; 422 N-glycosites from 241 glycoproteins were common in both approaches (Figure 3A and Additional file 4: Figure S4).
PMC3938046-1-3	2	77	gly	N-glycosites	330:341	arg2	605 distinct N-glycosites			605 distinct N-glycosites						N-glycosites	We also identified 605 distinct N-glycosites for 330 unique glycoproteins by WCC and 1267 distinct N-glycosites for 671 unique glycoproteins by CMC; 422 N-glycosites from 241 glycoproteins were common in both approaches (Figure 3A and Additional file 4: Figure S4).
PMC3938046-1-3	2	119	gly	422 N-glycosites	447:462	arg2	422 N-glycosites			422 N-glycosites						422 N-glycosites	We also identified 605 distinct N-glycosites for 330 unique glycoproteins by WCC and 1267 distinct N-glycosites for 671 unique glycoproteins by CMC; 422 N-glycosites from 241 glycoproteins were common in both approaches (Figure 3A and Additional file 4: Figure S4).
PMC6243375-1-3	2	66	gly	glycopeptides	379:391	arg2	27 glycopeptides			27 glycopeptides						glycopeptides	With 1% FDR, HCD‐MS2 and ETD‐MS2 identified 85 and 40 unique intact glycopeptides, respectively, with 27 glycopeptides identified in both modes (Dataset EV5).
PMC6243375-1-3	2	80	gly	glycopeptides	342:354	arg2	85 and 40 unique intact glycopeptides			85 and 40 unique intact glycopeptides						glycopeptides	With 1% FDR, HCD‐MS2 and ETD‐MS2 identified 85 and 40 unique intact glycopeptides, respectively, with 27 glycopeptides identified in both modes (Dataset EV5).
PMC5643531-1-fig6	0	2	gly	glycosylation	14:26	arg1	Fz8 receptor	Fz8 receptor				OGER		Fz8 receptor	Q9H461		OTG regulates glycosylation of Fz8 receptor.
PMC6243375-1-5	27	177	gly	glycoproteins	5822:5834	arg1	mucin‐type glycoproteins	mucin‐type glycoproteins				Fterm		glycoproteins			The use of EXoO therefore is advantageous to reveal new biological insight regarding mucin‐type glycoproteins.
PMC5976746-1-fig3	6	54	gly	microheterogeneity	555:572	arg1	22 of 28 BG505 NFL N-glycosylation sites			22 of 28 BG505 NFL N-glycosylation sites						sites	Relative quantification of the microheterogeneity of 22 of 28 BG505 NFL N-glycosylation sites is shown.
PMC5976746-1-fig3	6	65	gly	N-glycosylation	596:610	arg2	22 of 28 BG505 NFL N-glycosylation sites			22 of 28 BG505 NFL N-glycosylation sites						sites	Relative quantification of the microheterogeneity of 22 of 28 BG505 NFL N-glycosylation sites is shown.
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.
PMC7124471-1-3	12	90	gly	deglycopeptides	1875:1889	arg2	some N-linked deglycopeptides			some N-linked deglycopeptides						deglycopeptides	Accordingly, some N-linked deglycopeptides with this modification were identified in both UDGP and FDGP data sets (supplemental Table S2).
PMC4595782-1-7	40	707	gly	O-glycosylation	8071:8085	arg2	two potential O-glycosylation sites			two potential O-glycosylation sites						sites	In silico analysis of SAC-Par-4-GFP-SEKDEL using NetOGlyc 4.0.0.13 software affirmed two potential O-glycosylation sites at positions 20 and 21 located in SAC-Par-4-GFP.
PMC3942810-1-fig2	5	63	gly	N-glycopeptides	1186:1200	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	D is the distribution of N-glycopeptides identified by orbitrap-based MS and triple TOF-based MS using hydrazide enrichment.
PMC7081908-1-fig7	2	2	gly	occupied	348:355	arg2	the site			the site						site	Green and purple bars indicate the proportions of oligomannose glycans and complex glycans, respectively, and gray bars indicate that the site was not occupied by a glycan.
PMC5795011-1-4	96	387	gly	glycopeptide	16329:16340	arg2	the frequently used glycopeptide identification Byonic software			the frequently used glycopeptide identification Byonic software						glycopeptide	A recent study scrutinizing the frequently used glycopeptide identification Byonic software, also indicated that the glycome size, proteome size and number of modifications can have a profound impact on the search outcome.
PMC3942810-1-fig2	0	45	gly	N-glycopeptides	16:30	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	Distribution of N-glycopeptides analyzed by different enriched methods and instruments of royal jelly proteins.
PMC6243375-1-5	17	228	gly	glycosylation	3898:3910	arg2	specific glycosylation sites			specific glycosylation sites						sites	The effectiveness of the method derives from the specific enrichment of O‐linked glycopeptides at specific glycosylation sites using the tandem action of a solid support and the O‐linked glycan‐specific OpeRATOR enzyme.
PMC6243375-1-5	17	387	gly	glycopeptides	3872:3884	arg2	O‐linked glycopeptides			O‐linked glycopeptides						glycopeptides	The effectiveness of the method derives from the specific enrichment of O‐linked glycopeptides at specific glycosylation sites using the tandem action of a solid support and the O‐linked glycan‐specific OpeRATOR enzyme.
PMC5795011-1-3	7	161	gly	glycopeptides	1184:1196	arg2	the glycopeptides			the glycopeptides						glycopeptides	However, the fragmentation of the glycopeptides can be fine-tuned by the NCE values used for HCD fragmentation.
PMC3942810-2-2	20	343	gly	glycosylated	2974:2985	arg1	glycosylated proteins	glycosylated proteins				Fterm		proteins			Interestingly, the majority of glycosylated proteins identifed here are enzymes associated with the metabolic pathways of carbohydrates and proteins.
PMC5643531-1-8	2	13	gly	glycosylated	262:273	arg1	glycosylated proteins	glycosylated proteins				Fterm		proteins			Glycosylation of proteins begins in the ER; from there, glycosylated proteins are further modified in the Golgi complex before leaving for their final destinations.
PMC5643531-1-8	2	48	gly	Glycosylation	206:218	arg1	proteins	proteins				Fterm		proteins			Glycosylation of proteins begins in the ER; from there, glycosylated proteins are further modified in the Golgi complex before leaving for their final destinations.
PMC3938046-1-7	4	34	gly	N-glycosylated	760:773	arg1	N-glycosylated proteins	N-glycosylated proteins				Fterm		proteins			Further, N-glycosylated proteins were enriched in many pathways that are linked to the plasma membrane, such as cell adhesion molecules (CAMs), ECM-receptor interactions, cytokine-cytokine receptor interactions, and Toll-like receptor signaling (Additional file 8: Table S10).
PMC5795011-1-4	27	380	gly	glycopeptide	4515:4526	arg2	mono-sialylated di-antennary glycopeptide variant			mono-sialylated di-antennary glycopeptide variant						glycopeptide	The next major glycopeptide variants included the di-sialylated tri-antennary and mono-sialylated di-antennary glycopeptide variant without and with fucose residues (Supplementary Table 5).
PMC5795011-1-4	27	566	gly	glycopeptide	4419:4430	arg2	The next major glycopeptide variants			The next major glycopeptide variants						glycopeptide	The next major glycopeptide variants included the di-sialylated tri-antennary and mono-sialylated di-antennary glycopeptide variant without and with fucose residues (Supplementary Table 5).
PMC5795011-1-4	27	620	gly	mono-sialylated	4486:4500	arg1	mono-sialylated di-antennary glycopeptide variant	mono-sialylated di-antennary glycopeptide variant				Fterm		variant			The next major glycopeptide variants included the di-sialylated tri-antennary and mono-sialylated di-antennary glycopeptide variant without and with fucose residues (Supplementary Table 5).
PMC7124471-1-4	24	187	gly	glycosite	4227:4235	arg2	glycosite			glycosite						glycosite	There were 80.4% and 76.2% overlaps of identifications at glycoprotein and glycosite levels respectively (Fig. 3).
PMC7124471-1-4	24	308	gly	glycoprotein	4210:4221	arg1	glycoprotein	glycoprotein				Fterm		glycoprotein			There were 80.4% and 76.2% overlaps of identifications at glycoprotein and glycosite levels respectively (Fig. 3).
PMC3942810-1-2	5	241	gly	glycosylation	747:759	arg2	the 53 identified N-linked glycosylation sites			the 53 identified N-linked glycosylation sites						sites	Among the 53 identified N-linked glycosylation sites, 42 were confidentially mapped in RJ proteins for the first time (Table 2).
PMC7124471-1-10	11	42	gly	glycosites	1153:1162	arg1	N630			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	42	gly	glycosites	1153:1162	arg1	N432			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N432			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	the three glycosites N432, N630 and N637			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N637			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N630			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	42	gly	glycosites	1153:1162	arg1	N432			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N432			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	the three glycosites N432, N630 and N637			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N637			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N630			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N432			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	the three glycosites N432, N630 and N637			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N637			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N630			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	the three glycosites N432, N630 and N637			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N637			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N630			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N637			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N630			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC7124471-1-10	11	63	gly	glycosites	1153:1162	arg2	N630			glycosites N432, N630 and N637						glycosites N432, N630 and N637	Notably, the three glycosites N432, N630 and N637 were reported to locating at the interface of serotransferrin and pathogenic Neisseria transferrin-binding protein A (TbpA) (supplemental Fig.
PMC5795011-1-fig2	2	10	gly	glycopeptides	371:383	arg2	the glycopeptides			the glycopeptides						glycopeptides	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.
PMC5795011-1-fig2	2	24	gly	glycoprotein	454:465	arg1	the custom glycoprotein database	the custom glycoprotein database				Fterm		glycoprotein			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.
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.
PMC5795011-1-4	14	18	gly	sialylated	2398:2407	arg1	the above sialylated glycopeptides			the above sialylated glycopeptides						glycopeptides	Some of the above sialylated glycopeptides were also identified with attached fucose residues.
PMC5795011-1-4	14	1146	gly	glycopeptides	2409:2421	arg2	the above sialylated glycopeptides			the above sialylated glycopeptides						glycopeptides	Some of the above sialylated glycopeptides were also identified with attached fucose residues.
PMC5795011-1-3	1	3	gly	glycopeptides	152:164	arg2	O-linked glycopeptides			O-linked glycopeptides						glycopeptides	The feasibility of the Mascot search engine for automated annotation of both N- and O-linked glycopeptides was validated using two standard bovine glycoproteins (alpha-1-acid glycoprotein and fetuin).
PMC5795011-1-3	1	158	gly	glycoproteins	206:218	arg1	alpha-1-acid glycoprotein	alpha-1-acid glycoprotein				Fterm		glycoprotein			The feasibility of the Mascot search engine for automated annotation of both N- and O-linked glycopeptides was validated using two standard bovine glycoproteins (alpha-1-acid glycoprotein and fetuin).
PMC5795011-1-3	1	158	gly	glycoproteins	206:218	arg1	fetuin	fetuin				Fterm		fetuin			The feasibility of the Mascot search engine for automated annotation of both N- and O-linked glycopeptides was validated using two standard bovine glycoproteins (alpha-1-acid glycoprotein and fetuin).
PMC5795011-1-3	1	158	gly	glycoproteins	206:218	arg1	two standard bovine glycoproteins	two standard bovine glycoproteins				Fterm		glycoproteins			The feasibility of the Mascot search engine for automated annotation of both N- and O-linked glycopeptides was validated using two standard bovine glycoproteins (alpha-1-acid glycoprotein and fetuin).
PMC5795011-1-3	1	212	gly	glycoprotein	234:245	arg1	alpha-1-acid glycoprotein	alpha-1-acid glycoprotein				Fterm		glycoprotein			The feasibility of the Mascot search engine for automated annotation of both N- and O-linked glycopeptides was validated using two standard bovine glycoproteins (alpha-1-acid glycoprotein and fetuin).
PMC5795011-1-3	1	212	gly	glycoprotein	234:245	arg1	two standard bovine glycoproteins	two standard bovine glycoproteins				Fterm		glycoproteins			The feasibility of the Mascot search engine for automated annotation of both N- and O-linked glycopeptides was validated using two standard bovine glycoproteins (alpha-1-acid glycoprotein and fetuin).
PMC3942810-2-2	32	457	gly	glycosylation	4719:4731	arg1	these RJ proteins	these RJ proteins				Fterm		proteins			Overall, the glycosylation of these RJ proteins suggests that they may be involved in the above biological roles benefitting both honeybee and humans.
PMC3938046-1-1	15	15	gly	N-glycopeptides	2325:2339	arg2	capturing N-glycopeptides			capturing N-glycopeptides						N-glycopeptides	To obtain a wide range of glycopeptides and improve the coverage of the N-glycoproteome, an additional analysis was performed by crude membrane fraction capturing (CMC), a method that is based on capturing N-glycopeptides from crude membrane fractions using a combination of CM methods 1 and 2 and N-glyco-FASP.
PMC3938046-1-1	15	149	gly	glycopeptides	2145:2157	arg2	glycopeptides			glycopeptides						glycopeptides	To obtain a wide range of glycopeptides and improve the coverage of the N-glycoproteome, an additional analysis was performed by crude membrane fraction capturing (CMC), a method that is based on capturing N-glycopeptides from crude membrane fractions using a combination of CM methods 1 and 2 and N-glyco-FASP.
PMC6731604-1-fig1	0	10	gly	glycosite	63:71	arg2	glycosite			glycosite						glycosite	Assembly of the mass spectrometry-based human glycoprotein and glycosite database (N-GlycositeAtlas).
PMC6731604-1-fig1	0	11	gly	glycoprotein	46:57	arg1	the mass spectrometry-based human glycoprotein	the mass spectrometry-based human glycoprotein				Fterm		glycoprotein			Assembly of the mass spectrometry-based human glycoprotein and glycosite database (N-GlycositeAtlas).
PMC5795011-1-fig3	1	7	gly	O-glycoprotein	218:231	arg1	the custom O-glycoprotein database	the custom O-glycoprotein database				Fterm		O-glycoprotein			Bovine fetuin was digested with trypsin, analyzed by LC-MS using the stepped NCE function (15, 25 and 35) and searched against the custom O-glycoprotein database.
PMC3938046-1-5	10	24	gly	1450 N-glycosites	1340:1356	arg2	our 1450 N-glycosites			our 1450 N-glycosites						1450 N-glycosites	As shown in Additional file 4: Figure S6B, of our 1450 N-glycosites, 834 had with the same position, whereas 616 N-glycosylation sites were unique.
PMC3938046-1-5	10	36	gly	616 N-glycosylation	1399:1417	arg2	616 N-glycosylation sites			616 N-glycosylation sites						sites	As shown in Additional file 4: Figure S6B, of our 1450 N-glycosites, 834 had with the same position, whereas 616 N-glycosylation sites were unique.
PMC5795011-1-2	1	6	gly	glycopeptide	326:337	arg2	the glycopeptide sequence			the glycopeptide sequence						glycopeptide sequence	After manual annotation of various glycopeptide MS2 spectra, linear glycan sequences were defined based on the criteria that they should i) cover the maximum possible intense peaks in the MS2 spectrum and ii) provide close to complete information about the glycopeptide sequence.
PMC5795011-1-2	1	76	gly	glycopeptide	104:115	arg2	various glycopeptide MS2 spectra			various glycopeptide MS2 spectra						glycopeptide	After manual annotation of various glycopeptide MS2 spectra, linear glycan sequences were defined based on the criteria that they should i) cover the maximum possible intense peaks in the MS2 spectrum and ii) provide close to complete information about the glycopeptide sequence.
PMC7124471-1-6	19	69	gly	deglycopeptide	3636:3649	arg2	human serum N-linked deglycopeptide library			human serum N-linked deglycopeptide library						deglycopeptide	When searching the N-linked intact glycopeptide data sets from ovalbumin standard against human serum N-linked deglycopeptide library and the 739 N-glycan masses library, only 12 GPSMs were returned.
PMC7124471-1-6	19	169	gly	glycopeptide	3560:3571	arg2	the N-linked intact glycopeptide data sets			the N-linked intact glycopeptide data sets						glycopeptide	When searching the N-linked intact glycopeptide data sets from ovalbumin standard against human serum N-linked deglycopeptide library and the 739 N-glycan masses library, only 12 GPSMs were returned.
PMC5795011-1-3	27	56	gly	glycopeptides	4126:4138	arg2	The Mascot annotated glycopeptides			The Mascot annotated glycopeptides						glycopeptides	The Mascot annotated glycopeptides were compared to the previously published data, where software assistance and manual data analysis was performed and the majority (11/13 glycopeptides) of the previously confirmed O-glycopeptides were identified automatically (Supplementary Table 2).
PMC5795011-1-3	27	114	gly	O-glycopeptides	4320:4334	arg2	the previously confirmed O-glycopeptides			the previously confirmed O-glycopeptides						O-glycopeptides	The Mascot annotated glycopeptides were compared to the previously published data, where software assistance and manual data analysis was performed and the majority (11/13 glycopeptides) of the previously confirmed O-glycopeptides were identified automatically (Supplementary Table 2).
PMC5795011-1-3	27	191	gly	glycopeptides	4277:4289	arg2	11/13 glycopeptides			11/13 glycopeptides						glycopeptides	The Mascot annotated glycopeptides were compared to the previously published data, where software assistance and manual data analysis was performed and the majority (11/13 glycopeptides) of the previously confirmed O-glycopeptides were identified automatically (Supplementary Table 2).
PMC7124471-1-3	18	121	gly	deglycopeptides	2919:2933	arg2	3328 N-linked deglycopeptides			3328 N-linked deglycopeptides						deglycopeptides	A total of 3328 N-linked deglycopeptides have been identified in human sera after combining the results from UDGP and FDGP.
PMC3942810-2-2	5	475	gly	glycoproteins	798:810	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Hydrazide chemistry can efficiently capture glycoproteins once oxidized by sodium periodate, and is thus extremely useful for the identification of glycopeptides[54].
PMC6731604-1-fig3	1	2	gly	glycoproteins	269:281	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			The blue columns represent the glycosites (a) and glycoproteins (b) identified from human tissues or body fluids; the orange columns represent the glycosites (a) and glycoproteins (b) identified from the related cell lines.
PMC6731604-1-fig3	1	5	gly	glycosites	134:143	arg2	the glycosites			the glycosites						glycosites	The blue columns represent the glycosites (a) and glycoproteins (b) identified from human tissues or body fluids; the orange columns represent the glycosites (a) and glycoproteins (b) identified from the related cell lines.
PMC6731604-1-fig3	1	6	gly	glycoproteins	153:165	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			The blue columns represent the glycosites (a) and glycoproteins (b) identified from human tissues or body fluids; the orange columns represent the glycosites (a) and glycoproteins (b) identified from the related cell lines.
PMC6731604-1-fig3	1	12	gly	glycosites	250:259	arg2	the glycosites			the glycosites						glycosites	The blue columns represent the glycosites (a) and glycoproteins (b) identified from human tissues or body fluids; the orange columns represent the glycosites (a) and glycoproteins (b) identified from the related cell lines.
PMC6123398-1-fig3	7	50	gly	glycosylation	848:860	arg2	Asn 297			Asn 297				CD20	P11836	Asn 297	(f) The “omit” electron density map of the glycosylation site at Asn 297 in the recombinant mAb Fc fragment, contoured at 1.0 σ.
PMC6123398-1-fig3	7	50	gly	glycosylation	848:860	arg2	the glycosylation site			the glycosylation site						site	(f) The “omit” electron density map of the glycosylation site at Asn 297 in the recombinant mAb Fc fragment, contoured at 1.0 σ.
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.
PMC7124471-1-11	11	238	gly	glycopeptide	1483:1494	arg2	a given glycopeptide constant			a given glycopeptide constant						glycopeptide	However, in DDA employed here, it is not uncommon that a given GPSM fails to be identified in some runs, and it was difficult to keep the retention time of a given glycopeptide constant among multiple LC runs without retention time correction using standard peptides.
PMC6731604-1-1	22	177	gly	glycoprotein	4831:4842	arg1	glycoprotein	glycoprotein				Fterm		glycoprotein			Additional information about the detailed mass spectrometers and search parameters for the identification of a given glycosite or glycoprotein can be obtained from the original publications listed in the database.
PMC6731604-1-1	22	205	gly	glycosite	4818:4826	arg2	a given glycosite			a given glycosite						glycosite	Additional information about the detailed mass spectrometers and search parameters for the identification of a given glycosite or glycoprotein can be obtained from the original publications listed in the database.
PMC5795011-1-3	17	117	gly	glycopeptides	2509:2521	arg2	O-linked glycopeptides			O-linked glycopeptides						glycopeptides	The feasibility of the Mascot search engine for the analysis of O-linked glycopeptides was validated by analyzing the mass spectrometry data of bovine fetuin against a custom O-glycoprotein sequence of fetuin.
PMC5795011-1-3	17	154	gly	O-glycoprotein	2611:2624	arg1	a custom O-glycoprotein sequence	a custom O-glycoprotein sequence				Fterm		O-glycoprotein			The feasibility of the Mascot search engine for the analysis of O-linked glycopeptides was validated by analyzing the mass spectrometry data of bovine fetuin against a custom O-glycoprotein sequence of fetuin.
PMC3938046-1-4	5	104	gly	glycoproteins	727:739	arg1	all identified glycoproteins	all identified glycoproteins				Fterm		glycoproteins			According to process of GO analysis in crude membrane proteome, we established a general GO classification for all identified glycoproteins (Figure 4B).
PMC5795011-1-4	24	492	gly	glycoproteins	4001:4013	arg1	257 glycoproteins	257 glycoproteins				Fterm		glycoproteins			Using this approach, a total of 257 glycoproteins were identified from the 24 serum samples (Supplementary Table 3).
PMC6243375-1-5	14	338	gly	glycoproteins	3221:3233	arg1	O‐linked glycoproteins	O‐linked glycoproteins				Fterm		glycoproteins			By contrast, both IGHA1 and MUC1, known O‐linked glycoproteins, showed no detectable change between normal and tumor tissue indicating that the changes in O‐linked glycoproteins observed in tumor tissue are highly selective.
PMC6243375-1-5	14	341	gly	glycoproteins	3106:3118	arg1	O‐linked glycoproteins	O‐linked glycoproteins				Fterm		glycoproteins			By contrast, both IGHA1 and MUC1, known O‐linked glycoproteins, showed no detectable change between normal and tumor tissue indicating that the changes in O‐linked glycoproteins observed in tumor tissue are highly selective.
PMC3938046-1-4	8	94	gly	760 N-glycoproteins	1327:1345	arg1	760 N-glycoproteins	760 N-glycoproteins				Fterm		760 N-glycoproteins			Considering the nonexclusive localization in GO, 42% of the N-glycoproteome lay on the outside of or beyond the plasma membrane (321 of 760 N-glycoproteins with a GO annotation).
PMC7124471-1-4	33	104	gly	deglycopeptide	5754:5767	arg2	deglycopeptide samples			deglycopeptide samples						deglycopeptide	They are the top three proteins with the most glycosites identified in deglycopeptide samples including UDGP and FDGP.
PMC7124471-1-4	33	197	gly	glycosites	5729:5738	arg2	the most glycosites			the most glycosites						glycosites	They are the top three proteins with the most glycosites identified in deglycopeptide samples including UDGP and FDGP.
PMC6731604-1-2	13	0	gly	glycoproteins	1976:1988	arg1	identified serum glycoproteins [14]	identified serum glycoproteins [14]				Fterm		glycoproteins			Removal of these high abundant proteins before mass spectrometry-based proteomic or sub-proteomic analyses would increase the number of identified serum glycoproteins [14].
PMC5795011-1-fig4	2	12	gly	glycopeptides	230:242	arg2	the N-linked sialylated glycopeptides			the N-linked sialylated glycopeptides						glycopeptides	Next, the N-linked sialylated glycopeptides were enriched with TiO2 beads, followed by LC-MS analysis using a Q Exactive mass spectrometer applying stepped NCE for HCD fragmentation.
PMC5795011-1-fig4	2	22	gly	sialylated	219:228	arg1	the N-linked sialylated glycopeptides			the N-linked sialylated glycopeptides						glycopeptides	Next, the N-linked sialylated glycopeptides were enriched with TiO2 beads, followed by LC-MS analysis using a Q Exactive mass spectrometer applying stepped NCE for HCD fragmentation.
PMC5795011-1-4	74	347	gly	glycopeptide	12595:12606	arg2	intact glycopeptide identifications			intact glycopeptide identifications						glycopeptide	The FDR estimation for intact glycopeptide identifications is debatable and especially in case of glycopeptide identifications in relatively small numbers, the accurate estimation of FDR values is not possible.
PMC5795011-1-4	74	873	gly	glycopeptide	12663:12674	arg2	glycopeptide			glycopeptide						glycopeptide	The FDR estimation for intact glycopeptide identifications is debatable and especially in case of glycopeptide identifications in relatively small numbers, the accurate estimation of FDR values is not possible.
PMC5795011-1-4	131	839	gly	glycopeptide	22618:22629	arg2	O-linked glycopeptide spectra			O-linked glycopeptide spectra						glycopeptide	Though, at this point it does not solve all the problems associated with glycoproteomics, this single tool collectively allows the (i) elucidation of both N- and O-linked glycopeptide spectra, (ii) matching glycopeptides to known protein sequences, (iii) scoring and ranking of potential glycopeptides, (iv) usage of product ion spectra, and (v) high-throughput and batch-wise analysis.
PMC5795011-1-4	131	879	gly	glycopeptides	22654:22666	arg2	glycopeptides			glycopeptides						glycopeptides	Though, at this point it does not solve all the problems associated with glycoproteomics, this single tool collectively allows the (i) elucidation of both N- and O-linked glycopeptide spectra, (ii) matching glycopeptides to known protein sequences, (iii) scoring and ranking of potential glycopeptides, (iv) usage of product ion spectra, and (v) high-throughput and batch-wise analysis.
PMC5795011-1-4	131	1025	gly	glycopeptides	22735:22747	arg2	potential glycopeptides			potential glycopeptides						glycopeptides	Though, at this point it does not solve all the problems associated with glycoproteomics, this single tool collectively allows the (i) elucidation of both N- and O-linked glycopeptide spectra, (ii) matching glycopeptides to known protein sequences, (iii) scoring and ranking of potential glycopeptides, (iv) usage of product ion spectra, and (v) high-throughput and batch-wise analysis.
PMC5643531-1-9	46	129	gly	glycosylation	6006:6018	arg2	potential N-linked glycosylation sites			potential N-linked glycosylation sites						sites	We found that OTG binds to the N-terminal region of Fz8 which contains potential N-linked glycosylation sites.
PMC5795011-1-3	21	25	gly	O-glycopeptide	3263:3276	arg2	O-glycopeptide			O-glycopeptide						O-glycopeptide	Similar to N-linked glycopeptides, the b1, b2 and b3 ions at m/z values of 292.102 (Neu5Ac), 454.155 (Neu5Ac-Hex) and 657.233 (Neu5Ac-Hex-HexNAc) covered the low mass glycan fragment ions and provided an additional layer of confirmation about the O-glycopeptide spectra.
PMC5795011-1-3	21	83	gly	glycopeptides	3036:3048	arg2	N-linked glycopeptides			N-linked glycopeptides						glycopeptides	Similar to N-linked glycopeptides, the b1, b2 and b3 ions at m/z values of 292.102 (Neu5Ac), 454.155 (Neu5Ac-Hex) and 657.233 (Neu5Ac-Hex-HexNAc) covered the low mass glycan fragment ions and provided an additional layer of confirmation about the O-glycopeptide spectra.
PMC3938046-1-8	8	37	gly	glycosylated	1190:1201	arg1	89 proteins	89 proteins				Fterm		proteins			Notably, 78% (89 proteins) of CD antigens were glycosylated, and 54% (61 proteins) was multiply glycosylated, demonstrating the robustness of cell surface phenotyping with our proteomics approaches—ie, crude membrane fractionation and enrichment of N-glycosylation sites.
PMC3938046-1-8	8	90	gly	glycosylated	1239:1250	arg1	61 proteins	61 proteins				Fterm		proteins			Notably, 78% (89 proteins) of CD antigens were glycosylated, and 54% (61 proteins) was multiply glycosylated, demonstrating the robustness of cell surface phenotyping with our proteomics approaches—ie, crude membrane fractionation and enrichment of N-glycosylation sites.
PMC3938046-1-8	8	125	gly	N-glycosylation	1392:1406	arg2	N-glycosylation sites			N-glycosylation sites						sites	Notably, 78% (89 proteins) of CD antigens were glycosylated, and 54% (61 proteins) was multiply glycosylated, demonstrating the robustness of cell surface phenotyping with our proteomics approaches—ie, crude membrane fractionation and enrichment of N-glycosylation sites.
PMC3942810-2-2	35	253	gly	N-glycosylated	5250:5263	arg1	N-glycosylated RJ peptides			N-glycosylated RJ peptides						peptides	In addition, the identified conservative motif of amino acid sequence of N-glycosylated RJ peptides may have structural and functional importance for RJ proteins in future studies[82,83].
PMC5795011-1-4	32	399	gly	glycopeptides	5221:5233	arg2	the glycopeptides			the glycopeptides						glycopeptides	To find out any quantitative differences at the glycosylation level, the glycopeptides were segmented based on the glycan structures irrespective of the protein origin and the corresponding ratios were plotted as violin plots.
PMC5457524-1-7	2	96	gly	N-glycosite	183:193	arg2	Each N-glycosite			Each N-glycosite						N-glycosite	Each N-glycosite may contain a different population of N-glycan modifications (micro-heterogeneity), which can be predictive markers for disease states or specific biological function1013.
PMC5457524-1-7	1	301	gly	N-glycosite	113:123	arg2	N-glycosite			N-glycosite						N-glycosite	We have shown above that Fbs1 GYR significantly improves N-glycosite identification (deglycoproteomics) from human serum.
PMC7124471-1-11	30	120	gly	glycoprotein	3951:3962	arg1	glycoprotein standards	glycoprotein standards				Fterm		glycoprotein			We used a set of glycoprotein standards to validate the setting of semi-tryptic digestion, and the results showed semi-tryptic digestion dramatically increased the number of confident GPSMs of these protein standards' glycopeptides.
PMC7124471-1-11	30	335	gly	glycopeptides	4152:4164	arg2	these protein standards' glycopeptides			these protein standards' glycopeptides						glycopeptides	We used a set of glycoprotein standards to validate the setting of semi-tryptic digestion, and the results showed semi-tryptic digestion dramatically increased the number of confident GPSMs of these protein standards' glycopeptides.
PMC7124471-1-11	33	318	gly	glycosites	4397:4406	arg2	glycosites			glycosites						glycosites	By comparing the GPSMs, glycosites and N-glycan masses obtained from these standards and the two human serum data sets under four different sets of search parameters, it showed more than 80% GPSMs were shared by setting 16 variable PTMs and by setting 3 variable PTMs (supplemental Fig.
PMC7124471-1-3	1	136	gly	deglycopeptide	132:145	arg2	N-linked deglycopeptide identification			N-linked deglycopeptide identification						deglycopeptide	The two data sets FDGP and UDGP underwent protein sequence database search for N-linked deglycopeptide identification.
PMC6731604-1-3	13	2	gly	glycoproteins	1832:1844	arg1	1845 glycoproteins	1845 glycoproteins				Fterm		glycoproteins			Among 1845 glycoproteins identified in serum, 827 (44.8%) were also identified in urine.
PMC4804330-1-2	31	178	gly	glycosylation	5331:5343	arg2	three potential N-linked glycosylation sites			three potential N-linked glycosylation sites						sites	Nonetheless, given that B4GALT2 contains three potential N-linked glycosylation sites (NXS/T) at amino acids 66, 71, and 35724, we treated V957 cells ectopically expressing wild-type or A146V mutant proteins with either a pan N- and O-glycosidase or a specific N-linked glycosidase (PNGase F) to assess for N-linked glycosylation of wild-type versus mutant protein.
PMC4804330-1-2	31	336	gly	glycosylation	5581:5593	arg1	wild-type versus mutant protein	wild-type versus mutant protein				Fterm		protein			Nonetheless, given that B4GALT2 contains three potential N-linked glycosylation sites (NXS/T) at amino acids 66, 71, and 35724, we treated V957 cells ectopically expressing wild-type or A146V mutant proteins with either a pan N- and O-glycosidase or a specific N-linked glycosidase (PNGase F) to assess for N-linked glycosylation of wild-type versus mutant protein.
PMC5795011-1-4	40	32	gly	glycoproteins	7012:7024	arg1	68 glycoproteins	68 glycoproteins				Fterm		glycoproteins			Irrespective of the databases, 68 glycoproteins were consistently identified in all four different databases (Supplementary Fig. 6).
PMC6731604-1-fig5	3	36	gly	N-glycosylation	337:351	arg2	N-glycosylation motif			N-glycosylation motif						motif	The database can be searched online according to the protein accession number, gene name, protein name, glycosylation site location, glycosite-containing peptide, N-glycosylation motif (N-X-S/T), name of tissue/liquid/cell line, year of publication, and/or reference.
PMC6731604-1-fig5	3	61	gly	glycosylation	278:290	arg2	glycosylation site location			glycosylation site location						site	The database can be searched online according to the protein accession number, gene name, protein name, glycosylation site location, glycosite-containing peptide, N-glycosylation motif (N-X-S/T), name of tissue/liquid/cell line, year of publication, and/or reference.
PMC3938046-1-fig6	1	25	gly	N-glycopeptide	137:150	arg2	N-glycopeptide capture			N-glycopeptide capture						N-glycopeptide	Overview of 114 CD antigens identified in BV-2 cells by crude membrane fractionation and N-glycopeptide capture.
PMC5795011-1-4	9	419	gly	glycopeptides	1628:1640	arg2	tetra-antennary (Fig. 5C) glycopeptides			tetra-antennary (Fig. 5C) glycopeptides						glycopeptides	Almost all the intense peaks in the MS2 spectra of mono-sialylated bi- (Fig. 5A), tri- (Fig. 5B) and tetra-antennary (Fig. 5C) glycopeptides were annotated by Mascot, confirming the presence of these glycan structures.
PMC5795011-1-4	127	340	gly	glycopeptide	21725:21736	arg2	glycopeptide analysis			glycopeptide analysis						glycopeptide	The necessary changes to establish Mascot for glycopeptide analysis are simply done by defining the letters (O, J, U) in the unimod.xml file (Supplementary Fig. 1) and updating the Mascot server with the glycoprotein database.
PMC5795011-1-4	127	874	gly	glycoprotein	21883:21894	arg1	the glycoprotein database	the glycoprotein database				Fterm		glycoprotein			The necessary changes to establish Mascot for glycopeptide analysis are simply done by defining the letters (O, J, U) in the unimod.xml file (Supplementary Fig. 1) and updating the Mascot server with the glycoprotein database.
PMC5795011-1-4	38	702	gly	glycopeptide	6428:6439	arg2	automated glycopeptide identification			automated glycopeptide identification						glycopeptide	Summarized, the presented data shows the ease and feasibility of the proposed workflow for automated glycopeptide identification and quantification.
PMC5795011-1-fig3	2	3	gly	glycopeptide	312:323	arg2	mono- (A,C) and di-sialylated (B,D) core-1 O-linked glycopeptide spectra			mono- (A,C) and di-sialylated (B,D) core-1 O-linked glycopeptide spectra						glycopeptide	Mascot annotated mono- (A,C) and di-sialylated (B,D) core-1 O-linked glycopeptide spectra from two different peptide sequences.
PMC3938046-1-fig3	3	8	gly	N-glycoproteins	354:368	arg1	N-glycoproteins	N-glycoproteins				Fterm		N-glycoproteins			Orange bars and green bars represent the number of N-glycosylation sites and N-glycoproteins, respectively.
PMC3938046-1-fig3	3	15	gly	N-glycosylation	328:342	arg2	N-glycosylation sites			N-glycosylation sites						sites	Orange bars and green bars represent the number of N-glycosylation sites and N-glycoproteins, respectively.
PMC5457524-1-7	44	550	gly	labelled	7133:7140	arg1	Asn			Asn						Asn	PNGase F specifically liberates N-glycans for accurate identification and if the hydrolysis reaction is conducted in the presence of 18O water the site of protein attachment will be distinctly labelled (Asn to Asp-18O).
PMC7124471-1-6	3	175	gly	glycosites	475:484	arg2	five glycosites			five glycosites						glycosites	From the commercial serotransferrin protein standard, we identified five glycosites and varied number of glycan masses on each site (supplemental Table S16).
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	arg2	Asn 93	alpha-1-acid glycoprotein 1		Asn 93		OGER		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.
PMC5795011-1-fig5	0	26	gly	glycosylation	118:130	arg2	a single glycosylation site	alpha-1-acid glycoprotein 1		site		OGER		alpha-1-acid glycoprotein 1	P02763	site	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	Asn 93	alpha-1-acid glycoprotein 1		Asn 93		OGER		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.
PMC5795011-1-fig5	0	34	gly	varied	52:57	arg1	a single glycosylation site	alpha-1-acid glycoprotein 1		site		OGER		alpha-1-acid glycoprotein 1	P02763	site	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.
PMC5457524-1-2	12	102	gly	glycoprotein	1541:1552	arg1	a complex N-linked glycoprotein	a complex N-linked glycoprotein				Fterm		glycoprotein			The data from this experiment show a marked increase in the affinity of Fbs1 for a complex N-linked glycoprotein in high-salt conditions (Fig. 2c, Lane 1 versus Lane 2).
PMC7124471-1-6	12	130	gly	glycosites	1823:1832	arg2	the two glycosites	ovalbumin		glycosites		Fterm		ovalbumin		glycosites	Notably, the two glycosites of ovalbumin, i.e. N293 and N312 were identified only by setting semi-tryptic digestion (Fig. 5A–5D, supplemental Table S20).
PMC7124471-1-10	23	89	gly	N-glycosites	2439:2450	arg2	the two N-glycosites	transferrin receptor 1		N-glycosites		OGER		transferrin receptor 1	P02787	N-glycosites	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	arg2	the two N-glycosites	serotransferrin		N-glycosites		OGER		serotransferrin	P02787	N-glycosites	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		N-glycosites		OGER		transferrin receptor 1	P02787	N-glycosites	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		N-glycosites		OGER		serotransferrin	P02787	N-glycosites	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.
PMC5795011-1-3	9	260	gly	glycopeptide	1427:1438	arg2	the di-sialylated bi-antennary glycopeptide MS2 spectra			the di-sialylated bi-antennary glycopeptide MS2 spectra						glycopeptide	At NCE values of 15 and 25, the di-sialylated bi-antennary glycopeptide MS2 spectra displayed glycosidic fragment ions (Fig. 2A,B).
PMC3938046-1-6	5	27	gly	N-glycosylation	1147:1161	arg2	several N-glycosylation sites			several N-glycosylation sites						sites	Also, several N-glycosylation sites in microglia markers were identified in our N-glycoproteome, allowing us to distinguish microglia from other macrophages and monocytes in the CNS.
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.
PMC5457524-1-7	11	142	gly	N-glycopeptides	2171:2185	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	Following Fbs1 GYR enrichment 66% of total spectra were assigned to N-glycopeptides, while only 49% and 3.3% of spectra were assigned as N-glycopeptides in lectin enrichment and pre-enrichment samples, respectively (Fig. 7a).
PMC5457524-1-7	11	566	gly	N-glycopeptides	2102:2116	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	Following Fbs1 GYR enrichment 66% of total spectra were assigned to N-glycopeptides, while only 49% and 3.3% of spectra were assigned as N-glycopeptides in lectin enrichment and pre-enrichment samples, respectively (Fig. 7a).
PMC3938046-1-3	1	100	gly	N-glycopeptides	222:236	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	In analysis of BV-2 N-glycoproteome, we identified 1450 unique N-glycosites and 760 unique glycoproteins by WCC and CMC after removing the redundancy from all datasets and selecting N-glycopeptides that contained the canonical motif (Figure 3A and Table 1).
PMC3938046-1-3	1	104	gly	glycoproteins	131:143	arg1	760 unique glycoproteins	760 unique glycoproteins				Fterm		glycoproteins			In analysis of BV-2 N-glycoproteome, we identified 1450 unique N-glycosites and 760 unique glycoproteins by WCC and CMC after removing the redundancy from all datasets and selecting N-glycopeptides that contained the canonical motif (Figure 3A and Table 1).
PMC3938046-1-3	1	129	gly	N-glycosites	103:114	arg2	1450 unique N-glycosites			1450 unique N-glycosites						N-glycosites	In analysis of BV-2 N-glycoproteome, we identified 1450 unique N-glycosites and 760 unique glycoproteins by WCC and CMC after removing the redundancy from all datasets and selecting N-glycopeptides that contained the canonical motif (Figure 3A and Table 1).
PMC5795011-1-4	113	304	gly	glycopeptide	19521:19532	arg2	intact large scale glycopeptide identification			intact large scale glycopeptide identification						glycopeptide	SweetNET, a recently introduced bioinformatics workflow uses an iterative process where glycan derived oxonium ion are used to filter the MS2 data for glycopeptides, the resulting set is then searched against protein databases to generate molecular networks for intact large scale glycopeptide identification.
PMC5795011-1-4	113	903	gly	glycopeptides	19391:19403	arg2	glycopeptides			glycopeptides						glycopeptides	SweetNET, a recently introduced bioinformatics workflow uses an iterative process where glycan derived oxonium ion are used to filter the MS2 data for glycopeptides, the resulting set is then searched against protein databases to generate molecular networks for intact large scale glycopeptide identification.
PMC6243375-1-1	7	0	gly	glycopeptides	1286:1298	arg2	intact O‐linked glycopeptides			intact O‐linked glycopeptides						glycopeptides	In addition, the chemical conjugation of peptides to a solid support allows efficient washing and specific enzymatic release of intact O‐linked glycopeptides.
PMC7124471-1-11	67	130	gly	N-glycosylation	9474:9488	arg2	the canonical N-glycosylation motifs			the canonical N-glycosylation motifs						motifs	However, it is unclear how this newly identified motif is different from the canonical N-glycosylation motifs in terms of its recognition and processing by OSTs.
PMC5976746-1-4	3	50	gly	positions	564:572	arg1	N230			positions N289 and N230				BG505 NFL trimers	P07196	positions N289 and N230	In the first approach, we compared neutralization of BG505 T332N pseudovirus against pseudoviruses that possess N-glycan PNG motifs restored at positions N289 and N230, respectively.
PMC5976746-1-4	3	50	gly	positions	564:572	arg1	N289			positions N289 and N230				BG505 NFL trimers	P07196	positions N289 and N230	In the first approach, we compared neutralization of BG505 T332N pseudovirus against pseudoviruses that possess N-glycan PNG motifs restored at positions N289 and N230, respectively.
PMC5976746-1-4	3	50	gly	positions	564:572	arg1	N289			positions N289 and N230				BG505 NFL trimers	P07196	positions N289 and N230	In the first approach, we compared neutralization of BG505 T332N pseudovirus against pseudoviruses that possess N-glycan PNG motifs restored at positions N289 and N230, respectively.
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.
PMC7124471-1-fig6	0	27	gly	glycopeptide	2:13	arg2	A glycopeptide spectrum			A glycopeptide spectrum						glycopeptide	A glycopeptide spectrum identified by pMatchGlyco in UGP data set.
PMC2538527-1-4	44	272	gly	N-glycosylation	7029:7043	arg1	proper protein folding [45]	proper protein folding [45]				Fterm		protein			N-glycosylation in particular, is often required for proper protein folding [45], protein-protein interactions, stability and optimal pharmacokinetics [46].
PMC6731604-1-2	12	3	gly	glycoproteins	1736:1748	arg1	these glycoproteins	these glycoproteins				Fterm		glycoproteins			The possible reason is that serum contains many high abundant glycoproteins, and these glycoproteins might inhibit the identification of low abundant glycoproteins in serum.
PMC6731604-1-2	12	50	gly	glycoproteins	1799:1811	arg1	low abundant glycoproteins	low abundant glycoproteins				Fterm		glycoproteins			The possible reason is that serum contains many high abundant glycoproteins, and these glycoproteins might inhibit the identification of low abundant glycoproteins in serum.
PMC6731604-1-2	12	63	gly	glycoproteins	1711:1723	arg1	many high abundant glycoproteins	many high abundant glycoproteins				Fterm		glycoproteins			The possible reason is that serum contains many high abundant glycoproteins, and these glycoproteins might inhibit the identification of low abundant glycoproteins in serum.
PMC5457524-1-5	3	30	gly	non-glycosylated	338:353	arg1	non-glycosylated peptides			non-glycosylated peptides						peptides	Trypsin-treated RNaseB contains non-glycosylated peptides and multiple species of high-mannose N-linked glycopeptides (major species labelled as: M5N2-NLTK and M6N2-NLTK).
PMC5457524-1-5	3	76	gly	glycopeptides	410:422	arg2	high-mannose N-linked glycopeptides			high-mannose N-linked glycopeptides						glycopeptides	Trypsin-treated RNaseB contains non-glycosylated peptides and multiple species of high-mannose N-linked glycopeptides (major species labelled as: M5N2-NLTK and M6N2-NLTK).
PMC7124471-1-7	1	13	gly	N-glycoproteins	123:137	arg1	The identified 526 serum N-glycoproteins	The identified 526 serum N-glycoproteins				Fterm		N-glycoproteins			The identified 526 serum N-glycoproteins were mapped to biological pathways using the KEGG mapping tool (23), and the significance of each pathway enriched given by the STRING database (24).
PMC7124471-1-4	25	18	gly	glycosites	4388:4397	arg2	the occupied serum N-linked glycosites			the occupied serum N-linked glycosites						glycosites	This comparison revealed that the constructed N-linked deglycopeptide library covers most of the occupied serum N-linked glycosites.
PMC7124471-1-4	25	134	gly	deglycopeptide	4322:4335	arg2	the constructed N-linked deglycopeptide library			the constructed N-linked deglycopeptide library						deglycopeptide	This comparison revealed that the constructed N-linked deglycopeptide library covers most of the occupied serum N-linked glycosites.
PMC5457524-1-4	9	62	gly	glycopeptide	1320:1331	arg2	glycopeptide			glycopeptide						glycopeptide	The GYR variant was tested for binding to SGP-TMR and three glycopeptide derivatives created by enzymatic trimming.
PMC3942810-1-2	6	17	gly	N-glycoproteins	904:918	arg1	seven proteins	seven proteins				Fterm		proteins			In the YELLOW/MRJP family, seven proteins were identified as N-glycoproteins, glycosylated on 12 unique peptides, each carrying a single N-glycosylated site (Table 2).
PMC3942810-1-2	6	17	gly	N-glycoproteins	904:918	arg1	N-glycoproteins	N-glycoproteins				Fterm		N-glycoproteins			In the YELLOW/MRJP family, seven proteins were identified as N-glycoproteins, glycosylated on 12 unique peptides, each carrying a single N-glycosylated site (Table 2).
PMC6731604-1-fig5	8	27	gly	glycoprotein	1020:1031	arg1	the glycoprotein	the glycoprotein				Fterm		glycoprotein			In the second display page, the following information is shown: c glycoprotein information; d glycosite and glycosite-containing peptide information of the glycoprotein as well as their references; and e glycosites (red) and glycosite-containing peptides (bold font) highlighted in the protein sequence
PMC6731604-1-fig5	8	50	gly	glycoprotein	930:941	arg1	c glycoprotein information	c glycoprotein information				Fterm		glycoprotein			In the second display page, the following information is shown: c glycoprotein information; d glycosite and glycosite-containing peptide information of the glycoprotein as well as their references; and e glycosites (red) and glycosite-containing peptides (bold font) highlighted in the protein sequence
PMC6731604-1-fig5	8	30	gly	glycosites	1068:1077	arg2	e glycosites	glycoprotein		glycosites		Fterm		glycoprotein		glycosites	In the second display page, the following information is shown: c glycoprotein information; d glycosite and glycosite-containing peptide information of the glycoprotein as well as their references; and e glycosites (red) and glycosite-containing peptides (bold font) highlighted in the protein sequence
PMC6731604-1-fig5	8	59	gly	glycosite	958:966	arg2	d glycosite	glycoprotein		glycosite		Fterm		glycoprotein		glycosite	In the second display page, the following information is shown: c glycoprotein information; d glycosite and glycosite-containing peptide information of the glycoprotein as well as their references; and e glycosites (red) and glycosite-containing peptides (bold font) highlighted in the protein sequence
PMC6731604-1-fig2	0	27	gly	glycoprotein	22:33	arg1	the human glycoprotein	the human glycoprotein				Fterm		glycoprotein			Overview of the human glycoprotein and glycosite database.
PMC6731604-1-fig2	0	31	gly	glycosite	39:47	arg2	glycosite			glycosite						glycosite	Overview of the human glycoprotein and glycosite database.
PMC7124471-1-7	12	42	gly	N-glycosite	1529:1539	arg2	each N-glycosite			each N-glycosite						N-glycosite	However, the number of glycans identified on each N-glycosite varied (Fig. 6A, supplemental Table S24).
PMC5457524-1-7	61	35	gly	N-glycopeptide	9366:9379	arg2	N-glycopeptide enrichment			N-glycopeptide enrichment						N-glycopeptide	The following features facilitate the application of the GYR variant in a simple workflow for N-glycopeptide enrichment: (1) the SNAP fusion partner enables rapid, efficient immobilization; (2) alternatively, the SNAP-Fbs1 fusion protein can also be employed in an N-glyco-FASP protocol; (3) N-glycopeptide capture may be accomplished in many buffer conditions, preferably a volatile low-salt buffer such as 50 mM ammonium acetate or ammonium bicarbonate; (4) enriched N-glycopeptides may be eluted in 50% acetonitrile or 50% formic acid and directly analysed by MS; and (5) substantially unbiased capture of intact N-glycopeptides (rather than liberated N-glycans or deglycosylated peptides) allows for simultaneous identification of N-glycan composition and the respective glycosite.
PMC5457524-1-7	61	59	gly	deglycosylated	9940:9953	arg1	deglycosylated peptides			deglycosylated peptides						peptides	The following features facilitate the application of the GYR variant in a simple workflow for N-glycopeptide enrichment: (1) the SNAP fusion partner enables rapid, efficient immobilization; (2) alternatively, the SNAP-Fbs1 fusion protein can also be employed in an N-glyco-FASP protocol; (3) N-glycopeptide capture may be accomplished in many buffer conditions, preferably a volatile low-salt buffer such as 50 mM ammonium acetate or ammonium bicarbonate; (4) enriched N-glycopeptides may be eluted in 50% acetonitrile or 50% formic acid and directly analysed by MS; and (5) substantially unbiased capture of intact N-glycopeptides (rather than liberated N-glycans or deglycosylated peptides) allows for simultaneous identification of N-glycan composition and the respective glycosite.
PMC5457524-1-7	61	375	gly	N-glycopeptide	9564:9577	arg2	(3) N-glycopeptide capture			(3) N-glycopeptide capture						N-glycopeptide	The following features facilitate the application of the GYR variant in a simple workflow for N-glycopeptide enrichment: (1) the SNAP fusion partner enables rapid, efficient immobilization; (2) alternatively, the SNAP-Fbs1 fusion protein can also be employed in an N-glyco-FASP protocol; (3) N-glycopeptide capture may be accomplished in many buffer conditions, preferably a volatile low-salt buffer such as 50 mM ammonium acetate or ammonium bicarbonate; (4) enriched N-glycopeptides may be eluted in 50% acetonitrile or 50% formic acid and directly analysed by MS; and (5) substantially unbiased capture of intact N-glycopeptides (rather than liberated N-glycans or deglycosylated peptides) allows for simultaneous identification of N-glycan composition and the respective glycosite.
PMC5457524-1-7	61	385	gly	N-glycopeptides	9741:9755	arg2	(4) enriched N-glycopeptides			(4) enriched N-glycopeptides						N-glycopeptides	The following features facilitate the application of the GYR variant in a simple workflow for N-glycopeptide enrichment: (1) the SNAP fusion partner enables rapid, efficient immobilization; (2) alternatively, the SNAP-Fbs1 fusion protein can also be employed in an N-glyco-FASP protocol; (3) N-glycopeptide capture may be accomplished in many buffer conditions, preferably a volatile low-salt buffer such as 50 mM ammonium acetate or ammonium bicarbonate; (4) enriched N-glycopeptides may be eluted in 50% acetonitrile or 50% formic acid and directly analysed by MS; and (5) substantially unbiased capture of intact N-glycopeptides (rather than liberated N-glycans or deglycosylated peptides) allows for simultaneous identification of N-glycan composition and the respective glycosite.
PMC5457524-1-7	61	411	gly	glycosite	10047:10055	arg2	the respective glycosite			the respective glycosite						glycosite	The following features facilitate the application of the GYR variant in a simple workflow for N-glycopeptide enrichment: (1) the SNAP fusion partner enables rapid, efficient immobilization; (2) alternatively, the SNAP-Fbs1 fusion protein can also be employed in an N-glyco-FASP protocol; (3) N-glycopeptide capture may be accomplished in many buffer conditions, preferably a volatile low-salt buffer such as 50 mM ammonium acetate or ammonium bicarbonate; (4) enriched N-glycopeptides may be eluted in 50% acetonitrile or 50% formic acid and directly analysed by MS; and (5) substantially unbiased capture of intact N-glycopeptides (rather than liberated N-glycans or deglycosylated peptides) allows for simultaneous identification of N-glycan composition and the respective glycosite.
PMC5457524-1-7	61	418	gly	N-glycopeptides	9888:9902	arg2	intact N-glycopeptides			intact N-glycopeptides						N-glycopeptides	The following features facilitate the application of the GYR variant in a simple workflow for N-glycopeptide enrichment: (1) the SNAP fusion partner enables rapid, efficient immobilization; (2) alternatively, the SNAP-Fbs1 fusion protein can also be employed in an N-glyco-FASP protocol; (3) N-glycopeptide capture may be accomplished in many buffer conditions, preferably a volatile low-salt buffer such as 50 mM ammonium acetate or ammonium bicarbonate; (4) enriched N-glycopeptides may be eluted in 50% acetonitrile or 50% formic acid and directly analysed by MS; and (5) substantially unbiased capture of intact N-glycopeptides (rather than liberated N-glycans or deglycosylated peptides) allows for simultaneous identification of N-glycan composition and the respective glycosite.
PMC6243375-1-3	5	139	gly	glycosylation	840:852	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	O‐linked glycosylation sites with core 1 O‐linked glycans in seven PSMs could not be located by ETD spectra (Dataset EV5).
PMC6243375-1-4	19	301	gly	glycoprotein	3947:3958	arg1	the glycoprotein	the glycoprotein				Fterm		glycoprotein			To overview the positional distribution of the O‐linked glycosylation sites identified, the relative position of the sites in the proteins was determined and arranged relative to the N‐terminus of the glycoprotein in question (Fig 2F lower panel).
PMC6243375-1-4	19	308	gly	glycosylation	3802:3814	arg2	the O‐linked glycosylation sites			the O‐linked glycosylation sites						sites	To overview the positional distribution of the O‐linked glycosylation sites identified, the relative position of the sites in the proteins was determined and arranged relative to the N‐terminus of the glycoprotein in question (Fig 2F lower panel).
PMC3942810-1-2	24	41	gly	N-glycosylated	4443:4456	arg1	42 novel N-glycosylated sites			42 novel N-glycosylated sites						sites	Overall, 13 novel proteins and 42 novel N-glycosylated sites in 25 N-glycosylated proteins were identified.
PMC3942810-1-2	24	209	gly	25 N-glycosylated	4467:4483	arg1	25 N-glycosylated proteins	25 N-glycosylated proteins				Fterm		proteins			Overall, 13 novel proteins and 42 novel N-glycosylated sites in 25 N-glycosylated proteins were identified.
PMC5643531-1-8	10	22	gly	glycoproteins	1310:1322	arg1	N-linked glycoproteins	N-linked glycoproteins				Fterm		glycoproteins			Moreover, a similar mobility shift of Fz8-Myc was observed after treatment with TM or endoglycosidase H, an enzyme which cleaves oligosaccharides from N-linked glycoproteins (Fig. 6F).
PMC5457524-1-7	9	592	gly	N-glycopeptides	1620:1634	arg2	more intact N-glycopeptides			more intact N-glycopeptides						N-glycopeptides	Most importantly, Fbs1 GYR enrichment revealed more intact N-glycopeptides relative to lectin enrichment.
PMC3942810-2-2	10	610	gly	N-glycosylation	1650:1664	arg2	Nine potential N-glycosylation sites			Nine potential N-glycosylation sites						sites	Nine potential N-glycosylation sites predicted by the Uniprot database (updated April 2013) were also verified.
PMC7107550-1-fig1	5	19	gly	glycosylation	605:617	arg2	Underlined N-linked glycosylation motifs			Underlined N-linked glycosylation motifs						motifs	Underlined N-linked glycosylation motifs were not present in the majority of sequences sampled from the RMs at day 14 p.i. Sites labeled with a filled star were found to be under selection in both the RMs and the SMs.
PMC3938046-1-4	9	76	gly	glycoproteins	1625:1637	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Nonsurface component categories, including the ER (18%), Golgi apparatus (12%), and cytoplasmic vesicles (9%), were overrepresented, but in nearly all cases, these annotations were nonexclusive (Additional file 7: Table S8) or validated experimentally as glycoproteins, according to the UniprotKB database.
PMC3942810-1-fig2	1	48	gly	N-glycopeptides	137:151	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	A is the distribution of N-glycopeptides enriched by lectin and hydrazide methods using mass spectrometry of Q-Exactive (orbitrap-based MS).
PMC3942810-1-fig2	2	15	gly	N-glycopeptides	270:284	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	21 and eight are N-glycopeptides uniquely identified by the lectin and hydrazide enrichment, respectively, and 18 are N-glycopeptides identified by both enrichment methods using orbitrap-based MS. B is the distribution of N-glycopeptides enriched by lectin and hydrazide methods using mass spectrometry of triple TOF 5600 (triple TOF-based MS).
PMC3942810-1-fig2	2	19	gly	N-glycopeptides	371:385	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	21 and eight are N-glycopeptides uniquely identified by the lectin and hydrazide enrichment, respectively, and 18 are N-glycopeptides identified by both enrichment methods using orbitrap-based MS. B is the distribution of N-glycopeptides enriched by lectin and hydrazide methods using mass spectrometry of triple TOF 5600 (triple TOF-based MS).
PMC3942810-1-fig2	2	37	gly	N-glycopeptides	475:489	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	21 and eight are N-glycopeptides uniquely identified by the lectin and hydrazide enrichment, respectively, and 18 are N-glycopeptides identified by both enrichment methods using orbitrap-based MS. B is the distribution of N-glycopeptides enriched by lectin and hydrazide methods using mass spectrometry of triple TOF 5600 (triple TOF-based MS).
PMC6243375-1-3	8	137	gly	glycopeptide	1318:1329	arg2	this glycopeptide			this glycopeptide						glycopeptide	The observation of two PSMs of the same precursor with different site localization suggested that the site localization for this glycopeptide might not be confident for site assignment.
PMC3938046-1-7	9	80	gly	N-glycosites	1538:1549	arg2	many N-glycosites			many N-glycosites						N-glycosites	For example, we noted many N-glycosites on proteins that are involved in Toll receptor signaling, integrin signaling, and chemokine- and cytokine-mediated inflammation (Figure 5B).
PMC6731604-1-fig2	2	4	gly	glycosite	166:174	arg2	each glycosite			each glycosite						glycosite	The identification frequencies of each glycosite were determined based on their identification in different samples, different studies or glycosite-containing peptides of various lengths (due to different enzyme digestion or different missed cleavages).
PMC5457524-1-7	46	34	gly	N-glycopeptide	7302:7315	arg2	unbiased N-glycopeptide enrichment			unbiased N-glycopeptide enrichment						N-glycopeptide	Our objective was to develop a method for unbiased N-glycopeptide enrichment that allows for simultaneous determination of glycan composition and the protein attachment site.
PMC5457524-1-7	74	67	gly	N-glycopeptide	11649:11662	arg2	N-glycopeptide abundance			N-glycopeptide abundance						N-glycopeptide	Hydrazide-based methods can improve N-glycopeptide abundance to 80–90% (refs 14, 53), but this either results in the loss of N-glycan information1214 or only sialyated glycans may be captured15.
PMC7124471-1-fig5	0	31	gly	glycosylation	14:26	arg1	serum glycoproteins	serum glycoproteins				Fterm		glycoproteins			Site-specific glycosylation of serum glycoproteins.
PMC7124471-1-fig5	0	37	gly	glycoproteins	37:49	arg1	serum glycoproteins	serum glycoproteins				Fterm		glycoproteins			Site-specific glycosylation of serum glycoproteins.
PMC6731604-1-fig5	6	19	gly	glycosylation	684:696	arg2	glycosylation site location			glycosylation site location						site	In the first display page, the glycoprotein accession number (UniProt), gene name, protein name and glycosylation site location are exhibited.
PMC6731604-1-fig5	6	54	gly	glycoprotein	615:626	arg1	the glycoprotein accession number	the glycoprotein accession number				Fterm		glycoprotein			In the first display page, the glycoprotein accession number (UniProt), gene name, protein name and glycosylation site location are exhibited.
PMC4804330-1-2	38	140	gly	glycoprotein	6880:6891	arg1	antifreeze glycoprotein	antifreeze glycoprotein				Fterm		glycoprotein			We assessed the impact of these mutations on encoded ST6GALNAC2 enzyme activity using antifreeze glycoprotein from Antarctic fish (AFGP) and asialofetuin (ASF) substrates26.
PMC5098438-1-1	21	36	gly	N-glycosylation	3170:3184	arg1	the mono- and di-glycosylated Tt/C2B8 variants	the mono- and di-glycosylated Tt/C2B8 variants				Fterm		variants			Following PNGase F treatment, only the aglycosylated species were present, confirming the identification of N-glycosylation of the mono- and di-glycosylated Tt/C2B8 variants.
PMC5098438-1-1	21	139	gly	di-glycosylated	3203:3217	arg1	the mono- and di-glycosylated Tt/C2B8 variants	the mono- and di-glycosylated Tt/C2B8 variants				Fterm		variants			Following PNGase F treatment, only the aglycosylated species were present, confirming the identification of N-glycosylation of the mono- and di-glycosylated Tt/C2B8 variants.
PMC5795011-1-4	63	902	gly	glycopeptides	10970:10982	arg2	both N-linked and O-linked glycopeptides			both N-linked and O-linked glycopeptides						glycopeptides	Software tools that can automatically annotate both N-linked and O-linked glycopeptides are of great advantage.
PMC2538527-1-fig7	1	7	gly	glycopeptide	162:173	arg2	the disialylated glycopeptide			the disialylated glycopeptide						glycopeptide	A) CID-MS/MS spectrum of the triply protonated ion at m/z 1426.8 corresponding to the disialylated glycopeptide of T84-112.
PMC2538527-1-fig7	1	12	gly	disialylated	149:160	arg1	the disialylated glycopeptide			the disialylated glycopeptide						glycopeptide	A) CID-MS/MS spectrum of the triply protonated ion at m/z 1426.8 corresponding to the disialylated glycopeptide of T84-112.
PMC5457524-1-6	17	77	gly	N-glycosites	2736:2747	arg2	only 183 unique N-glycosites			only 183 unique N-glycosites						N-glycosites	From the same amount of starting human serum tryptic peptides, 477 unique N-glycosites were identified after Fbs1 GYR enrichment, while only 183 unique N-glycosites were identified without Fbs1 GYR enrichment (pre-enrichment), of which 172 N-glycosites (94%) were also identified by Fbs1 GYR enrichment (Fig. 6d, left panel and Supplementary Data 1 and 2).
PMC5457524-1-6	17	89	gly	N-glycosites	2824:2835	arg2	172 N-glycosites			172 N-glycosites						N-glycosites	From the same amount of starting human serum tryptic peptides, 477 unique N-glycosites were identified after Fbs1 GYR enrichment, while only 183 unique N-glycosites were identified without Fbs1 GYR enrichment (pre-enrichment), of which 172 N-glycosites (94%) were also identified by Fbs1 GYR enrichment (Fig. 6d, left panel and Supplementary Data 1 and 2).
PMC5457524-1-6	17	140	gly	N-glycosites	2658:2669	arg2	477 unique N-glycosites			477 unique N-glycosites						N-glycosites	From the same amount of starting human serum tryptic peptides, 477 unique N-glycosites were identified after Fbs1 GYR enrichment, while only 183 unique N-glycosites were identified without Fbs1 GYR enrichment (pre-enrichment), of which 172 N-glycosites (94%) were also identified by Fbs1 GYR enrichment (Fig. 6d, left panel and Supplementary Data 1 and 2).
PMC5457524-1-4	12	6	gly	N-glycopeptide	1831:1844	arg2	highly efficient N-glycopeptide recovery			highly efficient N-glycopeptide recovery						N-glycopeptide	Importantly, the GYR variant enables highly efficient N-glycopeptide recovery and binding to diverse types of N-glycans is substantially unbiased.
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		glycosites		OGER		serotransferrin	P02787	glycosites	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.
PMC6731604-1-2	8	102	gly	glycoproteins	1181:1193	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Glycoproteomic analysis of these tissues will promote human glycoproteomics studies and enhance our understanding of the distribution and function of glycoproteins in different tissues.
PMC2538527-1-fig6	1	6	gly	glycoprotein	166:177	arg1	the glycoprotein molecule weight profile	the glycoprotein molecule weight profile				Fterm		glycoprotein			A) ESI mass spectrum exhibiting the glycoform profiles associated with each charge state of the protein and B) the glycoprotein molecule weight profile reconstructed from the mass spectrum in panel A.
PMC6243375-1-3	19	57	gly	glycosylation	3386:3398	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	EXoO may miss O‐linked glycosylation sites that are not in an appropriate peptide length for identification.
PMC5795011-1-4	102	453	gly	glycopeptide	17424:17435	arg2	glycopeptide			glycopeptide						glycopeptide sequences	Though the stepped HCD function used in the study provided both peptide and glycan information, we observed that this is not universal and for some glycopeptide sequences, no peptide fragmentation was observed.
PMC5795011-1-fig4	4	7	gly	glycoprotein	572:583	arg1	a custom glycoprotein database	a custom glycoprotein database				Fterm		glycoprotein			The data was searched against a custom glycoprotein database prepared from 21 linear N-linked sialylated glycans and proteins (444) known to be glycosylated in serum (PeptideAtlas N-Glyco build 2010).
PMC6243375-1-4	17	68	gly	glycoproteins	3324:3336	arg1	O‐linked glycoproteins	O‐linked glycoproteins				Fterm		glycoproteins			Analysis of biological process and molecular function suggested various activities and functionalities associated with O‐linked glycoproteins, consistent with their important role in different aspects of biology (Appendix Fig S3).
PMC5795011-1-4	41	888	gly	glycoproteins	7209:7221	arg1	121 glycoproteins	121 glycoproteins				Fterm		glycoproteins			There is a good level of agreement between the three plasma protein related databases because 121 glycoproteins were consistently identified.
PMC5795011-1-4	21	39	gly	attached	3526:3533	arg2	the core HexNAc or HexNAc residues AND the fucose			the core HexNAc or HexNAc residues	the fucose					residues	Therefore, it must be considered that the fucose is either attached to the core HexNAc or HexNAc residues following the core glycan structure when determining the position of fucose residues in Mascot output.
PMC3938046-1-5	22	6	gly	N-glycosites	3056:3067	arg2	N-glycosites			N-glycosites						N-glycosites	In addition, N-glycosites in Tlr1, Tlr4, Tlr7, Tlr9, and Tlr13 were identified in our N-glycoproteome.
PMC5795011-1-4	47	741	gly	glycopeptide	8501:8512	arg2	automated glycopeptide analysis			automated glycopeptide analysis						glycopeptide	In this report, we addressed these concerns by using the widely applied Mascot search engine for automated glycopeptide analysis.
PMC5457524-1-7	18	32	gly	glycosite	3657:3665	arg2	each glycosite			each glycosite						glycosite	In this case, Fbs1 GYR enrichment clearly allows identification of more glycan types and spectra at each glycosite relative to the pre-enrichment and lectin enrichment samples.
PMC7124471-1-fig5	2	5	gly	glycosites	281:290	arg1	the four glycosites	serotransferrin		glycosites N432, N630 and N637				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	5	gly	glycosites	281:290	arg1	N630	serotransferrin		glycosites N432, N630 and N637				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	5	gly	glycosites	281:290	arg1	N432	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg1	serotransferrin	serotransferrin		glycosites N432, N630 and N637		OGER		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	30	gly	glycosites	281:290	arg2	N630	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	the four glycosites	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N637	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N432	serotransferrin		glycosites N432, N630 and N637				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	5	gly	glycosites	281:290	arg1	N630	serotransferrin		glycosites N432, N630 and N637				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	5	gly	glycosites	281:290	arg1	N432	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg1	serotransferrin	serotransferrin		glycosites N432, N630 and N637		OGER		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	30	gly	glycosites	281:290	arg2	N630	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	the four glycosites	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N637	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N432	serotransferrin		glycosites N432, N630 and N637				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	5	gly	glycosites	281:290	arg1	N432	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg1	serotransferrin	serotransferrin		glycosites N432, N630 and N637		OGER		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	30	gly	glycosites	281:290	arg2	N630	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	the four glycosites	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N637	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N432	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg1	serotransferrin	serotransferrin		glycosites N432, N630 and N637		OGER		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	30	gly	glycosites	281:290	arg2	N630	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	the four glycosites	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N637	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N432	serotransferrin		glycosites N432, N630 and N637				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	10	gly	glycosites	347:356	arg1	N529	complement factor H		glycosites N529, N822, N882 and N1029				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	10	gly	glycosites	347:356	arg1	N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	10	gly	glycosites	347:356	arg1	N822	complement factor H		glycosites N529, N822, N882 and N1029				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	10	gly	glycosites	347:356	arg1	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N822	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	the four glycosites N529, N822, N882 and N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg1	complement factor H	complement factor H		glycosites N529, N822, N882 and N1029		OGER		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	47	gly	glycosites	347:356	arg2	N529	complement factor H		glycosites N529, N822, N882 and N1029				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	10	gly	glycosites	347:356	arg1	N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	10	gly	glycosites	347:356	arg1	N822	complement factor H		glycosites N529, N822, N882 and N1029				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	10	gly	glycosites	347:356	arg1	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N822	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	the four glycosites N529, N822, N882 and N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg1	complement factor H	complement factor H		glycosites N529, N822, N882 and N1029		OGER		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	47	gly	glycosites	347:356	arg2	N529	complement factor H		glycosites N529, N822, N882 and N1029				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	10	gly	glycosites	347:356	arg1	N822	complement factor H		glycosites N529, N822, N882 and N1029				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	10	gly	glycosites	347:356	arg1	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N822	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	the four glycosites N529, N822, N882 and N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg1	complement factor H	complement factor H		glycosites N529, N822, N882 and N1029		OGER		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	47	gly	glycosites	347:356	arg2	N529	complement factor H		glycosites N529, N822, N882 and N1029				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	10	gly	glycosites	347:356	arg1	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N822	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	the four glycosites N529, N822, N882 and N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg1	complement factor H	complement factor H		glycosites N529, N822, N882 and N1029		OGER		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	47	gly	glycosites	347:356	arg2	N529	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N822	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	the four glycosites N529, N822, N882 and N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg1	complement factor H	complement factor H		glycosites N529, N822, N882 and N1029		OGER		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	47	gly	glycosites	347:356	arg2	N529	complement factor H		glycosites N529, N822, N882 and N1029				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	30	gly	glycosites	281:290	arg2	N630	serotransferrin		glycosites N432, N630 and N637		OGER		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	30	gly	glycosites	281:290	arg2	the four glycosites	serotransferrin		glycosites N432, N630 and N637		OGER		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	30	gly	glycosites	281:290	arg2	N637	serotransferrin		glycosites N432, N630 and N637		OGER		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	30	gly	glycosites	281:290	arg2	N432	serotransferrin		glycosites N432, N630 and N637		OGER		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	30	gly	glycosites	281:290	arg2	the four glycosites	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N637	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N432	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N637	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N432	serotransferrin		glycosites N432, N630 and N637				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	30	gly	glycosites	281:290	arg2	N432	serotransferrin		glycosites N432, N630 and N637				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	47	gly	glycosites	347:356	arg2	N822	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	the four glycosites N529, N822, N882 and N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg1	complement factor H	complement factor H		glycosites N529, N822, N882 and N1029		OGER		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	47	gly	glycosites	347:356	arg2	N529	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N882	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	the four glycosites N529, N822, N882 and N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg1	complement factor H	complement factor H		glycosites N529, N822, N882 and N1029		OGER		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	47	gly	glycosites	347:356	arg2	N529	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	the four glycosites N529, N822, N882 and N1029	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg1	complement factor H	complement factor H		glycosites N529, N822, N882 and N1029		OGER		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	47	gly	glycosites	347:356	arg2	N529	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg1	complement factor H	complement factor H		glycosites N529, N822, N882 and N1029		OGER		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	47	gly	glycosites	347:356	arg2	N529	complement factor H		glycosites N529, N822, N882 and N1029				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	47	gly	glycosites	347:356	arg2	N529	complement factor H		glycosites N529, N822, N882 and N1029		OGER		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.
PMC5457524-1-5	10	74	gly	glycopeptides	1305:1317	arg2	high-mannose-containing glycopeptides M5N2-NLTK and M6N2-NLTK			high-mannose-containing glycopeptides M5N2-NLTK and M6N2-NLTK						glycopeptides	The extracted ion chromatogram data (shown as a bar graph, Fig. 5) also shows that the GYR variant performs well for capturing high-mannose-containing glycopeptides M5N2-NLTK and M6N2-NLTK.
PMC3942810-2-2	0	71	gly	N-glycosylated	8:21	arg1	N-glycosylated sites			N-glycosylated sites						sites	Mapping N-glycosylated sites.
PMC2538527-1-4	49	98	gly	disialylated	7906:7917	arg1	the purified protein	the purified protein				Fterm		protein			Approximately 50% of the purified protein is disialylated, while another 10% is monosialylated, in comparison to 50% and 30% respectively for leukocyte-derived IFN.
PMC2762462-1-1	1	18	gly	glycoprotein	297:308	arg1	an O-linked glycoprotein	an O-linked glycoprotein				Fterm		glycoprotein			ST6 catalyzes the transfer of N-acetylneuraminic acid (Neu5Ac - the most common type of sialic acid in higher animals) from the sugar donor CMP-Neu5Ac (or CMP-SA) onto a terminal β-D-galactopyranosyl (Gal) residue of an O-linked glycoprotein to generate an α 2-6 linkage [8].
PMC3942810-1-fig2	6	39	gly	N-glycopeptides	1362:1376	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	18 are N-glycopeptides identified by orbitrap-based MS alone, and eight are N-glycopeptides identified by both types of LC-MS/MS instruments with adoption of hydrazide enrichment.
PMC3942810-1-fig2	6	46	gly	N-glycopeptides	1293:1307	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	18 are N-glycopeptides identified by orbitrap-based MS alone, and eight are N-glycopeptides identified by both types of LC-MS/MS instruments with adoption of hydrazide enrichment.
PMC7124471-1-9	1	67	gly	deglycopeptides	176:190	arg2	N-linked deglycopeptides			N-linked deglycopeptides						deglycopeptides	The proposed method will achieve the highest accuracy by using a complete database of N-glycans as well as N-linked deglycopeptides derived from human serum.
PMC7081908-1-fig3	2	44	gly	occupied	399:406	arg2	the site			the site						site	Green and purple bars indicate the proportions of oligomannose glycans and complex glycans, respectively, and gray bars indicate that the site was not occupied by a glycan.
PMC3942810-2-2	8	218	gly	N-glycosylated	1515:1528	arg1	N-glycosylated sites			N-glycosylated sites						sites	Meanwhile, orbitrap-based MS seems to be more robust than Triple TOF-based MS in the identification of glycosylated sites in RJ, and the combined utilization of two different double high LC-MS/MS yielded identification of more number of N-glycosylated sites in RJ.
PMC3942810-2-2	8	405	gly	glycosylated	1381:1392	arg1	glycosylated sites			glycosylated sites						sites	Meanwhile, orbitrap-based MS seems to be more robust than Triple TOF-based MS in the identification of glycosylated sites in RJ, and the combined utilization of two different double high LC-MS/MS yielded identification of more number of N-glycosylated sites in RJ.
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.
PMC5643531-1-fig7	0	35	gly	N-glycosylation	9:23	arg2	Putative N-glycosylation sites	Fz8 receptor		sites		OGER		Fz8 receptor	Q9H461	sites	Putative N-glycosylation sites of Fz8 receptor are important for Wnt8 signaling.
PMC5795011-1-4	71	95	gly	glycosylation	12080:12092	arg2	a consensus glycosylation motif			a consensus glycosylation motif						motif	Due to the lack of a consensus glycosylation motif, while assembling the O-glycopeptide database, every serine and threonine peptide must be considered as a potential glycopeptide, thus challenging the large-scale O-glycoproteomics studies.
PMC5795011-1-4	71	250	gly	O-glycopeptide	12122:12135	arg2	the O-glycopeptide database			the O-glycopeptide database						O-glycopeptide	Due to the lack of a consensus glycosylation motif, while assembling the O-glycopeptide database, every serine and threonine peptide must be considered as a potential glycopeptide, thus challenging the large-scale O-glycoproteomics studies.
PMC5795011-1-4	71	765	gly	glycopeptide	12216:12227	arg2	every serine and threonine peptide			every serine and threonine peptide						serine and threonine peptide	Due to the lack of a consensus glycosylation motif, while assembling the O-glycopeptide database, every serine and threonine peptide must be considered as a potential glycopeptide, thus challenging the large-scale O-glycoproteomics studies.
PMC5795011-1-4	71	765	gly	glycopeptide	12216:12227	arg2	a potential glycopeptide			a potential glycopeptide						glycopeptide	Due to the lack of a consensus glycosylation motif, while assembling the O-glycopeptide database, every serine and threonine peptide must be considered as a potential glycopeptide, thus challenging the large-scale O-glycoproteomics studies.
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.
PMC5457524-1-7	62	410	gly	N-glycopeptide	10129:10142	arg2	N-glycopeptide abundance			N-glycopeptide abundance						N-glycopeptide	In both deglycoproteomic (Fig. 6) and glycoproteomic (Fig. 7) studies, N-glycopeptide abundance in the human serum samples was increased to 66% after Fbs1 GYR enrichment.
PMC7124471-1-11	49	298	gly	glycopeptide	6765:6776	arg2	the N-linked intact glycopeptide			the N-linked intact glycopeptide						glycopeptide	If the peptide part (including sequence and PTMs) of a GPSM is correct, the mass of glycan part should also be correct if the precursor mass of the N-linked intact glycopeptide is accurate.
PMC5795011-1-4	52	665	gly	glycopeptide	9332:9343	arg2	glycopeptide analysis			glycopeptide analysis						glycopeptide	A considerable amount of research has been performed for developing efficient fragmentation tools for glycopeptide analysis.
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).
PMC6243375-1-5	9	75	gly	glycoprotein	1740:1751	arg1	a glycoprotein	a glycoprotein				Fterm		glycoprotein			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).
PMC6243375-1-fig3	2	27	gly	glycoproteins	338:350	arg1	592 glycoproteins	592 glycoproteins				Fterm		glycoproteins			A total of 592 glycoproteins are plotted in the Volcano plot according to their fold change (log2) and number of differential PSM between cancer and normal (log10).
PMC5976746-1-5	64	556	gly	homogeneity	10891:10901	arg1	the trimers	the trimers				Fterm		trimers			This favorable result (lack of robust tier 1 neutralizing responses) is probably due to the improved homogeneity of the trimers expressed in the CHO-M cell lines that do not expose the V3 region following purification and, more importantly, following multiple rounds of immunization with adjuvant in vivo.
PMC3942810-1-fig2	4	52	gly	N-glycopeptides	953:967	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	29 are N-glycopeptides uniquely identified by orbitrap-based MS, and four are uniquely identified by triple TOF-based MS, and 10 are N-glycopeptides identified by both MS systems using the lectin enrichment method.
PMC3942810-1-fig2	4	53	gly	N-glycopeptides	1079:1093	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	29 are N-glycopeptides uniquely identified by orbitrap-based MS, and four are uniquely identified by triple TOF-based MS, and 10 are N-glycopeptides identified by both MS systems using the lectin enrichment method.
PMC4876326-1-4	1	3	gly	glycosylation	166:178	arg2	the N-linked glycosylation sequons			the N-linked glycosylation sequons							Results of NetNGlyc across all study samples show that the N-linked glycosylation sequons in the F gene are relatively conserved.
PMC5457524-1-1	13	134	gly	glycopeptide	1969:1980	arg2	a naturally occurring glycopeptide			a naturally occurring glycopeptide						glycopeptide	Figure 1c illustrates that Fbs1 is capable of binding to SGP, a naturally occurring glycopeptide consisting of a six amino acid peptide (KVANKT) and a bi-antennary complex N-glycan with terminal sialic acid residues (structure shown in Fig. 1c, left panel).
PMC6243375-1-3	15	42	gly	glycopeptide	2598:2609	arg2	site‐specific O‐linked glycopeptide			site‐specific O‐linked glycopeptide						glycopeptide	These data could also be explained as that the major glycan composition for site‐specific O‐linked glycopeptide is the core 1 structure Hex(1)HexNAc(1) that is prevalent in a wide range of glycoproteins from different cell types compared to the relatively restricted presence of other core structures seen in specific tissue and cell types (Brockhausen & Stanley, 2015).
PMC6243375-1-3	15	169	gly	glycoproteins	2688:2700	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			These data could also be explained as that the major glycan composition for site‐specific O‐linked glycopeptide is the core 1 structure Hex(1)HexNAc(1) that is prevalent in a wide range of glycoproteins from different cell types compared to the relatively restricted presence of other core structures seen in specific tissue and cell types (Brockhausen & Stanley, 2015).
PMC6243375-1-3	15	208	gly	prevalent	2659:2667	arg1	the major glycan composition			the major glycan composition						position	These data could also be explained as that the major glycan composition for site‐specific O‐linked glycopeptide is the core 1 structure Hex(1)HexNAc(1) that is prevalent in a wide range of glycoproteins from different cell types compared to the relatively restricted presence of other core structures seen in specific tissue and cell types (Brockhausen & Stanley, 2015).
PMC7124471-1-9	6	80	gly	glycopeptides	790:802	arg2	N-linked intact glycopeptides			N-linked intact glycopeptides						glycopeptides	The results indicated that the size of N-glycan mass database significantly influenced the number of N-linked intact glycopeptides.
PMC3942810-2-2	3	57	gly	N-glycosylated	460:473	arg1	the N-glycosylated sites	RJ		sites		Cterm		RJ		sites	To the best of our knowledge, this is the most comprehensive assignment of the N-glycosylated sites of RJ.
PMC4876326-1-4	10	41	gly	glycosylation	1287:1299	arg2	85 predicted O-linked glycosylation sites			85 predicted O-linked glycosylation sites						sites	Genotype ON1 shows 85 predicted O-linked glycosylation sites, whereas genotype TN1 has 74 and 83 sites (in non-duplicated and duplicated genomes, respectively), genotype TN2 has 74 sites, and genotype GA5 has 72 sites.
PMC3942810-1-fig5	0	2	gly	N-glycosylated	0:13	arg1	N-glycosylated site motif			N-glycosylated site motif						motif	N-glycosylated site motif in royal jelly proteins.
PMC3942810-1-2	16	147	gly	glycoproteins	2934:2946	arg1	known glycoproteins	known glycoproteins				Fterm		glycoproteins			Specifically, only two known sites in known glycoproteins were repeatedly identified in the current study, and six potential sites in known glycoproteins and three potential sites in novel glycoproteins were also identified.
PMC3942810-1-2	16	151	gly	glycoproteins	2838:2850	arg1	known glycoproteins	known glycoproteins				Fterm		glycoproteins			Specifically, only two known sites in known glycoproteins were repeatedly identified in the current study, and six potential sites in known glycoproteins and three potential sites in novel glycoproteins were also identified.
PMC3942810-1-2	16	160	gly	glycoproteins	2983:2995	arg1	novel glycoproteins	novel glycoproteins				Fterm		glycoproteins			Specifically, only two known sites in known glycoproteins were repeatedly identified in the current study, and six potential sites in known glycoproteins and three potential sites in novel glycoproteins were also identified.
PMC6243375-1-2	7	52	gly	glycopeptides	1133:1145	arg2	1,982 O‐linked glycopeptides			1,982 O‐linked glycopeptides						glycopeptides	When the EXoO approach was applied to the analysis of T cells, 4,623 PSMs were assigned to contain 1,295 O‐linked glycosylation sites from 1,982 O‐linked glycopeptides and 590 glycoproteins (Dataset EV3).
PMC6243375-1-2	7	98	gly	glycoproteins	1155:1167	arg1	590 glycoproteins	590 glycoproteins				Fterm		glycoproteins			When the EXoO approach was applied to the analysis of T cells, 4,623 PSMs were assigned to contain 1,295 O‐linked glycosylation sites from 1,982 O‐linked glycopeptides and 590 glycoproteins (Dataset EV3).
PMC6243375-1-2	7	106	gly	glycosylation	1093:1105	arg2	1,295 O‐linked glycosylation sites			1,295 O‐linked glycosylation sites						sites	When the EXoO approach was applied to the analysis of T cells, 4,623 PSMs were assigned to contain 1,295 O‐linked glycosylation sites from 1,982 O‐linked glycopeptides and 590 glycoproteins (Dataset EV3).
PMC6731604-1-2	3	47	gly	glycosites	498:507	arg2	identified glycosites			identified glycosites						glycosites	Among eight tissues including prostate, liver, ovary, breast, pancreas, colon, lung and bladder, prostate has the most number of identified glycosites (> 6000; Fig. 3a) and glycoproteins (> 3000; Fig. 3b).
PMC6731604-1-2	3	104	gly	glycoproteins	531:543	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Among eight tissues including prostate, liver, ovary, breast, pancreas, colon, lung and bladder, prostate has the most number of identified glycosites (> 6000; Fig. 3a) and glycoproteins (> 3000; Fig. 3b).
PMC7107550-1-4	24	170	gly	positions	5802:5810	arg1	42			positions 30 and 42						positions 30 and 42	The partial reversion of this N-glyc site to its N-terminal position beyond day 70 p.i. is due to the reemergence of the presumably more immunologically evasive variants containing both of the N-glyc sites in V1 at amino acid positions 30 and 42 (see fig. 1).
PMC3938046-1-4	14	51	gly	glycoproteins	2364:2376	arg1	many glycoproteins	many glycoproteins				Fterm		glycoproteins			In addition, many glycoproteins in our data were enriched for immunity (p < 5.1×10-12), which is a central function of microglia in the brain.
PMC5795011-1-3	11	103	gly	glycopeptide	1725:1736	arg2	the glycopeptide sequence			the glycopeptide sequence						glycopeptide sequence	Hence, Mascot annotated mostly the peptide part of the glycopeptide sequence (Fig. 2C).
PMC5457524-1-7	73	126	gly	N-glycopeptide	11495:11508	arg2	intact N-glycopeptide identification			intact N-glycopeptide identification						N-glycopeptide	For intact N-glycopeptide identification, HILIC requires an additional chromatography step to achieve sufficient enrichment1819.
PMC7124471-1-10	19	60	gly	N-glycosites	2001:2012	arg2	the four N-glycosites	serotransferrin		N-glycosites		OGER		serotransferrin	P02787	N-glycosites	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.
PMC6243375-1-fig3	8	20	gly	glycoproteins	1033:1045	arg1	The 56 O‐linked glycoproteins	The 56 O‐linked glycoproteins				Fterm		glycoproteins			The 56 O‐linked glycoproteins with significant change between tumor and normal.
PMC7124471-1-8	1	53	gly	glycoproteins	285:297	arg1	the identified serum glycoproteins	the identified serum glycoproteins				Fterm		glycoproteins			Except for the component of complement and coagulation cascades, cell adhesion molecules and hematopoietic cell linage markers (CD molecules) were also enriched in the identified serum glycoproteins (supplementary Document S1).
PMC5795011-1-4	58	1014	gly	glycopeptide	10230:10241	arg2	glycopeptide MS2 spectra			glycopeptide MS2 spectra						glycopeptide	Therefore, we showed the advantages of using stepped HCD while generating glycopeptide MS2 spectra.
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.
PMC6243375-1-4	28	284	gly	glycoproteins	5150:5162	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			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.
PMC7124471-1-3	15	54	gly	glycosites	2378:2387	arg2	444 and 1536 N-linked glycosites			444 and 1536 N-linked glycosites						glycosites	Under 1% FDR, 915 and 2,724 N-linked deglycopeptides corresponding to 444 and 1536 N-linked glycosites from 219 and 724 N-linked glycoproteins were identified in UDGP and FDGP, respectively (Table I, supplemental Table S2).
PMC7124471-1-3	15	85	gly	deglycopeptides	2323:2337	arg2	915 and 2,724 N-linked deglycopeptides			915 and 2,724 N-linked deglycopeptides						deglycopeptides	Under 1% FDR, 915 and 2,724 N-linked deglycopeptides corresponding to 444 and 1536 N-linked glycosites from 219 and 724 N-linked glycoproteins were identified in UDGP and FDGP, respectively (Table I, supplemental Table S2).
PMC7124471-1-3	15	140	gly	glycoproteins	2415:2427	arg1	219 and 724 N-linked glycoproteins	219 and 724 N-linked glycoproteins				Fterm		glycoproteins			Under 1% FDR, 915 and 2,724 N-linked deglycopeptides corresponding to 444 and 1536 N-linked glycosites from 219 and 724 N-linked glycoproteins were identified in UDGP and FDGP, respectively (Table I, supplemental Table S2).
PMC5098438-1-1	19	12	gly	glycosylated	2888:2899	arg1	each glycosylated variant	each glycosylated variant				Fterm		variant			Glycan structures, confirmed by ion mobility mass spectrometry (discussed below), were identified within each glycosylated variant.
PMC5976746-1-5	39	308	gly	glycosylation	6187:6199	arg2	One glycosylation site			One glycosylation site						site	One glycosylation site that is different is at residue N197 where Man8GlcNAc2 is the most abundant structure on the trimer derived from CHO-M cells and Man9GlcNAc2 on trimer from 293F cells (21).
PMC5976746-1-5	39	399	gly	Man9GlcNAc2	6335:6345	arg1	trimer	trimer			Man9GlcNAc2	Fterm		trimer			One glycosylation site that is different is at residue N197 where Man8GlcNAc2 is the most abundant structure on the trimer derived from CHO-M cells and Man9GlcNAc2 on trimer from 293F cells (21).
PMC7107550-1-3	17	242	gly	identified	4129:4138	arg1	1 N-glyc motif			1 N-glyc motif						motif	Selection at sites 30 and 32 represent the RM-specific loss of 1 N-glyc motif at day 10 and 14 p.i. previously identified (Demma et al. 2005).
PMC6243375-1-1	2	25	gly	glycopeptides	185:197	arg2	the O‐linked glycopeptides			the O‐linked glycopeptides						glycopeptides	After washing, the O‐linked glycopeptides are enzymatically released from the support using an endo‐protease OpeRATOR that requires the presence of O‐linked glycans to specifically cleave on the N‐terminal side of O‐linked glycan‐occupied Ser or Thr (Fig 1A).
PMC6243375-1-fig3	1	13	gly	glycoproteins	275:287	arg1	differentially expressed O‐linked glycoproteins	differentially expressed O‐linked glycoproteins				Fterm		glycoproteins			Volcano plot of differentially expressed O‐linked glycoproteins between tumor and normal tissues.
PMC6731604-1-2	15	11	gly	glycoproteins	2115:2127	arg1	 > 1000 glycoproteins	 > 1000 glycoproteins				Fterm		glycoproteins			In addition, > 1000 glycoproteins have been detected from platelets and T cell cell lines, and > 500 glycoproteins have been identified from B-cell cell lines (Fig. 3).
PMC6731604-1-2	15	81	gly	glycoproteins	2196:2208	arg1	and > 500 glycoproteins	and > 500 glycoproteins				Fterm		glycoproteins			In addition, > 1000 glycoproteins have been detected from platelets and T cell cell lines, and > 500 glycoproteins have been identified from B-cell cell lines (Fig. 3).
PMC4595782-1-fig4	0	38	gly	Deglycosylation	0:14	arg1	recombinant apoplast-targeted SAC-Par-4-GFP				recombinant apoplast-targeted SAC-Par-4-GFP						Deglycosylation analysis of recombinant apoplast-targeted SAC-Par-4-GFP of transgenic line L3 and ER-targeted SAC-Par-4-GFP-SEKDEL of agroinfiltrated tobacco leaves protein extract.
PMC4595782-1-fig4	0	38	gly	Deglycosylation	0:14	arg1	ER-targeted SAC-Par-4-GFP-SEKDEL				ER-targeted SAC-Par-4-GFP-SEKDEL						Deglycosylation analysis of recombinant apoplast-targeted SAC-Par-4-GFP of transgenic line L3 and ER-targeted SAC-Par-4-GFP-SEKDEL of agroinfiltrated tobacco leaves protein extract.
PMC5795011-1-4	85	247	gly	glycopeptide	14604:14615	arg2	glycopeptide			glycopeptide						glycopeptide	The majority of the glycopeptide identification strategies consider the glycan structures as monosaccharide compositions, whereas we defined in our approach the glycan structures as linear sequences that best represents their behavior in the glycopeptide MS2 spectra.
PMC5795011-1-4	85	776	gly	glycopeptide	14382:14393	arg2	the glycopeptide identification strategies			the glycopeptide identification strategies						glycopeptide	The majority of the glycopeptide identification strategies consider the glycan structures as monosaccharide compositions, whereas we defined in our approach the glycan structures as linear sequences that best represents their behavior in the glycopeptide MS2 spectra.
PMC6243375-1-3	10	162	gly	glycopeptides	1713:1725	arg2	glycopeptides			glycopeptides						glycopeptides	HCD‐MS2 appeared to identify more unique glycopeptides compared to ETD‐MS2 that might be due to shorter glycopeptides with low charge states generated by trypsin and OpeRATOR digestion, while glycopeptides identified by ETD‐MS2 contained only +3 charge and above (Dataset EV5).
PMC6243375-1-3	10	172	gly	glycopeptides	1562:1574	arg2	more unique glycopeptides			more unique glycopeptides						glycopeptides	HCD‐MS2 appeared to identify more unique glycopeptides compared to ETD‐MS2 that might be due to shorter glycopeptides with low charge states generated by trypsin and OpeRATOR digestion, while glycopeptides identified by ETD‐MS2 contained only +3 charge and above (Dataset EV5).
PMC6243375-1-3	10	189	gly	glycopeptides	1625:1637	arg2	shorter glycopeptides			shorter glycopeptides						glycopeptides	HCD‐MS2 appeared to identify more unique glycopeptides compared to ETD‐MS2 that might be due to shorter glycopeptides with low charge states generated by trypsin and OpeRATOR digestion, while glycopeptides identified by ETD‐MS2 contained only +3 charge and above (Dataset EV5).
PMC7124471-1-8	4	5	gly	N-glycosite	599:609	arg2	N-glycosite	CD44		N-glycosite				CD44	P16070	N-glycosite N25	The N-glycosite N25 of CD44 locates at its extracellular part.
PMC3938046-1-fig4	2	22	gly	glycoproteins	203:215	arg1	identified glycoproteins	identified glycoproteins				Fterm		glycoproteins			(B) Gene ontology analysis of identified glycoproteins.
PMC7124471-1-4	32	27	gly	glycoproteins	5628:5640	arg1	serum glycoproteins	serum glycoproteins				Fterm		glycoproteins			This strategy enables elucidating the micro-heterogeneity of N-glycan in serum glycoproteins, as exemplified by MMRN1, LRP1 and APOB.
PMC6243375-1-4	14	244	gly	glycosylation	2672:2684	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	Overall enrichment of Pro was observed in the amino acids surrounding O‐linked glycosylation sites (Appendix Fig S2).
PMC5795011-1-4	79	163	gly	glycopeptide	13472:13483	arg2	glycopeptide			glycopeptide						glycopeptide	Moreover, it was even possible to extract the XIC values and quantitatively compare the glycopeptide identifications using Mascot Distiller.
PMC7124471-1-11	38	156	gly	deglycopeptide	5208:5221	arg2	deglycopeptide identifications			deglycopeptide identifications						deglycopeptide	In this regard, the FDR of deglycopeptide identifications was effectively controlled, and the tryptic peptides with some of the 16 PTMs and their unmodified versions will undergo matching and scoring in parallel.
PMC6243375-1-fig2	6	60	gly	glycosylation	625:637	arg2	the O‐linked glycosylation sites			the O‐linked glycosylation sites						sites	Landscape distribution of the O‐linked glycosylation sites and its frequency in proteins.
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		glycosites		Cterm		B	P02787	glycosites	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		glycosites		OGER		serotransferrin	P02787	glycosites	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	arg2	the eight glycosites	complement factor H		glycosites		OGER		complement factor H	P08603	glycosites	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		glycosites		Cterm		A	P08603	glycosites	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.
PMC7124471-1-10	18	36	gly	glycosite	1819:1827	arg2	The glycosite N523			The glycosite N523						glycosite N523	The glycosite N523 is distant from the binding interface, hence it has the least number of N-glycan masses identified.
PMC3942810-1-2	19	75	gly	N-glycosylated	3311:3324	arg1	N-glycosylated proteins	N-glycosylated proteins				Fterm		proteins			Site occupancy analyses showed that approximately 48% of N-glycosylated proteins carrying a single N-linked glycosylated site, 20% contained two sites, 16% retained three sites, and the rest carried four or more N-glycosylated sites (Figure 4).
PMC3942810-1-2	19	226	gly	N-glycosylated	3466:3479	arg1	four or more N-glycosylated sites			four or more N-glycosylated sites						sites	Site occupancy analyses showed that approximately 48% of N-glycosylated proteins carrying a single N-linked glycosylated site, 20% contained two sites, 16% retained three sites, and the rest carried four or more N-glycosylated sites (Figure 4).
PMC3942810-1-2	19	238	gly	glycosylated	3362:3373	arg1	a single N-linked glycosylated site			a single N-linked glycosylated site						site	Site occupancy analyses showed that approximately 48% of N-glycosylated proteins carrying a single N-linked glycosylated site, 20% contained two sites, 16% retained three sites, and the rest carried four or more N-glycosylated sites (Figure 4).
PMC5795011-1-4	51	114	gly	glycopeptide	9148:9159	arg2	potential glycopeptide identifications			potential glycopeptide identifications						glycopeptide	For any software tool, the MS2 spectra of intact glycopeptides should contain both peptide and glycan information in order to provide a scoring and ranking of potential glycopeptide identifications and matching the glycopeptides to protein sequences.
PMC5795011-1-4	51	337	gly	glycopeptides	9028:9040	arg2	intact glycopeptides			intact glycopeptides						glycopeptides	For any software tool, the MS2 spectra of intact glycopeptides should contain both peptide and glycan information in order to provide a scoring and ranking of potential glycopeptide identifications and matching the glycopeptides to protein sequences.
PMC5795011-1-4	51	862	gly	glycopeptides	9194:9206	arg2	the glycopeptides			the glycopeptides						glycopeptides	For any software tool, the MS2 spectra of intact glycopeptides should contain both peptide and glycan information in order to provide a scoring and ranking of potential glycopeptide identifications and matching the glycopeptides to protein sequences.
PMC7124471-1-11	74	36	gly	glycopeptide	10509:10520	arg2	serotransferrin glycopeptide			serotransferrin glycopeptide						glycopeptide	With the glycopetides identified here, a spectral library of serotransferrin glycopeptide can be constructed and applied to DIA workflow for its glycoform quantification.
PMC6243375-1-5	19	352	gly	glycopeptides	4426:4438	arg2	the released O‐linked glycopeptides			the released O‐linked glycopeptides						glycopeptides	The O‐linked glycan remains attached to the released O‐linked glycopeptides and provides oxonium ions in the MS/MS spectrum to facilitate confident identification.
PMC5795011-1-4	98	763	gly	glycoprotein	16828:16839	arg1	the custom glycoprotein databases	the custom glycoprotein databases				Fterm		glycoprotein			Considering the complexity involved in glycoproteomics, at this point we suggest using the custom glycoprotein databases that closely represent the samples used in the study.
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.
PMC5795011-1-4	16	1001	gly	attached	2698:2705	arg2	the core HexNAc residue AND the fucose			the core HexNAc residue	the fucose					residue	Though it is not possible to pinpoint the exact location of fucose residues, it can be easily concluded whether the fucose is attached to the core HexNAc residue or the HexNAc residues after the trimannosyl core glycan structure.
PMC5795011-1-4	16	1001	gly	attached	2698:2705	arg1	the HexNAc residues AND the fucose			the HexNAc residues	the fucose					residues	Though it is not possible to pinpoint the exact location of fucose residues, it can be easily concluded whether the fucose is attached to the core HexNAc residue or the HexNAc residues after the trimannosyl core glycan structure.
PMC7124471-1-7	7	21	gly	glycoproteins	1000:1012	arg1	the 526 serum glycoproteins	the 526 serum glycoproteins				Fterm		glycoproteins			The most enriched molecular function of the 526 serum glycoproteins is calcium ion binding and the second one is glycosaminoglycan (GAG) binding.
PMC3938046-1-5	11	71	gly	glycoproteins	1465:1477	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Considering the IPI_IDs of glycoproteins, 453 IPI_IDs overlapped between the 2 datasets, and 307 of 760 IPI_IDs (40%) were unique to our study (Additional file 4: Figure S6B).
PMC7124471-1-4	35	101	gly	glycopeptides	5983:5995	arg2	FGP, 11, 7, and 17 glycosites, 46, 40 and 281 glycopeptides			FGP, 11, 7, and 17 glycosites, 46, 40 and 281 glycopeptides						glycopeptides	In the intact glycopeptide data sets UGP and FGP, 11, 7, and 17 glycosites, 46, 40 and 281 glycopeptides, 45, 40, and 165 N-glycans were identified from MMRN1, LRP1 and APOB, respectively (supplemental Table S13).
PMC7124471-1-4	35	193	gly	glycosites	5956:5965	arg2	17 glycosites			17 glycosites						glycosites	In the intact glycopeptide data sets UGP and FGP, 11, 7, and 17 glycosites, 46, 40 and 281 glycopeptides, 45, 40, and 165 N-glycans were identified from MMRN1, LRP1 and APOB, respectively (supplemental Table S13).
PMC7124471-1-4	35	228	gly	glycopeptide	5906:5917	arg2	the intact glycopeptide data sets			the intact glycopeptide data sets						glycopeptide	In the intact glycopeptide data sets UGP and FGP, 11, 7, and 17 glycosites, 46, 40 and 281 glycopeptides, 45, 40, and 165 N-glycans were identified from MMRN1, LRP1 and APOB, respectively (supplemental Table S13).
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.
PMC5795011-1-4	54	599	gly	glycopeptide	9711:9722	arg2	glycopeptide			glycopeptide						glycopeptide sequences	The combination of collision based (HCD/CID) and electron transfer (ETD/ECD) based fragmentation techniques provide complementary information about the glycopeptide sequences.
PMC3942810-1-2	0	100	gly	N-glycosylated	8:21	arg1	N-glycosylated sites			N-glycosylated sites						sites	Mapping N-glycosylated sites.
PMC3938046-1-1	16	163	gly	glycopeptides	2440:2452	arg2	glycopeptides			glycopeptides						glycopeptides	Briefly, glycopeptides that were enriched from 300 μg of whole-cell lysates were analyzed on an Orbitrap Velos and Q Exactive.
PMC6243375-1-5	28	113	gly	glycosylation	5906:5918	arg2	these O‐linked glycosylation sites			these O‐linked glycosylation sites						sites	Motif analysis of the amino acid sequence surrounding these O‐linked glycosylation sites revealed that Pro was favored at the +3 and −1 positions.
PMC6243375-1-5	18	136	gly	glycosylation	4343:4355	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	The solid support specifically binds peptides and maximizes the removal of non‐bound molecules, while the OpeRATOR enzyme specifically cleaves on the N‐terminal side of glycan‐occupied Ser and Thr residues of the bound peptides to release O‐linked glycosylation sites at the N‐terminus of peptides enabling localization of O‐linked glycosylation sites.
PMC6243375-1-5	18	189	gly	glycosylation	4259:4271	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	The solid support specifically binds peptides and maximizes the removal of non‐bound molecules, while the OpeRATOR enzyme specifically cleaves on the N‐terminal side of glycan‐occupied Ser and Thr residues of the bound peptides to release O‐linked glycosylation sites at the N‐terminus of peptides enabling localization of O‐linked glycosylation sites.
PMC6243375-1-5	18	263	gly	Ser	4196:4198	arg1	residues			residues						Ser and Thr residues	The solid support specifically binds peptides and maximizes the removal of non‐bound molecules, while the OpeRATOR enzyme specifically cleaves on the N‐terminal side of glycan‐occupied Ser and Thr residues of the bound peptides to release O‐linked glycosylation sites at the N‐terminus of peptides enabling localization of O‐linked glycosylation sites.
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.
PMC6243375-1-4	24	169	gly	glycosylated	4433:4444	arg1	These heavily glycosylated proteins	These heavily glycosylated proteins				Fterm		proteins			These heavily glycosylated proteins appeared to show continuous clusters of many vincinal sites that nearly cover the whole proteins such as VCAN, mucin‐1 (MUC1), and aggrecan core protein (ACAN).
PMC5795011-1-4	67	829	gly	glycopeptide	11623:11634	arg2	O-linked glycopeptide analysis			O-linked glycopeptide analysis						glycopeptide	The obtained results using bovine fetuin documented that the Mascot search engine can indeed be used for O-linked glycopeptide analysis.
PMC3938046-1-1	17	0	gly	glycopeptides	2564:2576	arg2	glycopeptides			glycopeptides						glycopeptides	Also, glycopeptides that were captured from 300 μg of crude membrane fractions were analyzed on an LTQ Velos.
PMC5795011-1-4	30	267	gly	glycopeptides	4826:4838	arg2	the glycopeptides			the glycopeptides						glycopeptides	Label-free quantification of the glycopeptides (aggressive vs. indolent prostate cancer) was performed using the replicate quantitation protocol of Mascot Distiller.
PMC5795011-1-4	11	361	gly	glycopeptides	1886:1898	arg2	tetra-antennary glycopeptides			tetra-antennary glycopeptides						glycopeptides	MS2 spectra shown in Fig. 5 D–F were annotated to di-sialylated bi-, tri- and tetra-antennary glycopeptides, confirmed by a complete series of y ions representing both peptide and glycan cleavages.
PMC5795011-1-4	11	919	gly	both	1955:1958	arg1	peptide			peptide						peptide	MS2 spectra shown in Fig. 5 D–F were annotated to di-sialylated bi-, tri- and tetra-antennary glycopeptides, confirmed by a complete series of y ions representing both peptide and glycan cleavages.
PMC5795011-1-4	128	1005	gly	glycoprotein	21976:21987	arg1	a custom glycoprotein database	a custom glycoprotein database				Fterm		glycoprotein			The linear glycan sequences as well as the script to prepare a custom glycoprotein database are presented along with this report, and just needs to run a single command before the database is ready.
PMC5457524-1-5	9	36	gly	non-glycosylated	1073:1088	arg1	non-glycosylated peptides			non-glycosylated peptides						peptides	Importantly, non-glycosylated peptides are not enriched by either wt Fbs1 or the GYR variant.
PMC3942810-2-2	7	83	gly	glycosylation	1180:1192	arg2	comprehensive glycosylation sites			comprehensive glycosylation sites						sites	By adopting two different methods based on lectin and hydrazide enrichment, comprehensive glycosylation sites were assigned in RJ, namely 46 by lectin resin and 16 by hydrazide chemistry.
PMC3942810-2-2	4	215	gly	glycopeptides	668:680	arg2	glycopeptides			glycopeptides						glycopeptides	Capturing the maximum number of glycopeptides is of great importance for the analysis of mapping glycosylated sites[52,53], and is achievable using the complementary enrichment of glycopeptides with techniques such as hydrazide chemistry and lectin based protocols.
PMC3942810-2-2	4	442	gly	glycopeptides	520:532	arg2	glycopeptides			glycopeptides						glycopeptides	Capturing the maximum number of glycopeptides is of great importance for the analysis of mapping glycosylated sites[52,53], and is achievable using the complementary enrichment of glycopeptides with techniques such as hydrazide chemistry and lectin based protocols.
PMC3942810-2-2	4	630	gly	glycosylated	585:596	arg1	glycosylated sites[52,53]			glycosylated sites[52,53]						sites[52,53	Capturing the maximum number of glycopeptides is of great importance for the analysis of mapping glycosylated sites[52,53], and is achievable using the complementary enrichment of glycopeptides with techniques such as hydrazide chemistry and lectin based protocols.
PMC7124471-1-fig4	0	7	gly	glycoprotein	63:74	arg1	glycoprotein standards	glycoprotein standards				Fterm		glycoprotein			Validation of semi-tryptic digestion and 16 PTMs setting using glycoprotein standards and serum spiked with glycoprotein standards.
PMC7124471-1-fig4	0	17	gly	glycoprotein	108:119	arg1	glycoprotein standards	glycoprotein standards				Fterm		glycoprotein			Validation of semi-tryptic digestion and 16 PTMs setting using glycoprotein standards and serum spiked with glycoprotein standards.
PMC5098438-1-5	11	256	gly	glycoproteins	1964:1976	arg1	recombinant glycoproteins	recombinant glycoproteins				Fterm		glycoproteins			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.
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.
PMC5795011-1-4	42	443	gly	glycoproteins	7373:7385	arg1	the detectable glycoproteins	the detectable glycoproteins				Fterm		glycoproteins			The deamidated proteins (280 proteins) identified after the PNGaseF treatment potentially represent well the detectable glycoproteins present in the 24 serum samples.
PMC4595782-1-fig4	5	2	gly	deglycosylated	877:890	arg1	plant SAC-Par-4				plant SAC-Par-4						Arrows point to the deglycosylated form of plant SAC-Par-4.
PMC3942810-1-2	11	193	gly	N-glycosylated	1792:1805	arg1	those 53 unique N-glycosylated sites			those 53 unique N-glycosylated sites						sites	Among those 53 unique N-glycosylated sites, 21 were identified by lectin enrichment alone, eight were uniquely identified by the hydrazide enrichment, and 18 were identified by both enrichment methods using orbitrap-based MS (Figure 2A).
PMC6243375-1-5	16	78	gly	glycosylation	3619:3631	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	The main advantages of EXoO are (i) applicability for analysis of clinical samples including tissue, body fluid, and primary cells; (ii) precise localization of O‐linked glycosylation sites; (iii) simultaneous definition of O‐linked glycans at the glycosylation sites; and (iv) no requirement for ETD mass spectrometry for site localization.
PMC6243375-1-5	16	327	gly	glycosylation	3697:3709	arg2	the glycosylation sites			the glycosylation sites						sites	The main advantages of EXoO are (i) applicability for analysis of clinical samples including tissue, body fluid, and primary cells; (ii) precise localization of O‐linked glycosylation sites; (iii) simultaneous definition of O‐linked glycans at the glycosylation sites; and (iv) no requirement for ETD mass spectrometry for site localization.
PMC6731604-1-3	9	16	gly	glycoproteins	1222:1234	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			The urinary glycoproteins were also compared with glycoproteins from eight different tissues.
PMC6731604-1-3	9	61	gly	glycoproteins	1184:1196	arg1	The urinary glycoproteins	The urinary glycoproteins				Fterm		glycoproteins			The urinary glycoproteins were also compared with glycoproteins from eight different tissues.
PMC3942810-2-2	2	556	gly	glycosylation	331:343	arg2	42 novel N-linked glycosylation sites			42 novel N-linked glycosylation sites						sites	Among these, 42 novel N-linked glycosylation sites were reported in RJ proteins.
PMC6702745-2-2	3	0	gly	glycosylated	301:312	arg1	heavily glycosylated proteins	heavily glycosylated proteins				Fterm		proteins			Mucins are heavily glycosylated proteins where glycosylation is relevant to their function.
PMC7124471-1-11	27	76	gly	glycopeptide	3537:3548	arg2	N-linked intact glycopeptide identification			N-linked intact glycopeptide identification						glycopeptide	Compared with published workflows for N-linked intact glycopeptide identification, the widespread presence of truncated proteins or variable proteoforms in serum has been taken into account in the proposed workflow.
PMC6731604-1-2	4	14	gly	glycosites	595:604	arg2	more than 5000 glycosites			more than 5000 glycosites						glycosites	There were also more than 5000 glycosites and 2000 glycoproteins identified from liver and ovary.
PMC6731604-1-2	4	77	gly	glycoproteins	615:627	arg1	2000 glycoproteins	2000 glycoproteins				Fterm		glycoproteins			There were also more than 5000 glycosites and 2000 glycoproteins identified from liver and ovary.
PMC7124471-1-11	44	263	gly	glycopeptides	6129:6141	arg2	glycopeptides			glycopeptides						glycopeptides	It also helps to recognize those low-confidence N-glycan masses and glycopeptides identified, which is critical in completing the human serum N-glycan database.
PMC5976746-1-fig3	12	27	gly	Mn = number	1291:1301	arg1	H = hybrid residues			H = hybrid residues						residues	The glycan names are as previously described (43) and as follows: Mn = number (n) of mannose residues; An = number (n) of antennae (e.g., A2 = biantennary); Gn = number (n) of galactose residues; H = hybrid residues; F indicates the presence of a core fucose.
PMC7107550-1-3	16	63	gly	see	4005:4007	arg1	sites 30, 32, 104, and 105			sites 30, 32, 104, and 105						sites	Of the 6 RM-specific adaptive sites, 4 are part of N-glyc motifs (sites 30, 32, 104, and 105; see fig. 1).
PMC7124471-1-11	82	293	gly	glycoproteins	11541:11553	arg1	serum glycoproteins	serum glycoproteins				Fterm		glycoproteins			Accurate identification of each N-glycan composite is a prerequisite for functional investigation of site-specific glycoform of serum glycoproteins.
PMC7124471-1-11	82	439	gly	glycoform	11522:11530	arg1	serum glycoproteins	serum glycoproteins				Fterm		glycoproteins			Accurate identification of each N-glycan composite is a prerequisite for functional investigation of site-specific glycoform of serum glycoproteins.
PMC7124471-1-7	11	22	gly	N-glycosites	1401:1412	arg2	nine known N-glycosites			nine known N-glycosites						N-glycosites	There are nine known N-glycosites in CFH, from which 8 N-glycosites were identified in this study.
PMC7124471-1-7	11	57	gly	N-glycosites	1435:1446	arg2	8 N-glycosites			8 N-glycosites						N-glycosites	There are nine known N-glycosites in CFH, from which 8 N-glycosites were identified in this study.
PMC5795011-1-3	8	178	gly	glycoprotein	1314:1325	arg1	alpha-1-acid glycoprotein	alpha-1-acid glycoprotein				Fterm		glycoprotein			As an example, the tryptic peptides of alpha-1-acid glycoprotein were fragmented at different NCE values.
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.
PMC6702745-2-1	23	4	gly	glycoproteins	2961:2973	arg1	WNT proteins	WNT proteins				Fterm		proteins			WNT proteins are secreted glycoproteins, which bind an extracellular cysteine-rich domain of the Frizzled receptor family.
PMC6702745-2-1	23	4	gly	glycoproteins	2961:2973	arg1	secreted glycoproteins	secreted glycoproteins				Fterm		glycoproteins			WNT proteins are secreted glycoproteins, which bind an extracellular cysteine-rich domain of the Frizzled receptor family.
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	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).
PMC5795011-1-4	64	181	gly	glycosylation	11134:11146	arg1	serum alpha-1-acid glycoprotein 1	alpha-1-acid glycoprotein 1		Asn 93		OGER		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).
PMC5795011-1-4	64	181	gly	glycosylation	11134:11146	arg1	serum alpha-1-acid glycoprotein 1	alpha-1-acid glycoprotein 1		site		OGER		alpha-1-acid glycoprotein 1	P02763	site	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).
PMC6243375-1-5	2	108	gly	glycoproteins	289:301	arg1	56 O‐linked glycoproteins	56 O‐linked glycoproteins				Fterm		glycoproteins			This identified 56 O‐linked glycoproteins as exhibiting significant change using scoring criteria of at least a twofold change together with a difference in at least 10 PSMs between normal and tumor samples (Fig 3B and Appendix Table S1).
PMC5795011-1-4	36	165	gly	glycopeptide	5885:5896	arg2	the median glycopeptide ratio			the median glycopeptide ratio						glycopeptide	For example, the median glycopeptide ratio of the tri-sialylated tri-antennary glycopeptides is near 1.0 based on 77 values, whereas the mono- (73 values) and di-fucosylated (19 values) versions have a median peptide ratio slightly above 1.0.
PMC5795011-1-4	36	730	gly	tri-sialylated	5911:5924	arg1	the tri-sialylated tri-antennary glycopeptides			the tri-sialylated tri-antennary glycopeptides						glycopeptides	For example, the median glycopeptide ratio of the tri-sialylated tri-antennary glycopeptides is near 1.0 based on 77 values, whereas the mono- (73 values) and di-fucosylated (19 values) versions have a median peptide ratio slightly above 1.0.
PMC5795011-1-4	36	1030	gly	glycopeptides	5940:5952	arg2	the tri-sialylated tri-antennary glycopeptides			the tri-sialylated tri-antennary glycopeptides						glycopeptides	For example, the median glycopeptide ratio of the tri-sialylated tri-antennary glycopeptides is near 1.0 based on 77 values, whereas the mono- (73 values) and di-fucosylated (19 values) versions have a median peptide ratio slightly above 1.0.
PMC5795011-1-4	73	8	gly	sialylated	12480:12489	arg1	N-linked sialylated glycopeptide variants	N-linked sialylated glycopeptide variants				Fterm		variants			Mascot annotated a total of 257 glycoproteins containing 4653 redundant N-linked sialylated glycopeptide variants with an estimated false discovery rate (FDR) of 8%.
PMC5795011-1-4	73	450	gly	glycopeptide	12491:12502	arg2	N-linked sialylated glycopeptide variants			N-linked sialylated glycopeptide variants						glycopeptide	Mascot annotated a total of 257 glycoproteins containing 4653 redundant N-linked sialylated glycopeptide variants with an estimated false discovery rate (FDR) of 8%.
PMC5795011-1-4	73	712	gly	glycoproteins	12431:12443	arg1	257 glycoproteins	257 glycoproteins				Fterm		glycoproteins			Mascot annotated a total of 257 glycoproteins containing 4653 redundant N-linked sialylated glycopeptide variants with an estimated false discovery rate (FDR) of 8%.
PMC7124471-1-6	24	157	gly	glycosites	4368:4377	arg2	5 glycosites			5 glycosites						glycosites	We identified this major glycan on 5 glycosites including N87, N216, N228, N285, and N298 in commercial HRP (supplemental Table S22).
PMC7124471-1-6	24	157	gly	glycosites	4368:4377	arg2	N228			N87, N216, N228, N285, and N298						N87, N216, N228, N285, and N298	We identified this major glycan on 5 glycosites including N87, N216, N228, N285, and N298 in commercial HRP (supplemental Table S22).
PMC7124471-1-6	24	157	gly	glycosites	4368:4377	arg2	N87			N87, N216, N228, N285, and N298						N87, N216, N228, N285, and N298	We identified this major glycan on 5 glycosites including N87, N216, N228, N285, and N298 in commercial HRP (supplemental Table S22).
PMC7124471-1-6	24	157	gly	glycosites	4368:4377	arg2	N298			N87, N216, N228, N285, and N298						N87, N216, N228, N285, and N298	We identified this major glycan on 5 glycosites including N87, N216, N228, N285, and N298 in commercial HRP (supplemental Table S22).
PMC7124471-1-6	24	157	gly	glycosites	4368:4377	arg2	N87			N87, N216, N228, N285, and N298						N87, N216, N228, N285, and N298	We identified this major glycan on 5 glycosites including N87, N216, N228, N285, and N298 in commercial HRP (supplemental Table S22).
PMC7124471-1-6	24	157	gly	glycosites	4368:4377	arg2	N298			N87, N216, N228, N285, and N298						N87, N216, N228, N285, and N298	We identified this major glycan on 5 glycosites including N87, N216, N228, N285, and N298 in commercial HRP (supplemental Table S22).
PMC7124471-1-6	24	157	gly	glycosites	4368:4377	arg2	N298			N87, N216, N228, N285, and N298						N87, N216, N228, N285, and N298	We identified this major glycan on 5 glycosites including N87, N216, N228, N285, and N298 in commercial HRP (supplemental Table S22).
PMC5457524-1-6	1	51	gly	N-glycopeptide	71:84	arg2	N-glycopeptide enrichment			N-glycopeptide enrichment						N-glycopeptide	We assessed N-glycopeptide enrichment from a biological sample using Fbs1 GYR.
PMC6243375-1-1	9	68	gly	glycopeptides	1750:1762	arg2	O‐linked glycopeptides			O‐linked glycopeptides						glycopeptides	The analysis of fetuin demonstrated the ability of EXoO to enrich and identify O‐linked glycopeptides at specific O‐linked glycosylation sites and their corresponding O‐linked glycans.
PMC6243375-1-1	9	73	gly	glycosylation	1785:1797	arg2	specific O‐linked glycosylation sites			specific O‐linked glycosylation sites						sites	The analysis of fetuin demonstrated the ability of EXoO to enrich and identify O‐linked glycopeptides at specific O‐linked glycosylation sites and their corresponding O‐linked glycans.
PMC6243375-1-4	9	172	gly	glycosylation	1962:1974	arg2	new O‐linked glycosylation sites			new O‐linked glycosylation sites						sites	In the case of IGHA1, four of the five known sites on Ser residues and two new sites on Thr residues were mapped supportive of EXoO's capacity to both localize known and discover new O‐linked glycosylation sites.
PMC7124471-1-9	4	20	gly	glycopeptide	431:442	arg2	N-linked glycopeptide identification			N-linked glycopeptide identification						glycopeptide	In another serum glycoproteomic study, about 200 kind of N-glycans were used for N-linked glycopeptide identification (7).
PMC6243375-1-3	13	168	gly	composition	2215:2225	arg1	glycan composition Hex			position	glycan composition Hex					position	Analysis of our data from tissue, serum, and cells revealed that approximately 69% of total PSM contained glycan composition Hex(1)HexNAc(1) that was most likely to be core 1 mucin‐type glycan Gal‐GalNAc.
PMC6731604-1-3	5	39	gly	glycoproteins	783:795	arg1	47.6 ± 16.5% glycoproteins	47.6 ± 16.5% glycoproteins				Fterm		glycoproteins			An average of 47.6 ± 16.5% glycoproteins identified in tissues were also detected in serum.
PMC3942810-1-2	2	94	gly	N-glycopeptides	449:463	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	The introduction of 18O-water in the process of PNGase F digestion added to confidence to the identification of N-glycopeptides.
PMC7124471-1-9	7	69	gly	glycosite	872:880	arg2	N-linked glycosite			N-linked glycosite						glycosite	It also influenced the number of N-linked glycoprotein or N-linked glycosite but was insignificant.
PMC7124471-1-9	7	112	gly	glycoprotein	847:858	arg1	N-linked glycoprotein	N-linked glycoprotein				Fterm		glycoprotein			It also influenced the number of N-linked glycoprotein or N-linked glycosite but was insignificant.
PMC7124471-1-4	26	243	gly	glycopeptides	4430:4442	arg2	N-linked intact glycopeptides			N-linked intact glycopeptides						glycopeptides	The number of N-linked intact glycopeptides increased by 8320 when using 701 N-linked glycan masses database compared to that using 194 N-glycan masses database, indicating that the number of human N-glycans in GlycomeDB database is underestimated.
PMC5795011-1-fig2	0	5	gly	N-glycopeptide	61:74	arg2	a di-sialylated bi-antennary N-glycopeptide			a di-sialylated bi-antennary N-glycopeptide						N-glycopeptide	Mascot annotated MS2 spectra of a di-sialylated bi-antennary N-glycopeptide (m/z 1177.81373+) fragmented at different NCE values.
PMC5795011-1-fig2	0	28	gly	di-sialylated	34:46	arg1	a di-sialylated bi-antennary N-glycopeptide			a di-sialylated bi-antennary N-glycopeptide						N-glycopeptide	Mascot annotated MS2 spectra of a di-sialylated bi-antennary N-glycopeptide (m/z 1177.81373+) fragmented at different NCE values.
PMC2538527-1-4	13	290	gly	glycoform	1748:1756	arg1	this protein	this protein				Fterm		protein			The masses of the principal glycoform of this protein correspond to the mature IFNα2b peptide chain plus the glycans indicated (Fig. 6B).
PMC5457524-1-6	16	135	gly	N-glycosites	2570:2581	arg2	many more unique N-glycosites			many more unique N-glycosites						N-glycosites	This enabled the identification of many more unique N-glycosites.
PMC3942810-1-fig3	2	0	gly	glycoprotein	165:176	arg1	known glycoprotein	known glycoprotein				Fterm		glycoprotein			“6” is potential sites predicted in known glycoprotein, and “3” is potential glycosylation sites identified in novel glycoprotein.
PMC3942810-1-fig3	2	7	gly	glycoprotein	240:251	arg1	novel glycoprotein	novel glycoprotein				Fterm		glycoprotein			“6” is potential sites predicted in known glycoprotein, and “3” is potential glycosylation sites identified in novel glycoprotein.
PMC3942810-1-fig3	2	17	gly	glycosylation	200:212	arg2	potential glycosylation sites			potential glycosylation sites						sites	“6” is potential sites predicted in known glycoprotein, and “3” is potential glycosylation sites identified in novel glycoprotein.
PMC5795011-1-2	0	41	gly	glycopeptide	11:22	arg2	Linearized glycopeptide sequences			Linearized glycopeptide sequences						glycopeptide sequences	Linearized glycopeptide sequences and custom glycoprotein databases.
PMC5795011-1-2	0	46	gly	glycoprotein	45:56	arg1	custom glycoprotein databases	custom glycoprotein databases				Fterm		glycoprotein			Linearized glycopeptide sequences and custom glycoprotein databases.
PMC5795011-1-4	37	332	gly	tri-sialylated	6108:6121	arg1	The tri-sialylated tetra-antennary glycopeptides			The tri-sialylated tetra-antennary glycopeptides						glycopeptides	The tri-sialylated tetra-antennary glycopeptides had two different populations at median peptide ratios of 1.0 and 1.5, whereas the fucosylated version had a median peptide ratios slightly above 1.0 (Supplementary Fig. 5).
PMC5795011-1-4	37	668	gly	glycopeptides	6139:6151	arg2	The tri-sialylated tetra-antennary glycopeptides			The tri-sialylated tetra-antennary glycopeptides						glycopeptides	The tri-sialylated tetra-antennary glycopeptides had two different populations at median peptide ratios of 1.0 and 1.5, whereas the fucosylated version had a median peptide ratios slightly above 1.0 (Supplementary Fig. 5).
PMC5457524-1-6	8	87	gly	N-glycopeptides	1073:1087	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	We also examined the recovery efficiency of N-glycopeptides in the Fbs1 GYR enrichment sample.
PMC6243375-1-5	22	26	gly	glycosylation	4872:4884	arg2	the more than 3,000 O‐linked glycosylation sites			the more than 3,000 O‐linked glycosylation sites						sites	Analysis of the more than 3,000 O‐linked glycosylation sites identified by EXoO revealed many glycoproteins that were previously not known to be modified by O‐linked glycosylation.
PMC6243375-1-5	22	170	gly	glycoproteins	4925:4937	arg1	many glycoproteins	many glycoproteins				Fterm		glycoproteins			Analysis of the more than 3,000 O‐linked glycosylation sites identified by EXoO revealed many glycoproteins that were previously not known to be modified by O‐linked glycosylation.
PMC2538527-1-4	1	8	gly	glycosylated	172:183	arg1	a glycosylated active protein	a glycosylated active protein				Fterm		protein			One of the major interests for producing IFNα2b in mammalian cells is to generate a glycosylated active protein.
PMC7124471-1-6	18	122	gly	glycopeptides	3396:3408	arg2	the intact glycopeptides' spectra			the intact glycopeptides' spectra						glycopeptides	An alternative way of evaluating the FDR is by searching the intact glycopeptides' spectra from a glycoprotein standard against the protein and glycan mass database from another unrelated species.
PMC7124471-1-6	18	223	gly	glycoprotein	3426:3437	arg1	a glycoprotein	a glycoprotein				Fterm		glycoprotein			An alternative way of evaluating the FDR is by searching the intact glycopeptides' spectra from a glycoprotein standard against the protein and glycan mass database from another unrelated species.
PMC3942810-1-fig1	1	0	gly	N-glycosylated	106:119	arg1	the N-glycosylated site			the N-glycosylated site						site	The tandem mass spectrum of the N-glycosylated site is identified in peptide GESLN(+2.99)KSLPILHEWK using 18O-water labeling.
PMC6731604-1-3	0	53	gly	glycoproteins	32:44	arg1	urinary glycoproteins	urinary glycoproteins				Fterm		glycoproteins			Comparison of serum and urinary glycoproteins with tissue-derived glycoproteins.
PMC6731604-1-3	0	89	gly	glycoproteins	66:78	arg1	tissue-derived glycoproteins	tissue-derived glycoproteins				Fterm		glycoproteins			Comparison of serum and urinary glycoproteins with tissue-derived glycoproteins.
PMC6243375-1-2	2	109	gly	glycopeptides	299:311	arg2	O‐linked glycopeptides			O‐linked glycopeptides						glycopeptides	To do this, O‐linked glycopeptides were extracted using EXoO and fractionated into 24 fractions and then subjected to LC‐MS/MS analysis (Fig 2A).
PMC5795011-1-4	45	1154	gly	glycopeptide	7890:7901	arg2	automated glycopeptide analysis			automated glycopeptide analysis						glycopeptide	A large variety of informatics tools have been developed for automated glycopeptide analysis which advanced the glycoproteomics field.
PMC6243375-1-3	20	184	gly	glycosylation	3601:3613	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	It can be anticipated that using enzymes other than trypsin for generating peptides will increase the identification of O‐linked glycosylation sites (Choudhary et al, 2003).
PMC5457524-1-6	7	110	gly	N-glycopeptides	1012:1026	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	This suggests that a majority of the enriched peptides are N-glycopeptides.
PMC7124471-1-fig6	3	24	gly	glycopeptide	284:295	arg2	this glycopeptide's			this glycopeptide's						glycopeptide	B, Extracted ion chromatographs of the first six isotopic peaks of this glycopeptide's precursor ion.
PMC3942810-2-2	1	544	gly	25 N-glycoproteins	238:255	arg1	25 N-glycoproteins	25 N-glycoproteins				Fterm		25 N-glycoproteins			By using two complementary enrichment protocols (hydrazide chemistry and lectin resin) and two orbitrap-based and triple TOF-based double high LC-MS/MS systems, we have achieved an in-depth identification of 25 N-glycoproteins that mapped on to 53 sites on RJ proteins.
PMC6731604-1-1	20	79	gly	glycosites	4282:4291	arg2	glycosites			glycosites						glycosites	Our results showed that although the identified human glycoproteins and glycosites have been steadily increasing since 2003 when the first two glycoproteomic studies were published [12, 16], the huge increase mainly occurred in recent years (Fig. 2b).
PMC6731604-1-1	20	169	gly	glycoproteins	4264:4276	arg1	the identified human glycoproteins	the identified human glycoproteins				Fterm		glycoproteins			Our results showed that although the identified human glycoproteins and glycosites have been steadily increasing since 2003 when the first two glycoproteomic studies were published [12, 16], the huge increase mainly occurred in recent years (Fig. 2b).
PMC5795011-1-3	6	43	gly	glycopeptide	1087:1098	arg2	glycopeptide sequences			glycopeptide sequences						glycopeptide sequences	The lack of peptide fragmentation information in the MS2 spectrum might create difficulties in differentiating glycopeptide sequences resulting in similar Mascot ion scores.
PMC5795011-1-3	0	125	gly	glycopeptides	34:46	arg2	glycopeptides			glycopeptides						glycopeptides	Identification of N- and O-linked glycopeptides by Mascot.
PMC6731604-1-3	3	23	gly	glycoproteins	577:589	arg1	tissue glycoproteins	tissue glycoproteins				Fterm		glycoproteins			Using the data in N-GlycositeAtlas, we compared the glycoprotein contents between serum and eight different tissues (cell line-related glycoproteins were not included) to investigate the detectability of tissue glycoproteins in serum.
PMC6731604-1-3	3	85	gly	glycoprotein	418:429	arg1	the glycoprotein contents	the glycoprotein contents				Fterm		glycoprotein			Using the data in N-GlycositeAtlas, we compared the glycoprotein contents between serum and eight different tissues (cell line-related glycoproteins were not included) to investigate the detectability of tissue glycoproteins in serum.
PMC6731604-1-3	3	96	gly	glycoproteins	501:513	arg1	cell line-related glycoproteins	cell line-related glycoproteins				Fterm		glycoproteins			Using the data in N-GlycositeAtlas, we compared the glycoprotein contents between serum and eight different tissues (cell line-related glycoproteins were not included) to investigate the detectability of tissue glycoproteins in serum.
PMC3942810-1-2	4	23	gly	25 N-glycoproteins	591:608	arg1	25 N-glycoproteins	25 N-glycoproteins				Fterm		25 N-glycoproteins			Overall, 25 N-glycoproteins carrying 53 unique N-linked glycosylation sites represented 60% of the total identified proteins in RJ.
PMC3942810-1-2	4	168	gly	glycosylation	638:650	arg2	53 unique N-linked glycosylation sites			53 unique N-linked glycosylation sites						sites	Overall, 25 N-glycoproteins carrying 53 unique N-linked glycosylation sites represented 60% of the total identified proteins in RJ.
PMC7081908-1-5	1	84	gly	PNGS	123:126	arg1	glycan composition			glycan composition						position,	Finally, we sought to test whether any observed lot-to-lot variations in PNGS occupancy and glycan composition, no matter how minor they might be, had an effect on key antigenic features of these proteins.
PMC5457524-1-6	11	125	gly	N-glycopeptides	1569:1583	arg2	the N-glycopeptides			the N-glycopeptides						N-glycopeptides	These N-glycan profiles suggest Fbs1 GYR efficiently binds most N-glycans and thus recovers most of the N-glycopeptides from human serum samples.
PMC5795011-1-4	62	73	gly	glycopeptide	10830:10841	arg2	glycopeptide annotation			glycopeptide annotation						glycopeptide	A large number of available software tools for glycopeptide annotation deals mainly with N-linked glycosylation.
PMC5795011-1-4	80	1067	gly	glycopeptide	13552:13563	arg2	glycopeptide			glycopeptide						glycopeptide	The protein as well as the glycopeptide ratios indicated very little to no significant differences between indolent and aggressive serum prostate cancer samples.
PMC3942810-2-2	9	572	gly	53 N-glycosylation	1560:1577	arg2	the 53 N-glycosylation sites			the 53 N-glycosylation sites						sites	Together, of the 53 N-glycosylation sites assigned in RJ proteins, 42 were mapped as novel.
PMC7124471-1-fig3	1	29	gly	glycopeptide	140:151	arg2	serum N-linked intact glycopeptide identification			serum N-linked intact glycopeptide identification						glycopeptide	A, The distribution of 739 N-glycan masses used for serum N-linked intact glycopeptide identification.
PMC5795011-1-4	76	168	gly	glycopeptides	13020:13032	arg2	all the glycopeptides			all the glycopeptides						glycopeptides	Provided fragmentation information of both peptide and glycans of all the glycopeptides, FDR tools provided in Mascot can be confidently used.
PMC6243375-1-5	32	195	gly	glycoproteins	6913:6925	arg1	O‐linked glycoproteins	O‐linked glycoproteins				Fterm		glycoproteins			It also identified aberrant expression of O‐linked glycoproteins in kidney tumor tissue compared to normal tissue pointing to its utility in clinical investigations.
PMC6731604-1-4	9	63	gly	glycosylation	2069:2081	arg2	the glycosylation sites			the glycosylation sites						sites	The following information is included in the database: (1) UniProt accession numbers of glycoproteins; (2) whether the protein has been reviewed in the UniProt database; (3) protein names; (4) gene names; (5) location of the glycosylation sites; (6) identified glycosite-containing peptides; (7) the protein sequence at ± 20 amino acids surrounding the identified glycosylation site; (8) names of tissues/body fluids/cell lines where the glycosite-containing peptide was identified; (9) year of publication; and (10) references.
PMC6731604-1-4	9	102	gly	glycosylation	2208:2220	arg2	the identified glycosylation site			the identified glycosylation site						site	The following information is included in the database: (1) UniProt accession numbers of glycoproteins; (2) whether the protein has been reviewed in the UniProt database; (3) protein names; (4) gene names; (5) location of the glycosylation sites; (6) identified glycosite-containing peptides; (7) the protein sequence at ± 20 amino acids surrounding the identified glycosylation site; (8) names of tissues/body fluids/cell lines where the glycosite-containing peptide was identified; (9) year of publication; and (10) references.
PMC6731604-1-4	9	119	gly	glycoproteins	1932:1944	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			The following information is included in the database: (1) UniProt accession numbers of glycoproteins; (2) whether the protein has been reviewed in the UniProt database; (3) protein names; (4) gene names; (5) location of the glycosylation sites; (6) identified glycosite-containing peptides; (7) the protein sequence at ± 20 amino acids surrounding the identified glycosylation site; (8) names of tissues/body fluids/cell lines where the glycosite-containing peptide was identified; (9) year of publication; and (10) references.
PMC5457524-1-7	8	255	gly	N-glycopeptides	1353:1367	arg2	Intact N-glycopeptides			Intact N-glycopeptides						N-glycopeptides	Intact N-glycopeptides were identified by using Byonic software to compare the HCD spectra against the human proteome database (uniprot human up000005640) and the 57 most common N-glycan structures in human plasma.
PMC2762462-1-3	15	102	gly	glycoprotein	2461:2472	arg1	a donor glycoprotein	a donor glycoprotein				Fterm		glycoprotein			Using a novel assay for sialyltransferase activity, we found that the ST6 enzyme produced in these engineered strains is catalytically active in the transfer of sialic acid onto a donor glycoprotein.
PMC2538527-1-fig7	2	51	gly	glycopeptide	296:307	arg2	the doubly protonated glycopeptide ion			the doubly protonated glycopeptide ion						glycopeptide	The spectrum is dominated by the sequential neutral loss of the glycan components from the doubly protonated glycopeptide ion.
PMC3942810-1-2	9	115	gly	N-glycosylated	1484:1497	arg1	one unique peptide			peptide						peptide	Of the two proteins implicated in the regulation of morphological development, IDGF 4 was N-glycosylated on one unique peptide with a single site, and N-glycosylated protein takeout had one unique peptide carrying two sites (Table 2).
PMC6243375-1-4	3	59	gly	glycosylation	516:528	arg2	2,580 novel O‐linked glycosylation sites			2,580 novel O‐linked glycosylation sites						sites	Remarkably, EXoO identified 2,580 novel O‐linked glycosylation sites, an approximately 94% increase in the known sites, which however are mapped primarily using engineered cell lines.
PMC6731604-1-4	8	56	gly	glycoprotein	1695:1706	arg1	the glycoprotein database	the glycoprotein database				Fterm		glycoprotein			In addition, the entire human glycoprotein and glycosite database as well as the glycoprotein database for each individual tissue or body fluid can also be downloaded from the N-GlycositeAtlas website in a Microsoft Excel format.
PMC6731604-1-4	8	73	gly	glycoprotein	1644:1655	arg1	the entire human glycoprotein and glycosite database	the entire human glycoprotein and glycosite database				Fterm		glycoprotein			In addition, the entire human glycoprotein and glycosite database as well as the glycoprotein database for each individual tissue or body fluid can also be downloaded from the N-GlycositeAtlas website in a Microsoft Excel format.
PMC6731604-1-4	8	94	gly	glycosite	1661:1669	arg2	the entire human glycoprotein and glycosite database			the entire human glycoprotein and glycosite database						glycosite	In addition, the entire human glycoprotein and glycosite database as well as the glycoprotein database for each individual tissue or body fluid can also be downloaded from the N-GlycositeAtlas website in a Microsoft Excel format.
PMC4595782-1-7	43	51	gly	glycosylation	8561:8573	arg1	SAC-Par-4-GFP-SEKDEL protein	SAC-Par-4-GFP-SEKDEL protein				Fterm		protein			Besides this, effective glycosylation of SAC-Par-4-GFP-SEKDEL protein and its enhanced stability could be the other reasons for increasing the therapeutic value of plant derived SAC-Par-4-GFP-SEKDEL protein.
PMC5795011-1-4	112	374	gly	glycopeptide	19205:19216	arg2	the commercially available glycopeptide identification tools			the commercially available glycopeptide identification tools						glycopeptide	SimGlycan, GlycoQuest and Byonic are among the commercially available glycopeptide identification tools.
PMC5795011-1-4	117	975	gly	glycopeptides	20107:20119	arg2	glycopeptides			glycopeptides						glycopeptides	Byonic identifies glycopeptides at the level of peptide sequence and glycan composition by searching the predefined or user-defined separate glycan and protein databases.
PMC5795011-1-fig5	2	31	gly	glycopeptide	277:288	arg2	The nine different glycopeptide variants			The nine different glycopeptide variants						glycopeptide	The nine different glycopeptide variants included the mono-sialylated bi- (A), tri- (B), tetra-antennary (C), and the di-sialylated bi- (D), tri- (E), tetra-antennary (F).
PMC5457524-1-7	72	191	gly	N-glycopeptide	11414:11427	arg2	N-glycopeptide			N-glycopeptide						N-glycopeptide	Notably, HILIC enrichment is not specific for N-glycans and N-glycopeptide enrichment to only 30% has been achieved previously53.
PMC7124471-1-4	34	203	gly	glycosites	5816:5825	arg2	20, 18 and 18 glycosites			20, 18 and 18 glycosites						glycosites	20, 18 and 18 glycosites were identified from them, respectively (supplemental Table S2).
PMC3938046-1-5	8	70	gly	N-glycosylation	1001:1015	arg2	the N-glycosylation sites			the N-glycosylation sites						sites	We also compared the N-glycosylation sites in our study with the largest N-glycoproteome dataset, reported by Zielinska et al. [18].
PMC5457524-1-7	29	58	gly	attached	5404:5411	arg2	the innermost GlcNAc residue AND α1,6-linked fucose			the innermost GlcNAc residue	α1,6-linked fucose					residue	Specifically, we show that an immobilized form of Fbs1 is able to bind to both high-mannose and complex N-glycans regardless of the presence or absence of α1,6-linked fucose attached to the innermost GlcNAc residue.
PMC3938046-1-fig4	3	21	gly	glycoproteins	235:247	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Gene ontology of glycoproteins was analyzed using bioinformatics tools and categorized into 3 groups (cellular component, molecular function, and biological process).
PMC3938046-1-fig4	0	29	gly	N-glycoproteins	40:54	arg1	N-glycoproteins	N-glycoproteins				Fterm		N-glycoproteins			Functional classification of identified N-glycoproteins.
PMC6243375-1-1	4	89	gly	glycosylation	680:692	arg2	Ser‐290			Ser‐290						Ser‐290	In addition, a new O‐linked glycosylation site at Ser‐290 was also identified (Dataset EV1 and Appendix Fig S1).
PMC6243375-1-1	4	89	gly	glycosylation	680:692	arg2	a new O‐linked glycosylation site			a new O‐linked glycosylation site						site	In addition, a new O‐linked glycosylation site at Ser‐290 was also identified (Dataset EV1 and Appendix Fig S1).
PMC3942810-1-2	23	120	gly	glycoprotein/glycopeptides	4331:4356	arg2	glycoprotein/glycopeptides enrichment			glycoprotein/glycopeptides enrichment						glycoprotein/glycopeptides	To gain a new understanding of innate biochemical properties of RJ at the proteome and glycoproteome levels, RJ was analyzed for the identification of novel proteins hidden in RJ and mapped for N-glycosylation sites using the double high LC-MS/MS system (orbitrap and triple TOF) and complementary methods of glycoprotein/glycopeptides enrichment (hydrazide chemistry and lectin).
PMC3942810-1-2	23	187	gly	N-glycosylation	4216:4230	arg2	N-glycosylation sites			N-glycosylation sites						sites	To gain a new understanding of innate biochemical properties of RJ at the proteome and glycoproteome levels, RJ was analyzed for the identification of novel proteins hidden in RJ and mapped for N-glycosylation sites using the double high LC-MS/MS system (orbitrap and triple TOF) and complementary methods of glycoprotein/glycopeptides enrichment (hydrazide chemistry and lectin).
PMC5098438-1-1	17	69	gly	Fig. 2	2599:2604	arg1	amino acids sequence			amino acids sequence						sequence	To confirm the presence of Tt/C2B8 glycosylation variants and to precisely determine its molecular weight, we measured the intact antibody by high-resolution native mass spectrometry (Fig. 2; amino acids sequence in Supplementary Information).
PMC3942810-1-2	7	85	gly	N-glycosylation	1151:1165	arg2	a single N-glycosylation site			a single N-glycosylation site						site	Of the proteins involved in metabolic processes, seven were N-glycosylated on 16 unique N-glycopeptides: all but on each contained a single N-glycosylation site and one unique N-glycopeptide carried two sites (Table 2).
PMC3942810-1-2	7	111	gly	N-glycopeptide	1187:1200	arg2	one unique N-glycopeptide			one unique N-glycopeptide						N-glycopeptide	Of the proteins involved in metabolic processes, seven were N-glycosylated on 16 unique N-glycopeptides: all but on each contained a single N-glycosylation site and one unique N-glycopeptide carried two sites (Table 2).
PMC3942810-1-2	7	234	gly	N-glycopeptides	1099:1113	arg2	16 unique N-glycopeptides			16 unique N-glycopeptides						N-glycopeptides	Of the proteins involved in metabolic processes, seven were N-glycosylated on 16 unique N-glycopeptides: all but on each contained a single N-glycosylation site and one unique N-glycopeptide carried two sites (Table 2).
PMC3942810-1-2	7	221	gly	N-glycosylated	1071:1084	arg2	16 unique N-glycopeptides			N-glycopeptides						N-glycopeptides	Of the proteins involved in metabolic processes, seven were N-glycosylated on 16 unique N-glycopeptides: all but on each contained a single N-glycosylation site and one unique N-glycopeptide carried two sites (Table 2).
PMC6123398-1-3	4	31	gly	N-glycosylation	567:581	arg1	the conserved Asn297 site			the conserved Asn297 site				CD20	P11836	Asn297 site	N-glycosylation was only observed at the conserved Asn297 site for both mAbs.
PMC5098438-1-fig6	4	64	gly	glycoform	771:779	arg1	the Man3GlcNAc2 glycoform				the Man3GlcNAc2 glycoform						The T. thermophila oligomannose-type glycoform is a model of the Glc3Man9GlcNAc2 isomer generated by the superimposition of the NMR structure of a glucosylated oligomannose glycan and the crystal structure of the Man3GlcNAc2 glycoform (PDB ID: 1H3U).
PMC7124471-1-10	6	22	gly	glycoproteins	707:719	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			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).
PMC7124471-1-10	6	59	gly	glycosites	618:627	arg2	those glycosites	serotransferrin		glycosites		OGER		serotransferrin	P02787	glycosites	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).
PMC7124471-1-4	12	184	gly	glycopeptides	2330:2342	arg2	these glycopeptides			these glycopeptides						glycopeptides	When these glycopeptides have identical peptide backbone, and their precursor ions are from isotopic peaks, their pMatchGlyco score sometimes are identical.
PMC3942810-1-fig3	0	3	gly	N-glycosylated	16:29	arg1	N-glycosylated sites			N-glycosylated sites						sites	Distribution of N-glycosylated sites in royal jelly proteins.
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.
PMC2762462-1-1	2	73	gly	glycoprotein	406:417	arg1	a type II transmembrane glycoprotein	a type II transmembrane glycoprotein				Fterm		glycoprotein			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.
PMC3938046-1-fig7	1	17	gly	N-glycosylated	177:190	arg1	7 membrane and N-glycosylated proteins	7 membrane and N-glycosylated proteins				Fterm		proteins			The abundance of 5 proteins that are closely associated with microglial functions (A) and 7 membrane and N-glycosylated proteins and 1 cytosolic protein (B) was measured by western blot in control (RIPA) and crude membrane fraction samples.
PMC7124471-1-fig2	0	1	gly	glycoproteins	32:44	arg1	the identified serum glycoproteins	the identified serum glycoproteins				Fterm		glycoproteins			Overlap of the identified serum glycoproteins and glycosites using the two glycan mass databases.
PMC7124471-1-fig2	0	5	gly	glycosites	50:59	arg2	glycosites			glycosites						glycosites	Overlap of the identified serum glycoproteins and glycosites using the two glycan mass databases.
PMC3942810-2-2	17	123	gly	glycosylated	2521:2532	arg1	glycosylated proteins	glycosylated proteins				Fterm		proteins			Since glycosylated proteins have roles in immunity[62], the weak immunity of the young honeybee larvae (the first 48 h) may be promoted by feeding glycosylated MRJPs to ensure normal development[63].
PMC7124471-1-6	10	177	gly	glycopeptides	1604:1616	arg2	corresponding N-linked intact glycopeptides			corresponding N-linked intact glycopeptides						glycopeptides	7 N-glycan masses from Armoracia rusticana and 51 N-glycan masses from Gallus gallus based on species annotation in GlycomeDB were used to identify corresponding N-linked intact glycopeptides.
PMC3938046-1-4	6	23	gly	N-glycosylated	792:805	arg1	N-glycosylated proteins	N-glycosylated proteins				Fterm		proteins			Our GO analysis indicated that 75% of N-glycosylated proteins belonged to the category “membrane;” 66% (506 proteins) matched the category “integral to membrane;” and only 2% (16 proteins) was annotated as “cytosol” in the GO cellular compartment (GOCC) term.
PMC7124471-1-11	66	256	gly	alpha-1B-glycoprotein	9300:9320	arg1	alpha-1B-glycoprotein	alpha-1B-glycoprotein				Fterm		alpha-1B-glycoprotein			They included the previously reported glycosite N63 of alpha-1B-glycoprotein and N68 of albumin (7), suggesting that our method was reliable.
PMC7124471-1-11	66	337	gly	glycosite	9283:9291	arg2	the previously reported glycosite N63			the previously reported glycosite N63						glycosite N63	They included the previously reported glycosite N63 of alpha-1B-glycoprotein and N68 of albumin (7), suggesting that our method was reliable.
PMC7124471-1-4	21	107	gly	glycoproteins	3753:3765	arg1	507 N-linked glycoproteins	507 N-linked glycoproteins				Fterm		glycoproteins			In comparison, 981 N-linked glycosites and 13,874 N-linked intact glycopeptides from 507 N-linked glycoproteins were identified when using the database of 194 N-glycan masses (Table III, supplemental Table S8, S9, and S10).
PMC7124471-1-4	21	218	gly	glycosites	3683:3692	arg2	981 N-linked glycosites			981 N-linked glycosites						glycosites	In comparison, 981 N-linked glycosites and 13,874 N-linked intact glycopeptides from 507 N-linked glycoproteins were identified when using the database of 194 N-glycan masses (Table III, supplemental Table S8, S9, and S10).
PMC7124471-1-4	21	50	gly	glycopeptides	3721:3733	arg2	13,874 N-linked intact glycopeptides	glycoproteins		glycopeptides		Fterm		glycoproteins		glycopeptides	In comparison, 981 N-linked glycosites and 13,874 N-linked intact glycopeptides from 507 N-linked glycoproteins were identified when using the database of 194 N-glycan masses (Table III, supplemental Table S8, S9, and S10).
PMC3938046-1-6	8	32	gly	N-glycoproteins	1628:1642	arg1	N-glycoproteins	N-glycoproteins				Fterm		N-glycoproteins			Also, a detailed list of functional classes for TMD-containing proteins and N-glycoproteins is provided in Additional file 8: Table S9.
PMC6243375-1-2	8	107	gly	glycosylation	1445:1457	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	Finally, we studied human serum that contains a number of highly glycosylated proteins and has been previously subjected to detailed mapping of N‐linked glycosylation sites and N‐linked glycans but for which there has been little success in mapping of O‐linked glycosylation sites and O‐linked glycans (Zhang et al, 2005; Stumpo & Reinhold, 2010; Yabu et al, 2014; Darula et al, 2016; Hoffmann et al, 2016).
PMC6243375-1-2	8	118	gly	glycosylation	1337:1349	arg2	N‐linked glycosylation sites			N‐linked glycosylation sites						sites	Finally, we studied human serum that contains a number of highly glycosylated proteins and has been previously subjected to detailed mapping of N‐linked glycosylation sites and N‐linked glycans but for which there has been little success in mapping of O‐linked glycosylation sites and O‐linked glycans (Zhang et al, 2005; Stumpo & Reinhold, 2010; Yabu et al, 2014; Darula et al, 2016; Hoffmann et al, 2016).
PMC6243375-1-2	8	120	gly	glycosylated	1249:1260	arg1	highly glycosylated proteins	highly glycosylated proteins				Fterm		proteins			Finally, we studied human serum that contains a number of highly glycosylated proteins and has been previously subjected to detailed mapping of N‐linked glycosylation sites and N‐linked glycans but for which there has been little success in mapping of O‐linked glycosylation sites and O‐linked glycans (Zhang et al, 2005; Stumpo & Reinhold, 2010; Yabu et al, 2014; Darula et al, 2016; Hoffmann et al, 2016).
PMC5795011-1-4	2	704	gly	glycopeptides	495:507	arg2	sialylated glycopeptides			sialylated glycopeptides						glycopeptides	Tryptic peptides from serum samples were desalted using zwitterionic chromatography-hydrophilic interaction liquid chromatography solid phase extraction (ZIC-HILIC SPE) to enrich glycopeptides, followed by enrichment of sialylated glycopeptides with TiO2 beads (Fig. 4).
PMC5795011-1-4	2	951	gly	glycopeptides	443:455	arg2	glycopeptides			glycopeptides						glycopeptides	Tryptic peptides from serum samples were desalted using zwitterionic chromatography-hydrophilic interaction liquid chromatography solid phase extraction (ZIC-HILIC SPE) to enrich glycopeptides, followed by enrichment of sialylated glycopeptides with TiO2 beads (Fig. 4).
PMC5795011-1-4	2	1073	gly	sialylated	484:493	arg1	sialylated glycopeptides			sialylated glycopeptides						glycopeptides	Tryptic peptides from serum samples were desalted using zwitterionic chromatography-hydrophilic interaction liquid chromatography solid phase extraction (ZIC-HILIC SPE) to enrich glycopeptides, followed by enrichment of sialylated glycopeptides with TiO2 beads (Fig. 4).
PMC6934601-1-3	22	209	gly	glycosylated	3881:3892	arg1	its highly glycosylated extracellular domain			its highly glycosylated extracellular domain						domain	While MUC1 is normally expressed in epithelial cells, where its highly glycosylated extracellular domain acts as a protective barrier, we decided to include MUC1 in our screen validation work due to the possible functional similarity between MUC1 and SPN (both proteins carry extensive O-linked glycan structures).
PMC7124471-1-11	4	258	gly	glycosite	666:674	arg2	glycosite	serotransferrin		glycosite				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).
PMC5976746-1-5	74	176	gly	homogeneity	12793:12803	arg1	the trimers	the trimers				Fterm		trimers			The differences in neutralization may be due to improved homogeneity of the trimers produced in the CHO-M cell lines, but more likely is due to adjuvant.
PMC7124471-1-11	21	93	gly	list	2594:2597	arg1	all other N-linked intact glycopeptide carrying N630	serotransferrin		all other N-linked intact glycopeptide carrying N630				serotransferrin	P02787	N630	For all other N-linked intact glycopeptide carrying N630, a spectrum sequence list (.
PMC7124471-1-11	21	149	gly	glycopeptide	2546:2557	arg2	all other N-linked intact glycopeptide carrying N630			all other N-linked intact glycopeptide carrying N630						glycopeptide	For all other N-linked intact glycopeptide carrying N630, a spectrum sequence list (.
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.
PMC3942810-1-fig2	3	26	gly	N-glycopeptides	732:746	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	Eight and two are N-glycopeptides specifically identified by the lectin and hydrazide enrichment protocols, respectively, and six are N-glycopeptides identified by both enrichment methods using triple TOF-based MS. C is the distribution of N-glycopeptides identified by the orbitrap-based MS and triple TOF-based MS using lectin enrichment method.
PMC3942810-1-fig2	3	41	gly	N-glycopeptides	838:852	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	Eight and two are N-glycopeptides specifically identified by the lectin and hydrazide enrichment protocols, respectively, and six are N-glycopeptides identified by both enrichment methods using triple TOF-based MS. C is the distribution of N-glycopeptides identified by the orbitrap-based MS and triple TOF-based MS using lectin enrichment method.
PMC3942810-1-fig2	3	61	gly	N-glycopeptides	616:630	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	Eight and two are N-glycopeptides specifically identified by the lectin and hydrazide enrichment protocols, respectively, and six are N-glycopeptides identified by both enrichment methods using triple TOF-based MS. C is the distribution of N-glycopeptides identified by the orbitrap-based MS and triple TOF-based MS using lectin enrichment method.
PMC5795011-1-4	17	102	gly	glycopeptides	2905:2917	arg2	tri-sialylated tri-antennary and di-sialylated tetra-antennary glycopeptides			tri-sialylated tri-antennary and di-sialylated tetra-antennary glycopeptides						glycopeptides	For example, the top scoring matches of tri-sialylated tri-antennary and di-sialylated tetra-antennary glycopeptides indicated a fucose residue after the core structure.
PMC5795011-1-4	17	215	gly	tri-sialylated	2842:2855	arg1	tri-sialylated tri-antennary and di-sialylated tetra-antennary glycopeptides			tri-sialylated tri-antennary and di-sialylated tetra-antennary glycopeptides						glycopeptides	For example, the top scoring matches of tri-sialylated tri-antennary and di-sialylated tetra-antennary glycopeptides indicated a fucose residue after the core structure.
PMC5795011-1-4	17	961	gly	di-sialylated	2875:2887	arg1	tri-sialylated tri-antennary and di-sialylated tetra-antennary glycopeptides			tri-sialylated tri-antennary and di-sialylated tetra-antennary glycopeptides						glycopeptides	For example, the top scoring matches of tri-sialylated tri-antennary and di-sialylated tetra-antennary glycopeptides indicated a fucose residue after the core structure.
PMC5795011-1-fig6	0	28	gly	glycopeptide	30:41	arg2	glycopeptide			glycopeptide						glycopeptide	Violin plots representing the glycopeptide ratios (aggressive vs. indolent prostate cancer) of the three most frequent glycopeptide variants identified in the current study.
PMC5795011-1-fig6	0	29	gly	glycopeptide	119:130	arg2	the three most frequent glycopeptide variants			the three most frequent glycopeptide variants						glycopeptide	Violin plots representing the glycopeptide ratios (aggressive vs. indolent prostate cancer) of the three most frequent glycopeptide variants identified in the current study.
PMC4595782-1-5	5	10	gly	glycosylated	1192:1203	arg1	this protein	this protein				Fterm		protein			The enhanced stability of ER-targeted SAC-Par-4-GFP-SEKDEL could be attributed to the fact that this protein is getting effectively glycosylated.
PMC2538527-1-fig7	0	67	gly	glycopeptides	36:48	arg2	the tryptic glycopeptides			the tryptic glycopeptides						glycopeptides	CID and ETD analysis of the tryptic glycopeptides from IFNα2b.
PMC7124471-1-11	23	67	gly	glycopeptides	2871:2883	arg2	N-linked intact glycopeptides			N-linked intact glycopeptides						glycopeptides	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.
PMC7124471-1-11	23	358	gly	N-glycosite	2905:2915	arg2	the same N-glycosite			the same N-glycosite						N-glycosite	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.
PMC6731604-1-4	10	0	gly	glycosite	2470:2478	arg2	glycosite			glycosite						glycosite	It should be noted that each line of text only contains one glycosite-containing peptide and one glycosite location.
PMC6731604-1-4	13	17	gly	glycosite	2774:2782	arg2	glycosite			glycosite						glycosite	The detailed information for each identified glycosite or glycosite-containing protein can be acquired from their original publications that are listed after each record.
PMC5643531-1-9	1	137	gly	sites	226:230	arg1	two putative N-glycosylation sites			two putative N-glycosylation sites						sites	In order to assess potential roles of Fz8 glycosylation, we tested the activity of Fz8 mutants with Asn (N) to Ala (A) substitution at two putative N-glycosylation sites (Asn44 and Asn147) (Fig. 7A).
PMC5643531-1-9	1	294	gly	N-glycosylation	210:224	arg2	two putative N-glycosylation sites			two putative N-glycosylation sites						sites	In order to assess potential roles of Fz8 glycosylation, we tested the activity of Fz8 mutants with Asn (N) to Ala (A) substitution at two putative N-glycosylation sites (Asn44 and Asn147) (Fig. 7A).
PMC5643531-1-9	1	137	gly	sites	226:230	arg1	Asn44			Asn44 and Asn147				Fz8	Q9H461	Asn44 and Asn147	In order to assess potential roles of Fz8 glycosylation, we tested the activity of Fz8 mutants with Asn (N) to Ala (A) substitution at two putative N-glycosylation sites (Asn44 and Asn147) (Fig. 7A).
PMC5643531-1-9	1	294	gly	N-glycosylation	210:224	arg2	Asn44			Asn44 and Asn147				Fz8	Q9H461	Asn44 and Asn147	In order to assess potential roles of Fz8 glycosylation, we tested the activity of Fz8 mutants with Asn (N) to Ala (A) substitution at two putative N-glycosylation sites (Asn44 and Asn147) (Fig. 7A).
PMC3942810-1-2	12	6	gly	N-glycopeptides	2025:2039	arg2	eight N-glycopeptides			eight N-glycopeptides						N-glycopeptides	Similarly, eight N-glycopeptides were specifically identified by the lectin enrichment protocol, two were specifically identified by the hydrazide chemistry, and six were identified by both enrichment methods using triple TOF-based MS (Figure 2B).
PMC6731604-1-3	11	4	gly	glycoproteins	1507:1519	arg1	More tissue-derived glycoproteins	More tissue-derived glycoproteins				Fterm		glycoproteins			More tissue-derived glycoproteins were detected in urine than in serum, which could be attributed to the larger number of glycoproteins that were identified in urine compared to serum.
PMC6731604-1-3	11	26	gly	glycoproteins	1609:1621	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			More tissue-derived glycoproteins were detected in urine than in serum, which could be attributed to the larger number of glycoproteins that were identified in urine compared to serum.
PMC6731604-1-3	4	3	gly	glycoproteins	687:699	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			The results indicated that different tissues had different numbers and percentages of glycoproteins overlapped with serum-derived glycoproteins (Fig. 4a).
PMC6731604-1-3	4	21	gly	glycoproteins	731:743	arg1	serum-derived glycoproteins	serum-derived glycoproteins				Fterm		glycoproteins			The results indicated that different tissues had different numbers and percentages of glycoproteins overlapped with serum-derived glycoproteins (Fig. 4a).
PMC3942810-1-2	14	76	gly	18 N-glycopeptides	2488:2505	arg2	18 N-glycopeptides			18 N-glycopeptides						18 N-glycopeptides	Likewise, 18 N-glycopeptides were identified by orbitrap-based MS alone, and eight were identified by both types of LC-MS/MS instruments with adoption of hydrazide enrichment (Figure 2D).
PMC5795011-1-4	61	125	gly	glycopeptides	10741:10753	arg2	synthetic glycopeptides			synthetic glycopeptides						glycopeptides	A recent study also showed the same effect using low and high energy CID on a Q-TOF instrument for synthetic glycopeptides and standard glycoproteins.
PMC5795011-1-4	61	265	gly	glycoproteins	10768:10780	arg1	standard glycoproteins	standard glycoproteins				Fterm		glycoproteins			A recent study also showed the same effect using low and high energy CID on a Q-TOF instrument for synthetic glycopeptides and standard glycoproteins.
PMC7124471-1-11	65	73	gly	glycoproteins	9142:9154	arg1	26 N-linked glycoproteins	26 N-linked glycoproteins				Fterm		glycoproteins			By including them into the spectral library, 26 N-linked glycoproteins carrying 29 N-linked glycosites were identified with NXV motif (supplemental Table S27).
PMC7124471-1-11	65	331	gly	glycosites	9177:9186	arg2	29 N-linked glycosites			29 N-linked glycosites						glycosites	By including them into the spectral library, 26 N-linked glycoproteins carrying 29 N-linked glycosites were identified with NXV motif (supplemental Table S27).
PMC5795011-1-4	126	72	gly	glycopeptide	21638:21649	arg2	glycopeptide analysis			glycopeptide analysis						glycopeptide	Mascot as a computational tool is continuously followed up since two decades, widely acclaimed and established in the proteomics community across the world and easily adaptable for glycopeptide analysis as described here.
PMC7081908-1-2	20	83	gly	occupied	3029:3036	arg2	N262			N262				gp120 proteins	Q14624	N262	For example, N262 in clade B proteins was almost 100% occupied but the 293-produced protein carried an equal mixture of oligomannose and complex glycans and the CHO-produced protein had almost exclusively oligomannose glycans at this site.
PMC6731604-1-2	14	93	gly	glycoproteins	2012:2024	arg1	Several hundred glycoproteins	Several hundred glycoproteins				Fterm		glycoproteins			Several hundred glycoproteins have also been identified from saliva and cerebrospinal fluid (CSF).
PMC6731604-1-fig5	0	9	gly	glycoprotein	73:84	arg1	an N-linked glycoprotein	an N-linked glycoprotein				Fterm		glycoprotein			Representative N-GlycositeAtlas web interface output showing an N-linked glycoprotein and its glycosites.
PMC6731604-1-fig5	0	22	gly	glycosites	94:103	arg2	its glycosites			its glycosites						glycosites	Representative N-GlycositeAtlas web interface output showing an N-linked glycoprotein and its glycosites.
PMC3938046-1-1	25	31	gly	N-glycosylation	3626:3640	arg2	1450 unique N-glycosylation sites			1450 unique N-glycosylation sites						sites	Combining data from the quadruplicate analysis of N-glycosylated peptides per biological repeat, we obtained 760 glycoproteins from 1450 unique N-glycosylation sites with a 1% FDR that incorporated 18O-deamidated asparagine and the N-glycosylation sites of which were consistent with the canonical N!P-[S/T/rarely C] motif.
PMC3938046-1-1	25	71	gly	N-glycosylated	3532:3545	arg1	N-glycosylated peptides			N-glycosylated peptides						peptides	Combining data from the quadruplicate analysis of N-glycosylated peptides per biological repeat, we obtained 760 glycoproteins from 1450 unique N-glycosylation sites with a 1% FDR that incorporated 18O-deamidated asparagine and the N-glycosylation sites of which were consistent with the canonical N!P-[S/T/rarely C] motif.
PMC3938046-1-1	25	113	gly	glycoproteins	3595:3607	arg1	760 glycoproteins	760 glycoproteins				Fterm		glycoproteins			Combining data from the quadruplicate analysis of N-glycosylated peptides per biological repeat, we obtained 760 glycoproteins from 1450 unique N-glycosylation sites with a 1% FDR that incorporated 18O-deamidated asparagine and the N-glycosylation sites of which were consistent with the canonical N!P-[S/T/rarely C] motif.
PMC3938046-1-1	25	167	gly	N-glycosylation	3714:3728	arg2	the N-glycosylation sites			the N-glycosylation sites						sites	Combining data from the quadruplicate analysis of N-glycosylated peptides per biological repeat, we obtained 760 glycoproteins from 1450 unique N-glycosylation sites with a 1% FDR that incorporated 18O-deamidated asparagine and the N-glycosylation sites of which were consistent with the canonical N!P-[S/T/rarely C] motif.
PMC7081908-1-fig1	4	17	gly	glycosylation	504:516	arg2	glycosylation site distributions			glycosylation site distributions						site	(B) Summary of glycosylation site distributions among the four gp120 proteins.
PMC5457524-1-5	4	0	gly	non-glycosylated	614:629	arg1	non-glycosylated peptides			non-glycosylated peptides						peptides	The desired result was equivalent enrichment of each type of N-glycopeptide (sialylated versus high mannose) without contamination with non-glycosylated peptides.
PMC5457524-1-5	4	40	gly	N-glycopeptide	539:552	arg2	N-glycopeptide			N-glycopeptide						N-glycopeptide	The desired result was equivalent enrichment of each type of N-glycopeptide (sialylated versus high mannose) without contamination with non-glycosylated peptides.
PMC5098438-1-5	40	304	gly	hemiglycosylation	6931:6947	arg1	the Fc region			the Fc region						region	These differences in glycosylation can lead to hemiglycosylation of the Fc region of the antibody.
PMC7124471-1-10	3	1	gly	glycopeptides	279:291	arg2	The identified N-linked intact glycopeptides			The identified N-linked intact glycopeptides						glycopeptides	The identified N-linked intact glycopeptides using 739 N-glycan masses database were used to construct glycoform for a given glycosite.
PMC7124471-1-10	3	84	gly	used	333:336	arg2	The identified N-linked intact glycopeptides			The identified N-linked intact glycopeptides						glycopeptides	The identified N-linked intact glycopeptides using 739 N-glycan masses database were used to construct glycoform for a given glycosite.
PMC7124471-1-10	3	91	gly	glycosite	373:381	arg2	a given glycosite			a given glycosite						glycosite	The identified N-linked intact glycopeptides using 739 N-glycan masses database were used to construct glycoform for a given glycosite.
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.
PMC3938046-1-4	4	11	gly	glycoproteins	553:565	arg1	most glycoproteins	most glycoproteins				Fterm		glycoproteins			TargetP [44] predicted a secretion motif in 429 (60%) of all glycoproteins, indicating that they are cleaved and secreted, despite most glycoproteins being membrane-bound (Figure 4A).
PMC3938046-1-4	4	81	gly	glycoproteins	478:490	arg1	all glycoproteins	all glycoproteins				Fterm		glycoproteins			TargetP [44] predicted a secretion motif in 429 (60%) of all glycoproteins, indicating that they are cleaved and secreted, despite most glycoproteins being membrane-bound (Figure 4A).
PMC5457524-1-6	15	173	gly	N-glycopeptide	2372:2385	arg2	N-glycopeptide			N-glycopeptide						N-glycopeptide	Figure 6c and Supplementary Data 1 and 2 show Fbs1 GYR enrichment greatly increases the N-glycopeptide fraction in the samples (65.5% in Fbs1 GYR enrichment versus 8.5% in pre-enrichment), thus greatly reducing the sample complexity.
PMC3938046-1-3	17	64	gly	16759 N-glycosylation	2912:2932	arg2	16759 N-glycosylation sites			16759 N-glycosylation sites						sites	By CMC, 12,889 (76.0%) of 16759 N-glycosylation sites matched the canonical motif without removing the redundancy (Figure 4C).
PMC7081908-1-2	18	118	gly	glycosylated	2805:2816	arg1	the CHO-produced protein	the CHO-produced protein				Fterm		protein			Clade B proteins showed the largest variation, with the CHO-produced protein being more glycosylated than the 293-produced protein.
PMC5457524-1-7	76	63	gly	N-glycosites	12056:12067	arg2	N-glycosites			N-glycosites						position and N-glycosites	This substantially unbiased and 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 allows large-scale N-glycoproteomic studies due to greatly reduced sample complexity.
PMC5457524-1-7	76	454	gly	N-glycopeptide	11956:11969	arg2	This substantially unbiased and highly efficient N-glycopeptide enrichment method			This substantially unbiased and highly efficient N-glycopeptide enrichment method						N-glycopeptide	This substantially unbiased and 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 allows large-scale N-glycoproteomic studies due to greatly reduced sample complexity.
PMC3938046-1-fig1	4	33	gly	N-glycopeptides	405:419	arg2	N-glycopeptides			N-glycopeptides						N-glycopeptides	To enrich N-glycopeptides, N-glyco-FASP was performed on whole-cell lysates or crude membrane fractions.
PMC5643531-1-fig7	1	31	gly	N-glycosylation	122:136	arg2	putative N-glycosylation sites			putative N-glycosylation sites						sites	(A) Schematic representation of putative N-glycosylation sites in zebrafish Fz8a receptor.
PMC3938046-1-3	3	52	gly	N-glycosites	702:713	arg2	unique N-glycosites			unique N-glycosites						N-glycosites	As shown in Additional file 4: Figure S5, the technical variation between all replicates was reasonable (overlap of 45% to 74% for unique N-glycosites and overlap of 52% to 81% for unique glycoproteins).
PMC3938046-1-3	3	112	gly	glycoproteins	752:764	arg1	unique glycoproteins	unique glycoproteins				Fterm		glycoproteins			As shown in Additional file 4: Figure S5, the technical variation between all replicates was reasonable (overlap of 45% to 74% for unique N-glycosites and overlap of 52% to 81% for unique glycoproteins).
PMC6243375-1-3	6	58	gly	glycosylation	998:1010	arg2	the O‐linked glycosylation site			the O‐linked glycosylation site						site	One PSM was identified to have the O‐linked glycosylation site assigned at the sixth amino acid position on a serine (Dataset EV5).
PMC5795011-1-4	8	894	gly	glycosylation	1472:1484	arg2	this glycosylation site			this glycosylation site						site	Mascot annotated nine different mono-, di-, tri- and tetra-sialylated N-glycan structures on this glycosylation site (Fig. 5).
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.
PMC4876326-1-4	4	85	gly	glycosylation	570:582	arg2	three predicted N-linked glycosylation sites			three predicted N-linked glycosylation sites						sites	Genotype ON1 shows three predicted N-linked glycosylation sites; clades TN1, TN2, and GA5 have five, four, and five sites, respectively (Fig. 3).
PMC3938046-1-5	20	15	gly	N-glycosylation	2772:2786	arg2	556 novel N-glycosylation sites			556 novel N-glycosylation sites						sites	Thus, we identified 556 novel N-glycosylation sites that have not been annotated in PHOSIDA or the UniprotKB database, most of which were linked to microglial function.
PMC6731604-1-2	0	123	gly	glycoproteins	16:28	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Distribution of glycoproteins and glycosites across tissues and biological fluids.
PMC6731604-1-2	0	126	gly	glycosites	34:43	arg2	glycosites			glycosites						glycosites	Distribution of glycoproteins and glycosites across tissues and biological fluids.
PMC3942810-1-2	13	240	gly	29 N-glycopeptides	2268:2285	arg2	29 N-glycopeptides			29 N-glycopeptides						29 N-glycopeptides	In general, 29 N-glycopeptides were uniquely identified by orbitrap-based MS, four were uniquely identified by triple TOF-based MS, and 10 were identified by both MS systems using the lectin enrichment method (Figure 2C).
PMC7081908-1-1	2	54	gly	glycoproteins	395:407	arg1	The glycoproteins	The glycoproteins				Fterm		glycoproteins			The glycoproteins represent three primary isolates from clades A, B, and C, as well as a consensus variant from the AE clade.
PMC7124471-1-9	11	21	gly	glycoproteins	1264:1276	arg1	138 serum N-linked glycoproteins	138 serum N-linked glycoproteins				Fterm		glycoproteins			In total, 138 serum N-linked glycoproteins with 192 N-linked glycosites were identified to carry these modified N-glycans (supplemental Table S25).
PMC7124471-1-9	11	109	gly	glycosites	1296:1305	arg2	192 N-linked glycosites			192 N-linked glycosites						glycosites	In total, 138 serum N-linked glycoproteins with 192 N-linked glycosites were identified to carry these modified N-glycans (supplemental Table S25).
PMC5795011-1-4	84	861	gly	glycopeptide	14293:14304	arg2	intact glycopeptide analysis			intact glycopeptide analysis						glycopeptide	Despite the significant results obtained with this approach, some issues regarding intact glycopeptide analysis are yet to be solved and are worth discussing.
PMC5795011-1-4	129	173	gly	glycopeptide	22265:22276	arg2	the glycopeptide identifications			the glycopeptide identifications						glycopeptide	Thus, no specific informatics skills are required to establish this workflow and a typical single LC-MS file from e.g. serum need a couple of minutes until the glycopeptide identifications are obtained.
PMC6243375-1-3	3	45	gly	glycopeptides	520:532	arg2	glycopeptides			glycopeptides						glycopeptides	Next, the ambiguity of O‐linked glycosylation site at the first amino acid position on glycopeptides was determined in the PSMs generated by ETD‐MS2.
PMC6243375-1-3	3	175	gly	glycosylation	465:477	arg2	O‐linked glycosylation site			O‐linked glycosylation site						site	Next, the ambiguity of O‐linked glycosylation site at the first amino acid position on glycopeptides was determined in the PSMs generated by ETD‐MS2.
PMC5795011-1-fig4	3	0	gly	glycopeptide	394:405	arg2	The intact glycopeptide mass spectra			The intact glycopeptide mass spectra						glycopeptide	The intact glycopeptide mass spectra were submitted to the Mascot search engine for identification and relative quantification with Mascot Distiller.
PMC6123398-1-6	34	404	gly	fucosylated	5606:5616	arg1	relatively fewer fucosylated residues			relatively fewer fucosylated residues						residues	Similar scenario was observed in recombinant vs. native human lactoferrin, the lactoferrin expressed in bovine milk had relatively fewer fucosylated residues compared to the native human lactoferrin.
PMC3942810-1-fig1	0	15	gly	N-glycosylated	26:39	arg1	N-glycosylated peptide			N-glycosylated peptide						peptide	Representative spectra of N-glycosylated peptide in royal jelly proteins.
PMC3938046-1-5	25	69	gly	glycoproteins	3612:3624	arg1	all identified glycoproteins	all identified glycoproteins				Fterm		glycoproteins			Finally, to determine whether the N-glycoproteins were expressed predominantly in mouse microglia, we examined their expression at the transcriptome level using BioGPS [46]—705 of all identified glycoproteins were mapped in the BioGPS database [46], and the gene expression profiles for normal mouse microglia were compared with those of 96 other normal mouse tissues and cells [47,48].
PMC3938046-1-5	25	114	gly	N-glycoproteins	3451:3465	arg1	the N-glycoproteins	the N-glycoproteins				Fterm		N-glycoproteins			Finally, to determine whether the N-glycoproteins were expressed predominantly in mouse microglia, we examined their expression at the transcriptome level using BioGPS [46]—705 of all identified glycoproteins were mapped in the BioGPS database [46], and the gene expression profiles for normal mouse microglia were compared with those of 96 other normal mouse tissues and cells [47,48].
PMC7124471-1-11	83	495	gly	glycopeptide	11598:11609	arg2	N-linked glycopeptide identification			N-linked glycopeptide identification						glycopeptide	The proposed LC-MS/MS method for N-linked glycopeptide identification and site-specific glycoform construction was validated in human serum sample.
PMC5457524-1-3	24	199	gly	alanine	3942:3948	arg1	Asp212			Asp154, Asp212 and Lys280				Fbs1	Q9HAH7	Asp154, Asp212 and Lys280	Other residues predicted to form direct contact to the RNase B glycan were mutated to alanine (human Asp154, Asp212 and Lys280) and two of the substitutions negatively affected substrate binding (Supplementary Fig. 7).
PMC5457524-1-3	24	199	gly	alanine	3942:3948	arg1	human Asp154			Asp154, Asp212 and Lys280				Fbs1	Q9HAH7	Asp154, Asp212 and Lys280	Other residues predicted to form direct contact to the RNase B glycan were mutated to alanine (human Asp154, Asp212 and Lys280) and two of the substitutions negatively affected substrate binding (Supplementary Fig. 7).
PMC5457524-1-3	24	199	gly	alanine	3942:3948	arg1	human Asp154			Asp154, Asp212 and Lys280				Fbs1	Q9HAH7	Asp154, Asp212 and Lys280	Other residues predicted to form direct contact to the RNase B glycan were mutated to alanine (human Asp154, Asp212 and Lys280) and two of the substitutions negatively affected substrate binding (Supplementary Fig. 7).
PMC5795011-1-4	82	223	gly	glycopeptide	14030:14041	arg2	multiple LC-MS glycopeptide data sets			multiple LC-MS glycopeptide data sets						glycopeptide	Due to the availability of well-established tools like Mascot Daemon, Mascot Distiller and Proteome Discoverer, relatively fast identification and comparison of multiple LC-MS glycopeptide data sets is possible.
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.
PMC5457524-1-7	60	50	gly	glycoproteins	9127:9139	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Given the emerging interest in glycoproteins as biomarkers, a need exists for readily isolating and characterizing low-abundance glycoproteins from complex biological samples.
PMC5457524-1-7	60	518	gly	glycoproteins	9225:9237	arg1	low-abundance glycoproteins	low-abundance glycoproteins				Fterm		glycoproteins			Given the emerging interest in glycoproteins as biomarkers, a need exists for readily isolating and characterizing low-abundance glycoproteins from complex biological samples.
PMC6243375-1-1	3	31	gly	glycosylation	506:518	arg2	the six known O‐linked glycosylation sites			the six known O‐linked glycosylation sites						sites	To demonstrate proof of principle, bovine fetuin was analyzed and the six known O‐linked glycosylation sites documented in the UniProt database were pinpointed at Ser‐271, Thr‐280, Ser‐282, Ser‐296, Thr‐334, and Ser‐341 (Dataset EV1).
PMC6243375-1-1	6	27	gly	glycopeptides	1127:1139	arg2	O‐linked glycopeptides			O‐linked glycopeptides						glycopeptides	The detection of oxonium ions in the MS/MS spectrum is particularly useful for obtaining the correct identification of O‐linked glycopeptides.
PMC7124471-1-11	31	429	gly	deglycopeptides	4269:4283	arg2	its N-linked deglycopeptides			its N-linked deglycopeptides						deglycopeptides	In the case of OVAL, it was necessary to set semi-tryptic digestion in order to identify its N-linked deglycopeptides.
PMC5457524-1-7	3	267	gly	N-glycosite	376:386	arg2	N-glycosite			N-glycosite						N-glycosite	Standard N-glycosite identification by PNGase F treatment in 18O water results in the loss of information pertaining to which N-glycans are present at each glycosite.
PMC5457524-1-7	3	569	gly	glycosite	523:531	arg2	each glycosite			each glycosite						glycosite	Standard N-glycosite identification by PNGase F treatment in 18O water results in the loss of information pertaining to which N-glycans are present at each glycosite.
PMC7124471-1-3	16	29	gly	glycoproteins	2533:2545	arg1	N-linked glycoproteins	N-linked glycoproteins				Fterm		glycoproteins			The number of N-linked glycoproteins, glycosites and deglycopeptides were increased by 249%, 283%, and 264%, respectively with the combination of ACN precipitation and high pH RP-LC fractionation.
PMC7124471-1-3	16	40	gly	glycosites	2548:2557	arg2	glycosites			glycosites						glycosites and deglycopeptides	The number of N-linked glycoproteins, glycosites and deglycopeptides were increased by 249%, 283%, and 264%, respectively with the combination of ACN precipitation and high pH RP-LC fractionation.
PMC7124471-1-3	16	44	gly	deglycopeptides	2563:2577	arg2	deglycopeptides			deglycopeptides						glycosites and deglycopeptides	The number of N-linked glycoproteins, glycosites and deglycopeptides were increased by 249%, 283%, and 264%, respectively with the combination of ACN precipitation and high pH RP-LC fractionation.
PMC4876326-1-4	3	98	gly	glycosylation	376:388	arg2	N-linked glycosylation sequons			N-linked glycosylation sequons							However, N-linked glycosylation sequons in the G gene appear to follow a genotype specific pattern, with multiple glycosylation patterns co-circulating simultaneously.
PMC6243375-1-2	5	63	gly	glycopeptides	741:753	arg2	2,804 O‐linked glycopeptides			2,804 O‐linked glycopeptides						glycopeptides	After analysis with 1% false discovery rate (FDR) at PSM level, 35,848 PSMs were assigned to 2,804 O‐linked glycopeptides containing 1,781 O‐linked glycosylation sites from 592 glycoproteins (Dataset EV2).
PMC6243375-1-2	5	79	gly	glycoproteins	810:822	arg1	592 glycoproteins	592 glycoproteins				Fterm		glycoproteins			After analysis with 1% false discovery rate (FDR) at PSM level, 35,848 PSMs were assigned to 2,804 O‐linked glycopeptides containing 1,781 O‐linked glycosylation sites from 592 glycoproteins (Dataset EV2).
PMC6243375-1-2	5	83	gly	glycosylation	781:793	arg2	1,781 O‐linked glycosylation sites			1,781 O‐linked glycosylation sites						sites	After analysis with 1% false discovery rate (FDR) at PSM level, 35,848 PSMs were assigned to 2,804 O‐linked glycopeptides containing 1,781 O‐linked glycosylation sites from 592 glycoproteins (Dataset EV2).
PMC5795011-1-4	124	831	gly	glycopeptides	21226:21238	arg2	glycopeptides			glycopeptides						glycopeptides	Some of the recent large-scale glycoproteomics studies also displayed the successful identification of thousands of glycopeptides.
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	N-glycosylated proteins	N-glycosylated proteins				Fterm		proteins			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.
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.
PMC7124471-1-11	84	116	gly	glycoform	11754:11762	arg1	serum glycoprotein	serum glycoprotein				Fterm		glycoprotein			It enables quantitative analysis of site-specific glycoform of serum glycoprotein, which helps to develop better approaches for diagnosis and treatment of CDG as well as other human diseases.
PMC7124471-1-11	84	341	gly	glycoprotein	11773:11784	arg1	serum glycoprotein	serum glycoprotein				Fterm		glycoprotein			It enables quantitative analysis of site-specific glycoform of serum glycoprotein, which helps to develop better approaches for diagnosis and treatment of CDG as well as other human diseases.
PMC5457524-1-7	6	489	gly	N-glycopeptide	1055:1068	arg2	intact N-glycopeptide identification			intact N-glycopeptide identification						N-glycopeptide	We also compared Fbs1 GYR enrichment with lectin (ConA, WGA and RCA120 mixture) enrichment for intact N-glycopeptide identification.
PMC5457524-1-1	25	63	gly	glycoprotein	4085:4096	arg1	a glycoprotein	a glycoprotein				Fterm		glycoprotein			In typical N-glycan profiling studies, N-glycans are removed from a glycoprotein by PNGase F digestion after which liberated N-glycans are labelled with a fluorophore at their reducing end.
PMC3942810-1-fig4	0	11	gly	N-glycosylated	16:29	arg1	N-glycosylated royal jelly proteins	N-glycosylated royal jelly proteins				Fterm		proteins			Distribution of N-glycosylated royal jelly proteins carrying different numbers of modification sites.
PMC4595782-1-7	32	763	gly	glycosylates	6281:6292	arg1	the recombinant protein	the recombinant protein				Fterm		protein			The major advantage of using plant as a bioreactor is that it glycosylates the recombinant protein along the secretory pathway as proteins move from the ER through the Golgi to their final destination.
PMC6243375-1-3	14	71	gly	site	2467:2470	arg1	sialic acid			site	sialic acid					site	Therefore, it is possible to define that the O‐linked glycopeptide contained Hex(1)HexNAc(1) or most likely to be Gal‐GalNAc with or without sialic acid at the site of O‐linked glycosylation.
PMC6243375-1-3	14	127	gly	glycosylation	2484:2496	arg2	the site			the site						site	Therefore, it is possible to define that the O‐linked glycopeptide contained Hex(1)HexNAc(1) or most likely to be Gal‐GalNAc with or without sialic acid at the site of O‐linked glycosylation.
PMC6243375-1-3	14	159	gly	glycopeptide	2361:2372	arg2	the O‐linked glycopeptide			the O‐linked glycopeptide						glycopeptide	Therefore, it is possible to define that the O‐linked glycopeptide contained Hex(1)HexNAc(1) or most likely to be Gal‐GalNAc with or without sialic acid at the site of O‐linked glycosylation.
PMC7143757-1-1	11	53	gly	glycosylated	1507:1518	arg1	the substrate protein	protein			all	Fterm		protein			These results indicated that the O-linked glycosylation system was efficiently expressed in YeO9_52212 and that almost all of the substrate protein had been glycosylated.
PMC5457524-1-7	27	540	gly	N-glycosylated	5114:5127	arg1	misfolded N-glycosylated proteins	misfolded N-glycosylated proteins				Fterm		proteins			We made use of the glycan-binding properties of Fbs1, a eukaryotic lectin-like protein that normally functions in a ubiquitin-mediated process to eliminate misfolded N-glycosylated proteins.
PMC4595782-1-4	0	85	gly	Deglycosylation	0:14	arg1	Plant-derived SAC-Par-4-GFP				Plant-derived SAC-Par-4-GFP						Deglycosylation Analysis of Plant-derived SAC-Par-4-GFP.
PMC3938046-1-5	17	19	gly	glycoproteins	2366:2378	arg1	137 glycoproteins	137 glycoproteins				Fterm		glycoproteins			In our study, 252 N-glycosites, corresponding to 137 glycoproteins, were identified, which has been confirmed experimentally in previous studies.
PMC3938046-1-5	17	107	gly	252 N-glycosites	2327:2342	arg2	252 N-glycosites			252 N-glycosites						252 N-glycosites	In our study, 252 N-glycosites, corresponding to 137 glycoproteins, were identified, which has been confirmed experimentally in previous studies.
PMC7124471-1-fig4	2	6	gly	glycoprotein	454:465	arg1	alpha-1-acid glycoprotein	alpha-1-acid glycoprotein				Fterm		glycoprotein			HRP, horseradish peroxidase; IOVO, ovomucoid; Oval, ovalbumin; Ogchi, alpha-1-acid glycoprotein; QSOX1, sulfhydryl oxidase 1.
PMC5795011-1-3	2	64	gly	glycoprotein	426:437	arg1	alpha-1-acid glycoprotein	alpha-1-acid glycoprotein				Fterm		glycoprotein			When searched against the custom glycoprotein database, the MS2 spectrum shown in Fig. 1A is annotated as a di-sialylated bi-antennary N-glycopeptide of alpha-1-acid glycoprotein, with a Mascot ion score of 24 (Fig. 2A).
PMC5795011-1-3	2	135	gly	glycoprotein	293:304	arg1	the custom glycoprotein database	the custom glycoprotein database				Fterm		glycoprotein			When searched against the custom glycoprotein database, the MS2 spectrum shown in Fig. 1A is annotated as a di-sialylated bi-antennary N-glycopeptide of alpha-1-acid glycoprotein, with a Mascot ion score of 24 (Fig. 2A).
PMC5795011-1-3	2	221	gly	di-sialylated	368:380	arg1	a di-sialylated bi-antennary N-glycopeptide			a di-sialylated bi-antennary N-glycopeptide						N-glycopeptide	When searched against the custom glycoprotein database, the MS2 spectrum shown in Fig. 1A is annotated as a di-sialylated bi-antennary N-glycopeptide of alpha-1-acid glycoprotein, with a Mascot ion score of 24 (Fig. 2A).
PMC5795011-1-3	2	214	gly	N-glycopeptide	395:408	arg2	a di-sialylated bi-antennary N-glycopeptide	glycoprotein		N-glycopeptide		Fterm		glycoprotein		N-glycopeptide	When searched against the custom glycoprotein database, the MS2 spectrum shown in Fig. 1A is annotated as a di-sialylated bi-antennary N-glycopeptide of alpha-1-acid glycoprotein, with a Mascot ion score of 24 (Fig. 2A).
PMC5795011-1-4	81	425	gly	glycopeptides	13797:13809	arg2	intact glycopeptides			intact glycopeptides						glycopeptides	Still, we showed here the possibility of high-throughput identification and relative quantification of intact glycopeptides using this large dataset of 24 LC-MS runs.
PMC3942810-1-2	20	60	gly	motif	3543:3547	arg1	the N-linked glycosylation site			the N-linked glycosylation site						site	To gain a better understanding the sequence motif of the N-linked glycosylation site in RJ, the surrounding sequences (five amino acids to both termini) of N-glycosylated sites were compared.
PMC3942810-1-2	20	131	gly	glycosylation	3565:3577	arg2	the N-linked glycosylation site			the N-linked glycosylation site						site	To gain a better understanding the sequence motif of the N-linked glycosylation site in RJ, the surrounding sequences (five amino acids to both termini) of N-glycosylated sites were compared.
PMC3942810-1-2	20	204	gly	N-glycosylated	3655:3668	arg1	N-glycosylated sites			N-glycosylated sites						sites	To gain a better understanding the sequence motif of the N-linked glycosylation site in RJ, the surrounding sequences (five amino acids to both termini) of N-glycosylated sites were compared.
PMC3942810-2-2	36	423	gly	glycosylation	5414:5426	arg2	the glycosylation sites			the glycosylation sites						sites	Although the glycan linkages associated with the glycosylation sites demand further investigation, this new catalog of knowledge may prove helpful in elucidating the biological implications of glycosylation for the RJ proteins through synthesizing the glycan to the identified sites.
PMC5795011-1-4	44	363	gly	glycoproteins	7753:7765	arg1	the glycoproteins	the glycoproteins				Fterm		glycoproteins			This result clearly indicates the authenticity of the glycoproteins identified by the workflow presented in this study.
PMC3938046-1-3	14	95	gly	2599 N-glycosylation	2476:2495	arg2	2599 N-glycosylation sites			2599 N-glycosylation sites						sites	By WCC, 2394 (92%) of 2599 N-glycosylation sites matched the canonical motif without removing the redundancy.
PMC3938046-1-3	22	90	gly	glycoproteins	3628:3640	arg1	Other glycoproteins	Other glycoproteins				Fterm		glycoproteins			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.
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.
PMC3938046-1-3	22	174	gly	N-glycosites	3658:3669	arg2	10 or more N-glycosites			10 or more N-glycosites						N-glycosites	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.
PMC2538527-1-4	15	338	gly	glycopeptides	2040:2052	arg2	the tryptic glycopeptides			the tryptic glycopeptides						glycopeptides	A MS/MS analysis of the tryptic glycopeptides confirms the composition of this glycan.
PMC3942810-1-fig3	3	5	gly	glycoprotein	359:370	arg1	novel glycoprotein	novel glycoprotein				Fterm		glycoprotein			“33” is the novel sites identified in known glycoprotein, and “9” is the novel sites identified in novel glycoprotein.
PMC3942810-1-fig3	3	22	gly	glycoprotein	298:309	arg1	known glycoprotein	known glycoprotein				Fterm		glycoprotein			“33” is the novel sites identified in known glycoprotein, and “9” is the novel sites identified in novel glycoprotein.
PMC3938046-1-8	14	94	gly	N-glycoprotein	2354:2367	arg1	N-glycoprotein enrichment	N-glycoprotein enrichment				Fterm		N-glycoprotein			The combination of crude membrane fractionation and N-glycoprotein enrichment with quantitative SRM assays will contribute significantly to the comprehensive and systematic validation of changes in the abundance of targeted cell surface proteins.
PMC5457524-1-7	12	110	gly	N-glycopeptides	2356:2370	arg2	2,559 unique, intact N-glycopeptides			2,559 unique, intact N-glycopeptides						N-glycopeptides	Combining all three MS runs, Fbs1 GYR enrichment enabled identification of 2,559 unique, intact N-glycopeptides, which is a 2.2-fold and 7-fold improvement over the unique peptides identified using lectin enrichment (1,172) and pre-enrichment (358), respectively (Fig. 7b).
PMC5457524-1-1	2	177	gly	glycopeptide	177:188	arg2	an N-linked glycopeptide enrichment method			an N-linked glycopeptide enrichment method						glycopeptide	With an aim of developing an N-linked glycopeptide enrichment method, we examined the ability of wt Fbs1 to bind to a variety of glycomolecules.
PMC3942810-2-2	29	412	gly	glycosylated	4432:4443	arg1	the glycosylated protein	the glycosylated protein				Fterm		protein			In addition, the glycosylated protein affects cell proliferation and regulates circadian rhythm[78].
PMC6731604-1-1	5	161	gly	glycosites	1026:1035	arg2	11,336 unique glycosites			11,336 unique glycosites						glycosites	Using this strategy, we collected 13,811 human glycosite-containing peptides representing 11,336 unique glycosites from 34 datasets generated in our laboratory (Fig. 1).
PMC6731604-1-3	12	72	gly	glycoproteins	1782:1794	arg1	the glycoproteins	the glycoproteins				Fterm		glycoproteins			To further investigate the potential of urine in clinical tests and biomarker discovery, we also compared the glycoproteins between urine and serum.
PMC6731604-1-2	11	110	gly	glycoproteins	1591:1603	arg1	more glycoproteins	more glycoproteins				Fterm		glycoproteins			Based on these results, we found that more glycoproteins were identified from urine than from serum.
PMC7124471-1-4	20	113	gly	glycosites	3434:3443	arg2	1030 N-linked glycosites			1030 N-linked glycosites						glycosites	Based on the above strategy, 1030 N-linked glycosites and 22,194 N-linked intact glycopeptides from 521 N-linked glycoproteins were identified from UGP and FGP data sets when using the database of 701 N-glycan masses (Table II, supplemental Table S5, S6, and S7).
PMC7124471-1-4	20	311	gly	glycoproteins	3504:3516	arg1	521 N-linked glycoproteins	521 N-linked glycoproteins				Fterm		glycoproteins			Based on the above strategy, 1030 N-linked glycosites and 22,194 N-linked intact glycopeptides from 521 N-linked glycoproteins were identified from UGP and FGP data sets when using the database of 701 N-glycan masses (Table II, supplemental Table S5, S6, and S7).
PMC7124471-1-4	20	10	gly	glycopeptides	3472:3484	arg2	22,194 N-linked intact glycopeptides	glycoproteins		glycopeptides		Fterm		glycoproteins		glycopeptides	Based on the above strategy, 1030 N-linked glycosites and 22,194 N-linked intact glycopeptides from 521 N-linked glycoproteins were identified from UGP and FGP data sets when using the database of 701 N-glycan masses (Table II, supplemental Table S5, S6, and S7).
PMC5795011-1-4	39	238	gly	glycoproteins	6962:6974	arg1	14120 glycoproteins	14120 glycoproteins				Fterm		glycoproteins			In addition to the database used in obtaining the above presented results, the LC-MS data sets of the 24 serum samples were also searched against differentially sized custom glycoprotein databases created from (i) all known plasma/serum proteins from PeptideAtlas build 2010 (2421 glycoproteins), (ii) all deamidated proteins identified following PNGaseF treatment of glycopeptides from the same 24 serum samples (280 glycoproteins) and (iii) Swiss-Prot annotated human proteome (14120 glycoproteins).
PMC5795011-1-4	39	272	gly	glycoproteins	6757:6769	arg1	2421 glycoproteins	2421 glycoproteins				Fterm		glycoproteins			In addition to the database used in obtaining the above presented results, the LC-MS data sets of the 24 serum samples were also searched against differentially sized custom glycoprotein databases created from (i) all known plasma/serum proteins from PeptideAtlas build 2010 (2421 glycoproteins), (ii) all deamidated proteins identified following PNGaseF treatment of glycopeptides from the same 24 serum samples (280 glycoproteins) and (iii) Swiss-Prot annotated human proteome (14120 glycoproteins).
PMC5795011-1-4	39	358	gly	glycoprotein	6650:6661	arg1	differentially sized custom glycoprotein databases	differentially sized custom glycoprotein databases				Fterm		glycoprotein			In addition to the database used in obtaining the above presented results, the LC-MS data sets of the 24 serum samples were also searched against differentially sized custom glycoprotein databases created from (i) all known plasma/serum proteins from PeptideAtlas build 2010 (2421 glycoproteins), (ii) all deamidated proteins identified following PNGaseF treatment of glycopeptides from the same 24 serum samples (280 glycoproteins) and (iii) Swiss-Prot annotated human proteome (14120 glycoproteins).
PMC5795011-1-4	39	847	gly	glycoproteins	6894:6906	arg1	280 glycoproteins	280 glycoproteins				Fterm		glycoproteins			In addition to the database used in obtaining the above presented results, the LC-MS data sets of the 24 serum samples were also searched against differentially sized custom glycoprotein databases created from (i) all known plasma/serum proteins from PeptideAtlas build 2010 (2421 glycoproteins), (ii) all deamidated proteins identified following PNGaseF treatment of glycopeptides from the same 24 serum samples (280 glycoproteins) and (iii) Swiss-Prot annotated human proteome (14120 glycoproteins).
PMC5795011-1-4	39	899	gly	glycopeptides	6844:6856	arg2	glycopeptides	glycoproteins		glycopeptides		Fterm		glycoproteins		glycopeptides	In addition to the database used in obtaining the above presented results, the LC-MS data sets of the 24 serum samples were also searched against differentially sized custom glycoprotein databases created from (i) all known plasma/serum proteins from PeptideAtlas build 2010 (2421 glycoproteins), (ii) all deamidated proteins identified following PNGaseF treatment of glycopeptides from the same 24 serum samples (280 glycoproteins) and (iii) Swiss-Prot annotated human proteome (14120 glycoproteins).
PMC5795011-1-4	26	497	gly	glycopeptide	4264:4275	arg2	these 3447 glycopeptide variants			these 3447 glycopeptide variants						glycopeptide	Of these 3447 glycopeptide variants, the most abundant are the di-sialylated bi-antennary glycans with no (377), one (291) and two fucose residues (169).
PMC6243375-1-1	5	14	gly	glycopeptides	841:853	arg2	the site‐specific O‐linked glycopeptides			the site‐specific O‐linked glycopeptides						glycopeptides	Of note, O‐linked glycans were still attached to the site‐specific O‐linked glycopeptides as confirmed by the detection of oxonium, peptide (Y0), and less commonly identified peptide + HexNAc (Y1) ions in the MS/MS spectrum (Fig 1B).
PMC5795011-1-3	19	169	gly	glycopeptides	2906:2918	arg2	the O-linked glycopeptides			the O-linked glycopeptides						glycopeptides	A series of y ions (y5 to y18) and b ions (b1, b2,b3) covering the most intense peaks (Fig. 3A,B) clearly confirmed that these MS2 spectra correspond to the O-linked glycopeptides.
PMC5457524-1-6	12	7	gly	N-glycosite	1661:1671	arg2	N-glycosite			N-glycosite						N-glycosite	Next we examined Fbs1 GYR enrichment in detail by N-glycosite identification or deglycoproteomics10 using PNGase F deglycosylation in the presence of 18O water, which tags the deglycosylated peptides with 2.988 daltons due to conversion of asparagine (N) at the N-glycosylation site to aspartic acid (D) and incorporation of 18O.
PMC5457524-1-6	12	50	gly	deglycosylated	1787:1800	arg1	the deglycosylated peptides			the deglycosylated peptides						peptides	Next we examined Fbs1 GYR enrichment in detail by N-glycosite identification or deglycoproteomics10 using PNGase F deglycosylation in the presence of 18O water, which tags the deglycosylated peptides with 2.988 daltons due to conversion of asparagine (N) at the N-glycosylation site to aspartic acid (D) and incorporation of 18O.
PMC5457524-1-6	12	83	gly	N-glycosylation	1873:1887	arg2	the N-glycosylation site			the N-glycosylation site						site	Next we examined Fbs1 GYR enrichment in detail by N-glycosite identification or deglycoproteomics10 using PNGase F deglycosylation in the presence of 18O water, which tags the deglycosylated peptides with 2.988 daltons due to conversion of asparagine (N) at the N-glycosylation site to aspartic acid (D) and incorporation of 18O.
PMC3938046-1-5	19	23	gly	glycoproteins	2611:2623	arg1	349 glycoproteins	349 glycoproteins				Fterm		glycoproteins			Notably, 450 N-glycosites, corresponding 349 glycoproteins, were novel N-glycosylation sites that were uncharacterized in the UniProtKB database (Additional file 7: Table S8).
PMC3938046-1-5	19	32	gly	450 N-glycosites	2575:2590	arg2	450 N-glycosites			450 N-glycosites						450 N-glycosites	Notably, 450 N-glycosites, corresponding 349 glycoproteins, were novel N-glycosylation sites that were uncharacterized in the UniProtKB database (Additional file 7: Table S8).
PMC3938046-1-5	19	123	gly	N-glycosylation	2637:2651	arg2	novel N-glycosylation sites			novel N-glycosylation sites						sites	Notably, 450 N-glycosites, corresponding 349 glycoproteins, were novel N-glycosylation sites that were uncharacterized in the UniProtKB database (Additional file 7: Table S8).
PMC5795011-1-2	2	25	gly	glycopeptide	392:403	arg2	the di-sialylated bi-antennary glycopeptide			the di-sialylated bi-antennary glycopeptide						glycopeptide	Considering the di-sialylated bi-antennary glycopeptide (Fig. 1A), the following linear sequence OJUUJOJJJOO-peptide fulfills the criteria mentioned above (Fig. 1B).
PMC5795011-1-2	2	29	gly	di-sialylated	365:377	arg1	the di-sialylated bi-antennary glycopeptide			the di-sialylated bi-antennary glycopeptide						glycopeptide	Considering the di-sialylated bi-antennary glycopeptide (Fig. 1A), the following linear sequence OJUUJOJJJOO-peptide fulfills the criteria mentioned above (Fig. 1B).
PMC3942810-1-fig3	1	15	gly	glycoprotein	109:120	arg1	known glycoprotein	known glycoprotein				Fterm		glycoprotein			“2” is the identified two known sites in known glycoprotein.
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).
PMC3938046-1-8	13	31	gly	glycopeptides	2204:2216	arg2	glycopeptides			glycopeptides						glycopeptides	In addition to Antibody-based applications, our data allow one to choose fragment ions of peptides and glycopeptides for MS workflows by peptide-targeted selected reaction monitoring (SRM) assay [52].
PMC7124471-1-4	11	150	gly	glycopeptide	2136:2147	arg2	identified glycopeptide precursor ions			identified glycopeptide precursor ions						glycopeptide	After 1% separate-FDR filtering, we observed that a subset of identified glycopeptide precursor ions determined by pParse software were prone to be isotopic peaks, because their charge states were the same, and their precursor ion masses differed by 1 Da.
PMC7124471-1-6	15	59	gly	glycoproteins	2494:2506	arg1	non-human glycoproteins	non-human glycoproteins				Fterm		glycoproteins			To validate the accuracy of this strategy, we spiked a set of non-human glycoproteins including HRP, IOVO, Ogchi, OVAL, and QSOX1 into serum and analyzed the change of identified N-glycan masses.
PMC7124471-1-6	7	18	gly	glycoproteins	1016:1028	arg1	four glycoproteins	four glycoproteins				Fterm		glycoproteins			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).
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).
PMC5457524-1-7	49	250	gly	glycopeptides	7700:7712	arg2	N-linked glycopeptides			N-linked glycopeptides						glycopeptides	Yet no single lectin has been exploited for selective enrichment of N-linked glycopeptides.
PMC5795011-1-1	5	81	gly	glycopeptide	940:951	arg2	glycopeptide MS2 spectrum			glycopeptide MS2 spectrum						glycopeptide	Assuming the glycan residues similar to amino acids, deducing the glycan structure from glycopeptide MS2 spectrum is similar to peptide sequencing.
PMC6731604-1-1	21	58	gly	glycosites	4496:4505	arg2	the glycosites			the glycosites						glycosites	We found that the majority of the glycosites (83.4%) in the database were published during 2010–2015 (Fig. 2c), and these sites were most likely identified with high confidence by using high resolution and high accurate mass spectrometry.
PMC5795011-1-4	119	41	gly	glycopeptides	20600:20612	arg2	the glycopeptides			the glycopeptides						glycopeptides	In addition to the peptide/glycopeptide fragments, the presence of common oxonium ions and glycopeptide ions (Pep + HexNAc) are also considered while scoring the glycopeptides.
PMC5795011-1-4	119	817	gly	peptide/glycopeptide	20457:20476	arg2	the peptide/glycopeptide fragments			the peptide/glycopeptide fragments						peptide/glycopeptide fragments	In addition to the peptide/glycopeptide fragments, the presence of common oxonium ions and glycopeptide ions (Pep + HexNAc) are also considered while scoring the glycopeptides.
PMC5795011-1-4	119	619	gly	glycopeptide	20529:20540	arg1	Pep + HexNAc			glycopeptide	Pep + HexNAc					glycopeptide	In addition to the peptide/glycopeptide fragments, the presence of common oxonium ions and glycopeptide ions (Pep + HexNAc) are also considered while scoring the glycopeptides.
PMC5795011-1-4	94	343	gly	glycoprotein	15930:15941	arg1	custom glycoprotein databases	custom glycoprotein databases				Fterm		glycoprotein			Using the total human proteome and glycome databases in preparing custom glycoprotein databases would of course have an impact on the quality of assignments.
PMC5795011-1-4	118	98	gly	glycopeptide	20339:20350	arg2	the potential glycopeptide candidates			the potential glycopeptide candidates						glycopeptide	Glycan residues are specified as monosaccharide compositions and the potential glycopeptide candidates are scored by placing each glycan on the consensus N-glycosylation motifs.
PMC5795011-1-4	118	167	gly	N-glycosylation	20414:20428	arg2	the consensus N-glycosylation motifs			the consensus N-glycosylation motifs						motifs	Glycan residues are specified as monosaccharide compositions and the potential glycopeptide candidates are scored by placing each glycan on the consensus N-glycosylation motifs.
PMC5795011-1-4	43	309	gly	glycoprotein	7434:7445	arg1	the glycoprotein databases	the glycoprotein databases				Fterm		glycoprotein			Comparing the glycoprotein databases created from deamidated proteins identified following PNGaseF treatment and plasma glycoproteins reported in Peptide Atlas, out of the 257 glycoproteins identified, 163 were found to be common representing 63% overlap (Supplementary Fig. 6).
PMC5795011-1-4	43	701	gly	glycoproteins	7596:7608	arg1	the 257 glycoproteins	the 257 glycoproteins				Fterm		glycoproteins			Comparing the glycoprotein databases created from deamidated proteins identified following PNGaseF treatment and plasma glycoproteins reported in Peptide Atlas, out of the 257 glycoproteins identified, 163 were found to be common representing 63% overlap (Supplementary Fig. 6).
PMC5795011-1-4	43	976	gly	glycoproteins	7540:7552	arg1	plasma glycoproteins	plasma glycoproteins				Fterm		glycoproteins			Comparing the glycoprotein databases created from deamidated proteins identified following PNGaseF treatment and plasma glycoproteins reported in Peptide Atlas, out of the 257 glycoproteins identified, 163 were found to be common representing 63% overlap (Supplementary Fig. 6).
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.
PMC7124471-1-6	2	109	gly	glycoprotein	265:276	arg1	The classical serum glycoprotein serotransferrin	The classical serum glycoprotein serotransferrin				Fterm		glycoprotein			The classical serum glycoprotein serotransferrin was used as a benchmark protein, as it was identified with thousands of GPSMs in the human serum data sets.
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	Wnt/β-catenin signaling	Wnt/β-catenin signaling				Fterm		Wnt/β-catenin			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.
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	63	86	gly	glycopeptide	8881:8892	arg2	N-linked intact glycopeptide identification			N-linked intact glycopeptide identification						glycopeptide	Here we included this motif in N-linked intact glycopeptide identification and adopted group-FDR strategy to separately estimate FDR in different motif subclasses.
PMC6243375-1-3	9	120	gly	glycosylation	1480:1492	arg2	the O‐linked glycosylation sites			the O‐linked glycosylation sites						sites	Therefore, ETD‐MS2 provided that a cleavage specificity by OpeRATOR was at the N‐termini of the O‐linked glycosylation sites with core 1 glycans.
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	80	gly	glycoprotein	1271:1282	arg1	The plant glycoprotein HRP	The plant glycoprotein HRP				Fterm		glycoprotein			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.
PMC7124471-1-6	9	96	gly	glycoproteins	1309:1321	arg1	the four chicken glycoproteins	the four chicken glycoproteins				Fterm		glycoproteins			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.
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-fig2	4	11	gly	glycosylation	510:522	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	Analysis of amino acid sequence surrounding O‐linked glycosylation sites.
PMC3938046-1-3	5	2	gly	glycoproteins	935:947	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			By CMC, 70% of unique N-glycosites and 69% of glycoproteins overlapped between replicates.
PMC3938046-1-3	5	72	gly	N-glycosites	911:922	arg2	unique N-glycosites			unique N-glycosites						N-glycosites	By CMC, 70% of unique N-glycosites and 69% of glycoproteins overlapped between replicates.
PMC3938046-1-5	18	79	gly	glycoproteins	2509:2521	arg1	384 glycoproteins	384 glycoproteins				Fterm		glycoproteins			A total of 740 N-glycosites, corresponding to 384 glycoproteins, were labeled as “potential” in UniProtKB.
PMC3938046-1-5	18	186	gly	740 N-glycosites	2470:2485	arg2	740 N-glycosites			740 N-glycosites						740 N-glycosites	A total of 740 N-glycosites, corresponding to 384 glycoproteins, were labeled as “potential” in UniProtKB.
PMC5795011-1-4	5	137	gly	glycoprotein	1125:1136	arg1	the custom glycoprotein database	the custom glycoprotein database				Fterm		glycoprotein			Considering zero missed cleavages, NxT/S/C motifs and a peptide length of 6–30 amino acids, A1AG1 potentially contained two N-glycosylation sites in the custom glycoprotein database (QDQCIYNTTYLNVQR, ENGTISR).
PMC5795011-1-4	5	880	gly	N-glycosylation	1089:1103	arg2	two N-glycosylation sites			two N-glycosylation sites						sites	Considering zero missed cleavages, NxT/S/C motifs and a peptide length of 6–30 amino acids, A1AG1 potentially contained two N-glycosylation sites in the custom glycoprotein database (QDQCIYNTTYLNVQR, ENGTISR).
PMC6731604-1-fig3	0	8	gly	glycoproteins	42:54	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			Distribution of identified glycosites and glycoproteins across different human tissues or body fluids.
PMC6731604-1-fig3	0	20	gly	glycosites	27:36	arg2	glycosites			glycosites						glycosites	Distribution of identified glycosites and glycoproteins across different human tissues or body fluids.
PMC6731604-1-1	4	178	gly	glycosylation	826:838	arg2	the glycosylation site			the glycosylation site						site	For each matched protein, the protein accession number, protein name, gene name, N-linked glycosylation location and the protein sequence at ± 20 amino acids surrounding the glycosylation site were extracted from the protein database to constitute the N-GlycositeAtlas.
PMC7124471-1-6	4	129	gly	glycopeptides	650:662	arg2	N-linked intact glycopeptides			N-linked intact glycopeptides						glycopeptides	This indicates it is feasible to use the proposed workflow in identifying N-linked intact glycopeptides in commercial protein samples.
PMC5795011-1-fig1	0	18	gly	glycopeptide	49:60	arg2	a di-sialylated bi-antennary glycopeptide			a di-sialylated bi-antennary glycopeptide						glycopeptide	HCD-MS2 spectrum of a di-sialylated bi-antennary glycopeptide (m/z 1177.81373+) derived from bovine alpha-1-acid glycoprotein 1.
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.
PMC5795011-1-fig1	0	35	gly	di-sialylated	22:34	arg1	a di-sialylated bi-antennary glycopeptide			a di-sialylated bi-antennary glycopeptide						glycopeptide	HCD-MS2 spectrum of a di-sialylated bi-antennary glycopeptide (m/z 1177.81373+) derived from bovine alpha-1-acid glycoprotein 1.
PMC5457524-1-7	24	534	gly	glycosylation	4593:4605	arg2	the associated glycosylation sites			the associated glycosylation sites						sites	Even as the data set grows, accurate determination of glycan composition and the associated glycosylation sites remains challenging51.
PMC2538527-1-fig7	7	47	gly	glycopeptide	926:937	arg2	glycopeptide			glycopeptide						glycopeptide	C) ETD MS/MS spectrum of the triply protonated, monosialylated T84-112 glycopeptide at m/z 1340.8.
PMC7124471-1-11	15	465	gly	glycopeptide	1906:1917	arg2	this N-linked intact glycopeptide			this N-linked intact glycopeptide						glycopeptide	The peak area of this N-linked intact glycopeptide was exported by Skyline (Fig. 7C).
PMC2538527-1-fig6	2	2	gly	disialylated	364:375	arg1	Hex1HexNAc1SA2				Hex1HexNAc1SA2						The most intense peak at 20,213 Da appears to be composed of the mature peptide chain plus a single core type-1 disialylated glycan (Hex1HexNAc1SA2).
PMC5795011-1-3	10	68	gly	glycopeptide	1518:1529	arg2	the same glycopeptide			the same glycopeptide						glycopeptide	However, the same glycopeptide contained a series of peptide cleavage type y ions (y4 to y9) at an NCE value of 35 with almost no information about the glycan structure.
PMC3938046-1-5	14	119	gly	N-glycosylation	1845:1859	arg2	N-glycosylation sites			N-glycosylation sites						sites	Further, N-glycosylation sites were compared against UniProtKB, which included N-glycosylation information of proteins with the qualifiers “Potential,” “By similarity,” and “Experimental.”
PMC7124471-1-3	13	161	gly	deglycopeptides	2059:2073	arg2	identified N-linked deglycopeptides			identified N-linked deglycopeptides						deglycopeptides	Notably, 51.04% (467/915) and 42.22% (1150/2724) of identified N-linked deglycopeptides were semi-tryptic peptides in UDGP and FDGP, respectively (supplemental Table S2).
PMC7124471-1-fig4	1	4	gly	glycoprotein	227:238	arg1	five non-human glycoprotein standards	five non-human glycoprotein standards				Fterm		glycoprotein			Four different set of search parameters are used to identify glycopeptides from five non-human glycoprotein standards and their GPSMs (A), N-linked glycosites (B), N-linked intact glycopeptides(C) and number of N-glycans (D) are compared.
PMC7124471-1-fig4	1	8	gly	glycopeptides	312:324	arg2	N-linked intact glycopeptides			N-linked intact glycopeptides						glycopeptides	Four different set of search parameters are used to identify glycopeptides from five non-human glycoprotein standards and their GPSMs (A), N-linked glycosites (B), N-linked intact glycopeptides(C) and number of N-glycans (D) are compared.
PMC7124471-1-fig4	1	10	gly	glycopeptides	193:205	arg2	glycopeptides			glycopeptides						glycopeptides	Four different set of search parameters are used to identify glycopeptides from five non-human glycoprotein standards and their GPSMs (A), N-linked glycosites (B), N-linked intact glycopeptides(C) and number of N-glycans (D) are compared.
PMC7124471-1-fig4	1	24	gly	glycosites	280:289	arg2	N-linked glycosites			N-linked glycosites						glycosites	Four different set of search parameters are used to identify glycopeptides from five non-human glycoprotein standards and their GPSMs (A), N-linked glycosites (B), N-linked intact glycopeptides(C) and number of N-glycans (D) are compared.
PMC4804330-1-3	18	134	gly	peptide	3385:3391	arg1	the peptide GalNAc				the peptide GalNAc						ST6GALNAC2 on the other hand adds a NeuNAc to the 6 position of the peptide GalNAc of O-glycan Core 1 or 3 structures thus terminating chain elongation2633.
PMC6243375-1-fig1	0	1	gly	glycosylation	129:141	arg2	O‐linked glycosylation sites			O‐linked glycosylation sites						sites	EXoO procedure for mapping the site‐specific O‐linked glycoproteome  Schematic of EXoO process for precision mapping of O‐linked glycosylation sites and site‐specific glycans.
PMC7124471-1-11	64	364	gly	deglycopeptides	9053:9067	arg2	143 deglycopeptides			143 deglycopeptides						deglycopeptides	In the UDGP and FDGP data sets, we also identified 143 deglycopeptides with NXV motif.
PMC6731604-1-1	8	9	gly	glycoproteins	1611:1623	arg1	7204 glycoproteins	7204 glycoproteins				Fterm		glycoproteins			Altogether, the N-GlycositeAtlas contains 30,872 unique glycosite-containing peptides that match to 14,644 unique glycosites in 7204 glycoproteins (Fig. 1 and Additional file 1: Table S1).
PMC6731604-1-1	8	168	gly	glycosites	1592:1601	arg2	14,644 unique glycosites			14,644 unique glycosites						glycosites	Altogether, the N-GlycositeAtlas contains 30,872 unique glycosite-containing peptides that match to 14,644 unique glycosites in 7204 glycoproteins (Fig. 1 and Additional file 1: Table S1).
PMC7124471-1-5	1	19	gly	glycopeptide	137:148	arg2	serum N-linked intact glycopeptide identification			serum N-linked intact glycopeptide identification						glycopeptide	The distribution of 739 N-glycan masses used for serum N-linked intact glycopeptide identification is shown in Fig. 4A, which is close to a normal distribution.
PMC6731604-1-2	10	40	gly	glycoproteins	1468:1480	arg1	2645 and 1845 glycoproteins	2645 and 1845 glycoproteins				Fterm		glycoproteins			N-GlycositeAtlas contains 2645 and 1845 glycoproteins that were identified from urine and serum, respectively (Fig. 3).
PMC7124471-1-10	8	18	gly	glycosites	935:944	arg2	the mentioned glycosites	serotransferrin		glycosites		OGER		serotransferrin	P02787	glycosites	Among the mentioned glycosites of serotransferrin, N523 and N637 are not reported in Uniprot.
PMC6731604-1-3	10	22	gly	glycoproteins	1302:1314	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			The results indicated that a lot of glycoproteins were also commonly identified from urine and tissues, with an average of 63.1 ± 12.1% tissue-derived glycoproteins overlapping with urine-derived glycoproteins (Fig. 4b).
PMC6731604-1-3	10	27	gly	glycoproteins	1462:1474	arg1	urine-derived glycoproteins	urine-derived glycoproteins				Fterm		glycoproteins			The results indicated that a lot of glycoproteins were also commonly identified from urine and tissues, with an average of 63.1 ± 12.1% tissue-derived glycoproteins overlapping with urine-derived glycoproteins (Fig. 4b).
PMC6731604-1-3	10	107	gly	glycoproteins	1417:1429	arg1	63.1 ± 12.1% tissue-derived glycoproteins	63.1 ± 12.1% tissue-derived glycoproteins				Fterm		glycoproteins			The results indicated that a lot of glycoproteins were also commonly identified from urine and tissues, with an average of 63.1 ± 12.1% tissue-derived glycoproteins overlapping with urine-derived glycoproteins (Fig. 4b).
PMC6731604-1-1	15	12	gly	glycosites	2913:2922	arg2	5215 glycosites			5215 glycosites						glycosites	In N-GlycositeAtlas, 2247 glycosites were identified more than 10 times, 7182 glycosites were identified 2-10 times, and 5215 glycosites (35.6%) were identified only once in all different datasets (Fig. 2a).
PMC6731604-1-1	15	59	gly	glycosites	2865:2874	arg2	7182 glycosites			7182 glycosites						glycosites	In N-GlycositeAtlas, 2247 glycosites were identified more than 10 times, 7182 glycosites were identified 2-10 times, and 5215 glycosites (35.6%) were identified only once in all different datasets (Fig. 2a).
PMC6731604-1-1	15	207	gly	glycosites	2813:2822	arg2	2247 glycosites			2247 glycosites						glycosites	In N-GlycositeAtlas, 2247 glycosites were identified more than 10 times, 7182 glycosites were identified 2-10 times, and 5215 glycosites (35.6%) were identified only once in all different datasets (Fig. 2a).
PMC6731604-1-4	7	4	gly	glycosites	1534:1543	arg2	the identified glycosites			the identified glycosites						glycosites	In the second display page, the user will obtain the tissue/liquid/cell line types where the glycoprotein was identified (Fig. 5c), all glycosite-containing peptides identified at each glycosite with the reference information (Fig. 5d), as well as the highlighted the location of the identified glycosites and glycosite-containing peptides in the protein sequence (Fig. 5e).
PMC6731604-1-4	7	41	gly	glycosite	1424:1432	arg2	each glycosite			each glycosite						glycosite	In the second display page, the user will obtain the tissue/liquid/cell line types where the glycoprotein was identified (Fig. 5c), all glycosite-containing peptides identified at each glycosite with the reference information (Fig. 5d), as well as the highlighted the location of the identified glycosites and glycosite-containing peptides in the protein sequence (Fig. 5e).
PMC6731604-1-4	7	125	gly	glycoprotein	1332:1343	arg1	the glycoprotein	the glycoprotein				Fterm		glycoprotein			In the second display page, the user will obtain the tissue/liquid/cell line types where the glycoprotein was identified (Fig. 5c), all glycosite-containing peptides identified at each glycosite with the reference information (Fig. 5d), as well as the highlighted the location of the identified glycosites and glycosite-containing peptides in the protein sequence (Fig. 5e).
PMC5795011-1-4	108	420	gly	glycopeptide	18363:18374	arg2	automated glycopeptide identification studies			automated glycopeptide identification studies						glycopeptide	A large number of academically developed computational tools showed potential on automated glycopeptide identification studies for example, GlyDB, GlyPID, GlycoFragWork, GlycoMaster DB, GlycoPeptideSearch, GlycoPep Detector, GlycoPep Evaluator, GlycoPep Grader, Integrated Glyco- Proteome Analyzer, MAGIC, pGlyco, Protein Prospector, SweetNET, Sweet-Heart and a few more.
PMC6731604-1-fig2	3	25	gly	glycosites	448:457	arg2	unique glycosites			unique glycosites						glycosites	b Accumulation of identified glycosite-containing peptides, unique glycosites and glycoproteins with time.
PMC6731604-1-fig2	3	29	gly	glycoproteins	463:475	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			b Accumulation of identified glycosite-containing peptides, unique glycosites and glycoproteins with time.
PMC3938046-1-4	10	57	gly	N-glycoproteins	1721:1735	arg1	N-glycoproteins	N-glycoproteins				Fterm		N-glycoproteins			Many molecular functions that are common in N-glycoproteins were enriched in our dataset, including receptor activity, transporter activity, TMD receptor activity, TMD transporter activity, peptidase activity, and ion binding.
PMC6731604-1-2	5	55	gly	glycoproteins	707:719	arg1	311 glycoproteins	311 glycoproteins				Fterm		glycoproteins			In addition to the tissue glycoproteins, 311 glycoproteins with 585 glycosites were identified from spermatozoa [71].
PMC6731604-1-2	5	115	gly	glycosites	730:739	arg2	585 glycosites			585 glycosites						glycosites	In addition to the tissue glycoproteins, 311 glycoproteins with 585 glycosites were identified from spermatozoa [71].
PMC6731604-1-2	5	116	gly	glycoproteins	688:700	arg1	the tissue glycoproteins	the tissue glycoproteins				Fterm		glycoproteins			In addition to the tissue glycoproteins, 311 glycoproteins with 585 glycosites were identified from spermatozoa [71].
PMC5795011-1-4	25	61	gly	glycoproteins	4099:4111	arg1	these 257 glycoproteins	these 257 glycoproteins				Fterm		glycoproteins			Within these 257 glycoproteins, a total of 970 unique glycosylation sites and 3447 non-redundant glycopeptide variants were identified (Supplementary Tables 4, and 5).
PMC5795011-1-4	25	806	gly	glycosylation	4136:4148	arg2	970 unique glycosylation sites			970 unique glycosylation sites						sites	Within these 257 glycoproteins, a total of 970 unique glycosylation sites and 3447 non-redundant glycopeptide variants were identified (Supplementary Tables 4, and 5).
PMC5795011-1-4	25	813	gly	glycopeptide	4179:4190	arg2	3447 non-redundant glycopeptide variants			3447 non-redundant glycopeptide variants						glycopeptide	Within these 257 glycoproteins, a total of 970 unique glycosylation sites and 3447 non-redundant glycopeptide variants were identified (Supplementary Tables 4, and 5).
PMC5976746-1-fig3	10	69	gly	glycopeptide	1068:1079	arg2	glycopeptide			glycopeptide						glycopeptide	Details of glycopeptide peaks identified are shown in Table S2 in Supplementary Material.
PMC5795011-1-4	130	667	gly	glycopeptide	22424:22435	arg2	automated glycopeptide analysis			automated glycopeptide analysis						glycopeptide	In conclusion, we showed that Mascot, a widely accepted and used software could be easily implemented for automated glycopeptide analysis.
PMC6731604-1-4	11	39	gly	glycosite	2528:2536	arg2	more than one glycosite			more than one glycosite						glycosite	When a peptide contains more than one glycosite, each glycosite is displayed on a separate line.
PMC6731604-1-4	11	131	gly	glycosite	2544:2552	arg2	each glycosite			each glycosite						glycosite	When a peptide contains more than one glycosite, each glycosite is displayed on a separate line.
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).
PMC6731604-1-fig2	4	15	gly	glycosites	508:517	arg2	glycosites			glycosites						glycosites	c Classification of glycosites according to their year of publication
PMC3938046-1-3	11	33	gly	glycoproteins	2101:2113	arg1	374 glycoproteins	374 glycoproteins				Fterm		glycoproteins			In contrast, by CMC, the quadruplicate of 2 biological replicates identified an average of 670 N-glycosylation sites, corresponding to 374 glycoproteins.
PMC3938046-1-3	11	46	gly	670 N-glycosylation	2053:2071	arg2	670 N-glycosylation sites			670 N-glycosylation sites						sites	In contrast, by CMC, the quadruplicate of 2 biological replicates identified an average of 670 N-glycosylation sites, corresponding to 374 glycoproteins.
PMC5457524-1-6	19	164	gly	N-glycoproteins	3147:3161	arg1	Eighty-three (93%) N-glycoproteins	Eighty-three (93%) N-glycoproteins				Fterm		N-glycoproteins			Eighty-three (93%) N-glycoproteins identified in pre-enrichment samples were also identified in Fbs1 GYR enrichment samples.
PMC6934601-1-7	29	210	gly	sialylated	4688:4697	arg1	a sialylated epitope			a sialylated epitope						epitope	This antibody targeted a sialylated epitope on SPN that was expressed across all AML subtypes, but was not found on healthy monocytes, granulocytes, B cells or T cells.
PMC6123398-1-6	31	385	gly	fucosylated	5238:5248	arg1	fucosylated residues			fucosylated residues						residues in	This discrepancy could be due to the degradation of large fucosylated oligosaccharides by fucosidases, leaving only a small number of fucosylated residues in bovine milk.
PMC5457524-1-5	8	64	gly	non-glycosylated	1013:1028	arg1	the non-glycosylated peptides			the non-glycosylated peptides						peptides	The glycomolecules elute between 24 and 30 min, whereas the non-glycosylated peptides elute before 24 min.
PMC5795011-1-4	13	527	gly	glycosylation	2193:2205	arg2	the same glycosylation site			the same glycosylation site						site	Nine different glycan structures with varied degree of complexity and sialylation on the same glycosylation site, and near to complete information about both the peptide and glycan part proved the capability of the current approach for large scale automated glycopeptide analysis.
PMC5795011-1-4	13	693	gly	glycopeptide	2357:2368	arg2	large scale automated glycopeptide analysis			large scale automated glycopeptide analysis						glycopeptide	Nine different glycan structures with varied degree of complexity and sialylation on the same glycosylation site, and near to complete information about both the peptide and glycan part proved the capability of the current approach for large scale automated glycopeptide analysis.
PMC5795011-1-4	13	1128	gly	sialylation	2169:2179	arg1	the same glycosylation site			the same glycosylation site						site	Nine different glycan structures with varied degree of complexity and sialylation on the same glycosylation site, and near to complete information about both the peptide and glycan part proved the capability of the current approach for large scale automated glycopeptide analysis.
PMC7081908-1-1	4	21	gly	glycosylation	652:664	arg2	23 to 26 potential N-linked glycosylation sites			23 to 26 potential N-linked glycosylation sites						sites	They have 23 to 26 potential N-linked glycosylation sites (PNGSs), which are distributed throughout the sequence in similar but distinct manners (Fig. 1B).
PMC3938046-1-3	19	9	gly	760 N-glycosylated	3227:3244	arg1	760 N-glycosylated proteins	760 N-glycosylated proteins				Fterm		proteins			Of 760 N-glycosylated proteins, approximately two-thirds harbored a single N-glycosylation site (Figure 3D); 17% had 2 N-glycosylation sites, and 9% had 3 sites.
PMC3938046-1-3	19	98	gly	N-glycosylation	3299:3313	arg2	a single N-glycosylation site			a single N-glycosylation site						site	Of 760 N-glycosylated proteins, approximately two-thirds harbored a single N-glycosylation site (Figure 3D); 17% had 2 N-glycosylation sites, and 9% had 3 sites.
PMC3938046-1-3	19	151	gly	2 N-glycosylation	3341:3357	arg2	2 N-glycosylation sites			2 N-glycosylation sites						sites	Of 760 N-glycosylated proteins, approximately two-thirds harbored a single N-glycosylation site (Figure 3D); 17% had 2 N-glycosylation sites, and 9% had 3 sites.
PMC6243375-1-5	29	323	gly	glycosylation	6071:6083	arg2	the O‐linked glycosylation sites			the O‐linked glycosylation sites						sites	This was consistent with previous reports, which gives some validation of the O‐linked glycosylation sites identified using EXoO (Christlet & Veluraja, 2001; Julenius et al, 2005).
PMC3942810-1-2	1	181	gly	glycosylation	72:84	arg2	N-linked glycosylation sites			N-linked glycosylation sites						sites	To attain a comprehensive map of N-linked glycosylation sites in RJ, RJ proteins were extracted and enriched by two different enrichment methods (hydrazide and lectin), after which the N-glycosylation peptides were analyzed by two different double high LC-MS/MS (orbitrap-based MS and triple TOF-based MS).
PMC5457524-1-1	9	18	gly	glycoproteins	1448:1460	arg1	glycoproteins	glycoproteins				Fterm		glycoproteins			In addition to high-mannose N-glycoproteins, we demonstrate that Fbs1 also binds to glycoproteins with complex N-glycans.
PMC5457524-1-1	9	103	gly	N-glycoproteins	1392:1406	arg1	high-mannose N-glycoproteins	high-mannose N-glycoproteins				Fterm		N-glycoproteins			In addition to high-mannose N-glycoproteins, we demonstrate that Fbs1 also binds to glycoproteins with complex N-glycans.
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.
PMC5457524-1-7	0	327	gly	N-glycopeptide	25:38	arg2	intact N-glycopeptide identification			intact N-glycopeptide identification						N-glycopeptide	Fbs1 GYR improves intact N-glycopeptide identification.
PMC7124471-1-3	9	105	gly	deglycopeptides	1647:1661	arg2	serum N-linked deglycopeptides			serum N-linked deglycopeptides						deglycopeptides	Fifteen kinds of these modifications showed considerable frequencies in serum N-linked deglycopeptides (supplemental Fig.
PMC3938046-1-fig3	2	16	gly	N-glycoproteins	217:231	arg1	N-glycoproteins	N-glycoproteins				Fterm		N-glycoproteins			(B) Identification of N-glycosylation sites and N-glycoproteins in 16 replicates by 2 different approaches.
PMC3938046-1-fig3	2	18	gly	N-glycosylation	191:205	arg2	N-glycosylation sites			N-glycosylation sites						sites	(B) Identification of N-glycosylation sites and N-glycoproteins in 16 replicates by 2 different approaches.
PMC6243375-1-5	33	152	gly	glycosylation	7140:7152	arg1	proteins	proteins				Fterm		proteins			Given these advantages of EXoO, it is anticipated that it will be widely applied in studies to analyze O‐linked glycosylation of proteins.
PMC5098438-1-fig4	3	25	gly	MabThera®	291:299	arg1	encircled region			encircled region						region	(B) Mobility extracted singly charged ions from N-glycans released from rituximab (MabThera®, encircled region from panel A).
PMC5098438-1-5	71	200	gly	glycoform	13130:13138	arg1	the Man9GlcNAc2 glycoform				the Man9GlcNAc2 glycoform						Similarly, the extended mannosylated 3-arm would structurally resemble that reported by Crispin et al. for the Man9GlcNAc2 glycoform.
PMC3938046-1-fig6	3	23	gly	N-glycosylation	394:408	arg2	unique N-glycosylation sites			unique N-glycosylation sites						sites	Also, the inner color code of the red squares denotes the number of unique N-glycosylation sites per CD antigen for the N-glycoproteome in BV-2 cells.
PMC5457524-1-6	18	17	gly	N-glycoproteins	2993:3007	arg1	89 and 230 N-glycoproteins	89 and 230 N-glycoproteins				Fterm		N-glycoproteins			The unique N-glycosites were assigned to 89 and 230 N-glycoproteins in pre-enrichment and Fbs1 GYR enrichment samples, respectively (Fig. 6d, right panel and Supplementary Data 1 and 2).
PMC5457524-1-6	18	39	gly	N-glycosites	2952:2963	arg2	The unique N-glycosites			The unique N-glycosites						N-glycosites	The unique N-glycosites were assigned to 89 and 230 N-glycoproteins in pre-enrichment and Fbs1 GYR enrichment samples, respectively (Fig. 6d, right panel and Supplementary Data 1 and 2).
PMC7124471-1-11	40	229	gly	glycopeptide	5572:5583	arg2	large-scale N-linked intact glycopeptide identification			large-scale N-linked intact glycopeptide identification						glycopeptide	It is critical to validate the GPSMs in large-scale N-linked intact glycopeptide identification.
PMC6243375-1-1	8	30	gly	glycopeptide	1612:1623	arg2	O‐linked glycopeptide enrichment			O‐linked glycopeptide enrichment						glycopeptide	As a result, 193 peptide spectrum matches (PSMs) were assigned to fetuin site‐specific O‐linked glycopeptides with Ser or Thr at the N‐termini of peptides, glycan modification, and oxonium ions in the MS/MS spectra from a total of 270 assigned PSMs, indicating a specificity of approximately 71.5% for O‐linked glycopeptide enrichment using EXoO (Dataset EV1).
PMC6243375-1-1	8	83	gly	glycopeptides	1397:1409	arg2	fetuin site‐specific O‐linked glycopeptides			fetuin site‐specific O‐linked glycopeptides						glycopeptides	As a result, 193 peptide spectrum matches (PSMs) were assigned to fetuin site‐specific O‐linked glycopeptides with Ser or Thr at the N‐termini of peptides, glycan modification, and oxonium ions in the MS/MS spectra from a total of 270 assigned PSMs, indicating a specificity of approximately 71.5% for O‐linked glycopeptide enrichment using EXoO (Dataset EV1).
PMC3938046-1-3	21	147	gly	N-glycosylation	3522:3536	arg2	N-glycosylation sites			N-glycosylation sites						sites	The highest number of N-glycosylation sites per protein was 25 for prolow-density lipoprotein receptor-related protein 1.
PMC5976746-1-5	45	584	gly	positions	7307:7315	arg1	241			positions 241 and 289						positions 241 and 289	The N-glycan holes at positions 241 and 289 are the target for neutralizing Abs elicited in rabbits and NHPs immunized with BG505 SOSIP (25, 36, 55).
PMC4595782-1-7	33	471	gly	glycosylation	6446:6458	arg1	the apoplast-targeted SAC-Par-4-GFP and ER-targeted SAC-Par-4-GFP-SEKDEL protein	the apoplast-targeted SAC-Par-4-GFP and ER-targeted SAC-Par-4-GFP-SEKDEL protein				Fterm		protein			Therefore, the nature of glycosylation and proteolytic stability of the apoplast-targeted SAC-Par-4-GFP and ER-targeted SAC-Par-4-GFP-SEKDEL protein were analyzed (Figure ).