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GlyCosmos6-Glycan-Motif-Image

Id	Subject	Object	Predicate	Lexical cue	image
T1	278-289	Glycan_Motif	denotes	sialic acid	https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G81533KY
T2	933-939	Glycan_Motif	denotes	core-1	https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00031MO

sentences

Id	Subject	Object	Predicate	Lexical cue
T1	0-116	Sentence	denotes	LC-MS/MS characterization of O-glycosylation sites and glycan structures of human cerebrospinal fluid glycoproteins.
T2	117-252	Sentence	denotes	The GalNAc O-glycosylation on Ser/Thr residues of extracellular proteins has not been well characterized from a proteomics perspective.
T3	253-505	Sentence	denotes	We previously reported a sialic acid capture-and-release protocol to enrich tryptic N- and O-glycopeptides from human cerebrospinal fluid glycoproteins using nano-LC-ESI-MS/MS with collision-induced dissociation (CID) for glycopeptide characterization.
T4	506-782	Sentence	denotes	Here, we have introduced peptide N-glycosidase F (PNGase F) pretreatment of CSF samples to remove the N-glycans facilitating the selective characterization of O-glycopeptides and enabling the use of an automated CID-MS(2)/MS(3) search protocol for glycopeptide identification.
T5	783-1009	Sentence	denotes	We used electron-capture and -transfer dissociation (ECD/ETD) to pinpoint the glycosylation site(s) of the glycopeptides, identified as predominantly core-1-like HexHexNAc-O- structure attached to one to four Ser/Thr residues.
T6	1010-1177	Sentence	denotes	We characterized 106 O-glycosylations and found Pro residues preferentially in the n - 1, n + 1, and/or n + 3 positions in relation to the Ser/Thr attachment site (n).
T7	1178-1431	Sentence	denotes	The characterization of glycans and glycosylation sites in glycoproteins from human clinical samples provides a basis for future studies addressing the biological and diagnostic importance of specific protein glycosylations in relation to human disease.
T1	0-116	Sentence	denotes	LC-MS/MS characterization of O-glycosylation sites and glycan structures of human cerebrospinal fluid glycoproteins.
T2	117-252	Sentence	denotes	The GalNAc O-glycosylation on Ser/Thr residues of extracellular proteins has not been well characterized from a proteomics perspective.
T3	253-505	Sentence	denotes	We previously reported a sialic acid capture-and-release protocol to enrich tryptic N- and O-glycopeptides from human cerebrospinal fluid glycoproteins using nano-LC-ESI-MS/MS with collision-induced dissociation (CID) for glycopeptide characterization.
T4	506-782	Sentence	denotes	Here, we have introduced peptide N-glycosidase F (PNGase F) pretreatment of CSF samples to remove the N-glycans facilitating the selective characterization of O-glycopeptides and enabling the use of an automated CID-MS(2)/MS(3) search protocol for glycopeptide identification.
T5	783-1009	Sentence	denotes	We used electron-capture and -transfer dissociation (ECD/ETD) to pinpoint the glycosylation site(s) of the glycopeptides, identified as predominantly core-1-like HexHexNAc-O- structure attached to one to four Ser/Thr residues.
T6	1010-1177	Sentence	denotes	We characterized 106 O-glycosylations and found Pro residues preferentially in the n - 1, n + 1, and/or n + 3 positions in relation to the Ser/Thr attachment site (n).
T7	1178-1431	Sentence	denotes	The characterization of glycans and glycosylation sites in glycoproteins from human clinical samples provides a basis for future studies addressing the biological and diagnostic importance of specific protein glycosylations in relation to human disease.

GlyCosmos6-Glycan-Motif-Structure

Id	Subject	Object	Predicate	Lexical cue
T1	278-289	https://glytoucan.org/Structures/Glycans/G81533KY	denotes	sialic acid
T2	933-939	https://glytoucan.org/Structures/Glycans/G00031MO	denotes	core-1

Glycosmos6-MAT

Id	Subject	Object	Predicate	Lexical cue
T1	82-101	http://purl.obolibrary.org/obo/MAT_0000499	denotes	cerebrospinal fluid
T2	371-390	http://purl.obolibrary.org/obo/MAT_0000499	denotes	cerebrospinal fluid

Allie

Id	Subject	Object	Predicate	Lexical cue
SS1_23234360_2_0	434-464	expanded	denotes	collision-induced dissociation
SS2_23234360_2_0	466-469	abbr	denotes	CID
SS1_23234360_3_0	531-554	expanded	denotes	peptide N-glycosidase F
SS2_23234360_3_0	556-564	abbr	denotes	PNGase F
SS1_23234360_4_0	791-834	expanded	denotes	electron-capture and -transfer dissociation
SS2_23234360_4_0	836-843	abbr	denotes	ECD/ETD
AE1_23234360_2_0	SS1_23234360_2_0	SS2_23234360_2_0	abbreviatedTo	collision-induced dissociation,CID
AE1_23234360_3_0	SS1_23234360_3_0	SS2_23234360_3_0	abbreviatedTo	peptide N-glycosidase F,PNGase F
AE1_23234360_4_0	SS1_23234360_4_0	SS2_23234360_4_0	abbreviatedTo	electron-capture and -transfer dissociation,ECD/ETD

NGLY1-deficiency

Id	Subject	Object	Predicate	Lexical cue
PD-NGLY1-deficiency-B_T1	556-562	hgnc:17646	denotes	PNGase

GlyCosmos15-Glycan

Id	Subject	Object	Predicate	Lexical cue	image
T1	121-127	Glycan	denotes	GalNAc	https://api.glycosmos.org/wurcs2image/latest/png/binary/G39738WL
T2	933-939	Glycan	denotes	core-1	https://api.glycosmos.org/wurcs2image/latest/png/binary/G00031MO

mondo_disease

Id	Subject	Object	Predicate	Lexical cue	mondo_id
T1	836-839	Disease	denotes	ECD	http://purl.obolibrary.org/obo/MONDO_0018153\|http://purl.obolibrary.org/obo/MONDO_0020290

Glycan-GlyCosmos

Id	Subject	Object	Predicate	Lexical cue	image
T1	121-127	Glycan	denotes	GalNAc	https://api.glycosmos.org/wurcs2image/latest/png/binary/G39738WL

GlyCosmos15-UBERON

Id	Subject	Object	Predicate	Lexical cue	uberon_id
T1	82-101	Body_part	denotes	cerebrospinal fluid	http://purl.obolibrary.org/obo/UBERON_0001359
T2	167-180	Body_part	denotes	extracellular	http://purl.obolibrary.org/obo/GO_0005576
T3	371-390	Body_part	denotes	cerebrospinal fluid	http://purl.obolibrary.org/obo/UBERON_0001359
T4	1157-1172	Body_part	denotes	attachment site	http://purl.obolibrary.org/obo/UBERON_4200047

GlyCosmos15-MONDO

Id	Subject	Object	Predicate	Lexical cue	mondo_id
T1	1417-1430	Disease	denotes	human disease	MONDO:0700096

GlyCosmos15-Taxon

Id	Subject	Object	Predicate	Lexical cue	db_id
T1	76-81	Organism	denotes	human	9606
T2	365-370	Organism	denotes	human	9606
T3	1256-1261	Organism	denotes	human	9606
T4	1417-1422	Organism	denotes	human	9606

GlyCosmos15-Sentences

Id	Subject	Object	Predicate	Lexical cue
T1	0-116	Sentence	denotes	LC-MS/MS characterization of O-glycosylation sites and glycan structures of human cerebrospinal fluid glycoproteins.
T2	117-252	Sentence	denotes	The GalNAc O-glycosylation on Ser/Thr residues of extracellular proteins has not been well characterized from a proteomics perspective.
T3	253-505	Sentence	denotes	We previously reported a sialic acid capture-and-release protocol to enrich tryptic N- and O-glycopeptides from human cerebrospinal fluid glycoproteins using nano-LC-ESI-MS/MS with collision-induced dissociation (CID) for glycopeptide characterization.
T4	506-782	Sentence	denotes	Here, we have introduced peptide N-glycosidase F (PNGase F) pretreatment of CSF samples to remove the N-glycans facilitating the selective characterization of O-glycopeptides and enabling the use of an automated CID-MS(2)/MS(3) search protocol for glycopeptide identification.
T5	783-1009	Sentence	denotes	We used electron-capture and -transfer dissociation (ECD/ETD) to pinpoint the glycosylation site(s) of the glycopeptides, identified as predominantly core-1-like HexHexNAc-O- structure attached to one to four Ser/Thr residues.
T6	1010-1177	Sentence	denotes	We characterized 106 O-glycosylations and found Pro residues preferentially in the n - 1, n + 1, and/or n + 3 positions in relation to the Ser/Thr attachment site (n).
T7	1178-1431	Sentence	denotes	The characterization of glycans and glycosylation sites in glycoproteins from human clinical samples provides a basis for future studies addressing the biological and diagnostic importance of specific protein glycosylations in relation to human disease.

GlyCosmos15-FMA

Id	Subject	Object	Predicate	Lexical cue	db_id
T1	82-101	Body_part	denotes	cerebrospinal fluid	FMA:20935
T2	371-390	Body_part	denotes	cerebrospinal fluid	FMA:20935

GlyCosmos15-MAT

Id	Subject	Object	Predicate	Lexical cue	mat_id
T1	82-101	Body_part	denotes	cerebrospinal fluid	http://purl.obolibrary.org/obo/MAT_0000499
T2	371-390	Body_part	denotes	cerebrospinal fluid	http://purl.obolibrary.org/obo/MAT_0000499

NCBITAXON

Id	Subject	Object	Predicate	Lexical cue	db_id
T1	76-81	OrganismTaxon	denotes	human	9606
T2	365-370	OrganismTaxon	denotes	human	9606
T3	1256-1261	OrganismTaxon	denotes	human	9606
T4	1417-1422	OrganismTaxon	denotes	human	9606

Anatomy-UBERON

Id	Subject	Object	Predicate	Lexical cue	uberon_id
T1	82-101	Body_part	denotes	cerebrospinal fluid	http://purl.obolibrary.org/obo/UBERON_0001359
T2	167-180	Body_part	denotes	extracellular	http://purl.obolibrary.org/obo/GO_0005576
T3	371-390	Body_part	denotes	cerebrospinal fluid	http://purl.obolibrary.org/obo/UBERON_0001359
T4	1157-1172	Body_part	denotes	attachment site	http://purl.obolibrary.org/obo/UBERON_4200047

Anatomy-MAT

Id	Subject	Object	Predicate	Lexical cue	mat_id
T1	82-101	Body_part	denotes	cerebrospinal fluid	http://purl.obolibrary.org/obo/MAT_0000499
T2	371-390	Body_part	denotes	cerebrospinal fluid	http://purl.obolibrary.org/obo/MAT_0000499