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PubMed:19270074 JSONTXT

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sentences

Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-85 Sentence denotes De novo glycan structure search with the CID MS/MS spectra of native N-glycopeptides.
TextSentencer_T2 86-245 Sentence denotes The aim of our study is to automatically analyze the glycan and peptide structures of N-glycopeptides without a need to release glycans from the glycopeptides.
TextSentencer_T3 246-448 Sentence denotes Our wet laboratory raw data represent a series of MS/MS mass spectra obtained from a reverse-phase liquid chromatography run of size-exclusion-enriched tryptic-digested glycopeptides from glycoproteins.
TextSentencer_T4 449-599 Sentence denotes The MS/MS spectra are first analyzed in order to identify glycosylated peptides and N-glycan monosaccharide compositions present on each glycopeptide.
TextSentencer_T5 600-777 Sentence denotes We further developed a Branch-and-Bound algorithm to search de novo N-glycan structures, i.e., monosaccharide compositions and their ordered sequences from native glycopeptides.
TextSentencer_T6 778-937 Sentence denotes Our de novo algorithm is based on iterative growth and selection of a population of glycan structures and it does not use databases of known glycan structures.
TextSentencer_T7 938-1169 Sentence denotes We validate the algorithm with (i) in silico-generated spectra, with or without deteriorating deletions, (ii) with a purified glycoprotein transferrin, and (iii) with a complex mixture of N-glycopeptides enriched from human plasma.
TextSentencer_T8 1170-1280 Sentence denotes Our Branch-and-Bound algorithm depicted glycan structures from all the above-mentioned three input data types.
TextSentencer_T9 1281-1434 Sentence denotes Due to the large diversity of glycan structures, the results typically contained several proposed structures matching almost equally well to the spectra.
TextSentencer_T10 1435-1653 Sentence denotes In conclusion, this algorithm automatically identifies glycopeptides and their structures from the MS/MS spectra and thus greatly reduces the number of possible glycan structures from the vast amount of potential ones.
T1 0-85 Sentence denotes De novo glycan structure search with the CID MS/MS spectra of native N-glycopeptides.
T2 86-245 Sentence denotes The aim of our study is to automatically analyze the glycan and peptide structures of N-glycopeptides without a need to release glycans from the glycopeptides.
T3 246-448 Sentence denotes Our wet laboratory raw data represent a series of MS/MS mass spectra obtained from a reverse-phase liquid chromatography run of size-exclusion-enriched tryptic-digested glycopeptides from glycoproteins.
T4 449-599 Sentence denotes The MS/MS spectra are first analyzed in order to identify glycosylated peptides and N-glycan monosaccharide compositions present on each glycopeptide.
T5 600-777 Sentence denotes We further developed a Branch-and-Bound algorithm to search de novo N-glycan structures, i.e., monosaccharide compositions and their ordered sequences from native glycopeptides.
T6 778-937 Sentence denotes Our de novo algorithm is based on iterative growth and selection of a population of glycan structures and it does not use databases of known glycan structures.
T7 938-1169 Sentence denotes We validate the algorithm with (i) in silico-generated spectra, with or without deteriorating deletions, (ii) with a purified glycoprotein transferrin, and (iii) with a complex mixture of N-glycopeptides enriched from human plasma.
T8 1170-1280 Sentence denotes Our Branch-and-Bound algorithm depicted glycan structures from all the above-mentioned three input data types.
T9 1281-1434 Sentence denotes Due to the large diversity of glycan structures, the results typically contained several proposed structures matching almost equally well to the spectra.
T10 1435-1653 Sentence denotes In conclusion, this algorithm automatically identifies glycopeptides and their structures from the MS/MS spectra and thus greatly reduces the number of possible glycan structures from the vast amount of potential ones.
T1 0-85 Sentence denotes De novo glycan structure search with the CID MS/MS spectra of native N-glycopeptides.
T2 86-245 Sentence denotes The aim of our study is to automatically analyze the glycan and peptide structures of N-glycopeptides without a need to release glycans from the glycopeptides.
T3 246-448 Sentence denotes Our wet laboratory raw data represent a series of MS/MS mass spectra obtained from a reverse-phase liquid chromatography run of size-exclusion-enriched tryptic-digested glycopeptides from glycoproteins.
T4 449-599 Sentence denotes The MS/MS spectra are first analyzed in order to identify glycosylated peptides and N-glycan monosaccharide compositions present on each glycopeptide.
T5 600-777 Sentence denotes We further developed a Branch-and-Bound algorithm to search de novo N-glycan structures, i.e., monosaccharide compositions and their ordered sequences from native glycopeptides.
T6 778-937 Sentence denotes Our de novo algorithm is based on iterative growth and selection of a population of glycan structures and it does not use databases of known glycan structures.
T7 938-1169 Sentence denotes We validate the algorithm with (i) in silico-generated spectra, with or without deteriorating deletions, (ii) with a purified glycoprotein transferrin, and (iii) with a complex mixture of N-glycopeptides enriched from human plasma.
T8 1170-1280 Sentence denotes Our Branch-and-Bound algorithm depicted glycan structures from all the above-mentioned three input data types.
T9 1281-1434 Sentence denotes Due to the large diversity of glycan structures, the results typically contained several proposed structures matching almost equally well to the spectra.
T10 1435-1653 Sentence denotes In conclusion, this algorithm automatically identifies glycopeptides and their structures from the MS/MS spectra and thus greatly reduces the number of possible glycan structures from the vast amount of potential ones.

GlycoBiology-FMA

Id Subject Object Predicate Lexical cue
_T1 71-84 FMAID:82784 denotes glycopeptides
_T2 71-84 FMAID:196778 denotes glycopeptides
_T3 174-187 FMAID:82784 denotes glycopeptides
_T4 174-187 FMAID:196778 denotes glycopeptides
_T5 231-244 FMAID:196778 denotes glycopeptides
_T6 231-244 FMAID:82784 denotes glycopeptides
_T7 345-351 FMAID:85815 denotes liquid
_T8 415-428 FMAID:82784 denotes glycopeptides
_T9 415-428 FMAID:196778 denotes glycopeptides
_T10 434-447 FMAID:62925 denotes glycoproteins
_T11 434-447 FMAID:167256 denotes glycoproteins
_T12 542-556 FMAID:196730 denotes monosaccharide
_T13 542-556 FMAID:82741 denotes monosaccharide
_T14 557-569 FMAID:50603 denotes compositions
_T15 557-569 FMAID:146309 denotes compositions
_T16 586-598 FMAID:82784 denotes glycopeptide
_T17 586-598 FMAID:196778 denotes glycopeptide
_T18 623-629 FMAID:226028 denotes Branch
_T19 623-629 FMAID:226027 denotes Branch
_T20 695-709 FMAID:82741 denotes monosaccharide
_T21 695-709 FMAID:196730 denotes monosaccharide
_T22 710-722 FMAID:50603 denotes compositions
_T23 710-722 FMAID:146309 denotes compositions
_T24 763-776 FMAID:196778 denotes glycopeptides
_T25 763-776 FMAID:82784 denotes glycopeptides
_T26 812-821 FMAID:177808 denotes iterative
_T27 1064-1076 FMAID:62925 denotes glycoprotein
_T28 1064-1076 FMAID:167256 denotes glycoprotein
_T29 1128-1141 FMAID:82784 denotes glycopeptides
_T30 1128-1141 FMAID:196778 denotes glycopeptides
_T31 1162-1168 FMAID:162307 denotes plasma
_T32 1174-1180 FMAID:226028 denotes Branch
_T33 1174-1180 FMAID:226027 denotes Branch
_T34 1490-1503 FMAID:196778 denotes glycopeptides
_T35 1490-1503 FMAID:82784 denotes glycopeptides

uniprot-human

Id Subject Object Predicate Lexical cue
T1 45-47 http://www.uniprot.org/uniprot/Q99707 denotes MS
T2 48-50 http://www.uniprot.org/uniprot/Q99707 denotes MS
T3 296-298 http://www.uniprot.org/uniprot/Q99707 denotes MS
T4 299-301 http://www.uniprot.org/uniprot/Q99707 denotes MS
T5 453-455 http://www.uniprot.org/uniprot/Q99707 denotes MS
T6 456-458 http://www.uniprot.org/uniprot/Q99707 denotes MS
T7 1534-1536 http://www.uniprot.org/uniprot/Q99707 denotes MS
T8 1537-1539 http://www.uniprot.org/uniprot/Q99707 denotes MS
T9 1044-1046 http://www.uniprot.org/uniprot/Q8SNA0 denotes ii
T10 1077-1088 http://www.uniprot.org/uniprot/P02787 denotes transferrin

uniprot-mouse

Id Subject Object Predicate Lexical cue
T1 45-47 http://www.uniprot.org/uniprot/A6H5Y3 denotes MS
T2 48-50 http://www.uniprot.org/uniprot/A6H5Y3 denotes MS
T3 296-298 http://www.uniprot.org/uniprot/A6H5Y3 denotes MS
T4 299-301 http://www.uniprot.org/uniprot/A6H5Y3 denotes MS
T5 453-455 http://www.uniprot.org/uniprot/A6H5Y3 denotes MS
T6 456-458 http://www.uniprot.org/uniprot/A6H5Y3 denotes MS
T7 1534-1536 http://www.uniprot.org/uniprot/A6H5Y3 denotes MS
T8 1537-1539 http://www.uniprot.org/uniprot/A6H5Y3 denotes MS
T9 1044-1046 http://www.uniprot.org/uniprot/P04441 denotes ii
T10 1077-1088 http://www.uniprot.org/uniprot/Q63915 denotes transferrin

GO-BP

Id Subject Object Predicate Lexical cue
T1 406-414 http://purl.obolibrary.org/obo/GO_0007586 denotes digested
T2 507-519 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylated
T3 611-620 http://purl.obolibrary.org/obo/GO_0032502 denotes developed
T4 822-828 http://purl.obolibrary.org/obo/GO_0040007 denotes growth

GO-CC

Id Subject Object Predicate Lexical cue
T1 1095-1114 http://purl.obolibrary.org/obo/GO_0045275 denotes iii) with a complex

GlycoBiology-Motifs

Id Subject Object Predicate Lexical cue
T1 533-541 http://rdf.glycoinfo.org/glycan/G00027MO denotes N-glycan
T2 668-676 http://rdf.glycoinfo.org/glycan/G00027MO denotes N-glycan

GlyTouCan-IUPAC

Id Subject Object Predicate Lexical cue
GlycanIUPAC_T1 1233-1236 "http://rdf.glycoinfo.org/glycan/G41652MJ" denotes all
GlycanIUPAC_T2 1233-1236 "http://rdf.glycoinfo.org/glycan/G20761YC" denotes all
GlycanIUPAC_T3 1233-1236 "http://rdf.glycoinfo.org/glycan/G19807HM" denotes all
GlycanIUPAC_T4 1233-1236 "http://rdf.glycoinfo.org/glycan/G20351TE" denotes all
GlycanIUPAC_T5 1233-1236 "http://rdf.glycoinfo.org/glycan/G71957MR" denotes all
GlycanIUPAC_T6 1233-1236 "http://rdf.glycoinfo.org/glycan/G59040AE" denotes all
GlycanIUPAC_T7 1233-1236 "http://rdf.glycoinfo.org/glycan/G14987PW" denotes all
GlycanIUPAC_T8 1233-1236 "http://rdf.glycoinfo.org/glycan/G95064PC" denotes all
GlycanIUPAC_T9 1233-1236 "http://rdf.glycoinfo.org/glycan/G39143AQ" denotes all
GlycanIUPAC_T10 1233-1236 "http://rdf.glycoinfo.org/glycan/G65149OO" denotes all
GlycanIUPAC_T11 1233-1236 "http://rdf.glycoinfo.org/glycan/G02766SY" denotes all
GlycanIUPAC_T12 1233-1236 "http://rdf.glycoinfo.org/glycan/G26019KJ" denotes all
GlycanIUPAC_T13 1233-1236 "http://rdf.glycoinfo.org/glycan/G36429CZ" denotes all
GlycanIUPAC_T14 1233-1236 "http://rdf.glycoinfo.org/glycan/G89633TP" denotes all
GlycanIUPAC_T15 1233-1236 "http://rdf.glycoinfo.org/glycan/G28494FO" denotes all
GlycanIUPAC_T16 1233-1236 "http://rdf.glycoinfo.org/glycan/G06219CP" denotes all
GlycanIUPAC_T17 1233-1236 "http://rdf.glycoinfo.org/glycan/G44237SM" denotes all
GlycanIUPAC_T18 1233-1236 "http://rdf.glycoinfo.org/glycan/G57948RL" denotes all
GlycanIUPAC_T19 1233-1236 "http://rdf.glycoinfo.org/glycan/G64016DN" denotes all
GlycanIUPAC_T20 1233-1236 "http://rdf.glycoinfo.org/glycan/G14536PC" denotes all
GlycanIUPAC_T21 1233-1236 "http://rdf.glycoinfo.org/glycan/G14356FW" denotes all
GlycanIUPAC_T22 1233-1236 "http://rdf.glycoinfo.org/glycan/G34565UO" denotes all
GlycanIUPAC_T23 1233-1236 "http://rdf.glycoinfo.org/glycan/G67124MW" denotes all
GlycanIUPAC_T24 1233-1236 "http://rdf.glycoinfo.org/glycan/G71457ZU" denotes all
GlycanIUPAC_T25 1233-1236 "http://rdf.glycoinfo.org/glycan/G55228VZ" denotes all
GlycanIUPAC_T26 1233-1236 "http://rdf.glycoinfo.org/glycan/G31034MJ" denotes all
GlycanIUPAC_T27 1233-1236 "http://rdf.glycoinfo.org/glycan/G25776IP" denotes all
GlycanIUPAC_T28 1233-1236 "http://rdf.glycoinfo.org/glycan/G64442BV" denotes all
GlycanIUPAC_T29 1233-1236 "http://rdf.glycoinfo.org/glycan/G57018LE" denotes all
GlycanIUPAC_T30 1233-1236 "http://rdf.glycoinfo.org/glycan/G61761GX" denotes all
GlycanIUPAC_T31 1233-1236 "http://rdf.glycoinfo.org/glycan/G76318UX" denotes all
GlycanIUPAC_T32 1233-1236 "http://rdf.glycoinfo.org/glycan/G61906ER" denotes all
GlycanIUPAC_T33 1233-1236 "http://rdf.glycoinfo.org/glycan/G68723GR" denotes all
GlycanIUPAC_T34 1233-1236 "http://rdf.glycoinfo.org/glycan/G19540LE" denotes all
GlycanIUPAC_T35 1233-1236 "http://rdf.glycoinfo.org/glycan/G74944PO" denotes all
GlycanIUPAC_T36 1233-1236 "http://rdf.glycoinfo.org/glycan/G89489ZJ" denotes all
GlycanIUPAC_T37 1233-1236 "http://rdf.glycoinfo.org/glycan/G04434YU" denotes all
GlycanIUPAC_T38 1233-1236 "http://rdf.glycoinfo.org/glycan/G21450PB" denotes all
GlycanIUPAC_T39 1233-1236 "http://rdf.glycoinfo.org/glycan/G93629QY" denotes all
GlycanIUPAC_T40 1233-1236 "http://rdf.glycoinfo.org/glycan/G02603TR" denotes all
GlycanIUPAC_T41 1233-1236 "http://rdf.glycoinfo.org/glycan/G40280JP" denotes all
GlycanIUPAC_T42 1233-1236 "http://rdf.glycoinfo.org/glycan/G95259IC" denotes all
GlycanIUPAC_T43 1233-1236 "http://rdf.glycoinfo.org/glycan/G26900FE" denotes all
GlycanIUPAC_T44 1233-1236 "http://rdf.glycoinfo.org/glycan/G21346KK" denotes all
GlycanIUPAC_T45 1233-1236 "http://rdf.glycoinfo.org/glycan/G62509FF" denotes all
GlycanIUPAC_T46 1233-1236 "http://rdf.glycoinfo.org/glycan/G83932AK" denotes all
GlycanIUPAC_T47 1233-1236 "http://rdf.glycoinfo.org/glycan/G96978IB" denotes all
GlycanIUPAC_T48 1233-1236 "http://rdf.glycoinfo.org/glycan/G34275DN" denotes all
GlycanIUPAC_T49 1233-1236 "http://rdf.glycoinfo.org/glycan/G07071JF" denotes all
GlycanIUPAC_T50 1233-1236 "http://rdf.glycoinfo.org/glycan/G80639QD" denotes all
GlycanIUPAC_T51 1233-1236 "http://rdf.glycoinfo.org/glycan/G99460PJ" denotes all
GlycanIUPAC_T52 1233-1236 "http://rdf.glycoinfo.org/glycan/G22024BZ" denotes all
GlycanIUPAC_T53 1233-1236 "http://rdf.glycoinfo.org/glycan/G74097ZY" denotes all
GlycanIUPAC_T54 1233-1236 "http://rdf.glycoinfo.org/glycan/G84439YP" denotes all
GlycanIUPAC_T55 1233-1236 "http://rdf.glycoinfo.org/glycan/G52207WQ" denotes all
GlycanIUPAC_T56 1233-1236 "http://rdf.glycoinfo.org/glycan/G90695MS" denotes all
GlycanIUPAC_T57 1233-1236 "http://rdf.glycoinfo.org/glycan/G50398QX" denotes all
GlycanIUPAC_T58 1233-1236 "http://rdf.glycoinfo.org/glycan/G12166ZT" denotes all
GlycanIUPAC_T59 1233-1236 "http://rdf.glycoinfo.org/glycan/G48368BR" denotes all
GlycanIUPAC_T60 1233-1236 "http://rdf.glycoinfo.org/glycan/G57407RW" denotes all
GlycanIUPAC_T61 1233-1236 "http://rdf.glycoinfo.org/glycan/G00386TY" denotes all
GlycanIUPAC_T62 1233-1236 "http://rdf.glycoinfo.org/glycan/G18723JK" denotes all
GlycanIUPAC_T63 1233-1236 "http://rdf.glycoinfo.org/glycan/G93757OR" denotes all
GlycanIUPAC_T64 1233-1236 "http://rdf.glycoinfo.org/glycan/G29006SI" denotes all
GlycanIUPAC_T65 1233-1236 "http://rdf.glycoinfo.org/glycan/G03099OQ" denotes all
GlycanIUPAC_T66 1233-1236 "http://rdf.glycoinfo.org/glycan/G53739OW" denotes all
GlycanIUPAC_T67 1233-1236 "http://rdf.glycoinfo.org/glycan/G70440ZO" denotes all
GlycanIUPAC_T68 1233-1236 "http://rdf.glycoinfo.org/glycan/G29951RR" denotes all
GlycanIUPAC_T69 1233-1236 "http://rdf.glycoinfo.org/glycan/G58402TI" denotes all
GlycanIUPAC_T70 1233-1236 "http://rdf.glycoinfo.org/glycan/G39875TP" denotes all
GlycanIUPAC_T71 1233-1236 "http://rdf.glycoinfo.org/glycan/G83439QV" denotes all
GlycanIUPAC_T72 1233-1236 "http://rdf.glycoinfo.org/glycan/G41762RC" denotes all
GlycanIUPAC_T73 1233-1236 "http://rdf.glycoinfo.org/glycan/G91604UI" denotes all
GlycanIUPAC_T74 1233-1236 "http://rdf.glycoinfo.org/glycan/G88447WE" denotes all
GlycanIUPAC_T75 1233-1236 "http://rdf.glycoinfo.org/glycan/G93634BS" denotes all
GlycanIUPAC_T76 1233-1236 "http://rdf.glycoinfo.org/glycan/G02587BH" denotes all
GlycanIUPAC_T77 1233-1236 "http://rdf.glycoinfo.org/glycan/G43511MX" denotes all
GlycanIUPAC_T78 1233-1236 "http://rdf.glycoinfo.org/glycan/G64958DH" denotes all
GlycanIUPAC_T79 1233-1236 "http://rdf.glycoinfo.org/glycan/G30384TR" denotes all
GlycanIUPAC_T80 1233-1236 "http://rdf.glycoinfo.org/glycan/G15624EX" denotes all
GlycanIUPAC_T81 1233-1236 "http://rdf.glycoinfo.org/glycan/G22706ST" denotes all
GlycanIUPAC_T82 1233-1236 "http://rdf.glycoinfo.org/glycan/G57408PI" denotes all
GlycanIUPAC_T83 1233-1236 "http://rdf.glycoinfo.org/glycan/G86403XX" denotes all
GlycanIUPAC_T84 1233-1236 "http://rdf.glycoinfo.org/glycan/G78043YB" denotes all
GlycanIUPAC_T85 1233-1236 "http://rdf.glycoinfo.org/glycan/G18952JK" denotes all
GlycanIUPAC_T86 1233-1236 "http://rdf.glycoinfo.org/glycan/G49020ND" denotes all
GlycanIUPAC_T87 1233-1236 "http://rdf.glycoinfo.org/glycan/G63590YW" denotes all
GlycanIUPAC_T88 1233-1236 "http://rdf.glycoinfo.org/glycan/G22793KS" denotes all
GlycanIUPAC_T89 1233-1236 "http://rdf.glycoinfo.org/glycan/G64134SS" denotes all
GlycanIUPAC_T90 1233-1236 "http://rdf.glycoinfo.org/glycan/G17338HY" denotes all
GlycanIUPAC_T91 1233-1236 "http://rdf.glycoinfo.org/glycan/G99745XF" denotes all
GlycanIUPAC_T92 1233-1236 "http://rdf.glycoinfo.org/glycan/G27782HN" denotes all
GlycanIUPAC_T93 1233-1236 "http://rdf.glycoinfo.org/glycan/G57496DC" denotes all
GlycanIUPAC_T94 1233-1236 "http://rdf.glycoinfo.org/glycan/G93169WB" denotes all
GlycanIUPAC_T95 1233-1236 "http://rdf.glycoinfo.org/glycan/G05518TD" denotes all
GlycanIUPAC_T96 1233-1236 "http://rdf.glycoinfo.org/glycan/G62603DN" denotes all
GlycanIUPAC_T97 1233-1236 "http://rdf.glycoinfo.org/glycan/G59574FS" denotes all
GlycanIUPAC_T98 1233-1236 "http://rdf.glycoinfo.org/glycan/G47567WC" denotes all

NCBITAXON

Id Subject Object Predicate Lexical cue db_id
T1 1156-1161 OrganismTaxon denotes human 9606

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1162-1168 Body_part denotes plasma http://purl.obolibrary.org/obo/UBERON_0001969