PMC:7443692 / 12773-13789 JSONTXT

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T79","span":{"begin":221,"end":228},"obj":"Chemical"},{"id":"T80","span":{"begin":247,"end":256},"obj":"Chemical"},{"id":"T81","span":{"begin":280,"end":288},"obj":"Chemical"},{"id":"T82","span":{"begin":490,"end":498},"obj":"Chemical"},{"id":"T83","span":{"begin":561,"end":568},"obj":"Chemical"},{"id":"T84","span":{"begin":616,"end":623},"obj":"Chemical"},{"id":"T85","span":{"begin":679,"end":683},"obj":"Chemical"},{"id":"T86","span":{"begin":737,"end":744},"obj":"Chemical"},{"id":"T87","span":{"begin":745,"end":749},"obj":"Chemical"},{"id":"T88","span":{"begin":773,"end":780},"obj":"Chemical"},{"id":"T89","span":{"begin":790,"end":794},"obj":"Chemical"},{"id":"T90","span":{"begin":877,"end":881},"obj":"Chemical"},{"id":"T91","span":{"begin":953,"end":959},"obj":"Chemical"},{"id":"T92","span":{"begin":1003,"end":1015},"obj":"Chemical"}],"attributes":[{"id":"A82","pred":"chebi_id","subj":"T82","obj":"http://purl.obolibrary.org/obo/CHEBI_15356"},{"id":"A87","pred":"chebi_id","subj":"T87","obj":"http://purl.obolibrary.org/obo/CHEBI_24870"},{"id":"A84","pred":"chebi_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A89","pred":"chebi_id","subj":"T89","obj":"http://purl.obolibrary.org/obo/CHEBI_24870"},{"id":"A83","pred":"chebi_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A80","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_28300"},{"id":"A88","pred":"chebi_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A86","pred":"chebi_id","subj":"T86","obj":"http://purl.obolibrary.org/obo/CHEBI_29412"},{"id":"A92","pred":"chebi_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/CHEBI_24396"},{"id":"A91","pred":"chebi_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/CHEBI_33984"},{"id":"A81","pred":"chebi_id","subj":"T81","obj":"http://purl.obolibrary.org/obo/CHEBI_59520"},{"id":"A85","pred":"chebi_id","subj":"T85","obj":"http://purl.obolibrary.org/obo/CHEBI_24870"},{"id":"A79","pred":"chebi_id","subj":"T79","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A90","pred":"chebi_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/CHEBI_24870"}],"text":"(D) A representative Step-HCD fragmentation spectrum from mass-spectrometry analysis of a tryptic digest of S annotated manually based on search results from pGlyco 2.2. This spectrum defines the N terminus of the mature protein monomer as (pyro-)glutamine 0014. A representative N-glycan consistent with this annotation and our glycomics data (Figure 2) is overlaid by using the Symbol Nomenclature For Glycans (SNFG) code. This complex glycan occurs at N0017. Note, that as expected, the cysteine is carbamidomethylated, and the mass accuracy of the assigned peptide is 0.98 ppm. On the sequence of the N-terminal peptide and in the spectrum, the assigned b (blue) and y (red) ions are shown. In the spectrum, purple highlights glycan oxonium ions and green marks intact peptide fragment ions with various partial glycan sequences still attached. Note that the green-labeled ions allow for limited topology to be extracted including defining that the fucose is on the core and not the antennae of the glycopeptide."}

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T66","span":{"begin":0,"end":169},"obj":"Sentence"},{"id":"T67","span":{"begin":170,"end":262},"obj":"Sentence"},{"id":"T68","span":{"begin":263,"end":424},"obj":"Sentence"},{"id":"T69","span":{"begin":425,"end":461},"obj":"Sentence"},{"id":"T70","span":{"begin":462,"end":581},"obj":"Sentence"},{"id":"T71","span":{"begin":582,"end":694},"obj":"Sentence"},{"id":"T72","span":{"begin":695,"end":848},"obj":"Sentence"},{"id":"T73","span":{"begin":849,"end":1016},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"(D) A representative Step-HCD fragmentation spectrum from mass-spectrometry analysis of a tryptic digest of S annotated manually based on search results from pGlyco 2.2. This spectrum defines the N terminus of the mature protein monomer as (pyro-)glutamine 0014. A representative N-glycan consistent with this annotation and our glycomics data (Figure 2) is overlaid by using the Symbol Nomenclature For Glycans (SNFG) code. This complex glycan occurs at N0017. Note, that as expected, the cysteine is carbamidomethylated, and the mass accuracy of the assigned peptide is 0.98 ppm. On the sequence of the N-terminal peptide and in the spectrum, the assigned b (blue) and y (red) ions are shown. In the spectrum, purple highlights glycan oxonium ions and green marks intact peptide fragment ions with various partial glycan sequences still attached. Note that the green-labeled ions allow for limited topology to be extracted including defining that the fucose is on the core and not the antennae of the glycopeptide."}

{"project":"LitCovid-sample-UniProt","denotations":[{"id":"T1615","span":{"begin":605,"end":623},"obj":"Protein"}],"attributes":[{"id":"A1615","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/Q9DB14"},{"id":"A1616","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/Q9D2P6"},{"id":"A1617","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/Q9CYP0"},{"id":"A1618","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/Q9BS38"},{"id":"A1619","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/Q8CCZ3"},{"id":"A1620","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/Q6FHD0"},{"id":"A1621","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/Q06A28"},{"id":"A1622","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/P27682"},{"id":"A1623","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/P18844"},{"id":"A1624","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/P12961"},{"id":"A1625","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/P05408"},{"id":"A1626","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/P01165"},{"id":"A1627","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/P01164"},{"id":"A1628","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/A5HAK0"},{"id":"A1629","pred":"uniprot_id","subj":"T1615","obj":"https://www.uniprot.org/uniprot/A5A6J6"}],"text":"(D) A representative Step-HCD fragmentation spectrum from mass-spectrometry analysis of a tryptic digest of S annotated manually based on search results from pGlyco 2.2. This spectrum defines the N terminus of the mature protein monomer as (pyro-)glutamine 0014. A representative N-glycan consistent with this annotation and our glycomics data (Figure 2) is overlaid by using the Symbol Nomenclature For Glycans (SNFG) code. This complex glycan occurs at N0017. Note, that as expected, the cysteine is carbamidomethylated, and the mass accuracy of the assigned peptide is 0.98 ppm. On the sequence of the N-terminal peptide and in the spectrum, the assigned b (blue) and y (red) ions are shown. In the spectrum, purple highlights glycan oxonium ions and green marks intact peptide fragment ions with various partial glycan sequences still attached. Note that the green-labeled ions allow for limited topology to be extracted including defining that the fucose is on the core and not the antennae of the glycopeptide."}

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T58","span":{"begin":221,"end":228},"obj":"Body_part"},{"id":"T59","span":{"begin":247,"end":256},"obj":"Body_part"},{"id":"T60","span":{"begin":490,"end":498},"obj":"Body_part"},{"id":"T61","span":{"begin":953,"end":959},"obj":"Body_part"},{"id":"T62","span":{"begin":1003,"end":1015},"obj":"Body_part"}],"attributes":[{"id":"A61","pred":"fma_id","subj":"T61","obj":"http://purl.org/sig/ont/fma/fma82790"},{"id":"A60","pred":"fma_id","subj":"T60","obj":"http://purl.org/sig/ont/fma/fma82751"},{"id":"A59","pred":"fma_id","subj":"T59","obj":"http://purl.org/sig/ont/fma/fma82752"},{"id":"A62","pred":"fma_id","subj":"T62","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A58","pred":"fma_id","subj":"T58","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"(D) A representative Step-HCD fragmentation spectrum from mass-spectrometry analysis of a tryptic digest of S annotated manually based on search results from pGlyco 2.2. This spectrum defines the N terminus of the mature protein monomer as (pyro-)glutamine 0014. A representative N-glycan consistent with this annotation and our glycomics data (Figure 2) is overlaid by using the Symbol Nomenclature For Glycans (SNFG) code. This complex glycan occurs at N0017. Note, that as expected, the cysteine is carbamidomethylated, and the mass accuracy of the assigned peptide is 0.98 ppm. On the sequence of the N-terminal peptide and in the spectrum, the assigned b (blue) and y (red) ions are shown. In the spectrum, purple highlights glycan oxonium ions and green marks intact peptide fragment ions with various partial glycan sequences still attached. Note that the green-labeled ions allow for limited topology to be extracted including defining that the fucose is on the core and not the antennae of the glycopeptide."}

{"project":"LitCovid-sample-PD-MAT","denotations":[{"id":"T2","span":{"begin":987,"end":995},"obj":"http://purl.obolibrary.org/obo/MAT_0000086"}],"text":"(D) A representative Step-HCD fragmentation spectrum from mass-spectrometry analysis of a tryptic digest of S annotated manually based on search results from pGlyco 2.2. This spectrum defines the N terminus of the mature protein monomer as (pyro-)glutamine 0014. A representative N-glycan consistent with this annotation and our glycomics data (Figure 2) is overlaid by using the Symbol Nomenclature For Glycans (SNFG) code. This complex glycan occurs at N0017. Note, that as expected, the cysteine is carbamidomethylated, and the mass accuracy of the assigned peptide is 0.98 ppm. On the sequence of the N-terminal peptide and in the spectrum, the assigned b (blue) and y (red) ions are shown. In the spectrum, purple highlights glycan oxonium ions and green marks intact peptide fragment ions with various partial glycan sequences still attached. Note that the green-labeled ions allow for limited topology to be extracted including defining that the fucose is on the core and not the antennae of the glycopeptide."}