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LitCovid-sample-CHEBI

LitCovid-sample-PD-NCBITaxon

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T55","span":{"begin":117,"end":127},"obj":"Species"},{"id":"T56","span":{"begin":156,"end":166},"obj":"Species"},{"id":"T57","span":{"begin":697,"end":707},"obj":"Species"},{"id":"T58","span":{"begin":1095,"end":1103},"obj":"Species"},{"id":"T59","span":{"begin":1172,"end":1182},"obj":"Species"}],"attributes":[{"id":"A59","pred":"ncbi_taxonomy_id","subj":"T59","obj":"NCBItxid:2697049"},{"id":"A55","pred":"ncbi_taxonomy_id","subj":"T55","obj":"NCBItxid:2697049"},{"id":"A58","pred":"ncbi_taxonomy_id","subj":"T58","obj":"NCBItxid:694009"},{"id":"A56","pred":"ncbi_taxonomy_id","subj":"T56","obj":"NCBItxid:2697049"},{"id":"A57","pred":"ncbi_taxonomy_id","subj":"T57","obj":"NCBItxid:2697049"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"Glycomics-Informed Glycoproteomics Reveals Substantial Site-Specific Microheterogeneity of N-linked Glycosylation on SARS-CoV-2 S\n(A) Glycans released from SARS-CoV-2 S protein trimer immunogen were permethylated and analyzed by MSn. Structures were assigned and grouped by type and structural features, and prevalence was determined based on ion current. The pie chart shows basic division by broad N-glycan type. The bar graph provides additional detail about the glycans detected. The most abundant structure with a unique categorization by glycomics for each N-glycan type in the pie chart, or above each feature category in the bar graph, is indicated.\n(B–E) Glycopeptides were prepared from SARS-CoV-2 S protein trimer immunogen by using multiple combinations of proteases, analyzed by LC-MSn, and the resulting data were searched by using several different software packages. Four representative sites of N-linked glycosylation with specific features of interest were chosen and are presented here. N0074 (B) and N0149 (C) are shown that occur in variable insert regions of S compared to SARS-CoV and other related coronaviruses, and there are emerging variants of SARS-CoV-2 that disrupt these two sites of glycosylation in S. N0234 (D) contains the most high-mannose N-linked glycans. N0801 (D) is an example of glycosylation in the S2 region of the immunogen and displays a high degree of hybrid glycosylation compared to other sites. The abundance of each composition is graphed in terms of assigned spectral counts. Representative glycans (as determined by glycomics analysis) for several abundant compositions are shown in SNFG format. The abbreviations used here and throughout the manuscript are as follows: N, HexNAc; H, hexose; F, fucose; A, Neu5Ac; S, sulfation. Note that the graphs for the other 18 sites and other graphs grouping the microheterogeneity observed by other properties are presented in Supplemental Information."}

LitCovid-sample-sentences

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T86","span":{"begin":130,"end":233},"obj":"Sentence"},{"id":"T87","span":{"begin":234,"end":355},"obj":"Sentence"},{"id":"T88","span":{"begin":356,"end":414},"obj":"Sentence"},{"id":"T89","span":{"begin":415,"end":483},"obj":"Sentence"},{"id":"T90","span":{"begin":484,"end":657},"obj":"Sentence"},{"id":"T91","span":{"begin":658,"end":882},"obj":"Sentence"},{"id":"T92","span":{"begin":883,"end":1005},"obj":"Sentence"},{"id":"T93","span":{"begin":1006,"end":1234},"obj":"Sentence"},{"id":"T94","span":{"begin":1235,"end":1293},"obj":"Sentence"},{"id":"T95","span":{"begin":1294,"end":1444},"obj":"Sentence"},{"id":"T96","span":{"begin":1445,"end":1527},"obj":"Sentence"},{"id":"T97","span":{"begin":1528,"end":1648},"obj":"Sentence"},{"id":"T98","span":{"begin":1649,"end":1780},"obj":"Sentence"},{"id":"T99","span":{"begin":1781,"end":1945},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Glycomics-Informed Glycoproteomics Reveals Substantial Site-Specific Microheterogeneity of N-linked Glycosylation on SARS-CoV-2 S\n(A) Glycans released from SARS-CoV-2 S protein trimer immunogen were permethylated and analyzed by MSn. Structures were assigned and grouped by type and structural features, and prevalence was determined based on ion current. The pie chart shows basic division by broad N-glycan type. The bar graph provides additional detail about the glycans detected. The most abundant structure with a unique categorization by glycomics for each N-glycan type in the pie chart, or above each feature category in the bar graph, is indicated.\n(B–E) Glycopeptides were prepared from SARS-CoV-2 S protein trimer immunogen by using multiple combinations of proteases, analyzed by LC-MSn, and the resulting data were searched by using several different software packages. Four representative sites of N-linked glycosylation with specific features of interest were chosen and are presented here. N0074 (B) and N0149 (C) are shown that occur in variable insert regions of S compared to SARS-CoV and other related coronaviruses, and there are emerging variants of SARS-CoV-2 that disrupt these two sites of glycosylation in S. N0234 (D) contains the most high-mannose N-linked glycans. N0801 (D) is an example of glycosylation in the S2 region of the immunogen and displays a high degree of hybrid glycosylation compared to other sites. The abundance of each composition is graphed in terms of assigned spectral counts. Representative glycans (as determined by glycomics analysis) for several abundant compositions are shown in SNFG format. The abbreviations used here and throughout the manuscript are as follows: N, HexNAc; H, hexose; F, fucose; A, Neu5Ac; S, sulfation. Note that the graphs for the other 18 sites and other graphs grouping the microheterogeneity observed by other properties are presented in Supplemental Information."}

LitCovid-sample-PD-MONDO

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T39","span":{"begin":117,"end":127},"obj":"Disease"},{"id":"T40","span":{"begin":156,"end":166},"obj":"Disease"},{"id":"T41","span":{"begin":697,"end":707},"obj":"Disease"},{"id":"T42","span":{"begin":1095,"end":1103},"obj":"Disease"},{"id":"T43","span":{"begin":1172,"end":1182},"obj":"Disease"}],"attributes":[{"id":"A41","pred":"mondo_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A42","pred":"mondo_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A39","pred":"mondo_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A40","pred":"mondo_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"Glycomics-Informed Glycoproteomics Reveals Substantial Site-Specific Microheterogeneity of N-linked Glycosylation on SARS-CoV-2 S\n(A) Glycans released from SARS-CoV-2 S protein trimer immunogen were permethylated and analyzed by MSn. Structures were assigned and grouped by type and structural features, and prevalence was determined based on ion current. The pie chart shows basic division by broad N-glycan type. The bar graph provides additional detail about the glycans detected. The most abundant structure with a unique categorization by glycomics for each N-glycan type in the pie chart, or above each feature category in the bar graph, is indicated.\n(B–E) Glycopeptides were prepared from SARS-CoV-2 S protein trimer immunogen by using multiple combinations of proteases, analyzed by LC-MSn, and the resulting data were searched by using several different software packages. Four representative sites of N-linked glycosylation with specific features of interest were chosen and are presented here. N0074 (B) and N0149 (C) are shown that occur in variable insert regions of S compared to SARS-CoV and other related coronaviruses, and there are emerging variants of SARS-CoV-2 that disrupt these two sites of glycosylation in S. N0234 (D) contains the most high-mannose N-linked glycans. N0801 (D) is an example of glycosylation in the S2 region of the immunogen and displays a high degree of hybrid glycosylation compared to other sites. The abundance of each composition is graphed in terms of assigned spectral counts. Representative glycans (as determined by glycomics analysis) for several abundant compositions are shown in SNFG format. The abbreviations used here and throughout the manuscript are as follows: N, HexNAc; H, hexose; F, fucose; A, Neu5Ac; S, sulfation. Note that the graphs for the other 18 sites and other graphs grouping the microheterogeneity observed by other properties are presented in Supplemental Information."}

LitCovid-sample-UniProt

LitCovid-sample-PD-IDO

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T48","span":{"begin":55,"end":59},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T49","span":{"begin":903,"end":908},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T50","span":{"begin":1206,"end":1211},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T51","span":{"begin":1438,"end":1443},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T52","span":{"begin":1819,"end":1824},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"Glycomics-Informed Glycoproteomics Reveals Substantial Site-Specific Microheterogeneity of N-linked Glycosylation on SARS-CoV-2 S\n(A) Glycans released from SARS-CoV-2 S protein trimer immunogen were permethylated and analyzed by MSn. Structures were assigned and grouped by type and structural features, and prevalence was determined based on ion current. The pie chart shows basic division by broad N-glycan type. The bar graph provides additional detail about the glycans detected. The most abundant structure with a unique categorization by glycomics for each N-glycan type in the pie chart, or above each feature category in the bar graph, is indicated.\n(B–E) Glycopeptides were prepared from SARS-CoV-2 S protein trimer immunogen by using multiple combinations of proteases, analyzed by LC-MSn, and the resulting data were searched by using several different software packages. Four representative sites of N-linked glycosylation with specific features of interest were chosen and are presented here. N0074 (B) and N0149 (C) are shown that occur in variable insert regions of S compared to SARS-CoV and other related coronaviruses, and there are emerging variants of SARS-CoV-2 that disrupt these two sites of glycosylation in S. N0234 (D) contains the most high-mannose N-linked glycans. N0801 (D) is an example of glycosylation in the S2 region of the immunogen and displays a high degree of hybrid glycosylation compared to other sites. The abundance of each composition is graphed in terms of assigned spectral counts. Representative glycans (as determined by glycomics analysis) for several abundant compositions are shown in SNFG format. The abbreviations used here and throughout the manuscript are as follows: N, HexNAc; H, hexose; F, fucose; A, Neu5Ac; S, sulfation. Note that the graphs for the other 18 sites and other graphs grouping the microheterogeneity observed by other properties are presented in Supplemental Information."}

LitCovid-sample-PD-FMA

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T66","span":{"begin":169,"end":176},"obj":"Body_part"},{"id":"T67","span":{"begin":664,"end":677},"obj":"Body_part"},{"id":"T68","span":{"begin":710,"end":717},"obj":"Body_part"},{"id":"T69","span":{"begin":1268,"end":1275},"obj":"Body_part"},{"id":"T70","span":{"begin":1748,"end":1754},"obj":"Body_part"}],"attributes":[{"id":"A67","pred":"fma_id","subj":"T67","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A66","pred":"fma_id","subj":"T66","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A68","pred":"fma_id","subj":"T68","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A69","pred":"fma_id","subj":"T69","obj":"http://purl.org/sig/ont/fma/fma82801"},{"id":"A70","pred":"fma_id","subj":"T70","obj":"http://purl.org/sig/ont/fma/fma82790"}],"text":"Glycomics-Informed Glycoproteomics Reveals Substantial Site-Specific Microheterogeneity of N-linked Glycosylation on SARS-CoV-2 S\n(A) Glycans released from SARS-CoV-2 S protein trimer immunogen were permethylated and analyzed by MSn. Structures were assigned and grouped by type and structural features, and prevalence was determined based on ion current. The pie chart shows basic division by broad N-glycan type. The bar graph provides additional detail about the glycans detected. The most abundant structure with a unique categorization by glycomics for each N-glycan type in the pie chart, or above each feature category in the bar graph, is indicated.\n(B–E) Glycopeptides were prepared from SARS-CoV-2 S protein trimer immunogen by using multiple combinations of proteases, analyzed by LC-MSn, and the resulting data were searched by using several different software packages. Four representative sites of N-linked glycosylation with specific features of interest were chosen and are presented here. N0074 (B) and N0149 (C) are shown that occur in variable insert regions of S compared to SARS-CoV and other related coronaviruses, and there are emerging variants of SARS-CoV-2 that disrupt these two sites of glycosylation in S. N0234 (D) contains the most high-mannose N-linked glycans. N0801 (D) is an example of glycosylation in the S2 region of the immunogen and displays a high degree of hybrid glycosylation compared to other sites. The abundance of each composition is graphed in terms of assigned spectral counts. Representative glycans (as determined by glycomics analysis) for several abundant compositions are shown in SNFG format. The abbreviations used here and throughout the manuscript are as follows: N, HexNAc; H, hexose; F, fucose; A, Neu5Ac; S, sulfation. Note that the graphs for the other 18 sites and other graphs grouping the microheterogeneity observed by other properties are presented in Supplemental Information."}

LitCovid-sample-PD-GO-BP-0

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T46","span":{"begin":100,"end":113},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T47","span":{"begin":921,"end":934},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T48","span":{"begin":1215,"end":1228},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T49","span":{"begin":1321,"end":1334},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T50","span":{"begin":1406,"end":1419},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T51","span":{"begin":1770,"end":1779},"obj":"http://purl.obolibrary.org/obo/GO_0051923"}],"text":"Glycomics-Informed Glycoproteomics Reveals Substantial Site-Specific Microheterogeneity of N-linked Glycosylation on SARS-CoV-2 S\n(A) Glycans released from SARS-CoV-2 S protein trimer immunogen were permethylated and analyzed by MSn. Structures were assigned and grouped by type and structural features, and prevalence was determined based on ion current. The pie chart shows basic division by broad N-glycan type. The bar graph provides additional detail about the glycans detected. The most abundant structure with a unique categorization by glycomics for each N-glycan type in the pie chart, or above each feature category in the bar graph, is indicated.\n(B–E) Glycopeptides were prepared from SARS-CoV-2 S protein trimer immunogen by using multiple combinations of proteases, analyzed by LC-MSn, and the resulting data were searched by using several different software packages. Four representative sites of N-linked glycosylation with specific features of interest were chosen and are presented here. N0074 (B) and N0149 (C) are shown that occur in variable insert regions of S compared to SARS-CoV and other related coronaviruses, and there are emerging variants of SARS-CoV-2 that disrupt these two sites of glycosylation in S. N0234 (D) contains the most high-mannose N-linked glycans. N0801 (D) is an example of glycosylation in the S2 region of the immunogen and displays a high degree of hybrid glycosylation compared to other sites. The abundance of each composition is graphed in terms of assigned spectral counts. Representative glycans (as determined by glycomics analysis) for several abundant compositions are shown in SNFG format. The abbreviations used here and throughout the manuscript are as follows: N, HexNAc; H, hexose; F, fucose; A, Neu5Ac; S, sulfation. Note that the graphs for the other 18 sites and other graphs grouping the microheterogeneity observed by other properties are presented in Supplemental Information."}

LitCovid-sample-GO-BP

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T43","span":{"begin":100,"end":113},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T44","span":{"begin":921,"end":934},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T45","span":{"begin":1215,"end":1228},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T46","span":{"begin":1321,"end":1334},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T47","span":{"begin":1406,"end":1419},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T48","span":{"begin":1770,"end":1779},"obj":"http://purl.obolibrary.org/obo/GO_0051923"}],"text":"Glycomics-Informed Glycoproteomics Reveals Substantial Site-Specific Microheterogeneity of N-linked Glycosylation on SARS-CoV-2 S\n(A) Glycans released from SARS-CoV-2 S protein trimer immunogen were permethylated and analyzed by MSn. Structures were assigned and grouped by type and structural features, and prevalence was determined based on ion current. The pie chart shows basic division by broad N-glycan type. The bar graph provides additional detail about the glycans detected. The most abundant structure with a unique categorization by glycomics for each N-glycan type in the pie chart, or above each feature category in the bar graph, is indicated.\n(B–E) Glycopeptides were prepared from SARS-CoV-2 S protein trimer immunogen by using multiple combinations of proteases, analyzed by LC-MSn, and the resulting data were searched by using several different software packages. Four representative sites of N-linked glycosylation with specific features of interest were chosen and are presented here. N0074 (B) and N0149 (C) are shown that occur in variable insert regions of S compared to SARS-CoV and other related coronaviruses, and there are emerging variants of SARS-CoV-2 that disrupt these two sites of glycosylation in S. N0234 (D) contains the most high-mannose N-linked glycans. N0801 (D) is an example of glycosylation in the S2 region of the immunogen and displays a high degree of hybrid glycosylation compared to other sites. The abundance of each composition is graphed in terms of assigned spectral counts. Representative glycans (as determined by glycomics analysis) for several abundant compositions are shown in SNFG format. The abbreviations used here and throughout the manuscript are as follows: N, HexNAc; H, hexose; F, fucose; A, Neu5Ac; S, sulfation. Note that the graphs for the other 18 sites and other graphs grouping the microheterogeneity observed by other properties are presented in Supplemental Information."}

LitCovid-sample-Glycan

PMC:7443692 / 15383-17328 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7443692 / 15383-17328 JSON TXT