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LitCovid-sample-CHEBI

LitCovid-sample-PD-NCBITaxon

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T53","span":{"begin":64,"end":74},"obj":"Species"},{"id":"T54","span":{"begin":127,"end":137},"obj":"Species"},{"id":"T55","span":{"begin":1603,"end":1613},"obj":"Species"},{"id":"T56","span":{"begin":1642,"end":1652},"obj":"Species"},{"id":"T57","span":{"begin":2183,"end":2193},"obj":"Species"},{"id":"T58","span":{"begin":2581,"end":2589},"obj":"Species"},{"id":"T59","span":{"begin":2658,"end":2668},"obj":"Species"}],"attributes":[{"id":"A53","pred":"ncbi_taxonomy_id","subj":"T53","obj":"NCBItxid:2697049"},{"id":"A54","pred":"ncbi_taxonomy_id","subj":"T54","obj":"NCBItxid:2697049"},{"id":"A55","pred":"ncbi_taxonomy_id","subj":"T55","obj":"NCBItxid:2697049"},{"id":"A56","pred":"ncbi_taxonomy_id","subj":"T56","obj":"NCBItxid:2697049"},{"id":"A57","pred":"ncbi_taxonomy_id","subj":"T57","obj":"NCBItxid:2697049"},{"id":"A58","pred":"ncbi_taxonomy_id","subj":"T58","obj":"NCBItxid:694009"},{"id":"A59","pred":"ncbi_taxonomy_id","subj":"T59","obj":"NCBItxid:2697049"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"We utilized multiple approaches to examine glycosylation of the SARS-CoV-2 S trimer. First, the portfolio of glycans linked to SARS-CoV-2 S trimer immunogen was analyzed after their release from the polypeptide backbone. N-glycans were released from protein by treatment with PNGase F- and O-glycans were subsequently released by beta-elimination. After permethylation to enhance detection sensitivity and structural characterization, released glycans were analyzed by multi-stage mass spectrometry (MSn) (Aoki et al., 2007; Aoki et al., 2008). Mass spectra were processed by GRITS Toolbox, and the resulting annotations were validated manually (Weatherly et al., 2019). Glycan assignments were grouped by type and by additional structural features for relative quantification of profile characteristics (Figure 2 A; Table S3). This analysis quantified 49 N-glycans and revealed that 55% of the total glycan abundance was of the complex type, 17% was of the hybrid type, and 28% was high mannose. Among the complex and hybrid N-glycans, we observed a high degree of core fucosylation and significant abundance of bisected and LacDiNAc structures. We also observed sulfated N-linked glycans by using negative mode MSn analyses (Table S13), although signal intensity was too low in positive ion mode (at least 10-fold lower than any of the non-sulfated glycans) for accurate quantification. In addition, we detected 15 O-glycans released from the S trimer (Figure S5; Table S4).\nFigure 2 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":"T75","span":{"begin":0,"end":84},"obj":"Sentence"},{"id":"T76","span":{"begin":85,"end":220},"obj":"Sentence"},{"id":"T77","span":{"begin":221,"end":347},"obj":"Sentence"},{"id":"T78","span":{"begin":348,"end":544},"obj":"Sentence"},{"id":"T79","span":{"begin":545,"end":670},"obj":"Sentence"},{"id":"T80","span":{"begin":671,"end":827},"obj":"Sentence"},{"id":"T81","span":{"begin":828,"end":996},"obj":"Sentence"},{"id":"T82","span":{"begin":997,"end":1146},"obj":"Sentence"},{"id":"T83","span":{"begin":1147,"end":1388},"obj":"Sentence"},{"id":"T84","span":{"begin":1389,"end":1476},"obj":"Sentence"},{"id":"T85","span":{"begin":1477,"end":1615},"obj":"Sentence"},{"id":"T86","span":{"begin":1616,"end":1719},"obj":"Sentence"},{"id":"T87","span":{"begin":1720,"end":1841},"obj":"Sentence"},{"id":"T88","span":{"begin":1842,"end":1900},"obj":"Sentence"},{"id":"T89","span":{"begin":1901,"end":1969},"obj":"Sentence"},{"id":"T90","span":{"begin":1970,"end":2143},"obj":"Sentence"},{"id":"T91","span":{"begin":2144,"end":2368},"obj":"Sentence"},{"id":"T92","span":{"begin":2369,"end":2491},"obj":"Sentence"},{"id":"T93","span":{"begin":2492,"end":2720},"obj":"Sentence"},{"id":"T94","span":{"begin":2721,"end":2779},"obj":"Sentence"},{"id":"T95","span":{"begin":2780,"end":2930},"obj":"Sentence"},{"id":"T96","span":{"begin":2931,"end":3013},"obj":"Sentence"},{"id":"T97","span":{"begin":3014,"end":3134},"obj":"Sentence"},{"id":"T98","span":{"begin":3135,"end":3266},"obj":"Sentence"},{"id":"T99","span":{"begin":3267,"end":3431},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"We utilized multiple approaches to examine glycosylation of the SARS-CoV-2 S trimer. First, the portfolio of glycans linked to SARS-CoV-2 S trimer immunogen was analyzed after their release from the polypeptide backbone. N-glycans were released from protein by treatment with PNGase F- and O-glycans were subsequently released by beta-elimination. After permethylation to enhance detection sensitivity and structural characterization, released glycans were analyzed by multi-stage mass spectrometry (MSn) (Aoki et al., 2007; Aoki et al., 2008). Mass spectra were processed by GRITS Toolbox, and the resulting annotations were validated manually (Weatherly et al., 2019). Glycan assignments were grouped by type and by additional structural features for relative quantification of profile characteristics (Figure 2 A; Table S3). This analysis quantified 49 N-glycans and revealed that 55% of the total glycan abundance was of the complex type, 17% was of the hybrid type, and 28% was high mannose. Among the complex and hybrid N-glycans, we observed a high degree of core fucosylation and significant abundance of bisected and LacDiNAc structures. We also observed sulfated N-linked glycans by using negative mode MSn analyses (Table S13), although signal intensity was too low in positive ion mode (at least 10-fold lower than any of the non-sulfated glycans) for accurate quantification. In addition, we detected 15 O-glycans released from the S trimer (Figure S5; Table S4).\nFigure 2 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":"T37","span":{"begin":64,"end":74},"obj":"Disease"},{"id":"T38","span":{"begin":127,"end":137},"obj":"Disease"},{"id":"T39","span":{"begin":1603,"end":1613},"obj":"Disease"},{"id":"T40","span":{"begin":1642,"end":1652},"obj":"Disease"},{"id":"T41","span":{"begin":2183,"end":2193},"obj":"Disease"},{"id":"T42","span":{"begin":2581,"end":2589},"obj":"Disease"},{"id":"T43","span":{"begin":2658,"end":2668},"obj":"Disease"}],"attributes":[{"id":"A37","pred":"mondo_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A38","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"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":"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":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"We utilized multiple approaches to examine glycosylation of the SARS-CoV-2 S trimer. First, the portfolio of glycans linked to SARS-CoV-2 S trimer immunogen was analyzed after their release from the polypeptide backbone. N-glycans were released from protein by treatment with PNGase F- and O-glycans were subsequently released by beta-elimination. After permethylation to enhance detection sensitivity and structural characterization, released glycans were analyzed by multi-stage mass spectrometry (MSn) (Aoki et al., 2007; Aoki et al., 2008). Mass spectra were processed by GRITS Toolbox, and the resulting annotations were validated manually (Weatherly et al., 2019). Glycan assignments were grouped by type and by additional structural features for relative quantification of profile characteristics (Figure 2 A; Table S3). This analysis quantified 49 N-glycans and revealed that 55% of the total glycan abundance was of the complex type, 17% was of the hybrid type, and 28% was high mannose. Among the complex and hybrid N-glycans, we observed a high degree of core fucosylation and significant abundance of bisected and LacDiNAc structures. We also observed sulfated N-linked glycans by using negative mode MSn analyses (Table S13), although signal intensity was too low in positive ion mode (at least 10-fold lower than any of the non-sulfated glycans) for accurate quantification. In addition, we detected 15 O-glycans released from the S trimer (Figure S5; Table S4).\nFigure 2 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":1541,"end":1545},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T49","span":{"begin":2389,"end":2394},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T50","span":{"begin":2692,"end":2697},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T51","span":{"begin":2924,"end":2929},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T52","span":{"begin":3305,"end":3310},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"We utilized multiple approaches to examine glycosylation of the SARS-CoV-2 S trimer. First, the portfolio of glycans linked to SARS-CoV-2 S trimer immunogen was analyzed after their release from the polypeptide backbone. N-glycans were released from protein by treatment with PNGase F- and O-glycans were subsequently released by beta-elimination. After permethylation to enhance detection sensitivity and structural characterization, released glycans were analyzed by multi-stage mass spectrometry (MSn) (Aoki et al., 2007; Aoki et al., 2008). Mass spectra were processed by GRITS Toolbox, and the resulting annotations were validated manually (Weatherly et al., 2019). Glycan assignments were grouped by type and by additional structural features for relative quantification of profile characteristics (Figure 2 A; Table S3). This analysis quantified 49 N-glycans and revealed that 55% of the total glycan abundance was of the complex type, 17% was of the hybrid type, and 28% was high mannose. Among the complex and hybrid N-glycans, we observed a high degree of core fucosylation and significant abundance of bisected and LacDiNAc structures. We also observed sulfated N-linked glycans by using negative mode MSn analyses (Table S13), although signal intensity was too low in positive ion mode (at least 10-fold lower than any of the non-sulfated glycans) for accurate quantification. In addition, we detected 15 O-glycans released from the S trimer (Figure S5; Table S4).\nFigure 2 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":"T63","span":{"begin":211,"end":219},"obj":"Body_part"},{"id":"T64","span":{"begin":250,"end":257},"obj":"Body_part"},{"id":"T65","span":{"begin":988,"end":995},"obj":"Body_part"},{"id":"T66","span":{"begin":1655,"end":1662},"obj":"Body_part"},{"id":"T67","span":{"begin":2150,"end":2163},"obj":"Body_part"},{"id":"T68","span":{"begin":2196,"end":2203},"obj":"Body_part"},{"id":"T69","span":{"begin":2754,"end":2761},"obj":"Body_part"},{"id":"T70","span":{"begin":3234,"end":3240},"obj":"Body_part"}],"attributes":[{"id":"A67","pred":"fma_id","subj":"T67","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A63","pred":"fma_id","subj":"T63","obj":"http://purl.org/sig/ont/fma/fma13478"},{"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":"A65","pred":"fma_id","subj":"T65","obj":"http://purl.org/sig/ont/fma/fma82801"},{"id":"A64","pred":"fma_id","subj":"T64","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":"We utilized multiple approaches to examine glycosylation of the SARS-CoV-2 S trimer. First, the portfolio of glycans linked to SARS-CoV-2 S trimer immunogen was analyzed after their release from the polypeptide backbone. N-glycans were released from protein by treatment with PNGase F- and O-glycans were subsequently released by beta-elimination. After permethylation to enhance detection sensitivity and structural characterization, released glycans were analyzed by multi-stage mass spectrometry (MSn) (Aoki et al., 2007; Aoki et al., 2008). Mass spectra were processed by GRITS Toolbox, and the resulting annotations were validated manually (Weatherly et al., 2019). Glycan assignments were grouped by type and by additional structural features for relative quantification of profile characteristics (Figure 2 A; Table S3). This analysis quantified 49 N-glycans and revealed that 55% of the total glycan abundance was of the complex type, 17% was of the hybrid type, and 28% was high mannose. Among the complex and hybrid N-glycans, we observed a high degree of core fucosylation and significant abundance of bisected and LacDiNAc structures. We also observed sulfated N-linked glycans by using negative mode MSn analyses (Table S13), although signal intensity was too low in positive ion mode (at least 10-fold lower than any of the non-sulfated glycans) for accurate quantification. In addition, we detected 15 O-glycans released from the S trimer (Figure S5; Table S4).\nFigure 2 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":"T43","span":{"begin":43,"end":56},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T44","span":{"begin":276,"end":284},"obj":"http://purl.obolibrary.org/obo/GO_0000224"},{"id":"T45","span":{"begin":1071,"end":1083},"obj":"http://purl.obolibrary.org/obo/GO_0036065"},{"id":"T46","span":{"begin":1586,"end":1599},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T47","span":{"begin":2407,"end":2420},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T48","span":{"begin":2701,"end":2714},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T49","span":{"begin":2807,"end":2820},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T50","span":{"begin":2892,"end":2905},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T51","span":{"begin":3256,"end":3265},"obj":"http://purl.obolibrary.org/obo/GO_0051923"}],"text":"We utilized multiple approaches to examine glycosylation of the SARS-CoV-2 S trimer. First, the portfolio of glycans linked to SARS-CoV-2 S trimer immunogen was analyzed after their release from the polypeptide backbone. N-glycans were released from protein by treatment with PNGase F- and O-glycans were subsequently released by beta-elimination. After permethylation to enhance detection sensitivity and structural characterization, released glycans were analyzed by multi-stage mass spectrometry (MSn) (Aoki et al., 2007; Aoki et al., 2008). Mass spectra were processed by GRITS Toolbox, and the resulting annotations were validated manually (Weatherly et al., 2019). Glycan assignments were grouped by type and by additional structural features for relative quantification of profile characteristics (Figure 2 A; Table S3). This analysis quantified 49 N-glycans and revealed that 55% of the total glycan abundance was of the complex type, 17% was of the hybrid type, and 28% was high mannose. Among the complex and hybrid N-glycans, we observed a high degree of core fucosylation and significant abundance of bisected and LacDiNAc structures. We also observed sulfated N-linked glycans by using negative mode MSn analyses (Table S13), although signal intensity was too low in positive ion mode (at least 10-fold lower than any of the non-sulfated glycans) for accurate quantification. In addition, we detected 15 O-glycans released from the S trimer (Figure S5; Table S4).\nFigure 2 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":"T41","span":{"begin":43,"end":56},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T42","span":{"begin":1071,"end":1083},"obj":"http://purl.obolibrary.org/obo/GO_0036065"},{"id":"T43","span":{"begin":1586,"end":1599},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T44","span":{"begin":2407,"end":2420},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T45","span":{"begin":2701,"end":2714},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T46","span":{"begin":2807,"end":2820},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T47","span":{"begin":2892,"end":2905},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T48","span":{"begin":3256,"end":3265},"obj":"http://purl.obolibrary.org/obo/GO_0051923"}],"text":"We utilized multiple approaches to examine glycosylation of the SARS-CoV-2 S trimer. First, the portfolio of glycans linked to SARS-CoV-2 S trimer immunogen was analyzed after their release from the polypeptide backbone. N-glycans were released from protein by treatment with PNGase F- and O-glycans were subsequently released by beta-elimination. After permethylation to enhance detection sensitivity and structural characterization, released glycans were analyzed by multi-stage mass spectrometry (MSn) (Aoki et al., 2007; Aoki et al., 2008). Mass spectra were processed by GRITS Toolbox, and the resulting annotations were validated manually (Weatherly et al., 2019). Glycan assignments were grouped by type and by additional structural features for relative quantification of profile characteristics (Figure 2 A; Table S3). This analysis quantified 49 N-glycans and revealed that 55% of the total glycan abundance was of the complex type, 17% was of the hybrid type, and 28% was high mannose. Among the complex and hybrid N-glycans, we observed a high degree of core fucosylation and significant abundance of bisected and LacDiNAc structures. We also observed sulfated N-linked glycans by using negative mode MSn analyses (Table S13), although signal intensity was too low in positive ion mode (at least 10-fold lower than any of the non-sulfated glycans) for accurate quantification. In addition, we detected 15 O-glycans released from the S trimer (Figure S5; Table S4).\nFigure 2 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

2_test

{"project":"2_test","denotations":[{"id":"32841605-17264077-19659503","span":{"begin":519,"end":523},"obj":"17264077"},{"id":"32841605-18725413-19659504","span":{"begin":538,"end":542},"obj":"18725413"},{"id":"32841605-30913289-19659505","span":{"begin":664,"end":668},"obj":"30913289"}],"text":"We utilized multiple approaches to examine glycosylation of the SARS-CoV-2 S trimer. First, the portfolio of glycans linked to SARS-CoV-2 S trimer immunogen was analyzed after their release from the polypeptide backbone. N-glycans were released from protein by treatment with PNGase F- and O-glycans were subsequently released by beta-elimination. After permethylation to enhance detection sensitivity and structural characterization, released glycans were analyzed by multi-stage mass spectrometry (MSn) (Aoki et al., 2007; Aoki et al., 2008). Mass spectra were processed by GRITS Toolbox, and the resulting annotations were validated manually (Weatherly et al., 2019). Glycan assignments were grouped by type and by additional structural features for relative quantification of profile characteristics (Figure 2 A; Table S3). This analysis quantified 49 N-glycans and revealed that 55% of the total glycan abundance was of the complex type, 17% was of the hybrid type, and 28% was high mannose. Among the complex and hybrid N-glycans, we observed a high degree of core fucosylation and significant abundance of bisected and LacDiNAc structures. We also observed sulfated N-linked glycans by using negative mode MSn analyses (Table S13), although signal intensity was too low in positive ion mode (at least 10-fold lower than any of the non-sulfated glycans) for accurate quantification. In addition, we detected 15 O-glycans released from the S trimer (Figure S5; Table S4).\nFigure 2 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."}

PMC:7443692 / 13897-17328 JSONTXT

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PMC:7443692 / 13897-17328 JSON TXT