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LitCovid-sample-CHEBI

LitCovid-sample-PD-NCBITaxon

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T160","span":{"begin":24,"end":34},"obj":"Species"}],"attributes":[{"id":"A160","pred":"ncbi_taxonomy_id","subj":"T160","obj":"NCBItxid:2697049"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"Three 10-μg aliquots of SARS-CoV-2 S protein and one 10-μg aliquot of ACE2 protein were reduced by incubating with 5 mM of dithiothreitol at 56°C and alkylated by 13.75 mM of iodoacetamide at room temperature in dark. The four aliquots were then digested respectively using trypsin, Lys-C, Arg-C, or a combination of trypsin and Lys-C. Following digestion, the proteins were deglycosylated by PNGaseF treatment and then digested with O-protease OpeRATOR®. The resulting peptides were separated on an Acclaim PepMap RSLC C18 column (75 μm x 15 cm) and eluted into the nano-electrospray ion source of an Orbitrap Fusion Lumos Tribrid mass spectrometer at a flow rate of 200 nL/min. The elution gradient consists of 1%–40% acetonitrile in 0.1% formic acid over 370 min followed by 10 min of 80% acetonitrile in 0.1% formic acid. The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C. Full MS scans were acquired from m/z 200 to 2000 at 60k resolution, and MS/MS scans following higher-energy collisional dissociation (HCD) with stepped collision energy (15%, 25%, 35%) or electron transfer dissociation (ETD) were collected in the Orbitrap at 15k resolution. The raw spectra were analyzed by Byonic (v3.8.13) with mass tolerance set as 20 ppm for both precursors and fragments. MS/MS filtering was applied to only allow for spectra where the oxonium ions of HexNAc were observed. The search output was filtered at 1% false discovery rate and 10 ppm mass error. The spectra assigned as O-linked glycopeptides were manually evaluated. Quantitation was performed by calculating spectral counts for each glycan composition at each site. Any O-linked glycan compositions identified by only one spectra were removed from quantitation. Occupancy of each O-linked glycosylation site was calculated using spectral counts assigned to any glycosylated peptides and their unmodified counterparts from searches without MS/MS filtering."}

LitCovid-sample-sentences

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T406","span":{"begin":0,"end":217},"obj":"Sentence"},{"id":"T407","span":{"begin":218,"end":335},"obj":"Sentence"},{"id":"T408","span":{"begin":336,"end":455},"obj":"Sentence"},{"id":"T409","span":{"begin":456,"end":679},"obj":"Sentence"},{"id":"T410","span":{"begin":680,"end":825},"obj":"Sentence"},{"id":"T411","span":{"begin":826,"end":923},"obj":"Sentence"},{"id":"T412","span":{"begin":924,"end":1198},"obj":"Sentence"},{"id":"T413","span":{"begin":1199,"end":1317},"obj":"Sentence"},{"id":"T414","span":{"begin":1318,"end":1419},"obj":"Sentence"},{"id":"T415","span":{"begin":1420,"end":1500},"obj":"Sentence"},{"id":"T416","span":{"begin":1501,"end":1572},"obj":"Sentence"},{"id":"T417","span":{"begin":1573,"end":1672},"obj":"Sentence"},{"id":"T418","span":{"begin":1673,"end":1768},"obj":"Sentence"},{"id":"T419","span":{"begin":1769,"end":1962},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Three 10-μg aliquots of SARS-CoV-2 S protein and one 10-μg aliquot of ACE2 protein were reduced by incubating with 5 mM of dithiothreitol at 56°C and alkylated by 13.75 mM of iodoacetamide at room temperature in dark. The four aliquots were then digested respectively using trypsin, Lys-C, Arg-C, or a combination of trypsin and Lys-C. Following digestion, the proteins were deglycosylated by PNGaseF treatment and then digested with O-protease OpeRATOR®. The resulting peptides were separated on an Acclaim PepMap RSLC C18 column (75 μm x 15 cm) and eluted into the nano-electrospray ion source of an Orbitrap Fusion Lumos Tribrid mass spectrometer at a flow rate of 200 nL/min. The elution gradient consists of 1%–40% acetonitrile in 0.1% formic acid over 370 min followed by 10 min of 80% acetonitrile in 0.1% formic acid. The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C. Full MS scans were acquired from m/z 200 to 2000 at 60k resolution, and MS/MS scans following higher-energy collisional dissociation (HCD) with stepped collision energy (15%, 25%, 35%) or electron transfer dissociation (ETD) were collected in the Orbitrap at 15k resolution. The raw spectra were analyzed by Byonic (v3.8.13) with mass tolerance set as 20 ppm for both precursors and fragments. MS/MS filtering was applied to only allow for spectra where the oxonium ions of HexNAc were observed. The search output was filtered at 1% false discovery rate and 10 ppm mass error. The spectra assigned as O-linked glycopeptides were manually evaluated. Quantitation was performed by calculating spectral counts for each glycan composition at each site. Any O-linked glycan compositions identified by only one spectra were removed from quantitation. Occupancy of each O-linked glycosylation site was calculated using spectral counts assigned to any glycosylated peptides and their unmodified counterparts from searches without MS/MS filtering."}

LitCovid-sample-PD-UBERON

{"project":"LitCovid-sample-PD-UBERON","denotations":[{"id":"T11","span":{"begin":896,"end":905},"obj":"Body_part"}],"attributes":[{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0001982"}],"text":"Three 10-μg aliquots of SARS-CoV-2 S protein and one 10-μg aliquot of ACE2 protein were reduced by incubating with 5 mM of dithiothreitol at 56°C and alkylated by 13.75 mM of iodoacetamide at room temperature in dark. The four aliquots were then digested respectively using trypsin, Lys-C, Arg-C, or a combination of trypsin and Lys-C. Following digestion, the proteins were deglycosylated by PNGaseF treatment and then digested with O-protease OpeRATOR®. The resulting peptides were separated on an Acclaim PepMap RSLC C18 column (75 μm x 15 cm) and eluted into the nano-electrospray ion source of an Orbitrap Fusion Lumos Tribrid mass spectrometer at a flow rate of 200 nL/min. The elution gradient consists of 1%–40% acetonitrile in 0.1% formic acid over 370 min followed by 10 min of 80% acetonitrile in 0.1% formic acid. The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C. Full MS scans were acquired from m/z 200 to 2000 at 60k resolution, and MS/MS scans following higher-energy collisional dissociation (HCD) with stepped collision energy (15%, 25%, 35%) or electron transfer dissociation (ETD) were collected in the Orbitrap at 15k resolution. The raw spectra were analyzed by Byonic (v3.8.13) with mass tolerance set as 20 ppm for both precursors and fragments. MS/MS filtering was applied to only allow for spectra where the oxonium ions of HexNAc were observed. The search output was filtered at 1% false discovery rate and 10 ppm mass error. The spectra assigned as O-linked glycopeptides were manually evaluated. Quantitation was performed by calculating spectral counts for each glycan composition at each site. Any O-linked glycan compositions identified by only one spectra were removed from quantitation. Occupancy of each O-linked glycosylation site was calculated using spectral counts assigned to any glycosylated peptides and their unmodified counterparts from searches without MS/MS filtering."}

LitCovid-sample-PD-MONDO

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T98","span":{"begin":24,"end":34},"obj":"Disease"}],"attributes":[{"id":"A98","pred":"mondo_id","subj":"T98","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"Three 10-μg aliquots of SARS-CoV-2 S protein and one 10-μg aliquot of ACE2 protein were reduced by incubating with 5 mM of dithiothreitol at 56°C and alkylated by 13.75 mM of iodoacetamide at room temperature in dark. The four aliquots were then digested respectively using trypsin, Lys-C, Arg-C, or a combination of trypsin and Lys-C. Following digestion, the proteins were deglycosylated by PNGaseF treatment and then digested with O-protease OpeRATOR®. The resulting peptides were separated on an Acclaim PepMap RSLC C18 column (75 μm x 15 cm) and eluted into the nano-electrospray ion source of an Orbitrap Fusion Lumos Tribrid mass spectrometer at a flow rate of 200 nL/min. The elution gradient consists of 1%–40% acetonitrile in 0.1% formic acid over 370 min followed by 10 min of 80% acetonitrile in 0.1% formic acid. The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C. Full MS scans were acquired from m/z 200 to 2000 at 60k resolution, and MS/MS scans following higher-energy collisional dissociation (HCD) with stepped collision energy (15%, 25%, 35%) or electron transfer dissociation (ETD) were collected in the Orbitrap at 15k resolution. The raw spectra were analyzed by Byonic (v3.8.13) with mass tolerance set as 20 ppm for both precursors and fragments. MS/MS filtering was applied to only allow for spectra where the oxonium ions of HexNAc were observed. The search output was filtered at 1% false discovery rate and 10 ppm mass error. The spectra assigned as O-linked glycopeptides were manually evaluated. Quantitation was performed by calculating spectral counts for each glycan composition at each site. Any O-linked glycan compositions identified by only one spectra were removed from quantitation. Occupancy of each O-linked glycosylation site was calculated using spectral counts assigned to any glycosylated peptides and their unmodified counterparts from searches without MS/MS filtering."}

LitCovid-sample-UniProt

LitCovid-sample-PD-IDO

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T159","span":{"begin":1667,"end":1671},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T160","span":{"begin":1810,"end":1814},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"Three 10-μg aliquots of SARS-CoV-2 S protein and one 10-μg aliquot of ACE2 protein were reduced by incubating with 5 mM of dithiothreitol at 56°C and alkylated by 13.75 mM of iodoacetamide at room temperature in dark. The four aliquots were then digested respectively using trypsin, Lys-C, Arg-C, or a combination of trypsin and Lys-C. Following digestion, the proteins were deglycosylated by PNGaseF treatment and then digested with O-protease OpeRATOR®. The resulting peptides were separated on an Acclaim PepMap RSLC C18 column (75 μm x 15 cm) and eluted into the nano-electrospray ion source of an Orbitrap Fusion Lumos Tribrid mass spectrometer at a flow rate of 200 nL/min. The elution gradient consists of 1%–40% acetonitrile in 0.1% formic acid over 370 min followed by 10 min of 80% acetonitrile in 0.1% formic acid. The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C. Full MS scans were acquired from m/z 200 to 2000 at 60k resolution, and MS/MS scans following higher-energy collisional dissociation (HCD) with stepped collision energy (15%, 25%, 35%) or electron transfer dissociation (ETD) were collected in the Orbitrap at 15k resolution. The raw spectra were analyzed by Byonic (v3.8.13) with mass tolerance set as 20 ppm for both precursors and fragments. MS/MS filtering was applied to only allow for spectra where the oxonium ions of HexNAc were observed. The search output was filtered at 1% false discovery rate and 10 ppm mass error. The spectra assigned as O-linked glycopeptides were manually evaluated. Quantitation was performed by calculating spectral counts for each glycan composition at each site. Any O-linked glycan compositions identified by only one spectra were removed from quantitation. Occupancy of each O-linked glycosylation site was calculated using spectral counts assigned to any glycosylated peptides and their unmodified counterparts from searches without MS/MS filtering."}

LitCovid-sample-PD-FMA

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T198","span":{"begin":37,"end":44},"obj":"Body_part"},{"id":"T199","span":{"begin":75,"end":82},"obj":"Body_part"},{"id":"T200","span":{"begin":361,"end":369},"obj":"Body_part"},{"id":"T201","span":{"begin":896,"end":905},"obj":"Body_part"},{"id":"T202","span":{"begin":1144,"end":1147},"obj":"Body_part"},{"id":"T203","span":{"begin":1534,"end":1547},"obj":"Body_part"}],"attributes":[{"id":"A198","pred":"fma_id","subj":"T198","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A199","pred":"fma_id","subj":"T199","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A200","pred":"fma_id","subj":"T200","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A201","pred":"fma_id","subj":"T201","obj":"http://purl.org/sig/ont/fma/fma63194"},{"id":"A202","pred":"fma_id","subj":"T202","obj":"http://purl.org/sig/ont/fma/fma67781"},{"id":"A203","pred":"fma_id","subj":"T203","obj":"http://purl.org/sig/ont/fma/fma82784"}],"text":"Three 10-μg aliquots of SARS-CoV-2 S protein and one 10-μg aliquot of ACE2 protein were reduced by incubating with 5 mM of dithiothreitol at 56°C and alkylated by 13.75 mM of iodoacetamide at room temperature in dark. The four aliquots were then digested respectively using trypsin, Lys-C, Arg-C, or a combination of trypsin and Lys-C. Following digestion, the proteins were deglycosylated by PNGaseF treatment and then digested with O-protease OpeRATOR®. The resulting peptides were separated on an Acclaim PepMap RSLC C18 column (75 μm x 15 cm) and eluted into the nano-electrospray ion source of an Orbitrap Fusion Lumos Tribrid mass spectrometer at a flow rate of 200 nL/min. The elution gradient consists of 1%–40% acetonitrile in 0.1% formic acid over 370 min followed by 10 min of 80% acetonitrile in 0.1% formic acid. The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C. Full MS scans were acquired from m/z 200 to 2000 at 60k resolution, and MS/MS scans following higher-energy collisional dissociation (HCD) with stepped collision energy (15%, 25%, 35%) or electron transfer dissociation (ETD) were collected in the Orbitrap at 15k resolution. The raw spectra were analyzed by Byonic (v3.8.13) with mass tolerance set as 20 ppm for both precursors and fragments. MS/MS filtering was applied to only allow for spectra where the oxonium ions of HexNAc were observed. The search output was filtered at 1% false discovery rate and 10 ppm mass error. The spectra assigned as O-linked glycopeptides were manually evaluated. Quantitation was performed by calculating spectral counts for each glycan composition at each site. Any O-linked glycan compositions identified by only one spectra were removed from quantitation. Occupancy of each O-linked glycosylation site was calculated using spectral counts assigned to any glycosylated peptides and their unmodified counterparts from searches without MS/MS filtering."}

LitCovid-sample-PD-GO-BP-0

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T125","span":{"begin":290,"end":295},"obj":"http://purl.obolibrary.org/obo/GO_0043870"},{"id":"T126","span":{"begin":346,"end":355},"obj":"http://purl.obolibrary.org/obo/GO_0007586"},{"id":"T127","span":{"begin":393,"end":400},"obj":"http://purl.obolibrary.org/obo/GO_0000224"},{"id":"T128","span":{"begin":1112,"end":1129},"obj":"http://purl.obolibrary.org/obo/GO_0022904"},{"id":"T129","span":{"begin":1796,"end":1809},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Three 10-μg aliquots of SARS-CoV-2 S protein and one 10-μg aliquot of ACE2 protein were reduced by incubating with 5 mM of dithiothreitol at 56°C and alkylated by 13.75 mM of iodoacetamide at room temperature in dark. The four aliquots were then digested respectively using trypsin, Lys-C, Arg-C, or a combination of trypsin and Lys-C. Following digestion, the proteins were deglycosylated by PNGaseF treatment and then digested with O-protease OpeRATOR®. The resulting peptides were separated on an Acclaim PepMap RSLC C18 column (75 μm x 15 cm) and eluted into the nano-electrospray ion source of an Orbitrap Fusion Lumos Tribrid mass spectrometer at a flow rate of 200 nL/min. The elution gradient consists of 1%–40% acetonitrile in 0.1% formic acid over 370 min followed by 10 min of 80% acetonitrile in 0.1% formic acid. The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C. Full MS scans were acquired from m/z 200 to 2000 at 60k resolution, and MS/MS scans following higher-energy collisional dissociation (HCD) with stepped collision energy (15%, 25%, 35%) or electron transfer dissociation (ETD) were collected in the Orbitrap at 15k resolution. The raw spectra were analyzed by Byonic (v3.8.13) with mass tolerance set as 20 ppm for both precursors and fragments. MS/MS filtering was applied to only allow for spectra where the oxonium ions of HexNAc were observed. The search output was filtered at 1% false discovery rate and 10 ppm mass error. The spectra assigned as O-linked glycopeptides were manually evaluated. Quantitation was performed by calculating spectral counts for each glycan composition at each site. Any O-linked glycan compositions identified by only one spectra were removed from quantitation. Occupancy of each O-linked glycosylation site was calculated using spectral counts assigned to any glycosylated peptides and their unmodified counterparts from searches without MS/MS filtering."}

LitCovid-sample-GO-BP

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T118","span":{"begin":346,"end":355},"obj":"http://purl.obolibrary.org/obo/GO_0007586"},{"id":"T119","span":{"begin":1112,"end":1129},"obj":"http://purl.obolibrary.org/obo/GO_0022904"},{"id":"T120","span":{"begin":1457,"end":1462},"obj":"http://purl.obolibrary.org/obo/GO_0071878"},{"id":"T121","span":{"begin":1457,"end":1462},"obj":"http://purl.obolibrary.org/obo/GO_0071877"},{"id":"T122","span":{"begin":1796,"end":1809},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Three 10-μg aliquots of SARS-CoV-2 S protein and one 10-μg aliquot of ACE2 protein were reduced by incubating with 5 mM of dithiothreitol at 56°C and alkylated by 13.75 mM of iodoacetamide at room temperature in dark. The four aliquots were then digested respectively using trypsin, Lys-C, Arg-C, or a combination of trypsin and Lys-C. Following digestion, the proteins were deglycosylated by PNGaseF treatment and then digested with O-protease OpeRATOR®. The resulting peptides were separated on an Acclaim PepMap RSLC C18 column (75 μm x 15 cm) and eluted into the nano-electrospray ion source of an Orbitrap Fusion Lumos Tribrid mass spectrometer at a flow rate of 200 nL/min. The elution gradient consists of 1%–40% acetonitrile in 0.1% formic acid over 370 min followed by 10 min of 80% acetonitrile in 0.1% formic acid. The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C. Full MS scans were acquired from m/z 200 to 2000 at 60k resolution, and MS/MS scans following higher-energy collisional dissociation (HCD) with stepped collision energy (15%, 25%, 35%) or electron transfer dissociation (ETD) were collected in the Orbitrap at 15k resolution. The raw spectra were analyzed by Byonic (v3.8.13) with mass tolerance set as 20 ppm for both precursors and fragments. MS/MS filtering was applied to only allow for spectra where the oxonium ions of HexNAc were observed. The search output was filtered at 1% false discovery rate and 10 ppm mass error. The spectra assigned as O-linked glycopeptides were manually evaluated. Quantitation was performed by calculating spectral counts for each glycan composition at each site. Any O-linked glycan compositions identified by only one spectra were removed from quantitation. Occupancy of each O-linked glycosylation site was calculated using spectral counts assigned to any glycosylated peptides and their unmodified counterparts from searches without MS/MS filtering."}

LitCovid-sample-Glycan

PMC:7443692 / 60174-62136 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7443692 / 60174-62136 JSON TXT