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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T159","span":{"begin":108,"end":116},"obj":"Body_part"},{"id":"T160","span":{"begin":295,"end":308},"obj":"Body_part"},{"id":"T161","span":{"begin":609,"end":622},"obj":"Body_part"},{"id":"T162","span":{"begin":917,"end":926},"obj":"Body_part"},{"id":"T163","span":{"begin":1768,"end":1780},"obj":"Body_part"},{"id":"T164","span":{"begin":1893,"end":1900},"obj":"Body_part"},{"id":"T165","span":{"begin":1916,"end":1928},"obj":"Body_part"},{"id":"T166","span":{"begin":2425,"end":2437},"obj":"Body_part"},{"id":"T167","span":{"begin":2453,"end":2463},"obj":"Body_part"}],"attributes":[{"id":"A159","pred":"fma_id","subj":"T159","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A160","pred":"fma_id","subj":"T160","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A161","pred":"fma_id","subj":"T161","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A162","pred":"fma_id","subj":"T162","obj":"http://purl.org/sig/ont/fma/fma63194"},{"id":"A163","pred":"fma_id","subj":"T163","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A164","pred":"fma_id","subj":"T164","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A165","pred":"fma_id","subj":"T165","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A166","pred":"fma_id","subj":"T166","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A167","pred":"fma_id","subj":"T167","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T10","span":{"begin":338,"end":341},"obj":"Body_part"},{"id":"T11","span":{"begin":917,"end":926},"obj":"Body_part"}],"attributes":[{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_2001840"},{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0001982"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T95","span":{"begin":1104,"end":1107},"obj":"Disease"},{"id":"T96","span":{"begin":1178,"end":1181},"obj":"Disease"},{"id":"T97","span":{"begin":1227,"end":1230},"obj":"Disease"}],"attributes":[{"id":"A95","pred":"mondo_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/MONDO_0012956"},{"id":"A96","pred":"mondo_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/MONDO_0012956"},{"id":"A97","pred":"mondo_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/MONDO_0012956"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-sample-PD-IDO

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T88","span":{"begin":1260,"end":1265},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T89","span":{"begin":2574,"end":2578},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

LitCovid-sample-PD-FMA

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T157","span":{"begin":108,"end":116},"obj":"Body_part"},{"id":"T158","span":{"begin":295,"end":308},"obj":"Body_part"},{"id":"T159","span":{"begin":609,"end":622},"obj":"Body_part"},{"id":"T160","span":{"begin":917,"end":926},"obj":"Body_part"},{"id":"T161","span":{"begin":1768,"end":1780},"obj":"Body_part"},{"id":"T162","span":{"begin":1893,"end":1900},"obj":"Body_part"},{"id":"T163","span":{"begin":1916,"end":1928},"obj":"Body_part"},{"id":"T164","span":{"begin":2425,"end":2437},"obj":"Body_part"},{"id":"T165","span":{"begin":2453,"end":2463},"obj":"Body_part"}],"attributes":[{"id":"A160","pred":"fma_id","subj":"T160","obj":"http://purl.org/sig/ont/fma/fma63194"},{"id":"A162","pred":"fma_id","subj":"T162","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A163","pred":"fma_id","subj":"T163","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A159","pred":"fma_id","subj":"T159","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A158","pred":"fma_id","subj":"T158","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A157","pred":"fma_id","subj":"T157","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A164","pred":"fma_id","subj":"T164","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A165","pred":"fma_id","subj":"T165","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A161","pred":"fma_id","subj":"T161","obj":"http://purl.org/sig/ont/fma/fma82784"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

LitCovid-sample-CHEBI

LitCovid-sample-PD-NCBITaxon

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T202","span":{"begin":589,"end":595},"obj":"Species"}],"attributes":[{"id":"A202","pred":"ncbi_taxonomy_id","subj":"T202","obj":"NCBItxid:76720"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

LitCovid-sample-sentences

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T175","span":{"begin":0,"end":107},"obj":"Sentence"},{"id":"T176","span":{"begin":108,"end":252},"obj":"Sentence"},{"id":"T177","span":{"begin":253,"end":396},"obj":"Sentence"},{"id":"T178","span":{"begin":397,"end":608},"obj":"Sentence"},{"id":"T179","span":{"begin":609,"end":837},"obj":"Sentence"},{"id":"T180","span":{"begin":838,"end":985},"obj":"Sentence"},{"id":"T181","span":{"begin":986,"end":1117},"obj":"Sentence"},{"id":"T182","span":{"begin":1118,"end":1236},"obj":"Sentence"},{"id":"T183","span":{"begin":1237,"end":1379},"obj":"Sentence"},{"id":"T184","span":{"begin":1380,"end":1421},"obj":"Sentence"},{"id":"T185","span":{"begin":1422,"end":1469},"obj":"Sentence"},{"id":"T186","span":{"begin":1470,"end":1767},"obj":"Sentence"},{"id":"T187","span":{"begin":1768,"end":1915},"obj":"Sentence"},{"id":"T188","span":{"begin":1916,"end":2127},"obj":"Sentence"},{"id":"T189","span":{"begin":2128,"end":2222},"obj":"Sentence"},{"id":"T190","span":{"begin":2223,"end":2316},"obj":"Sentence"},{"id":"T191","span":{"begin":2317,"end":2361},"obj":"Sentence"},{"id":"T192","span":{"begin":2362,"end":2579},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

LitCovid-sample-PD-UBERON

{"project":"LitCovid-sample-PD-UBERON","denotations":[{"id":"T10","span":{"begin":338,"end":341},"obj":"Body_part"},{"id":"T11","span":{"begin":917,"end":926},"obj":"Body_part"}],"attributes":[{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_2001840"},{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0001982"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

LitCovid-sample-PD-MONDO

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T90","span":{"begin":1104,"end":1107},"obj":"Disease"},{"id":"T91","span":{"begin":1178,"end":1181},"obj":"Disease"},{"id":"T92","span":{"begin":1227,"end":1230},"obj":"Disease"}],"attributes":[{"id":"A91","pred":"mondo_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/MONDO_0012956"},{"id":"A92","pred":"mondo_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/MONDO_0012956"},{"id":"A90","pred":"mondo_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/MONDO_0012956"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

LitCovid-sample-Pubtator

LitCovid-sample-UniProt

LitCovid-sample-GO-BP

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T53","span":{"begin":2322,"end":2327},"obj":"http://purl.obolibrary.org/obo/GO_0071878"},{"id":"T54","span":{"begin":2322,"end":2327},"obj":"http://purl.obolibrary.org/obo/GO_0071877"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T175","span":{"begin":0,"end":107},"obj":"Sentence"},{"id":"T176","span":{"begin":108,"end":252},"obj":"Sentence"},{"id":"T177","span":{"begin":253,"end":396},"obj":"Sentence"},{"id":"T178","span":{"begin":397,"end":608},"obj":"Sentence"},{"id":"T179","span":{"begin":609,"end":837},"obj":"Sentence"},{"id":"T180","span":{"begin":838,"end":985},"obj":"Sentence"},{"id":"T181","span":{"begin":986,"end":1117},"obj":"Sentence"},{"id":"T182","span":{"begin":1118,"end":1236},"obj":"Sentence"},{"id":"T183","span":{"begin":1237,"end":1379},"obj":"Sentence"},{"id":"T184","span":{"begin":1380,"end":1421},"obj":"Sentence"},{"id":"T185","span":{"begin":1422,"end":1469},"obj":"Sentence"},{"id":"T186","span":{"begin":1470,"end":1767},"obj":"Sentence"},{"id":"T187","span":{"begin":1768,"end":1915},"obj":"Sentence"},{"id":"T188","span":{"begin":1916,"end":2127},"obj":"Sentence"},{"id":"T189","span":{"begin":2128,"end":2222},"obj":"Sentence"},{"id":"T190","span":{"begin":2223,"end":2316},"obj":"Sentence"},{"id":"T191","span":{"begin":2317,"end":2361},"obj":"Sentence"},{"id":"T192","span":{"begin":2362,"end":2579},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36. Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega). Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol. Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific). Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid. Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%. Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000. The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54. The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D. Number of missed cleavages were set at 3. The following modifications were also included: Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1). Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.). Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed. The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions. MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence. A 1% false discovery rate (FDR) was applied. The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site."}

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