PMC:7640975 / 12867-14225 JSON TXT

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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T100","span":{"begin":661,"end":670},"obj":"Body_part"}],"attributes":[{"id":"A100","pred":"fma_id","subj":"T100","obj":"http://purl.org/sig/ont/fma/fma63194"}],"text":"2.6 LC-MS/MS Analysis\nLC-MS/MS analyses of the labeled peptides were carried out using a Q-Exactive mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) combined with an EASY-nLC 1200 system (Thermo Fisher Scientific). After loading 2 μg of the labeled peptides onto a C18 reversed phase HPLC column (Thermo Fisher Scientific), peptides were chromatographed for 120 min at a flow rate of 300 nL/min over gradients from 2–80% (mobile phase A comprising 0.1% (v/v) formic acid and 2% (v/v) acetonitrile; mobile phase B comprising 0.1% (v/v) formic acid and 80% (v/v) acetonitrile). The following ion source parameters, including spray voltage 1.8 kV, capillary temperature 275 °C and declustering potential 100 V, were set. The mass spectrometer was run using a data-dependent Top-20 acquisition mode, switching automatically between MS and MS/MS. A full MS scan ranging from 350 to 1300 m/z was conducted at 70 000 resolution with an automatic gain control (AGC) target value of 3 × 106 ions and a maximum ion transfer (IT) of 20 ms. The precursor ions were fragmented by means of high-energy collisional dissociation (HCD), and all MS/MS spectra were scanned using the following parameters: resolution 17 500; AGC 1 × 105 ions; maximum IT 50 ms; dynamic exclusion duration 18 s; normalized collision energy 30%; and intensity threshold 1.6 × 105."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T20","span":{"begin":661,"end":670},"obj":"Body_part"}],"attributes":[{"id":"A20","pred":"uberon_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/UBERON_0001982"}],"text":"2.6 LC-MS/MS Analysis\nLC-MS/MS analyses of the labeled peptides were carried out using a Q-Exactive mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) combined with an EASY-nLC 1200 system (Thermo Fisher Scientific). After loading 2 μg of the labeled peptides onto a C18 reversed phase HPLC column (Thermo Fisher Scientific), peptides were chromatographed for 120 min at a flow rate of 300 nL/min over gradients from 2–80% (mobile phase A comprising 0.1% (v/v) formic acid and 2% (v/v) acetonitrile; mobile phase B comprising 0.1% (v/v) formic acid and 80% (v/v) acetonitrile). The following ion source parameters, including spray voltage 1.8 kV, capillary temperature 275 °C and declustering potential 100 V, were set. The mass spectrometer was run using a data-dependent Top-20 acquisition mode, switching automatically between MS and MS/MS. A full MS scan ranging from 350 to 1300 m/z was conducted at 70 000 resolution with an automatic gain control (AGC) target value of 3 × 106 ions and a maximum ion transfer (IT) of 20 ms. The precursor ions were fragmented by means of high-energy collisional dissociation (HCD), and all MS/MS spectra were scanned using the following parameters: resolution 17 500; AGC 1 × 105 ions; maximum IT 50 ms; dynamic exclusion duration 18 s; normalized collision energy 30%; and intensity threshold 1.6 × 105."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T70","span":{"begin":0,"end":22},"obj":"Sentence"},{"id":"T71","span":{"begin":23,"end":230},"obj":"Sentence"},{"id":"T72","span":{"begin":231,"end":591},"obj":"Sentence"},{"id":"T73","span":{"begin":592,"end":733},"obj":"Sentence"},{"id":"T74","span":{"begin":734,"end":857},"obj":"Sentence"},{"id":"T75","span":{"begin":858,"end":1044},"obj":"Sentence"},{"id":"T76","span":{"begin":1045,"end":1358},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.6 LC-MS/MS Analysis\nLC-MS/MS analyses of the labeled peptides were carried out using a Q-Exactive mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) combined with an EASY-nLC 1200 system (Thermo Fisher Scientific). After loading 2 μg of the labeled peptides onto a C18 reversed phase HPLC column (Thermo Fisher Scientific), peptides were chromatographed for 120 min at a flow rate of 300 nL/min over gradients from 2–80% (mobile phase A comprising 0.1% (v/v) formic acid and 2% (v/v) acetonitrile; mobile phase B comprising 0.1% (v/v) formic acid and 80% (v/v) acetonitrile). The following ion source parameters, including spray voltage 1.8 kV, capillary temperature 275 °C and declustering potential 100 V, were set. The mass spectrometer was run using a data-dependent Top-20 acquisition mode, switching automatically between MS and MS/MS. A full MS scan ranging from 350 to 1300 m/z was conducted at 70 000 resolution with an automatic gain control (AGC) target value of 3 × 106 ions and a maximum ion transfer (IT) of 20 ms. The precursor ions were fragmented by means of high-energy collisional dissociation (HCD), and all MS/MS spectra were scanned using the following parameters: resolution 17 500; AGC 1 × 105 ions; maximum IT 50 ms; dynamic exclusion duration 18 s; normalized collision energy 30%; and intensity threshold 1.6 × 105."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"249","span":{"begin":340,"end":348},"obj":"Chemical"},{"id":"250","span":{"begin":475,"end":486},"obj":"Chemical"},{"id":"251","span":{"begin":500,"end":512},"obj":"Chemical"},{"id":"252","span":{"begin":551,"end":562},"obj":"Chemical"},{"id":"253","span":{"begin":577,"end":589},"obj":"Chemical"}],"attributes":[{"id":"A249","pred":"tao:has_database_id","subj":"249","obj":"MESH:D010455"},{"id":"A250","pred":"tao:has_database_id","subj":"250","obj":"MESH:C030544"},{"id":"A251","pred":"tao:has_database_id","subj":"251","obj":"MESH:C032159"},{"id":"A252","pred":"tao:has_database_id","subj":"252","obj":"MESH:C030544"},{"id":"A253","pred":"tao:has_database_id","subj":"253","obj":"MESH:C032159"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"2.6 LC-MS/MS Analysis\nLC-MS/MS analyses of the labeled peptides were carried out using a Q-Exactive mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) combined with an EASY-nLC 1200 system (Thermo Fisher Scientific). After loading 2 μg of the labeled peptides onto a C18 reversed phase HPLC column (Thermo Fisher Scientific), peptides were chromatographed for 120 min at a flow rate of 300 nL/min over gradients from 2–80% (mobile phase A comprising 0.1% (v/v) formic acid and 2% (v/v) acetonitrile; mobile phase B comprising 0.1% (v/v) formic acid and 80% (v/v) acetonitrile). The following ion source parameters, including spray voltage 1.8 kV, capillary temperature 275 °C and declustering potential 100 V, were set. The mass spectrometer was run using a data-dependent Top-20 acquisition mode, switching automatically between MS and MS/MS. A full MS scan ranging from 350 to 1300 m/z was conducted at 70 000 resolution with an automatic gain control (AGC) target value of 3 × 106 ions and a maximum ion transfer (IT) of 20 ms. The precursor ions were fragmented by means of high-energy collisional dissociation (HCD), and all MS/MS spectra were scanned using the following parameters: resolution 17 500; AGC 1 × 105 ions; maximum IT 50 ms; dynamic exclusion duration 18 s; normalized collision energy 30%; and intensity threshold 1.6 × 105."}