PMC:7692688 / 9533-11435 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/7692688","sourcedb":"PMC","sourceid":"7692688","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7692688","text":"2.11. Targeted Analysis by SPS–MS3\nMass spectrometry data were acquired in centroid mode on an Orbitrap Fusion Lumos mass spectrometer hyphenated to an easy-nLC 1200 nano HPLC system using a nanoFlex ion source (ThermoFisher Scientific) applying a spray voltage of 2.6 kV with the transfer tube heated to 300 °C and a funnel RF of 30%. Internal mass calibration was enabled (lock mass 445.12003 m/z). Peptides were separated on a self-made, 32 cm long, 75 µm ID fused-silica column, packed in house with 1.9 µm C18 particles (ReproSil-Pur, Dr. Maisch, Ammerbuch-Entringen, Germany) and heated to 50 °C using an integrated column oven (Sonation, Biberach, Germany). The HPLC solvents consisted of 0.1% formic acid in water (Buffer A) and 0.1% formic acid with 80% acetonitrile in water (Buffer B).\nDependent scans were performed on precursors matching a mass list of viral peptides modified with TMTpro reagents and their charge states (mass tolerance was set to 5 ppm for matching precursors). Peptides were eluted by a non-linear gradient from 5% to 40% B over 30 min, followed by a step-wise increase to 95% B in 6 min, which was held for another 9 min. Full scan MS spectra (350–1500 m/z) were acquired with a resolution of 120,000 at m/z 200, a maximum injection time of 100 ms, and an automatic gain control (AGC) target value of 4 × 105. The 10 most intense precursors matching the target list per full scan were selected for fragmentation (“Top 10”) and isolated with a quadrupole isolation window of 0.4 Th. MS2 scans were performed in the Orbitrap using a maximum injection time of 300 ms, an AGC target value of 1.5 × 104, and fragmented using HCD with a normalized collision energy (NCE) of 35% and a fixed first mass of 110 m/z. Repeated sequencing of already acquired precursors was limited by setting a dynamic exclusion of 20 s and 10 ppm and advanced peak determination was deactivated.","divisions":[{"label":"title","span":{"begin":0,"end":34}},{"label":"p","span":{"begin":35,"end":796}}],"tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"227","span":{"begin":468,"end":474},"obj":"Chemical"},{"id":"228","span":{"begin":511,"end":514},"obj":"Chemical"},{"id":"229","span":{"begin":701,"end":712},"obj":"Chemical"},{"id":"230","span":{"begin":716,"end":721},"obj":"Chemical"},{"id":"231","span":{"begin":742,"end":753},"obj":"Chemical"},{"id":"232","span":{"begin":763,"end":775},"obj":"Chemical"},{"id":"233","span":{"begin":779,"end":784},"obj":"Chemical"},{"id":"236","span":{"begin":1516,"end":1519},"obj":"Species"},{"id":"237","span":{"begin":895,"end":910},"obj":"Chemical"}],"attributes":[{"id":"A227","pred":"tao:has_database_id","subj":"227","obj":"MESH:D012822"},{"id":"A228","pred":"tao:has_database_id","subj":"228","obj":"MESH:C109760"},{"id":"A229","pred":"tao:has_database_id","subj":"229","obj":"MESH:C030544"},{"id":"A230","pred":"tao:has_database_id","subj":"230","obj":"MESH:D014867"},{"id":"A231","pred":"tao:has_database_id","subj":"231","obj":"MESH:C030544"},{"id":"A232","pred":"tao:has_database_id","subj":"232","obj":"MESH:C032159"},{"id":"A233","pred":"tao:has_database_id","subj":"233","obj":"MESH:D014867"},{"id":"A236","pred":"tao:has_database_id","subj":"236","obj":"Tax:2710868"},{"subj":"227","pred":"source","obj":"LitCovid-PubTator"},{"subj":"228","pred":"source","obj":"LitCovid-PubTator"},{"subj":"229","pred":"source","obj":"LitCovid-PubTator"},{"subj":"230","pred":"source","obj":"LitCovid-PubTator"},{"subj":"231","pred":"source","obj":"LitCovid-PubTator"},{"subj":"232","pred":"source","obj":"LitCovid-PubTator"},{"subj":"233","pred":"source","obj":"LitCovid-PubTator"},{"subj":"236","pred":"source","obj":"LitCovid-PubTator"},{"subj":"237","pred":"source","obj":"LitCovid-PubTator"}],"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_"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T85","span":{"begin":0,"end":5},"obj":"Sentence"},{"id":"T86","span":{"begin":6,"end":34},"obj":"Sentence"},{"id":"T87","span":{"begin":35,"end":335},"obj":"Sentence"},{"id":"T88","span":{"begin":336,"end":400},"obj":"Sentence"},{"id":"T89","span":{"begin":401,"end":664},"obj":"Sentence"},{"id":"T90","span":{"begin":665,"end":796},"obj":"Sentence"},{"id":"T91","span":{"begin":797,"end":993},"obj":"Sentence"},{"id":"T92","span":{"begin":994,"end":1155},"obj":"Sentence"},{"id":"T93","span":{"begin":1156,"end":1343},"obj":"Sentence"},{"id":"T94","span":{"begin":1344,"end":1515},"obj":"Sentence"},{"id":"T95","span":{"begin":1516,"end":1740},"obj":"Sentence"},{"id":"T96","span":{"begin":1741,"end":1902},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T85","pred":"source","obj":"LitCovid-sentences"},{"subj":"T86","pred":"source","obj":"LitCovid-sentences"},{"subj":"T87","pred":"source","obj":"LitCovid-sentences"},{"subj":"T88","pred":"source","obj":"LitCovid-sentences"},{"subj":"T89","pred":"source","obj":"LitCovid-sentences"},{"subj":"T90","pred":"source","obj":"LitCovid-sentences"},{"subj":"T91","pred":"source","obj":"LitCovid-sentences"},{"subj":"T92","pred":"source","obj":"LitCovid-sentences"},{"subj":"T93","pred":"source","obj":"LitCovid-sentences"},{"subj":"T94","pred":"source","obj":"LitCovid-sentences"},{"subj":"T95","pred":"source","obj":"LitCovid-sentences"},{"subj":"T96","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PubTator","color":"#93ec9f","default":true},{"id":"LitCovid-sentences","color":"#ec93a0"}]}]}}