{"response":{"docs":[{"system_create_dtsi":"2017-10-27T02:52:32Z","system_modified_dtsi":"2018-08-01T18:40:06Z","has_model_ssim":["Article"],"id":"bc387099c","accessControl_ssim":["87823b20-ed61-4be0-8719-29cc9455fce1"],"hasRelatedMediaFragment_ssim":["bc387100x"],"hasRelatedImage_ssim":["bc387100x"],"depositor_ssim":["greiskd@ucmail.uc.edu"],"depositor_tesim":["greiskd@ucmail.uc.edu"],"title_tesim":["Systematic evaluation of data-independent acquisition for sensitive and reproducible proteomics—a prototype design for a single injection assay"],"date_uploaded_dtsi":"2017-03-03T00:00:00Z","date_modified_dtsi":"2017-04-07T00:00:00Z","isPartOf_ssim":["admin_set/default"],"proxy_depositor_ssim":["dungavjk@mail.uc.edu"],"doi_tesim":["10.1002/jms.3716"],"journal_title_tesim":["Journal of Mass Spectrometry"],"college_tesim":["Medicine"],"department_tesim":["Cancer \u0026 Cell Biology"],"note_tesim":["This work was part of a pilot \"mediated-deposit model\" where library staff found potential works, later submitted for faculty review"],"creator_tesim":["Haffey, Wendy D.","Norris, Jeremy L.","McCullumsmith, Robert E.","Heaven, Michael R.","Cobbs, Archie L.","Funk, Adam J.","Greis, Kenneth D."],"subject_tesim":["Cancer Biology"],"language_tesim":["English"],"description_tesim":["Data-independent acquisition (DIA)-based proteomics has become increasingly complicated in recent years because of the vast number of workflows described, coupled with a lack of studies indicating a rational framework for selecting effective settings to use. To address this issue and provide a resource for the proteomics community, we compared 12 DIA methods that assay tryptic peptides using various mass-isolation windows. Our findings indicate that the most sensitive single injection LC-DIA method uses 6 m/z isolation windows to analyze the densely populated tryptic peptide range from 450 to 730 m/z, which allowed quantification of 4465 Escherichia coli peptides. In contrast, using the sequential windowed acquisition of all theoretical fragmentions (SWATH) approach with 26 m/z isolation windows across the entire 400–1200 m/z range, allowed quantification of only 3309 peptides. This reduced sensitivity with 26 m/z windows is caused by an increase in co-eluting compounds with similar precursor values detected in the same tandemMS spectra, which lowers the signal-to-noise of peptide fragment-ion chromatograms and reduces the amount of low abundance peptides that can be quantified from 410 to 920 m/z. Above 920 m/z, more peptides were quantified with 26 m/z windows because of substantial peptide 13C isotope distributions that parse peptide ions into separate isolation windows. Because reproducible quantification has been a long-standing aimof quantitative proteomics, and is a socalled trait of DIA, we sought to determine whether precursor-level chromatograms used in some methods rather than their fragment-level counterparts have similar precision. Our data show that extracted fragment-ion chromatograms are the reason DIA provides superior reproducibility. Copyright © 2015 John Wiley \u0026 Sons, Ltd."],"license_tesim":["http://rightsstatements.org/vocab/InC/1.0/"],"date_created_tesim":["2016-01"],"source_tesim":["Journal of Mass Spectrometry"],"thumbnail_path_ss":"/downloads/bc387100x?file=thumbnail","suppressed_bsi":false,"actionable_workflow_roles_ssim":["admin_set/default-default-depositing"],"workflow_state_name_ssim":["deposited"],"member_ids_ssim":["bc387100x"],"file_set_ids_ssim":["bc387100x"],"visibility_ssi":"open","admin_set_tesim":["Default Admin Set"],"sort_title_ssi":"SYSTEMATIC EVALUATION OF DATAINDEPENDENT ACQUISITION FOR SENSITIVE AND REPRODUCIBLE PROTEOMICSA PROTOTYPE DESIGN FOR A SINGLE INJECTION ASSAY","human_readable_type_tesim":["Article"],"read_access_group_ssim":["public"],"read_access_person_ssim":["konecnmc@ucmail.uc.edu"],"edit_access_person_ssim":["greiskd@ucmail.uc.edu"],"nesting_collection__pathnames_ssim":["bc387099c"],"nesting_collection__deepest_nested_depth_isi":1,"_version_":1697127424824705024,"timestamp":"2021-04-15T17:13:56.724Z","score":0.00049999997}],"facets":[{"name":"human_readable_type_sim","items":[{"value":"Article","hits":1,"label":"Article"}],"label":"Human Readable Type Sim"},{"name":"creator_sim","items":[{"value":"Cobbs, Archie L.","hits":1,"label":"Cobbs, Archie L."},{"value":"Funk, Adam J.","hits":1,"label":"Funk, Adam J."},{"value":"Greis, Kenneth D.","hits":1,"label":"Greis, Kenneth D."},{"value":"Haffey, Wendy D.","hits":1,"label":"Haffey, Wendy D."},{"value":"Heaven, Michael R.","hits":1,"label":"Heaven, Michael R."},{"value":"McCullumsmith, Robert E.","hits":1,"label":"McCullumsmith, Robert E."}],"label":"Creator Sim"},{"name":"subject_sim","items":[{"value":"Cancer Biology","hits":1,"label":"Cancer Biology"}],"label":"Subject Sim"},{"name":"college_sim","items":[{"value":"Medicine","hits":1,"label":"Medicine"}],"label":"College Sim"},{"name":"department_sim","items":[{"value":"Cancer \u0026 Cell Biology","hits":1,"label":"Cancer \u0026 Cell Biology"}],"label":"Department Sim"},{"name":"language_sim","items":[{"value":"English","hits":1,"label":"English"}],"label":"Language Sim"},{"name":"publisher_sim","items":[],"label":"Publisher Sim"},{"name":"date_created_sim","items":[{"value":"2016-01","hits":1,"label":"2016-01"}],"label":"Date Created Sim"},{"name":"member_of_collection_ids_ssim","items":[],"label":"Member Of Collection Ids Ssim"},{"name":"generic_type_sim","items":[{"value":"Work","hits":1,"label":"Work"}],"label":"Generic Type Sim"}],"pages":{"current_page":1,"next_page":null,"prev_page":null,"total_pages":1,"limit_value":10,"offset_value":0,"total_count":1,"first_page?":true,"last_page?":true}}}