{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:01Z","timestamp":1772138041406,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2020,10,17]],"date-time":"2020-10-17T00:00:00Z","timestamp":1602892800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Data mining and data quality evaluation are indispensable constituents of quantitative proteomics, but few integrated tools available.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduced obaDIA, a one-step pipeline to generate visualizable and comprehensive results for quantitative proteomics data. obaDIA supports fragment-level, peptide-level and protein-level abundance matrices from DIA technique, as well as protein-level abundance matrices from other quantitative proteomic techniques. The result contains abundance matrix statistics, differential expression analysis, protein functional annotation and enrichment analysis. Additionally, enrichment strategies which use total proteins or expressed proteins as background are optional, and HTML based interactive visualization for differentially expressed proteins in the KEGG pathway is offered, which helps biological significance mining. In short, obaDIA is an automatic tool for bioinformatics analysis for quantitative proteomics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>obaDIA is freely available from https:\/\/github.com\/yjthu\/obaDIA.git.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa893","type":"journal-article","created":{"date-parts":[[2020,10,2]],"date-time":"2020-10-02T15:11:58Z","timestamp":1601651518000},"page":"2066-2067","source":"Crossref","is-referenced-by-count":3,"title":["obaDIA: one-step biological analysis pipeline for data-independent acquisition and other quantitative proteomics data"],"prefix":"10.1093","volume":"37","author":[{"given":"Jun","family":"Yan","sequence":"first","affiliation":[{"name":"Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University , Beijing 100094, China"},{"name":"Department of Bioinformatics, Beijing Mingde Zhengkang Medical Research Co., Ltd. , Beijing 102206, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongning","family":"Zhai","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Beijing Mingde Zhengkang Medical Research Co., Ltd. , Beijing 102206, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ling","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of College English, Inner Mongolia Medical University , Huhehot, Inner Mongolia 010110, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sasha","family":"Sa","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Beijing Mingde Zhengkang Medical Research Co., Ltd. , Beijing 102206, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaojun","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Beijing Mingde Zhengkang Medical Research Co., Ltd. , Beijing 102206, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,10,17]]},"reference":[{"key":"2023061310292891500_btaa893-B1","article-title":"Gene set enrichment analysis with topGO","volume":"27","author":"Alexa","year":"2009","journal-title":"Bioconductor Improv"},{"key":"2023061310292891500_btaa893-B2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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