{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:09Z","timestamp":1772138049487,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,10,12]],"date-time":"2021-10-12T00:00:00Z","timestamp":1633996800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100007214","name":"Velux Foundation","doi-asserted-by":"publisher","award":["00028116"],"award-info":[{"award-number":["00028116"]}],"id":[{"id":"10.13039\/100007214","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Liquid-chromatography mass-spectrometry (LC-MS) is the established standard for analyzing the proteome in biological samples by identification and quantification of thousands of proteins. Machine learning (ML) promises to considerably improve the analysis of the resulting data, however, there is yet to be any tool that mediates the path from raw data to modern ML applications. More specifically, ML applications are currently hampered by three major limitations: (i) absence of balanced training data with large sample size; (ii) unclear definition of sufficiently information-rich data representations for e.g. peptide identification; (iii) lack of benchmarking of ML methods on specific LC-MS problems.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We created the MS2AI pipeline that automates the process of gathering vast quantities of MS data for large-scale ML applications. The software retrieves raw data from either in-house sources or from the proteomics identifications database, PRIDE. Subsequently, the raw data are stored in a standardized format amenable for ML, encompassing MS1\/MS2 spectra and peptide identifications. This tool bridges the gap between MS and AI, and to this effect we also present an ML application in the form of a convolutional neural network for the identification of oxidized peptides.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>An open-source implementation of the software can be found at https:\/\/gitlab.com\/roettgerlab\/ms2ai<\/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\/btab701","type":"journal-article","created":{"date-parts":[[2021,10,11]],"date-time":"2021-10-11T15:33:00Z","timestamp":1633966380000},"page":"875-877","source":"Crossref","is-referenced-by-count":6,"title":["MS2AI: automated repurposing of public peptide LC-MS data for machine learning applications"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1190-9485","authenticated-orcid":false,"given":"Tobias Greisager","family":"Rehfeldt","sequence":"first","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Southern Denmark , Odense, Denmark"}]},{"given":"Konrad","family":"Krawczyk","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Southern Denmark , Odense, Denmark"}]},{"given":"Mathias","family":"B\u00f8gebjerg","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Southern Denmark , Odense, Denmark"}]},{"given":"Veit","family":"Schw\u00e4mmle","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , Odense, Denmark"}]},{"given":"Richard","family":"R\u00f6ttger","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Southern Denmark , Odense, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2021,10,12]]},"reference":[{"key":"2023020108475185900_btab701-B1","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1093\/bioinformatics\/btx724","article-title":"Deep learning for tumor classification in imaging mass spectrometry","volume":"34","author":"Behrmann","year":"2018","journal-title":"Bioinformatics"},{"key":"2023020108475185900_btab701-B2","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"Cox","year":"2008","journal-title":"Nat. Biotechnol"},{"key":"2023020108475185900_btab701-B3","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1021\/acs.jproteome.9b00328","article-title":"ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion","volume":"19","author":"Hulstaert","year":"2020","journal-title":"J. Proteome Res"},{"key":"2023020108475185900_btab701-B4","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1146\/annurev-biodatasci-080917-013516","article-title":"Computational methods for understanding mass spectrometry-based shotgun proteomics data","volume":"1","author":"Sinitcyn","year":"2018","journal-title":"Ann. Rev. Biomed. Data Sci"},{"key":"2023020108475185900_btab701-B5","doi-asserted-by":"crossref","first-page":"11033","DOI":"10.1093\/nar\/gkw880","article-title":"2016 update of the PRIDE database and its related tools","volume":"44","author":"Vizca\u00edno","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020108475185900_btab701-B6","doi-asserted-by":"crossref","first-page":"9724","DOI":"10.1021\/acs.analchem.9b01262","article-title":"MS\/MS spectrum prediction for modified peptides using pDeep2 trained by transfer learning","volume":"91","author":"Zeng","year":"2019","journal-title":"Anal. Chem"},{"key":"2023020108475185900_btab701-B7","doi-asserted-by":"crossref","first-page":"17168","DOI":"10.1038\/s41598-019-52954-4","article-title":"DeepIso: a deep learning model for peptide feature detection from LC-MS map","volume":"9","author":"Zohora","year":"2019","journal-title":"Sci. Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab701\/40839683\/btab701.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/3\/875\/49007328\/btab701.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/3\/875\/49007328\/btab701.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T15:04:01Z","timestamp":1675263841000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/3\/875\/6390792"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,10,12]]},"references-count":7,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2022,1,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab701","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.01.27.428375","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,2,1]]},"published":{"date-parts":[[2021,10,12]]}}}