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To comprehensively analyze selenoproteomes, previously developed selenocysteine\u2010specific mass spectrometry (SecMS) and the selenocysteine insertion sequence (SECIS)\u2010independent selenoprotein database (SIS) have provided effective tools for analyzing the selenoproteome and, more importantly, hold the potential to uncover new selenoproteins. In this study, a deep learning approach is employed to develop the DeepSecMS method. Given the rarity of Sec and its chemical similarity to cysteine (Cys, C), a proxy training strategy is utilized using a large dataset of Cys\u2010containing peptides to generate a large\u2010scale theoretical library of Sec\u2010containing peptides. It is shown that DeepSecMS enables the accurate prediction of critical features of Sec\u2010containing peptides, including MS2, retention time (RT), and ion mobility (IM). By integrating DeepSecMS with data\u2010independent acquisition (DIA) methods, the identification of known selenoproteins is significantly enhanced across diverse cell types and tissues. More importantly, it facilitates the identification of numerous highly scored, potential novel selenoproteins. These findings highlight the powerful potential of DeepSecMS in advancing selenoprotein research. Moreover, the proxy training strategy may be extended to the analysis of other rare post\u2010translational modifications.<\/jats:p>","DOI":"10.1002\/advs.202504109","type":"journal-article","created":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T09:27:38Z","timestamp":1753176458000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["DeepSecMS Advances DIA\u2010Based Selenoproteome Profiling Through Cys\u2010to\u2010Sec Proxy Training"],"prefix":"10.1002","volume":"12","author":[{"given":"Chenfang","family":"Si","sequence":"first","affiliation":[{"name":"Interdisciplinary Research Center on Biology and Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences  100 Haike Rd. Shanghai 201210 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yamei","family":"Yuan","sequence":"additional","affiliation":[{"name":"Interdisciplinary Research Center on Biology and Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences  100 Haike Rd. Shanghai 201210 China"},{"name":"University of Chinese Academy of Sciences  Beijing 100049 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Zong","sequence":"additional","affiliation":[{"name":"Department of Chemistry Fudan University  Shanghai 200000 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liang","family":"Qiao","sequence":"additional","affiliation":[{"name":"Department of Chemistry Fudan University  Shanghai 200000 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen\u2010Feng","family":"Zeng","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease Research &amp; School of Engineering Westlake University  Hangzhou 310024 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5363-9834","authenticated-orcid":false,"given":"Yaoyang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Interdisciplinary Research Center on Biology and Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences  100 Haike Rd. Shanghai 201210 China"},{"name":"Shanghai Key Laboratory of Aging Studies Chinese Academy of Sciences  100 Haike Rd. Shanghai 201210 China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2025,7,22]]},"reference":[{"key":"e_1_2_9_1_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.freeradbiomed.2018.09.014"},{"key":"e_1_2_9_1_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncb3064"},{"key":"e_1_2_9_1_3","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.11.048"},{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.freeradbiomed.2018.02.030"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-nutr-071811-150740"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1160\/TH14-07-0603"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(11)61452-9"},{"key":"e_1_2_9_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2010.09.015"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1152\/physrev.00039.2013"},{"key":"e_1_2_9_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/bs.mie.2021.10.022"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2018.08.006"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35740-1"},{"key":"e_1_2_9_8_2","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201400270"},{"key":"e_1_2_9_8_3","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.8b05734"},{"key":"e_1_2_9_8_4","first-page":"2024","volume":"2024","author":"Saxena G.","year":"2012","journal-title":"bioRxiv"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15346-1"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201900335"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.8b02386"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0426-7"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.7b02566"},{"key":"e_1_2_9_13_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.9b01262"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0427-6"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13866-z"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.9b04867"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-26979-1"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-024-00875-x"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34904-3"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.21203\/rs.3.rs\u20106900872\/v1"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr401277r"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4256"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth1113"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1021\/ac0341261"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0638-x"}],"container-title":["Advanced Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/advanced.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/advs.202504109","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/advanced.onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/advs.202504109","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/advanced.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/advs.202504109","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T19:32:24Z","timestamp":1773084744000},"score":1,"resource":{"primary":{"URL":"https:\/\/advanced.onlinelibrary.wiley.com\/doi\/10.1002\/advs.202504109"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,22]]},"references-count":33,"journal-issue":{"issue":"38","published-print":{"date-parts":[[2025,10]]}},"alternative-id":["10.1002\/advs.202504109"],"URL":"https:\/\/doi.org\/10.1002\/advs.202504109","archive":["Portico"],"relation":{},"ISSN":["2198-3844","2198-3844"],"issn-type":[{"value":"2198-3844","type":"print"},{"value":"2198-3844","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,22]]},"assertion":[{"value":"2025-03-05","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-07-22","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e04109"}}