{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T13:59:45Z","timestamp":1790949585843,"version":"4.1.0"},"reference-count":31,"publisher":"American Chemical Society (ACS)","issue":"10","license":[{"start":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T00:00:00Z","timestamp":1789862400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T00:00:00Z","timestamp":1789862400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T00:00:00Z","timestamp":1789862400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100023581","name":"National Science Foundation Graduate Research Fellowship Program","doi-asserted-by":"publisher","award":["2140004"],"award-info":[{"award-number":["2140004"]}],"id":[{"id":"10.13039\/100023581","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["U01 DK137097"],"award-info":[{"award-number":["U01 DK137097"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R24 GM141156"],"award-info":[{"award-number":["R24 GM141156"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2245300"],"award-info":[{"award-number":["2245300"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>One critical step in any targeted mass spectrometry experiment is selecting, from each protein of interest, a small number of peptides that respond well in the mass spectrometer and can serve as reliable proxies for protein quantification. Existing methods select target peptides either by relying on prior empirical measurements, limiting their applicability to previously observed peptides, or using machine learning to predict peptide behavior from sequence alone. However, current machine learning tools suffer from various limitations, including using detectability as an indirect proxy for intensity, relying on small training sets, or ignoring the precursor charge state. In this study, we introduce Bromo, a transformer-based deep learning model that ranks peptide precursors from a given protein by their relative response, taking charge state into account. Trained on millions of annotated peptide pairs derived from large-scale, publicly available data-independent acquisition mass spectrometry data, Bromo consistently outperforms existing sequence-based methods across diverse, independent data sets. Furthermore, we show that fine-tuning Bromo on experiment-specific data can account for differences in sample preparation, sample matrix, and instrument platform, all of which influence which peptides serve as optimal targets. This adaptability makes Bromo a practical tool for selecting target peptides for selected reaction monitoring and parallel reaction monitoring assay development across a wide range of experimental conditions.<\/jats:p>","DOI":"10.1021\/acs.jproteome.6c00457","type":"journal-article","created":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T15:02:16Z","timestamp":1789916536000},"page":"5469-5479","source":"Crossref","is-referenced-by-count":0,"title":["Prioritizing\nPeptides for Targeted Mass Spectrometry\nExperiments Using Deep Learning"],"prefix":"10.1021","volume":"25","author":[{"given":"Shreyash","family":"Sonthalia","sequence":"first","affiliation":[{"name":"University of Washington , , , ,","place":["Seattle, Washington, United States, 98195"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2261-3150","authenticated-orcid":true,"given":"Bo","family":"Wen","sequence":"additional","affiliation":[{"name":"University of Washington , , , ,","place":["Seattle, Washington, United States, 98195"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priank","family":"Dasgupta","sequence":"additional","affiliation":[{"name":"University of Washington , , , ,","place":["Seattle, Washington, United States, 98195"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0846-6126","authenticated-orcid":true,"given":"Chris","family":"Hsu","sequence":"additional","affiliation":[{"name":"University of Washington , , , ,","place":["Seattle, Washington, United States, 98195"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1853-0256","authenticated-orcid":true,"given":"Michael J.","family":"MacCoss","sequence":"additional","affiliation":[{"name":"University of Washington , , , ,","place":["Seattle, Washington, United States, 98195"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7283-4715","authenticated-orcid":true,"given":"William Stafford","family":"Noble","sequence":"additional","affiliation":[{"name":"University of Washington , , , ,","place":["Seattle, Washington, United States, 98195"]},{"name":"University of Washington , , , ,","place":["Seattle, Washington, United States, 98195"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,20]]},"reference":[{"issue":"12","key":"2026100208412773500_cit1","doi-asserted-by":"publisher","first-page":"6940","DOI":"10.1073\/pnas.0832254100","article-title":"Absolute quantification of proteins and phosphoproteins\nfrom cell lysates by tandem ms","volume":"100","author":"Gerber","year":"2003","journal-title":"Proc. Natl.\nAcad. Sci. U. S. A."},{"issue":"3","key":"2026100208412773500_cit2","doi-asserted-by":"publisher","first-page":"658","DOI":"10.1021\/pr034124x","article-title":"Evaluation of a\ncleavable stable isotope labeled synthetic peptide for absolute protein\nquantification using lc- ms\/ms","volume":"3","author":"Barnidge","year":"2004","journal-title":"J. Proteome\nRes."},{"issue":"6","key":"2026100208412773500_cit3","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1038\/nmeth.2015","article-title":"Selected reaction\nmonitoring\u2013based proteomics:\nworkflows, potential, pitfalls and future directions","volume":"9","author":"Picotti","year":"2012","journal-title":"Nat. Methods"},{"issue":"11","key":"2026100208412773500_cit4","doi-asserted-by":"publisher","first-page":"1475","DOI":"10.1074\/mcp.o112.020131","article-title":"Parallel reaction monitoring for high resolution and\nhigh mass accuracy quantitative, targeted proteomics","volume":"11","author":"Peterson","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"issue":"12","key":"2026100208412773500_cit5","doi-asserted-by":"publisher","first-page":"1709","DOI":"10.1074\/mcp.o112.019802","article-title":"Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer","volume":"11","author":"Gallien","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"2026100208412773500_cit6","doi-asserted-by":"publisher","first-page":"100165","DOI":"10.1016\/j.mcpro.2021.100165","article-title":"An introduction to advanced targeted\nacquisition methods","volume":"20","author":"van Bentum","year":"2021","journal-title":"Mol. Cell. Proteomics"},{"key":"2026100208412773500_cit7","doi-asserted-by":"publisher","first-page":"101506","DOI":"10.1016\/j.mcpro.2026.101506","article-title":"Development of highly\nmultiplex targeted proteomics assays in biofluids\nusing a nominal mass ion trap mass spectrometer","volume":"25","author":"Plubell","year":"2026","journal-title":"Mol. Cell. Proteomics"},{"issue":"3","key":"2026100208412773500_cit8","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1074\/mcp.m113.036095","article-title":"Targeted peptide measurements\nin biology and medicine: best practices for mass spectrometry-based\nassay development using a fit-for-purpose approach","volume":"13","author":"Carr","year":"2014","journal-title":"Mol. Cell. 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