{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T01:20:43Z","timestamp":1767921643787,"version":"3.49.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2018,8,20]],"date-time":"2018-08-20T00:00:00Z","timestamp":1534723200000},"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\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["5R01GM086688"],"award-info":[{"award-number":["5R01GM086688"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["5U19AI107775"],"award-info":[{"award-number":["5U19AI107775"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Peptides crosslinked with cleavable chemical crosslinkers are identified with mass spectrometry by independent database search of spectra associated with the two linked peptides. A major challenge is to combine together the evidence of the two peptides into an overall assessment of the two-peptide crosslink.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we describe software that models crosslink specific information to automatically validate XL-MS cleavable peptide crosslinks. Using a dataset of crosslinked protein mixtures, we demonstrate that it computes accurate and highly discriminating probabilities, enabling as many as 75% more identifications than was previously possible using only search scores and a predictable false discovery rate.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>XLinkProphet software is freely available on the web at http:\/\/brucelab.gs.washington.edu.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty720","type":"journal-article","created":{"date-parts":[[2018,8,17]],"date-time":"2018-08-17T19:34:40Z","timestamp":1534534480000},"page":"895-897","source":"Crossref","is-referenced-by-count":29,"title":["Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks"],"prefix":"10.1093","volume":"35","author":[{"given":"Andrew","family":"Keller","sequence":"first","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, WA, USA"}]},{"given":"Juan D","family":"Chavez","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, WA, USA"}]},{"given":"James E","family":"Bruce","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, WA, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,8,20]]},"reference":[{"key":"2023013107251520000_bty720-B1","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1016\/j.chembiol.2016.05.012","article-title":"In vivo conformational dynamics of Hsp90 and its interactors","volume":"23","author":"Chavez","year":"2016","journal-title":"Cell Chem. 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