{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:17Z","timestamp":1772138057770,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T00:00:00Z","timestamp":1674604800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM121818"],"award-info":[{"award-number":["R01GM121818"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory"},{"name":"Battelle for the U.S. Department of Energy"},{"name":"Linus Pauling Distinguished Postdoctoral Fellowship"},{"DOI":"10.13039\/100011661","name":"Pacific Northwest National Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011661","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Battelle Memorial Institute for the United States Department of Energy","award":["DE-AC06-76RLO"],"award-info":[{"award-number":["DE-AC06-76RLO"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,2,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Interpretation of newly acquired mass spectrometry data can be improved by identifying, from an online repository, previous mass spectrometry runs that resemble the new data. However, this retrieval task requires computing the similarity between an arbitrary pair of mass spectrometry runs. This is particularly challenging for runs acquired using different experimental protocols.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose a method, MS1Connect, that calculates the similarity between a pair of runs by examining only the intact peptide (MS1) scans, and we show evidence that the MS1Connect score is accurate. Specifically, we show that MS1Connect outperforms several baseline methods on the task of predicting the species from which a given proteomics sample originated. In addition, we show that MS1Connect scores are highly correlated with similarities computed from fragment (MS2) scans, even though these data are not used by MS1Connect.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The MS1Connect software is available at https:\/\/github.com\/bmx8177\/MS1Connect.<\/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\/btad058","type":"journal-article","created":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T16:35:39Z","timestamp":1674578139000},"source":"Crossref","is-referenced-by-count":1,"title":["MS1Connect: a mass spectrometry run similarity measure"],"prefix":"10.1093","volume":"39","author":[{"given":"Andy","family":"Lin","sequence":"first","affiliation":[{"name":"Chemical and Biological Signatures, Pacific Northwest National Laboratory , Richland, WA 99354, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brooke L","family":"Deatherage Kaiser","sequence":"additional","affiliation":[{"name":"Chemical and Biological Signatures, Pacific Northwest National Laboratory , Richland, WA 99354, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janine R","family":"Hutchison","sequence":"additional","affiliation":[{"name":"Chemical and Biological Signatures, Pacific Northwest National Laboratory , Richland, WA 99354, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey A","family":"Bilmes","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, University of Washington , Seattle, WA 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7283-4715","authenticated-orcid":false,"given":"William Stafford","family":"Noble","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA 98195, USA"},{"name":"Paul G. 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