{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T10:07:17Z","timestamp":1774001237381,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":425,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Systematic bias in mass measurement adversely affects data quality and negates the advantages of high precision instruments.<\/jats:p>\n               <jats:p>Results: We introduce the mzRefinery tool for calibration of mass spectrometry data files. Using confident peptide spectrum matches, three different calibration methods are explored and the optimal transform function is chosen. After calibration, systematic bias is removed and the mass measurement errors are centered at 0\u2009ppm. Because it is part of the ProteoWizard package, mzRefinery can read and write a wide variety of file formats.<\/jats:p>\n               <jats:p>Availability and implementation: The mzRefinery tool is part of msConvert, available with the ProteoWizard open source package at http:\/\/proteowizard.sourceforge.net\/<\/jats:p>\n               <jats:p>Contact: \u00a0samuel.payne@pnnl.gov<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv437","type":"journal-article","created":{"date-parts":[[2015,8,5]],"date-time":"2015-08-05T00:18:55Z","timestamp":1438733935000},"page":"3838-3840","source":"Crossref","is-referenced-by-count":51,"title":["Correcting systematic bias and instrument measurement drift with mzRefinery"],"prefix":"10.1093","volume":"31","author":[{"given":"Bryson C.","family":"Gibbons","sequence":"first","affiliation":[{"name":"1 Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99354 and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew C.","family":"Chambers","sequence":"additional","affiliation":[{"name":"2 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew E.","family":"Monroe","sequence":"additional","affiliation":[{"name":"1 Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99354 and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David L.","family":"Tabb","sequence":"additional","affiliation":[{"name":"2 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel H.","family":"Payne","sequence":"additional","affiliation":[{"name":"1 Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99354 and"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,8,4]]},"reference":[{"key":"2023020202423905000_btv437-B1","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/nbt.2377","article-title":"A cross-platform toolkit for mass spectrometry and proteomics","volume":"30","author":"Chambers","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"2023020202423905000_btv437-B2","doi-asserted-by":"crossref","first-page":"1383","DOI":"10.1002\/rcm.1060","article-title":"Flow injection of the lock mass standard for accurate mass measurement in electrospray ionization time-of-flight mass spectrometry coupled with liquid chromatography","volume":"17","author":"Charles","year":"2003","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"2023020202423905000_btv437-B3","doi-asserted-by":"crossref","first-page":"1373","DOI":"10.1007\/s13361-011-0142-8","article-title":"Software lock mass by two-dimensional minimization of peptide mass errors","volume":"22","author":"Cox","year":"2011","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2023020202423905000_btv437-B4","doi-asserted-by":"crossref","first-page":"2534","DOI":"10.1093\/bioinformatics\/btn323","article-title":"ProteoWizard: open source software for rapid proteomics tools development","volume":"24","author":"Kessner","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020202423905000_btv437-B5","doi-asserted-by":"crossref","first-page":"2010","DOI":"10.1074\/mcp.T500030-MCP200","article-title":"Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap","volume":"4","author":"Olsen","year":"2005","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020202423905000_btv437-B6","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1074\/mcp.M900217-MCP200","article-title":"DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets","volume":"9","author":"Petyuk","year":"2010","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020202423905000_btv437-B7","doi-asserted-by":"crossref","first-page":"9344","DOI":"10.1021\/ac201867h","article-title":"Improving proteomics mass accuracy by dynamic offline lock mass","volume":"83","author":"Zhang","year":"2011","journal-title":"Anal. 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