{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T23:15:20Z","timestamp":1777418120788,"version":"3.51.4"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Isotope trace (IT) detection is a fundamental step for liquid or gas chromatography mass spectrometry (XC-MS) data analysis that faces a multitude of technical challenges on complex samples. The Kalman filter (KF) application to IT detection addresses some of these challenges; it discriminates closely eluting ITs in the m\/z dimension, flexibly handles heteroscedastic m\/z variances and does not bin the m\/z axis. Yet, the behavior of this KF application has not been fully characterized, as no cost-free open-source implementation exists and incomplete evaluation standards for IT detection persist.<\/jats:p>\n               <jats:p>Results: Massifquant is an open-source solution for KF IT detection that has been subjected to novel and rigorous methods of performance evaluation. The presented evaluation with accompanying annotations and optimization guide sets a new standard for comparative IT detection. Compared with centWave, matchedFilter and MZMine2\u2014alternative IT detection engines\u2014Massifquant detected more true ITs in a real LC-MS complex sample, especially low-intensity ITs. It also offers competitive specificity and equally effective quantitation accuracy.<\/jats:p>\n               <jats:p>Availability and implementation: Massifquant is integrated into XCMS with GPL license \u2265 2.0 and hosted by Bioconductor: http:\/\/bioconductor.org . Annotation data are archived at http:\/\/hdl.lib.byu.edu\/1877\/3232 . Parameter optimization code and documentation is hosted at https:\/\/github.com\/topherconley\/optimize-it .<\/jats:p>\n               <jats:p>Contact: \u00a0cjconley@ucdavis.edu or jtprince@chem.byu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu359","type":"journal-article","created":{"date-parts":[[2014,5,29]],"date-time":"2014-05-29T03:33:46Z","timestamp":1401334426000},"page":"2636-2643","source":"Crossref","is-referenced-by-count":42,"title":["Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection"],"prefix":"10.1093","volume":"30","author":[{"given":"Christopher J.","family":"Conley","sequence":"first","affiliation":[{"name":"1 Department of Statistics, University of California Davis, Davis, CA 95616, 2 Department of Computer Science, Brigham Young University, Provo, UT 84606, USA, 3 Department of Analytical Chemistry, Stockholm University, SE-106 91, Stockholm, Sweden, 4 Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84606, 5 Department of Chemistry, 6 Department of Molecular Biology and 7 Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rob","family":"Smith","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, University of California Davis, Davis, CA 95616, 2 Department of Computer Science, Brigham Young University, Provo, UT 84606, USA, 3 Department of Analytical Chemistry, Stockholm University, SE-106 91, Stockholm, Sweden, 4 Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84606, 5 Department of Chemistry, 6 Department of Molecular Biology and 7 Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ralf J. 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