{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T00:22:56Z","timestamp":1772151776421,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,11,7]],"date-time":"2016-11-07T00:00:00Z","timestamp":1478476800000},"content-version":"vor","delay-in-days":882,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The use of liquid chromatography coupled to mass spectrometry has enabled the high-throughput profiling of the metabolite composition of biological samples. However, the large amount of data obtained can be difficult to analyse and often requires computational processing to understand which metabolites are present in a sample. This article looks at the dual problem of annotating peaks in a sample with a metabolite, together with putatively annotating whether a metabolite is present in the sample. The starting point of the approach is a Bayesian clustering of peaks into groups, each corresponding to putative adducts and isotopes of a single metabolite.<\/jats:p><jats:p>Results: The Bayesian modelling introduced here combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The results inherently contain a quantitative estimate of confidence in the peak annotations and allow an accurate trade-off between precision and recall. Extensive validation experiments using authentic chemical standards show that this system is able to produce more accurate putative identifications than other state-of-the-art systems, while at the same time giving a probabilistic measure of confidence in the annotations.<\/jats:p><jats:p>Availability and implementation : The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download at http:\/\/mzmatch.sourceforge.net\/ .<\/jats:p><jats:p>Contact: \u00a0Ronan.Daly@glasgow.ac.uk<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu370","type":"journal-article","created":{"date-parts":[[2014,6,11]],"date-time":"2014-06-11T03:13:01Z","timestamp":1402456381000},"page":"2764-2771","source":"Crossref","is-referenced-by-count":67,"title":["MetAssign: probabilistic annotation of metabolites from LC\u2013MS data using a Bayesian clustering approach"],"prefix":"10.1093","volume":"30","author":[{"given":"R\u00f3n\u00e1n","family":"Daly","sequence":"first","affiliation":[{"name":"1 School of Computing Science, University of Glasgow, Glasgow, 2 Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester and 3 Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK"}]},{"given":"Simon","family":"Rogers","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, University of Glasgow, Glasgow, 2 Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester and 3 Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK"}]},{"given":"Joe","family":"Wandy","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, University of Glasgow, Glasgow, 2 Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester and 3 Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK"}]},{"given":"Andris","family":"Jankevics","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, University of Glasgow, Glasgow, 2 Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester and 3 Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK"}]},{"given":"Karl E. V.","family":"Burgess","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, University of Glasgow, Glasgow, 2 Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester and 3 Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK"}]},{"given":"Rainer","family":"Breitling","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, University of Glasgow, Glasgow, 2 Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester and 3 Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK"}]}],"member":"286","published-online":{"date-parts":[[2014,6,9]]},"reference":[{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"6382","DOI":"10.1021\/ac800795f","article-title":"XCMS 2 : processing tandem mass spectrometry data for metabolite identification and structural characterization","volume":"80","author":"Benton","year":"2008","journal-title":"Anal. Chem."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1093\/bioinformatics\/btn603","article-title":"SIRIUS: decomposing isotope patterns for metabolite identification","volume":"25","author":"B\u00f6cker","year":"2009","journal-title":"Bioinformatics"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1093\/bioinformatics\/btr079","article-title":"Automated workflows for accurate mass-based putative metabolite identification in LC\/MS-derived metabolomic datasets","volume":"27","author":"Brown","year":"2011","journal-title":"Bioinformatics"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"8703","DOI":"10.1021\/ac2021823","article-title":"Toward global metabolomics analysis with hydrophilic interaction liquid chromatography-mass spectrometry: improved metabolite identification by retention time prediction","volume":"83","author":"Creek","year":"2011","journal-title":"Anal. Chem."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1093\/bioinformatics\/bts069","article-title":"Ideom: an Excel interface for analysis of LC-MS-based metabolomics data","volume":"28","author":"Creek","year":"2012","journal-title":"Bioinformatics"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1007\/s11306-012-0434-4","article-title":"Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics","volume":"9","author":"Dunn","year":"2012","journal-title":"Metabolomics"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1002\/jms.1777","article-title":"MassBank: a public repository for sharing mass spectral data for life sciences","volume":"45","author":"Horai","year":"2010","journal-title":"J. Mass Spectrom."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"1766","DOI":"10.1021\/ac902361f","article-title":"A statistically rigorous test for the identification of parent-fragment pairs in LC-MS datasets","volume":"82","author":"Ipsen","year":"2010","journal-title":"Anal. Chem."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"7319","DOI":"10.1021\/ac101278x","article-title":"Construction of confidence regions for isotopic abundance patterns in LC\/MS data sets for rigorous determination of molecular formulas","volume":"82","author":"Ipsen","year":"2010","journal-title":"Anal. Chem."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.aca.2008.04.043","article-title":"Interferences and contaminants encountered in modern mass spectrometry","volume":"627","author":"Keller","year":"2008","journal-title":"Anal. Chim. Acta."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1186\/1471-2105-7-234","article-title":"Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm","volume":"7","author":"Kind","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1021\/ac202450g","article-title":"CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography\/mass spectrometry data sets","volume":"84","author":"Kuhl","year":"2012","journal-title":"Anal. Chem."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1007\/s11306-013-0539-4","article-title":"Precursor mass prediction by clustering ionization products in LC-MS-based metabolomics","volume":"9","author":"Lee","year":"2013","journal-title":"Metabolomics"},{"key":"2023041303362362300_","first-page":"554","article-title":"The infinite Gaussian mixture model","volume-title":"Advances in Neural Information Processing Systems 12","author":"Rasmussen","year":"2000"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"2461","DOI":"10.1002\/rcm.6364","article-title":"Substructure-based annotation of high-resolution multistage MS n spectral trees","volume":"26","author":"Ridder","year":"2012","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1093\/bioinformatics\/btn642","article-title":"Probabilistic assignment of formulas to mass peaks in metabolomics experiments","volume":"25","author":"Rogers","year":"2009","journal-title":"Bioinformatics"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"5524","DOI":"10.1021\/ac2034216","article-title":"Metabolite identification using automated comparison of high-resolution multistage mass spectral trees","volume":"84","author":"Rojas-Cherto","year":"2012","journal-title":"Anal. Chem."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.4155\/bio.09.146","article-title":"A simple data reduction method for high resolution LC-MS data in metabolomics","volume":"1","author":"Scheltema","year":"2009","journal-title":"Bioanalysis"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"2786","DOI":"10.1021\/ac2000994","article-title":"PeakML\/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis","volume":"83","author":"Scheltema","year":"2011","journal-title":"Anal. Chem."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"1336","DOI":"10.1093\/bioinformatics\/btu019","article-title":"ProbMetab: an R package for Bayesian probabilistic annotation of LC\u2013MS-based metabolomics","volume":"30","author":"Silva","year":"2014","journal-title":"Bioinformatics"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1097\/01.ftd.0000179845.53213.39","article-title":"METLIN: a metabolite mass spectral database","volume":"27","author":"Smith","year":"2005","journal-title":"Ther. Drug Monit."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1016\/j.jasms.2007.05.016","article-title":"Efficient calculation of exact mass isotopic distributions","volume":"18","author":"Snider","year":"2007","journal-title":"J Am. Soc. Mass Spectrom."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1007\/s11306-007-0082-2","article-title":"Proposed minimum reporting standards for chemical analysis","volume":"3","author":"Sumner","year":"2007","journal-title":"Metabolomics"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.chemolab.2010.04.010","article-title":"MI-Pack: increased confidence of metabolite identification in mass spectra by integrating accurate masses and metabolic pathways","volume":"104","author":"Weber","year":"2010","journal-title":"Chem. Intell. Lab. Syst."},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1186\/1471-2105-11-148","article-title":"In silico fragmentation for computer assisted identification of metabolite mass spectra","volume":"11","author":"Wolf","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023041303362362300_","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1039\/C1MB05350G","article-title":"LC-MS-based metabolomics","volume":"8","author":"Zhou","year":"2012","journal-title":"Mol. Biosystems"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/19\/2764\/49872410\/bioinformatics_30_19_2764.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/19\/2764\/49872410\/bioinformatics_30_19_2764.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,14]],"date-time":"2023-07-14T05:37:02Z","timestamp":1689313022000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/19\/2764\/2422184"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,6,9]]},"references-count":26,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2014,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu370","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,10]]},"published":{"date-parts":[[2014,6,9]]}}}