{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T01:28:28Z","timestamp":1767922108826,"version":"3.49.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1415,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Stable isotope-labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography\u2013mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here, we describe mzMatch\u2013ISO, a new extension to the metabolomics analysis pipeline mzMatch.R.<\/jats:p>\n               <jats:p>Results: Targeted and untargeted isotope profiling using mzMatch\u2013ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono-isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab-delimited file. We demonstrate the power and versatility of mzMatch\u2013ISO by analysing a 13C-labelled metabolome dataset from trypanosomal parasites.<\/jats:p>\n               <jats:p>Availability: mzMatch.R and mzMatch\u2013ISO are available free of charge from http:\/\/mzmatch.sourceforge.net and can be used on Linux and Windows platforms running the latest version of R.<\/jats:p>\n               <jats:p>Contact: \u00a0rainer.breitling@manchester.ac.uk \u00a0.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts674","type":"journal-article","created":{"date-parts":[[2012,11,18]],"date-time":"2012-11-18T02:50:02Z","timestamp":1353207002000},"page":"281-283","source":"Crossref","is-referenced-by-count":93,"title":["mzMatch\u2013ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data"],"prefix":"10.1093","volume":"29","author":[{"given":"Achuthanunni","family":"Chokkathukalam","sequence":"first","affiliation":[{"name":"1 College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, 4Wellcome Trust Centre for Molecular Parasitology, College of Medical Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK and 5Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"}]},{"given":"Andris","family":"Jankevics","sequence":"additional","affiliation":[{"name":"1 College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, 4Wellcome Trust Centre for Molecular Parasitology, College of Medical Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK and 5Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"},{"name":"1 College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, 4Wellcome Trust Centre for Molecular Parasitology, College of Medical Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK and 5Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"}]},{"given":"Darren J.","family":"Creek","sequence":"additional","affiliation":[{"name":"1 College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, 4Wellcome Trust Centre for Molecular Parasitology, College of Medical Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK and 5Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"},{"name":"1 College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, 4Wellcome Trust Centre for Molecular Parasitology, College of Medical Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK and 5Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"}]},{"given":"Fiona","family":"Achcar","sequence":"additional","affiliation":[{"name":"1 College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, 4Wellcome Trust Centre for Molecular Parasitology, College of Medical Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK and 5Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"}]},{"given":"Michael P.","family":"Barrett","sequence":"additional","affiliation":[{"name":"1 College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, 4Wellcome Trust Centre for Molecular Parasitology, College of Medical Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK and 5Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"}]},{"given":"Rainer","family":"Breitling","sequence":"additional","affiliation":[{"name":"1 College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, 4Wellcome Trust Centre for Molecular Parasitology, College of Medical Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK and 5Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"},{"name":"1 College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, 4Wellcome Trust Centre for Molecular Parasitology, College of Medical Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK and 5Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"},{"name":"1 College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands, 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, 4Wellcome Trust Centre for Molecular Parasitology, College of Medical Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK and 5Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"}]}],"member":"286","published-online":{"date-parts":[[2012,11,17]]},"reference":[{"key":"2023012810220575000_bts674-B1","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1007\/s11306-006-0029-z","article-title":"Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data","volume":"2","author":"Breitling","year":"2006","journal-title":"Metabolomics"},{"key":"2023012810220575000_bts674-B2","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1093\/bioinformatics\/bts012","article-title":"MetExtract: a new software tool for the 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