{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T16:40:23Z","timestamp":1762101623244},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":691,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Developing liquid chromatography tandem mass spectrometry (LC-MS\/MS) analyses of (bio)chemicals is both time consuming and challenging, largely because of the large number of LC and MS instrument parameters that need to be optimized. This bottleneck significantly impedes our ability to establish new (bio)analytical methods in fields such as pharmacology, metabolomics and pesticide research. We report the development of a multi-platform, user-friendly software tool MUSCLE (multi-platform unbiased optimization of spectrometry via closed-loop experimentation) for the robust and fully automated multi-objective optimization of targeted LC-MS\/MS analysis. MUSCLE shortened the analysis times and increased the analytical sensitivities of targeted metabolite analysis, which was demonstrated on two different manufacturer\u2019s LC-MS\/MS instruments.<\/jats:p>\n               <jats:p>Availability and implementation: Available at http:\/\/www.muscleproject.org.<\/jats:p>\n               <jats:p>Contact: \u00a0info@muscleproject.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu740","type":"journal-article","created":{"date-parts":[[2014,11,12]],"date-time":"2014-11-12T04:44:24Z","timestamp":1415767464000},"page":"975-977","source":"Crossref","is-referenced-by-count":19,"title":["MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS\/MS analysis"],"prefix":"10.1093","volume":"31","author":[{"given":"James","family":"Bradbury","sequence":"first","affiliation":[{"name":"1 School of Computer Science and 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, 3Manchester Institute of Biotechnology, 4School of Chemistry and 5School of Computer Science, The University of Manchester, Manchester M13 9JD, UK"}]},{"given":"Gr\u00e9gory","family":"Genta-Jouve","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, 3Manchester Institute of Biotechnology, 4School of Chemistry and 5School of Computer Science, The University of Manchester, Manchester M13 9JD, UK"}]},{"given":"J. William","family":"Allwood","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, 3Manchester Institute of Biotechnology, 4School of Chemistry and 5School of Computer Science, The University of Manchester, Manchester M13 9JD, UK"}]},{"given":"Warwick B.","family":"Dunn","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, 3Manchester Institute of Biotechnology, 4School of Chemistry and 5School of Computer Science, The University of Manchester, Manchester M13 9JD, UK"}]},{"given":"Royston","family":"Goodacre","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, 3Manchester Institute of Biotechnology, 4School of Chemistry and 5School of Computer Science, The University of Manchester, Manchester M13 9JD, UK"},{"name":"1 School of Computer Science and 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, 3Manchester Institute of Biotechnology, 4School of Chemistry and 5School of Computer Science, The University of Manchester, Manchester M13 9JD, UK"}]},{"given":"Joshua D.","family":"Knowles","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, 3Manchester Institute of Biotechnology, 4School of Chemistry and 5School of Computer Science, The University of Manchester, Manchester M13 9JD, UK"}]},{"given":"Shan","family":"He","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, 3Manchester Institute of Biotechnology, 4School of Chemistry and 5School of Computer Science, The University of Manchester, Manchester M13 9JD, UK"}]},{"given":"Mark R.","family":"Viant","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK, 3Manchester Institute of Biotechnology, 4School of Chemistry and 5School of Computer Science, The University of Manchester, Manchester M13 9JD, UK"}]}],"member":"286","published-online":{"date-parts":[[2014,11,11]]},"reference":[{"key":"2023020116175459400_btu740-B1","first-page":"283","article-title":"PESA-II: region-based selection in evolutionary multiobjective optimization","volume-title":"Proceedings of the Genetic and Evolutionary Computation Conference, San Francisco - July 2001","author":"Corne","year":"2001"},{"key":"2023020116175459400_btu740-B2","first-page":"760","article-title":"jMetal: A Java framework for multi-objective optimization","volume-title":"Advances in Engineering Software","author":"Durillo","year":"2011"},{"key":"2023020116175459400_btu740-B3","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1109\/MCI.2009.933095","article-title":"Closed-loop evolutionary multiobjective optimization","volume":"4","author":"Knowles","year":"2009","journal-title":"IEEE Comput. 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