{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T03:07:23Z","timestamp":1771470443223,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Comprehensive 2D gas chromatography-mass spectrometry is an established method for the analysis of complex mixtures in analytical chemistry and metabolomics. It produces large amounts of data that require semiautomatic, but preferably automatic handling. This involves the location of significant signals (peaks) and their matching and alignment across different measurements. To date, there exist only a few openly available algorithms for the retention time alignment of peaks originating from such experiments that scale well with increasing sample and peak numbers, while providing reliable alignment results.<\/jats:p>\n               <jats:p>Results: We describe BiPACE 2D, an automated algorithm for retention time alignment of peaks from 2D gas chromatography-mass spectrometry experiments and evaluate it on three previously published datasets against the mSPA, SWPA and Guineu algorithms. We also provide a fourth dataset from an experiment studying the H2 production of two different strains of Chlamydomonas reinhardtii that is available from the MetaboLights database together with the experimental protocol, peak-detection results and manually curated multiple peak alignment for future comparability with newly developed algorithms.<\/jats:p>\n               <jats:p>Availability and implementation: BiPACE 2D is contained in the freely available Maltcms framework, version 1.3, hosted at http:\/\/maltcms.sf.net, under the terms of the L-GPL v3 or Eclipse Open Source licenses. The software used for the evaluation along with the underlying datasets is available at the same location. The C.reinhardtii dataset is freely available at http:\/\/www.ebi.ac.uk\/metabolights\/MTBLS37.<\/jats:p>\n               <jats:p>Contact: nils.hoffmann@cebitec.uni-bielefeld.de or jens.stoye@uni-bielefeld.de<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt738","type":"journal-article","created":{"date-parts":[[2013,12,21]],"date-time":"2013-12-21T03:17:47Z","timestamp":1387595867000},"page":"988-995","source":"Crossref","is-referenced-by-count":16,"title":["BiPACE 2D\u2014graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry"],"prefix":"10.1093","volume":"30","author":[{"given":"Nils","family":"Hoffmann","sequence":"first","affiliation":[{"name":"1 Genome Informatics, Faculty of Technology and CeBiTec, 2Algae Biotechnology & Bioenergy, 3Faculty of Biology and CeBiTec, 4Proteomics and Metabolomics Research, Bielefeld University, 33501 Bielefeld, Germany"}]},{"given":"Mathias","family":"Wilhelm","sequence":"additional","affiliation":[{"name":"1 Genome Informatics, Faculty of Technology and CeBiTec, 2Algae Biotechnology & Bioenergy, 3Faculty of Biology and CeBiTec, 4Proteomics and Metabolomics Research, Bielefeld University, 33501 Bielefeld, Germany"}]},{"given":"Anja","family":"Doebbe","sequence":"additional","affiliation":[{"name":"1 Genome Informatics, Faculty of Technology and CeBiTec, 2Algae Biotechnology & Bioenergy, 3Faculty of Biology and CeBiTec, 4Proteomics and Metabolomics Research, Bielefeld University, 33501 Bielefeld, Germany"},{"name":"1 Genome Informatics, Faculty of Technology and CeBiTec, 2Algae Biotechnology & Bioenergy, 3Faculty of Biology and CeBiTec, 4Proteomics and Metabolomics Research, Bielefeld University, 33501 Bielefeld, Germany"}]},{"given":"Karsten","family":"Niehaus","sequence":"additional","affiliation":[{"name":"1 Genome Informatics, Faculty of Technology and CeBiTec, 2Algae Biotechnology & Bioenergy, 3Faculty of Biology and CeBiTec, 4Proteomics and Metabolomics Research, Bielefeld University, 33501 Bielefeld, Germany"},{"name":"1 Genome Informatics, Faculty of Technology and CeBiTec, 2Algae Biotechnology & Bioenergy, 3Faculty of Biology and CeBiTec, 4Proteomics and Metabolomics Research, Bielefeld University, 33501 Bielefeld, Germany"}]},{"given":"Jens","family":"Stoye","sequence":"additional","affiliation":[{"name":"1 Genome Informatics, Faculty of Technology and CeBiTec, 2Algae Biotechnology & Bioenergy, 3Faculty of Biology and CeBiTec, 4Proteomics and Metabolomics Research, Bielefeld University, 33501 Bielefeld, Germany"}]}],"member":"286","published-online":{"date-parts":[[2013,12,20]]},"reference":[{"key":"2023012710455352500_btt738-B1","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/j.chroma.2007.10.041","article-title":"Quantification in comprehensive two-dimensional gas chromatography and a model of quantification based on selected summed modulated peaks","volume":"1184","author":"Amador-Mu\u00f1oz","year":"2008","journal-title":"J. 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