title: BiPACE 2D--graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry.
abstract: BACKGROUND
  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.
  
  
  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.
  
  
  METHODS
  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.
authors.affiliation: Genome Informatics, Faculty of Technology and CeBiTec, Algae Biotechnology & Bioenergy, Faculty of Biology and CeBiTec, Proteomics and Metabolomics Research, Bielefeld University, 33501 Bielefeld, Germany.
authors.forename: Nils
authors.initials: N
authors.lastname: Hoffmann
authors.forename: Mathias
authors.initials: M
authors.lastname: Wilhelm
authors.forename: Anja
authors.initials: A
authors.lastname: Doebbe
authors.forename: Karsten
authors.initials: K
authors.lastname: Niehaus
authors.forename: Jens
authors.initials: J
authors.lastname: Stoye
mesh_terms: D000465:Algorithms; D000818:Animals; D057205:Automation, Laboratory; D016825:Chlamydomonas reinhardtii / Q000737:chemistry; D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods*; D055432:Metabolomics / Q000379:methods*; D012984:Software