title: Comparative evaluation of eight software programs for alignment of gas chromatography-mass spectrometry chromatograms in metabolomics experiments.
abstract: Since retention times of compounds in GC-MS chromatograms always vary slightly from chromatogram to chromatogram, it is necessary to align chromatograms before comparing them in metabolomics experiments. Several software programs have been developed to automate this process. Here we report a comparative evaluation of the performance of eight programs using prepared samples of mixtures of chemicals, and an extract of tomato vines spiked with three concentrations of a mixture of alkanes. The programs included in the comparison were SpectConnect, MetaboliteDetector 2.01a, MetAlign 041012, MZmine 2.0, TagFinder 04, XCMS Online 1.21.01, MeltDB and GAVIN. Samples were analyzed by GC-MS, chromatograms were aligned using the selected programs, and the resulting data matrices were preprocessed and submitted to principal components analysis. In the first trial, SpectConnect, MetAlign and MetaboliteDetector correctly identified ≥90% of the true positives. In the second trial, MetAlign and MetaboliteDetector correctly identified 87% and 81% of the true positives, respectively. In addition, in both trials >90% of the peaks identified by MetAlign and MetaboliteDetector were true positives.
authors.affiliation: School of Life Science, Chongqing University, Chongqing 400044, China.
authors.forename: Weihuan
authors.initials: W
authors.lastname: Niu
authors.affiliation: Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3, Canada.
authors.forename: Elisa
authors.initials: E
authors.lastname: Knight
authors.affiliation: State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China.
authors.forename: Qingyou
authors.initials: Q
authors.lastname: Xia
authors.affiliation: Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3, Canada. Electronic address: bmcgarve@uwo.ca.
authors.forename: Brian D
authors.initials: BD
authors.lastname: McGarvey
mesh_terms: D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods*; D055432:Metabolomics / Q000379:methods*; D025341:Principal Component Analysis; D012984:Software
keywords: Gas chromatography–mass spectrometry (GC–MS); Metabolomics; Principal components analysis (PCA); Retention time alignment; Software comparison