Comparative evaluation of eight software programs for alignment of gas chromatography-mass spectrometry chromatograms in metabolomics experiments.

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.

[1]  W. Dunn,et al.  Measuring the metabolome: current analytical technologies. , 2005, The Analyst.

[2]  R. Dixon,et al.  Plant metabolomics: large-scale phytochemistry in the functional genomics era. , 2003, Phytochemistry.

[3]  Dietmar Schomburg,et al.  MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. , 2009, Analytical chemistry.

[4]  V. Shulaev,et al.  Metabolomics for plant stress response. , 2008, Physiologia plantarum.

[5]  Sonja Peters,et al.  Parameter selection for peak alignment in chromatographic sample profiling: objective quality indicators and use of control samples , 2009, Analytical and bioanalytical chemistry.

[6]  Joachim Kopka,et al.  TagFinder: preprocessing software for the fingerprinting and the profiling of gas chromatography-mass spectrometry based metabolome analyses. , 2012, Methods in molecular biology.

[7]  U. Roessner,et al.  Sampling and Sample Preparation , 2006 .

[8]  R. Abagyan,et al.  XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. , 2006, Analytical chemistry.

[9]  Steffen Neumann,et al.  Highly sensitive feature detection for high resolution LC/MS , 2008, BMC Bioinformatics.

[10]  Dirk Inzé,et al.  Plant cell factories in the post-genomic era: new ways to produce designer secondary metabolites. , 2004, Trends in plant science.

[11]  Serge Rudaz,et al.  UPLC-TOF-MS for plant metabolomics: a sequential approach for wound marker analysis in Arabidopsis thaliana. , 2008, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[12]  Jens Stoye,et al.  MeltDB: a software platform for the analysis and integration of metabolomics experiment data , 2008, Bioinform..

[13]  Ute Roessner,et al.  Plant metabolomics reveals conserved and divergent metabolic responses to salinity. , 2007, Physiologia plantarum.

[14]  Kishore K. Pasikanti,et al.  Gas chromatography/mass spectrometry in metabolic profiling of biological fluids. , 2008, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[15]  G. Siuzdak,et al.  XCMS Online: a web-based platform to process untargeted metabolomic data. , 2012, Analytical chemistry.

[16]  O. Fiehn.  Metabolomics – the link between genotypes and phenotypes , 2004, Plant Molecular Biology.

[17]  Mark P. Styczynski,et al.  Systematic identification of conserved metabolites in GC/MS data for metabolomics and biomarker discovery. , 2007, Analytical chemistry.

[18]  D. Kell,et al.  Comparative evaluation of software for deconvolution of metabolomics data based on GC-TOF-MS , 2007 .

[19]  S. Stein.  An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data , 1999 .

[20]  Robert C. Bolles,et al.  Random sample consensus: a paradigm for model fitting with applications to image analysis and automated cartography , 1981, CACM.

[21]  Ian D Wilson,et al.  Analytical strategies in metabonomics. , 2007, Journal of proteome research.

[22]  B. Hammock,et al.  Mass spectrometry-based metabolomics. , 2007, Mass spectrometry reviews.

[23]  J. Selbig,et al.  Metabolite profile analysis: from raw data to regression and classification. , 2007, Physiologia plantarum.

[24]  Chun Wei Yap,et al.  Comparative evaluation of software for retention time alignment of gas chromatography/time-of-flight mass spectrometry-based metabonomic data. , 2010, Journal of chromatography. A.

[25]  Alexander Erban,et al.  TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS)-based metabolite profiling experiments , 2008, Bioinform..

[26]  A. Smilde,et al.  Fusion of mass spectrometry-based metabolomics data. , 2005, Analytical chemistry.

[27]  A. Kushalappa,et al.  Mass Spectrometry Based Metabolomics to Identify Potential Biomarkers for Resistance in Barley against Fusarium Head Blight (Fusarium graminearum) , 2011, Journal of Chemical Ecology.

[28]  Royston Goodacre,et al.  Metabolomics: Current technologies and future trends , 2006, Proteomics.

[29]  C. Lim,et al.  Current developments in LC-MS for pharmaceutical analysis. , 2002, Biological & pharmaceutical bulletin.

[30]  Alexander Goesmann,et al.  MSEA: metabolite set enrichment analysis in the MeltDB metabolomics software platform: metabolic profiling of Corynebacterium glutamicum as an example , 2011, Metabolomics.

[31]  Matej Oresic,et al.  MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data , 2010, BMC Bioinformatics.

[32]  Arjen Lommen,et al.  MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. , 2009, Analytical chemistry.

[33]  Jacob G. Bundy,et al.  A software complement to AMDIS for processing GC-MS metabolomic data. , 2011, Analytical biochemistry.

[34]  R. A. van den Berg,et al.  Centering, scaling, and transformations: improving the biological information content of metabolomics data , 2006, BMC Genomics.

[35]  D. Goodenowe,et al.  Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry. , 2002, Omics : a journal of integrative biology.

[36]  Alexander Goesmann,et al.  MeltDB 2.0–advances of the metabolomics software system , 2013, Bioinform..

[37]  Arjen Lommen,et al.  MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware , 2011, Metabolomics.

[38]  Steffen Neumann,et al.  Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements , 2008, BMC Bioinformatics.

[39]  R. Powers.  NMR metabolomics and drug discovery , 2009, Magnetic resonance in chemistry : MRC.