title: MetPP: a computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics.
abstract: BACKGROUND
  Due to the high complexity of metabolome, the comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC×GC-TOF MS) is considered as a powerful analytical platform for metabolomics study. However, the applications of GC×GC-TOF MS in metabolomics are not popular owing to the lack of bioinformatics system for data analysis.
  
  
  RESULTS
  We developed a computational platform entitled metabolomics profiling pipeline (MetPP) for analysis of metabolomics data acquired on a GC×GC-TOF MS system. MetPP can process peak filtering and merging, retention index matching, peak list alignment, normalization, statistical significance tests and pattern recognition, using the peak lists deconvoluted from the instrument data as its input. The performance of MetPP software was tested with two sets of experimental data acquired in a spike-in experiment and a biomarker discovery experiment, respectively. MetPP not only correctly aligned the spiked-in metabolite standards from the experimental data, but also correctly recognized their concentration difference between sample groups. For analysis of the biomarker discovery data, 15 metabolites were recognized with significant concentration difference between the sample groups and these results agree with the literature results of histological analysis, demonstrating the effectiveness of applying MetPP software for disease biomarker discovery.
  
  
  BACKGROUND
  The source code of MetPP is available at http://metaopen.sourceforge.net
  
  
  BACKGROUND
  xiang.zhang@louisville.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Chemistry, Department of Bioinformatics and Biostatistics, Department of Pharmacology & Toxicology, Alcohol Research Center, Department of Medicine, University of Louisville and Robley Rex Louisville VAMC, Louisville, KY 40292, USA.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Wei
authors.forename: Xue
authors.initials: X
authors.lastname: Shi
authors.forename: Imhoi
authors.initials: I
authors.lastname: Koo
authors.forename: Seongho
authors.initials: S
authors.lastname: Kim
authors.forename: Robin H
authors.initials: RH
authors.lastname: Schmidt
authors.forename: Gavin E
authors.initials: GE
authors.lastname: Arteel
authors.forename: Walter H
authors.initials: WH
authors.lastname: Watson
authors.forename: Craig
authors.initials: C
authors.lastname: McClain
authors.forename: Xiang
authors.initials: X
authors.lastname: Zhang
mesh_terms: D000818:Animals; D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods*; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D051379:Mice; D012984:Software