title: MET-COFEA: a liquid chromatography/mass spectrometry data processing platform for metabolite compound feature extraction and annotation.
abstract: In this paper, we present a novel liquid chromatography/mass spectrometry (LC/MS) data processing and analysis platform, MET-COFEA (METabolite COmpound Feature Extraction and Annotation). MET-COFEA detects and clusters chromatographic peak features for each metabolite compound by first comprehensively evaluating retention time and peak shape criteria and then annotating the associations between each peak's observed m/z value with the corresponding metabolite compound's molecular mass. MET-COFEA integrates a series of innovative approaches, including novel mass trace based extracted-ion chromatogram (EIC) extraction, continuous wavelet transform (CWT)-based peak detection, and compound-associated peak clustering and peak annotation algorithms. On the basis of the deduced neutral molecular mass and retention time, we have also developed a new alignment algorithm that uses compound-associated peak groups instead of individual peaks to align the same metabolite compound across samples from different electrospray ionization (ESI) modes, different instruments, even different experimental conditions. MET-COFEA has been systematically tested on a series of LC/MS profiles of mixed standards at different concentrations as well as real untargeted LC/MS plant metabolomics data. We compared the performances of MET-COFEA with the existing publicly available tools at LC/MS peak analysis level and demonstrated its excellent performance in this arena. MET-COFEA is freely available at http://bioinfo.noble.org/manuscript-support/met-cofea/.
authors.affiliation: Plant Biology Division, The Samuel Roberts Noble Foundation , 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States.
authors.forename: Wenchao
authors.initials: W
authors.lastname: Zhang
authors.forename: Junil
authors.initials: J
authors.lastname: Chang
authors.forename: Zhentian
authors.initials: Z
authors.lastname: Lei
authors.forename: David
authors.initials: D
authors.lastname: Huhman
authors.forename: Lloyd W
authors.initials: LW
authors.lastname: Sumner
authors.forename: Patrick X
authors.initials: PX
authors.lastname: Zhao
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D055432:Metabolomics / Q000379:methods*; D012984:Software