MET-COFEA: A Liquid Chromatography/Mass Spectrometry Data Processing Platform for Metabolite Compound Feature Extraction and Annotation

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• 作者：Wenchao Zhang ; Junil Chang ; Zhentian Lei ; David Huhman ; Lloyd W. Sumner ; Patrick X. Zhao
• 刊名：Analytical Chemistry
• 出版年：2014
• 出版时间：July 1, 2014
• 年：2014
• 卷：86
• 期：13
• 页码：6245-6253
• 全文大小：493K
• ISSN：1520-6882

文摘

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鈥檚 observed m/z value with the corresponding metabolite compound鈥檚 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/.