XCMS:  Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification

Colin A. Smith, Elizabeth J. Want, Grace O'Maille, Ruben Abagyan, and Gary Siuzdak*
The Scripps Center for Mass Spectrometry and Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC-007, La Jolla, California 92037
Anal. Chem., 2006, 78 (3), pp 779–787
DOI: 10.1021/ac051437y
Publication Date (Web): January 7, 2006
Copyright © 2006 American Chemical Society
*

 To whom correspondence should be addressed. E-mail:  siuzdak@scripps.edu.

Abstract

Metabolite profiling in biomarker discovery, enzyme substrate assignment, drug activity/specificity determination, and basic metabolic research requires new data preprocessing approaches to correlate specific metabolites to their biological origin. Here we introduce an LC/MS-based data analysis approach, XCMS, which incorporates novel nonlinear retention time alignment, matched filtration, peak detection, and peak matching. Without using internal standards, the method dynamically identifies hundreds of endogenous metabolites for use as standards, calculating a nonlinear retention time correction profile for each sample. Following retention time correction, the relative metabolite ion intensities are directly compared to identify changes in specific endogenous metabolites, such as potential biomarkers. The software is demonstrated using data sets from a previously reported enzyme knockout study and a large-scale study of plasma samples. XCMS is freely available under an open-source license at http://metlin.scripps.edu/download/.

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History

  • Published In Issue February 01, 2006
  • Received for review August 10, 2005. Accepted November 23, 2005.

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