Introduction

Liquid chromatography/mass spectrometry (LC/MS) metabolite profiling has been widely used in comparative metabolomics studies; however, LC/MS-based comparative metabolomics currently faces several critical challenges. One of the greatest challenges is how to effectively align metabolites across different LC/MS profiles; a single metabolite can give rise to multiple peak features, and the grouped peak features that can be used to construct a spectrum pattern of single metabolite can vary greatly between biochemical experiments and even between instrument runs. Another major challenge is that the observed retention time for a single metabolite can also be significantly affected by experimental conditions. To overcome these two key challenges, we present a novel metabolite-based alignment approach entitled MET-XAlign to align metabolites across LC/MS metabolomics profiles. MET-XAlign takes the deduced molecular mass and estimated compound retention time information that can be extracted by our previously published tool, MET-COFEA, and aligns metabolites based on this information. We demonstrate that MET-XAlign is able to cross-align metabolite compounds, either known or unknown, in LC/MS profiles not only across different samples but also across different biological experiments and different electrospray ionization modes. Therefore, our proposed metabolite-based cross-alignment approach is a great step forward and its implementation, MET-XAlign, is a very useful tool in LC/MS-based comparative metabolomics. MET-XAlign has been successfully implemented with core algorithm coding in C++, making it very efficient, and visualization interface coding in the Microsoft.NET Framework. The MET-XAlign software along with demonstrative data is freely available at http://bioinfo.noble.org/manuscript-support/met-xalign/ .

Publications

  1. MET-XAlign: a metabolite cross-alignment tool for LC/MS-based comparative metabolomics.
    Cite this
    Zhang W, Lei Z, Huhman D, Sumner LW, Zhao PX, 2015-09-01 - Analytical chemistry

Credits

  1. Wenchao Zhang
    Developer

    Plant Biology Division, The Samuel Roberts Noble Foundation, United States of America

  2. Zhentian Lei
    Developer

    Plant Biology Division, The Samuel Roberts Noble Foundation, United States of America

  3. David Huhman
    Developer

    Plant Biology Division, The Samuel Roberts Noble Foundation, United States of America

  4. Lloyd W Sumner
    Developer

    Plant Biology Division, The Samuel Roberts Noble Foundation, United States of America

  5. Patrick X Zhao
    Investigator

    Plant Biology Division, The Samuel Roberts Noble Foundation, United States of America

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Summary
AccessionBT003057
Tool TypeApplication
Category
PlatformsWindows
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByPatrick X Zhao