title: MET-XAlign: a metabolite cross-alignment tool for LC/MS-based comparative metabolomics.
abstract: 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/ .
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.affiliation: Plant Biology Division, The Samuel Roberts Noble Foundation , 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States.
authors.forename: Zhentian
authors.initials: Z
authors.lastname: Lei
authors.affiliation: Plant Biology Division, The Samuel Roberts Noble Foundation , 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States.
authors.forename: David
authors.initials: D
authors.lastname: Huhman
authors.affiliation: Plant Biology Division, The Samuel Roberts Noble Foundation , 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States.
authors.forename: Lloyd W
authors.initials: LW
authors.lastname: Sumner
authors.affiliation: Plant Biology Division, The Samuel Roberts Noble Foundation , 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States.
authors.forename: Patrick X
authors.initials: PX
authors.lastname: Zhao
mesh_terms: D015415:Biomarkers / Q000378:metabolism; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D055432:Metabolomics / Q000379:methods*; D013223:Statistics as Topic / Q000379:methods*
chemical_list: D015415:Biomarkers