Washington University in St. Louis

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Metabolomics to elucidate novel biochemical mechanisms of disease
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A Protocol to Compare Methods for Untargeted Metabolomics

Wang L, Naser FJ, Spalding JL, and Patti GJ
A Protocol to Compare Methods for Untargeted Metabolomics
Methods in Molecular Biology, 1-15, 2018

There are thousands of published methods for profiling metabolites with liquid chromatography/mass spectrometry (LC/MS). While many have been evaluated and optimized for a small number of select metabolites, very few have been assessed on the basis of global metabolite coverage. Thus, when performing untargeted metabolomics, researchers often question which combination of extraction techniques, chromatographic separations, and mass spectrometers is best for global profiling. Method comparisons are complicated because thousands of LC/MS signals (so-called features) in a typical untargeted metabolomic experiment cannot be readily identified with current resources. It is therefore challenging to distinguish methods that increase signal number due to improved metabolite coverage from methods that increase signal number due to contamination and artifacts. Here, we present the credentialing protocol to remove the latter from untargeted metabolomic datasets without having to identify metabolite structures. This protocol can be used to compare or optimize methods pertaining to any step of the untargeted metabolomic workflow (e.g., extraction, chromatography, mass spectrometer, informatic software, etc.).

Washington University, Departments of Chemistry, Genetics, and Medicine. Saint Louis, Missouri 63110 USA