Cross-Platform Comparison of Methods for Quantitative Metabolomics of Primary Metabolism
- 23 February 2009
- journal article
- research article
- Published by American Chemical Society (ACS) in Analytical Chemistry
- Vol. 81 (6), 2135-2143
- https://doi.org/10.1021/ac8022857
Abstract
Quantitative metabolomics is under intense development, and no commonly accepted standard analytical technique has emerged, yet. The employed analytical methods were mostly chosen based on educated guesses. So far, there has been no systematic cross-platform comparison of different separation and detection methods for quantitative metabolomics. Generally, the chromatographic separation of metabolites followed by their selective detection in a mass spectrometer (MS) is the most promising approach in terms of sensitivity and separation power. Using a defined mixture of 91 metabolites (covering glycolysis, pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, redox metabolism, amino acids, and nucleotides), we compared six separation methods designed for the analysis of these mostly very polar primary metabolites, two methods each for gas chromatography (GC), liquid chromatography (LC), and capillary electrophoresis (CE). For analyses on a single platform, LC provides the best combination of both versatility and robustness. If a second platform can be used, it is best complemented by GC. Only liquid-phase separation systems can handle large polar metabolites, such as those containing multiple phosphate groups. As assessed by supplementing the defined mixture with 13C-labeled yeast extracts, matrix effects are a common phenomenon on all platforms. Therefore, suitable internal standards, such as 13C-labeled biomass extracts, are mandatory for quantitative metabolomics with any methods.Keywords
This publication has 37 references indexed in Scilit:
- Development of a quantitative, validated Capillary electrophoresis‐time of flight – mass spectrometry method with integrated high‐confidence analyte identification for metabolomicsElectrophoresis, 2008
- Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomesPhysical Biology, 2008
- A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic informationMolecular Systems Biology, 2007
- Pressure-assisted capillary electrophoresis mass spectrometry using combination of polarity reversion and electroosmotic flow for metabolomics anion analysisJournal of Bioscience and Bioengineering, 2006
- Mass Spectrometry and Protein AnalysisScience, 2006
- Integration of metabolome data with metabolic networks reveals reporter reactionsMolecular Systems Biology, 2006
- Putative regulatory sites unraveled by network‐embedded thermodynamic analysis of metabolome dataMolecular Systems Biology, 2006
- Evolution of metabolic diversityPhytochemistry, 2005
- Matrix effect in LC-ESI-MS and LC-APCI-MS with off-line and on-line extraction proceduresJournal of Chromatography A, 2004
- Mass spectrometry-based proteomicsNature, 2003