An assessment of extraction methods for global metabolic profiling of Escherichia coli

Accurate determination of intracellular metabolite variation requires well validated procedures for sampling and sample treatment. Therefore, we developed methods for efficient extraction of metabolites from Escherichia coli to determine the best methods to approach analysis of the metabolome. Using a strictly quantitative approach, we evaluated seven methods with extraction solvents (butanol, butanol added ammonium hydroxide and ethanol, ethanol, methanol, methanol added potassium phosphate, ethyl acetate, aqueous sodium hydroxide) coupled to sonication for metabolites extraction. The metabolite profiles were generated using gas chromatography-mass spectrometry (GC/MS). Method using butanol added ammonium and ethanol is the most efficient in the extraction of metabolites: detection of 289 masses, identification of amino acids, fatty acids, organic acids and amines of 58 metabolites. Other methods were achieved with methanol added potassium hydroxide, and methanol, which yielded nearly identical variations for the metabolites analyzed. According to our results, butanol added ammonium hydroxide and ethanol, methanol, and methanol added potassium hydroxide extraction methods are practical extraction methods.