Acidic Acetonitrile for Cellular Metabolome Extraction from Escherichia coli

Cellular metabolome analysis by chromatography?mass spectrometry (MS) requires prior metabolite extraction. We examined a diversity of solvent systems for extraction of water-soluble metabolites from Escherichia coli. Quantitative yields of ��100 different metabolites were measured by liquid chromatography?tandem MS and displayed in clustered heat map format. Many metabolites, including most amino acids and components of central carbon metabolism, were adequately extracted by a broad spectrum of solvent mixtures. For nucleotide triphosphates, however, mixtures of acidic (0.1 M formic acid-containing) acetonitrile/water (80:20) or acetonitrile/methanol/water (40:40:20) gave superior triphosphate yields. Experiments involving isotopic tracers revealed that the improved triphosphate yields in the acidic acetonitrile were in part due to reduced triphosphate decomposition, which is a major problem when extracting with other solvent systems such as methanol/water. We recommend acidic solvent mixtures containing acetonitrile for extraction of the E. coli metabolome.