TitleAcidic acetonitrile for cellular metabolome extraction from Escherichia coli.
Publication TypeJournal Article
Year of Publication2007
AuthorsRabinowitz, JD, Kimball, E
JournalAnal Chem
Date Published2007 Aug 15
KeywordsAcetonitriles, Amino Acids, Carbon, Chemical Fractionation, Escherichia coli, Gas Chromatography-Mass Spectrometry, Metabolism, Nucleotides, Solvents

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 approximately 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.

Alternate JournalAnal. Chem.