Acidic acetonitrile for cellular metabolome extraction from Escherichia coli

Joshua D. Rabinowitz, Elizabeth Kimball

Research output: Contribution to journalArticlepeer-review

268 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)6167-6173
Number of pages7
JournalAnalytical Chemistry
Issue number16
StatePublished - Aug 15 2007

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry


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