Acidic acetonitrile for cellular metabolome extraction from Escherichia coli

Anal Chem. 2007 Aug 15;79(16):6167-73. doi: 10.1021/ac070470c. Epub 2007 Jul 14.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acetonitriles*
  • Amino Acids / analysis
  • Carbon / analysis
  • Chemical Fractionation / methods
  • Escherichia coli / metabolism*
  • Gas Chromatography-Mass Spectrometry / methods*
  • Metabolism*
  • Nucleotides / analysis
  • Solvents


  • Acetonitriles
  • Amino Acids
  • Nucleotides
  • Solvents
  • Carbon
  • acetonitrile