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

Acidic acetonitrile for cellular metabolome extraction from Escherichia coli.

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Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.


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.

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