title: Acidic acetonitrile for cellular metabolome extraction from Escherichia coli.
abstract: 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.
authors.affiliation: Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA. joshr@princeton.edu
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Rabinowitz
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Kimball
mesh_terms: D000097:Acetonitriles; D000596:Amino Acids / Q000032:analysis; D002244:Carbon / Q000032:analysis; D005591:Chemical Fractionation / Q000379:methods; D004926:Escherichia coli / Q000378:metabolism*; D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods*; D008660:Metabolism; D009711:Nucleotides / Q000032:analysis; D012997:Solvents
chemical_list: D000097:Acetonitriles; D000596:Amino Acids; D009711:Nucleotides; D012997:Solvents; D002244:Carbon; C032159:acetonitrile