Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach (original) (raw)

• Rabinowitz, J.D. & Kimball, E. Acidic acetonitrile for cellular metabolome extraction from Escherichia coli. Anal. Chem. 79, 6167–6173 (2007).
  Article CAS PubMed Google Scholar
• Lu, W., Kwon, Y.K. & Rabinowitz, J.D. Isotope ratio-based profiling of microbial folates. J. Am. Soc. Mass Spectrom. 18, 898–909 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Yuan, J., Fowler, W.U., Kimball, E., Lu, W. & Rabinowitz, J.D. Kinetic flux profiling of nitrogen assimilation in Escherichia coli. Nat. Chem. Biol. 2, 529–530 (2006).
  Article CAS PubMed Google Scholar
• Lu, W., Kimball, E. & Rabinowitz, J.D. A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites. J. Am. Soc. Mass Spectrom. 17, 37–50 (2006).
  Article CAS PubMed Google Scholar
• Wu, L. et al. Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards. Anal. Biochem. 336, 164–171 (2005).
  Article CAS PubMed Google Scholar
• Mashego, M.R. et al. MIRACLE: mass isotopomer ratio analysis of U-C-13-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites. Biotechnol. Bioeng. 85, 620–628 (2004).
  Article CAS PubMed Google Scholar
• Brauer, M.J. et al. Conservation of the metabolomic response to starvation across two divergent microbes. Proc. Natl. Acad. Sci. USA 103, 19302–19307 (2006).
  Article CAS PubMed Google Scholar
• Ikeda, T.P., Shauger, A.E. & Kustu, S. Salmonella typhimurium apparently perceives external nitrogen limitation as internal glutamine limitation. J. Mol. Biol. 259, 589–607 (1996).
  Article CAS PubMed Google Scholar
• Rabinowitz, J.D. Cellular metabolomics of Escherchia coli. Expert Rev. Proteomics 4, 187–198 (2007).
  Article CAS PubMed Google Scholar
• Villas-Boas, S. & Bruheim, P. Cold glycerol-saline: the promising quenching solution for accurate intracellular metabolite analysis of microbial cells. Anal. Biochem. 370, 87–97 (2007).
  Article CAS PubMed Google Scholar
• Wittmann, C., Kromer, J.O., Kiefer, P., Binz, T. & Heinzle, E. Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria. Anal. Biochem. 327, 135–139 (2004).
  Article CAS Google Scholar
• Villas-Boas, S.G., Hojer-Pedersen, J., Akesson, M., Smedsgaard, J. & Nielsen, J. Global metabolite analysis of yeast: evaluation of sample preparation methods. Yeast 22, 1155–1169 (2005).
  Article CAS Google Scholar
• Maharjan, R.P. & Ferenci, T. Global metabolite analysis: the influence of extraction methodology on metabolome profiles of Escherichia coli. Anal. Biochem. 313, 145–154 (2003).
  Article PubMed Google Scholar
• Kimball, E. & Rabinowitz, J.D. Identifying decomposition products in extracts of cellular metabolites. Anal. Biochem. 358, 273–280 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Meyer, R.C. et al. The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 104, 4759–4764 (2007).
  Article CAS PubMed Google Scholar
• Monton, M.R. & Soga, T. Metabolome analysis by capillary electrophoresis-mass spectrometry. J. Chromatogr. A 1168, 237–246 discussion 236 (2007).
  Article CAS PubMed Google Scholar
• Bajad, S.U. et al. Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J. Chromatogr. A 1125, 76–88 (2006).
  Article CAS Google Scholar
• Tolstikov, V.V., Lommen, A., Nakanishi, K., Tanaka, N. & Fiehn, O. Monolithic silica-based capillary reversed-phase liquid chromatography/electrospray mass spectrometry for plant metabolomics. Anal. Chem. 75, 6737–6740 (2003).
  Article CAS PubMed Google Scholar
• Maruska, A., Rocco, A., Kornysova, O. & Fanali, S. Synthesis and evaluation of polymeric continuous bed (monolithic) reversed-phase gradient stationary phases for capillary liquid chromatography and capillary electrochromatography. J. Biochem. Biophys. Methods 70, 47–55 (2007).
  Article CAS PubMed Google Scholar
• Horie, K. et al. Highly efficient monolithic silica capillary columns modified with poly(acrylic acid) for hydrophilic interaction chromatography. J. Chromatogr. A 1164, 198–205 (2007).
  Article CAS PubMed Google Scholar
• Wilson, I.D. et al. HPLC-MS-based methods for the study of metabonomics. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 817, 67–76 (2005).
  Article CAS PubMed Google Scholar
• Nguyen, D.T. et al. High throughput liquid chromatography with sub-2 microm particles at high pressure and high temperature. J. Chromatogr. A 1167, 76–84 (2007).
  Article CAS PubMed Google Scholar
• Guillarme, D., Nguyen, D.T., Rudaz, S. & Veuthey, J.L. Method transfer for fast liquid chromatography in pharmaceutical analysis: application to short columns packed with small particle. Part I: isocratic separation. Eur. J. Pharm. Biopharm. 66, 475–482 (2007).
  Article CAS PubMed Google Scholar
• Yu, K., Little, D., Plumb, R. & Smith, B. High-throughput quantification for a drug mixture in rat plasma—a comparison of ultra performance liquid chromatography/tandem mass spectrometry with high-performance liquid chromatography/tandem mass spectrometry. Rapid Commun. Mass Spectrom. 20, 544–552 (2006).
  Article CAS PubMed Google Scholar
• Cai, S.S., Hanold, K.A. & Syage, J.A. Comparison of atmospheric pressure photoionization and atmospheric pressure chemical ionization for normal-phase LC/MS chiral analysis of pharmaceuticals. Anal. Chem. 79, 2491–2498 (2007).
  Article CAS PubMed Google Scholar
• Hu, Q. et al. The Orbitrap: a new mass spectrometer. J. Mass Spectrom 40, 430–443 (2005).
  Article CAS PubMed Google Scholar
• Wilson, S.D. & Horne, D.W. Evaluation of ascorbic acid in protecting labile folic acid derivatives. Proc. Natl. Acad. Sci. USA 80, 6500–6504 (1983).
  Article CAS PubMed Google Scholar
• Luo, B., Groenke, K., Takors, R., Wandrey, C. & Oldiges, M. Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. J. Chromatogr. A 1147, 153–164 (2007).
  Article CAS PubMed Google Scholar
• van Winden, W.A. et al. Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of 13C-labeled primary metabolites. FEMS Yeast Res. 5, 559–568 (2005).
  Article CAS PubMed Google Scholar
• Coulier, L. et al. Simultaneous quantitative analysis of metabolites using ion-pair liquid chromatography-electrospray ionization mass spectrometry. Anal. Chem. 78, 6573–6582 (2006).
  Article CAS PubMed Google Scholar
• Brown, A.F. & Dunn, G.A. Microinterferometry of the movement of dry matter in fibroblasts. J. Cell. Sci. 92 (Part 3): 379–389 (1989).
  PubMed Google Scholar