Chemoselective probes for metabolite enrichment and profiling (original) (raw)

References

  1. Brown, P.O. & Botstein, D. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21, 33–37 (1999).
    Article CAS PubMed Google Scholar
  2. Patterson, S.D. & Aebersold, R. Proteomics: the first decade and beyond. Nat. Genet. 33, 311–323 (2003).
    Article CAS PubMed Google Scholar
  3. Fiehn, O. Metabolomics—the link between genotypes and phenotypes. Plant Mol. Biol. 48, 155–171 (2002).
    Article CAS PubMed Google Scholar
  4. Saghatelian, A. & Cravatt, B.F. Global strategies to integrate the proteome and metabolome. Curr. Opin. Chem. Biol. 9, 62–68 (2005).
    Article CAS PubMed Google Scholar
  5. Kell, D.B. & Westerhoff, H.V. Towards a rationale approach to the optimization of flux in microbial biotransformations. Trends Biotechnol. 4, 137–142 (1986).
    Article CAS Google Scholar
  6. Fell, D.A. Enzymes, metabolites and fluxes. J. Exp. Bot. 56, 267–272 (2005).
    Article CAS PubMed Google Scholar
  7. Fernie, A.R., Trethewey, R.N., Krotzky, A.J. & Willmitzer, L. Metabolite profiling: from diagnostics to systems biology. Nat. Rev. Mol. Cell Biol. 5, 763–769 (2004).
    Article CAS PubMed Google Scholar
  8. Wenk, M.R. The emerging field of lipidomics. Nat. Rev. Drug Discov. 4, 594–610 (2005).
    Article CAS PubMed Google Scholar
  9. Saghatelian, A. et al. Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry 43, 14332–14339 (2004).
    Article CAS PubMed Google Scholar
  10. Chiang, K.P., Niessen, S., Saghatelian, A. & Cravatt, B.F. An enzyme that regulates ether lipid signaling pathways in cancer annotated by multidimensional profiling. Chem. Biol. 13, 1041–1050 (2006).
    Article CAS PubMed Google Scholar
  11. Speers, A.E. & Cravatt, B.F. Chemical strategies for activity-based proteomics. ChemBioChem 5, 41–47 (2004).
    Article CAS PubMed Google Scholar
  12. Evans, M.J. & Cravatt, B.F. Mechanism-based profiling of enzyme families. Chem. Rev. 106, 3279–3301 (2006).
    Article CAS PubMed Google Scholar
  13. Adam, G.C., Sorensen, E.J. & Cravatt, B.F. Chemical strategies for functional proteomics. Mol. Cell. Proteomics 1, 781–790 (2002).
    Article CAS PubMed Google Scholar
  14. Zhang, H., Yan, W. & Aebersold, R. Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes. Curr. Opin. Chem. Biol. 8, 66–75 (2004).
    Article CAS PubMed Google Scholar
  15. Daykin, C.A., Foxall, P.J.D., Connor, S.C., Lindon, J.C. & Nicholson, J.K. The comparison of plasma deproteinization methods for the detection of low-molecular-weight metabolites by (1)H nuclear magnetic resonance spectroscopy. Anal. Biochem. 304, 220–230 (2002).
    Article CAS PubMed Google Scholar
  16. Want, E.J. et al. Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry. Anal. Chem. 78, 743–752 (2006).
    Article CAS PubMed Google Scholar
  17. Chowdhury, S.M., Munske, G.R., Siems, W.F. & Bruce, J.E. A new maleimide-bound acid-cleavable solid-support reagent for profiling phosphorylation. Rapid Commun. Mass Spectrom. 19, 899–909 (2005).
    Article CAS PubMed Google Scholar
  18. Tumelty, D., Cao, K. & Holmes, C.P. Traceless solid-phase synthesis of substituted benzimidazoles via a base-cleavable linker. Org. Lett. 3, 83–86 (2001).
    Article CAS PubMed Google Scholar
  19. Williams, S.J., Hekmat, O. & Withers, S.G. Synthesis and testing of mechanism-based protein-profiling probes for retaining endo-glycosidases. ChemBioChem 7, 116–124 (2006).
    Article CAS PubMed Google Scholar
  20. Smith, C.A., Want, E.J., O'Maille, G., Abagyan, R. & Siuzdak, G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78, 779–787 (2006).
    Article CAS PubMed Google Scholar
  21. Roessner-Tunali, U. et al. Metabolic profiling of transgenic tomato plants overexpressing hexokinase reveals that the influence of hexose phosphorylation diminishes during fruit development. Plant Physiol. 133, 84–99 (2003).
    Article CAS PubMed PubMed Central Google Scholar
  22. Kell, D.B. Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7, 296–307 (2004).
    Article CAS PubMed Google Scholar
  23. Yalcin, T. & Harrison, A.G. Ion chemistry of protonated lysine derivatives. J. Mass Spectrom. 31, 1237–1243 (1996).
    Article CAS PubMed Google Scholar
  24. Menon, S.G., Coleman, M.C., Walsh, S.A., Spitz, D.R. & Goswami, P.C. Differential susceptibility of nonmalignant human breast epithelial cells and breast cancer cells to thiol antioxidant-induced G(1)-delay. Antioxid. Redox Signal. 7, 711–718 (2005).
    Article CAS PubMed Google Scholar
  25. Shibanuma, M., Kuroki, T. & Nose, K. Induction of DNA-replication and expression of proto-oncogene c-myc and c-fos in quiescent Balb/3T3 cells by xanthine-xanthine oxidase. Oncogene 3, 17–21 (1988).
    CAS Google Scholar
  26. Kim, K.Y., Rhim, T., Choi, I. & Kim, S.S. N-acetylcysteine induces cell cycle arrest in hepatic stellate cells through its reducing activity. J. Biol. Chem. 276, 40591–40598 (2001).
    Article CAS PubMed Google Scholar
  27. Menon, S.G. et al. Redox regulation of the G1 to S phase transition in the mouse embryo fibroblast cell cycle. Cancer Res. 63, 2109–2117 (2003).
    CAS PubMed Google Scholar
  28. 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 PubMed Google Scholar
  29. Breitling, R., Pitt, A.R. & Barrett, M.P. Precision mapping of the metabolome. Trends Biotechnol. 24, 543–548 (2006).
    Article CAS PubMed Google Scholar
  30. Hemstrom, P. & Irgum, K. Hydrophilic interaction chromatography. J. Sep. Sci. 29, 1784–1821 (2006).
    Article PubMed Google Scholar

Download references