Chemoselective probes for metabolite enrichment and profiling

Nature Methods

Volumn 4, Issue 5, 2007, Pages 429-435

  Carlson, Erin E ^a   Cravatt, Benjamin F ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLCYSTEINE; ANTIOXIDANT; PROTEINASE; PROTEOME; THIOL;

ARTICLE; BIOLOGY; CANCER CELL; ENZYME DEGRADATION; GENOMICS; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLITE; METABOLOMICS; MOLECULAR PROBE; MOLECULAR WEIGHT; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN TARGETING; PROTEOMICS; SYSTEMS BIOLOGY;

ACETYLCYSTEINE; ACRYLIC RESINS; ANTIOXIDANTS; BREAST NEOPLASMS; CHROMATOGRAPHY, LIQUID; HUMANS; POLYETHYLENE GLYCOLS; PROTEOMICS; SULFHYDRYL COMPOUNDS; TANDEM MASS SPECTROMETRY; TRYPSIN; TUMOR CELLS, CULTURED;

EID: 34250164588     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth1038     Document Type: Article

References (30)

1. Brown, P.O. & Botstein, D. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21, 33-37 (1999).
2. Patterson, S.D. & Aebersold, R. Proteomics: The first decade and beyond. Nat. Genet. 33, 311-323 (2003).
3. Fiehn, O. Metabolomics - the link between genotypes and phenotypes. Plant Mol. Biol. 48, 155-171 (2002).
4. Saghatelian, A. & Cravatt, B.F. Global strategies to integrate the proteome and metabolome. Curr. Opin. Chem. Biol. 9, 62-68 (2005).
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).
6. Fell, D.A. Enzymes, metabolites and fluxes. J. Exp. Bot. 56, 267-272 (2005).
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).
8. Wenk, M.R. The emerging field of lipidomics. Nat. Rev. Drug Discov. 4, 594-610 (2005).
9. Saghatelian, A. et al. Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry 43, 14332-14339 (2004).
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).
11. Speers, A.E. & Cravatt, B.F. Chemical strategies for activity-based proteomics. ChemBioChem 5, 41-47 (2004).
12. Evans, M.J. & Cravatt, B.F. Mechanism-based profiling of enzyme families. Chem. Rev. 106, 3279-3301 (2006).
13. Adam, G.C., Sorensen, E.J. & Cravatt, B.F. Chemical strategies for functional proteomics. Mol. Cell. Proteomics 1, 781-790 (2002).
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).
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).
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).
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).
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).
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).
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).
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).
22. Kell, D.B. Metabolomics and systems biology: Making sense of the soup. Curr. Opin. Microbiol. 7, 296-307 (2004).
23. Yalcin, T. & Harrison, A.G. Ion chemistry of protonated lysine derivatives. J. Mass Spectrom. 31, 1237-1243 (1996).
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).
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).
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).
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).
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).
29. Breitling, R., Pitt, A.R. & Barrett, M.P. Precision mapping of the metabolome. Trends Biotechnol. 24, 543-548 (2006).
30. Hemstrom, P. & Irgum, K. Hydrophilic interaction chromatography. J. Sep. Sci. 29, 1784-1821 (2006).