Metabolite profiling: From diagnostics to systems biology

Nature Reviews Molecular Cell Biology

Volumn 5, Issue 9, 2004, Pages 763-769

  Fernie, Alisdair R ^a   Trethewey, Richard N ^b   Krotzky, Arno J ^b   Willmitzer, Lothar ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^b Metanomics GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; BIOTECHNOLOGY; CHEMOMETRIC ANALYSIS; CLUSTER ANALYSIS; ECOTYPE; ELECTROSPRAY; GAS CHROMATOGRAPHY; GENE FUNCTION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MEDICAL RESEARCH; MEDICAL TECHNOLOGY; METABOLITE; METABOLITE PROFILING; NUCLEAR MAGNETIC RESONANCE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; TANDEM MASS SPECTROMETRY;

CELL PHYSIOLOGY; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY; METABOLISM; MOLECULAR DIAGNOSTIC TECHNIQUES; PROTEINS; PROTEOMICS;

EID: 4444277707     PISSN: 14710072     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrm1451     Document Type: Review

References (54)

1. Harrigan, G. G. & Goodacre, R. (eds). Metabolic Profiling: Its Role in Biomarker Discovery and Gene Functional Analysis (Kluwer Academic, Boston, 2003).
2. Fiehn, O. Metabolomics. The link between genotype and phenotype. Plant Mol. Biol. 48, 155-171 (2002).
3. Kell, D. B. Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7, 296-307 (2004).
4. Roessner, U. et al. Metabolite profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13, 11-29 (2001).
5. Fiehn, O. et al. Metabolite profiling for plant functional genomics. Nature Biotech. 18, 1157-1161 (2000).
6. Halket, J. M. et al. Deconvolution gas chromatography mass spectrometry of urinary organic acids. Potential for pattern recognition and automated identification of metabolic disorders. Rapid Commun. Mass Spectrom. 13, 279-284 (2003).
7. Aharoni, A. et al. Terpenoid metabolism in wild type and transgenic Arabidopsis plants. Plant Cell 15, 2866-2884 (2003).
8. Swart, P. J. et al. HPLC-UV atmospheric-pressure ionisation mass-spectrometric determination of the dopamine-D2 agonist N-0923 and its major metabolites after oxidative metabolism by rat liver, monkey liver and human liver microsomes. Toxicology Methods 3, 279-290 (1993).
9. Matuszewski, B. K., Constanzer, M. L. & Chavez-Eng, C. M. Strategies for the assessment of matrix effect in quantitative bioanalytical methods based on HPLC-MS/MS. Anal. Chem. 75, 3019-3030 (2003).
10. Plumb, R. S. et al. Use of liquid chromatography/time-of-flight mass spectrometry and multivariate statistical analysis shows promise for the detection of drug metabolites in biological fluids. Rapid Commun. Mass Spectrom. 17, 2632-2638 (2003).
11. Watkins, S. M. & German, J. B. Metabolomics and biochemical profiling in drug discovery and development. Curr. Opin. Mol. Ther. 4, 224-228 (2002).
12. Aharoni, A. et al. Nontargeted metabolome analysis by use of Fourier transform ion cyclotron mass spectrometry. OMICS 6, 217-234 (2002).
13. Soga, T. et al. Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J. Proteome Res. 2, 488-494 (2003).
14. Nobeli, I., Krissinel, E. B. & Thornton, J. M. B. A structure-based anatomy of the E. coli metabolome. J. Mol. Biol. 334, 697-719 (2003).
15. Hall, R. et al. Plant metabolomics: the missing link in functional genomics strategies. Plant Cell 14, 1437-1440 (2002).
16. 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).
17. Walles, M. et al. Verapamil drug metabolism studies by automated in-tube solid phase microextraction. J. Pharma. Biomed. Anal. 30, 307-319 (2002).
18. Kok, E. J. & Kuiper, H. A. Comparative safety assessment for biotech crops. Trends Biotech. 21, 438-444 (2003).
19. Sauter, H., Lauer, M. & Fritsch, H. Metabolite profiling of plants a new diagnostic technique. Abstr. Pap. Am. Chem. Soc. 195, 129 (1988).
20. Allen, J. et al. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nature Biotech. 21, 692-696 (2003).
21. 1H-NMR-based metabonomics. Nature Med. 8, 1439-1444 (2002).
22. Huhman, D. V. & Sumner, L. W. Metabolic profiling of saponins in Medicago sativa and Medicago trunculata using HPLC coupled to an electrospray ion-trap mass spectrometer. Phytochemistry 59, 347-360 (2002).
23. Kose, F., Weckwerth, W., Linke, T. & Fiehn, O. Visualizing plant metabolomic correlation networks using clique-metabolite matrices. Bioinformatics 17, 1198-1208 (2001).
24. Aranibar, N., Singh, B. K., Stockton, G. W. & Ott, K. H. Automated mode-of-action detection by metabolic profiling. Biochem. Biophys. Res. Commun. 286, 150-155 (2001).
25. Quackenbush, J. Computational analysis of microarray data. Nature Rev. Genet. 2, 418-427 (2001).
26. Griffin, J. L. et al. NMR spectroscopy based metabonomic studies on the comparative biochemistry of the kidney and urine of the bank vole (Clethrionomys glareolus), wood mouse (Apodemus sylvaticus), white toothed shrew (Crocidura suaveolens) and the laboratory rat. Comp. Biochem. Physiol. B 127, 357-367 (2000).
27. Kaderbhal, N. N., Broadhurst, D. I., Ellis, D. I., Goodacre, R. & Kell, D. B. Functional genomics via metabolic footprinting: monitoring metabolite secretion by Escherichia coli tryptophan metabolism mutants using FT-IR and direct injection electrospray mass spectrometry. Comp. Funct. Genomics 4, 376-391 (2003).
28. Hashed, M. S. et al. Screening blood spots for inborn errors of metabolism by electrospray tandem mass spectrometry with a microplate batch process and a computer algorithm from automated flagging of abnormal profiles. Clin. Chem. 43, 1129-1141 (1997).
29. Martzen, M. R. et al. A biochemical genomics approach fur identifying genes by the activity of their products. Science 286, 1153-1155 (1999).
30. Trethewey, R. N., Krotzky, A. J. & Willmitzer, L. Metabolic profiling: a Rosetta stone for genomics? Curr. Opin. Plant Biol. 2, 83-85 (1999).
31. Raamsdonk, L. M. et al. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nature Biotech. 19, 45-50 (2001).
32. Fehr, M., Lalonde, S., Lager, I., Wolff, M. W. & Frommer, W. B. In vivo imaging of the dynamics of glucose uptake in the cytosol of COS-7 cells by fluorescent nanosensors. J. Biol. Chem. 278, 19127-19133 (2003).
33. Barabasi, A. L. & Oltvai, Z. N. Network biology: understanding the cell's functional organisation. Nature Rev. Genet. 5, 101-113 (2004).
34. Wagner, A. & Fell, D. A. The small world inside large metabolic networks. Proc. R. Soc. Lond. B 268, 1803-1810 (2001).
35. Kamath, R. S. et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231-237 (2003).
36. Kacser, H. & Burns, J. A. The control of flux. Symposia Soc. Exp. Biol. 28, 65-104 (1974).
37. Fernie, A. R. et al. Metabolic profiling at the genome level. Plant Animal Genome Abstr. XI, W307 (2003).
38. Kitano, H. Perspectives on systems biology. New Generation Comput. 18, 199-216 (2000).
39. Ideker, T., Galitski, T. & Hood, L. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343-372 (2001).
40. Edwards, J. S., Ibarra, R. U. & Palsson, B. O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotech. 19, 125-130 (1999).
41. Baliga, N. S. et al. Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc. Natl Acad. Sci. USA 99, 14913-14918 (2002).
42. Davidson E. H. et al. A genomic regulatory network for development. Science 295, 1669-1678 (2002).
43. Nicholson, J. K. & Wilson I. D. Understanding 'global' systems biology: metabonomics and the continuum of metabolism. Nature Rev. Drug Discov. 2, 668-676 (2003).
44. Weckwerth, W. Metabolomics in systems biology. Annu. Rev. Plant Biol. 54, 669-689 (2003).
45. Urbanczyk-Wochniak, E. et al. Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Reports 4, 989-993 (2003).
46. Askenazi, M. et al. Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nature Biotech. 21, 150-156 (2003).
47. Gygi, S. P. et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotech. 17, 994-999 (1999).
48. Stein, S. E. An integrated method for spectrum extraction and compound identification from GC/MS data. J. Am. Soc. Mass Spectrom. 10, 770-781 (1999).
49. Wagner, C., Sefkow, M. & Kopka, J. Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochemistry 62, 887-900 (2003).
50. Frenzel, T., Miller, A. & Engel, K. H. A methodology for automated comparative analysis of metabolite profiling data. Eur. Food Res. Tecnnol. 216, 335-342 (2003).
51. Duran, A. L., Yang, J., Wang, L. & Sumner, L. W. Metabolomics spectral formatting, alignment and conversion tools (MSFACTs). Bioinformatics 19, 2283-2293 (2003).
52. 1H nuclear magnetic resonance spectroscopy. Analyst 128, 1082-1090 (2003).
53. Lindon, J. C. HPLC-NMR-MS: past, present and future. Drug Discov. Todays 8, 1021-1022 (2003).
54. 13C NMR spectra. J. Am. Chem. Soc. 124, 1868-1870 (2002).