Introduction to Metabolomics

  • Teresa Whei-Mei FanEmail author
  • Andrew N. Lane
  • Richard M. Higashi
Part of the Methods in Pharmacology and Toxicology book series (MIPT)


We provide an overview of metabolomics in its current practices, including sample processing, major techniques, example applications, and useful resources to the readership, as described in detail in the various chapters of the handbook. In our view, metabolomics can be defined as “a systematic interrogation of the metabolome in terms of metabolite concentration, structure, and transformation pathways.” We emphasize the use of stable isotope tracing methodologies both in vitro and in vivo. We further provide a brief introduction to some concepts of flux analyses at steady state and nonsteady state.

Key words

Stable isotope editing Metabolic pathways Flux analysis 


  1. 1.
    Harrigan GG, Brackett DJ, Boros LG (2005) Medicinal chemistry, metabolic profiling and drug target discovery: a role for metabolic profiling in reverse pharmacology and chemical genetics. Mini Rev Med Chem 5(1):13–20PubMedCrossRefGoogle Scholar
  2. 2.
    Whitfield PD, German AJ, Noble PJM (2004) Metabolomics: an emerging post-genomic tool for nutrition. Br J Nutr 92(4):549–55PubMedCrossRefGoogle Scholar
  3. 3.
    Kaddurah-Daouk R, Kristal BS, Weinshilboum RM (2008) Metabolomics: a global biochemical approach to drug response and disease. Annu Rev Pharmacol Toxicol 48:653–683CrossRefGoogle Scholar
  4. 4.
    Nicholson J (2005) Metabonomics and global systems biology approaches to molecular diagnostics. Drug Metab Rev 37:10–10Google Scholar
  5. 5.
    Bollard ME, Stanley EG, Lindon JC, Nicholson JK, Holmes E (2005) NMR-based metabonomic approaches for evaluating physiological influences on biofluid composition. NMR Biomed 18(3):143–62PubMedCrossRefGoogle Scholar
  6. 6.
    Fan TW-M, Lane AN, Higashi RM, Yan J (2011) Stable isotope resolved metabolomics of lung cancer in a SCID mouse model. Metabolomics 7:257–69PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Beger RD, Hansen DK, Schnackenberg LK, Cross BM, Fatollahi JJ, Lagunero FT, Sarnyai Z, Boros LG (2009) Single valproic acid treatment inhibits glycogen and RNA ribose turnover while disrupting glucose-derived cholesterol synthesis in liver as revealed by the [U-13C6]-D-glucose tracer in mice. Metabolomics 5:336–45PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Fan TW-M, Lane AN, Higashi RM, Bousamra M, Kloecker G, Miller DM (2009) Erlotinib-sensitive and resistant lung tumors show radically different metabolic profiles. Exp Mol Pathol 87:83–6PubMedCentralPubMedCrossRefGoogle Scholar
  9. 9.
    Fan TW, Lane AN, Higashi RM, Farag MA, Gao H, Bousamra M, Miller DM (2009) Altered regulation of metabolic pathways in human lung cancer discerned by 13C stable isotope-resolved metabolomics (SIRM). Mol Cancer 8:41PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Lane AN, Fan TW-M, Bousamra M II, Higashi RM, Yan J, Miller DM (2011) Clinical applications of stable isotope-resolved metabolomics (SIRM) in non-small cell lung cancer. Omics 15:173–82PubMedCrossRefGoogle Scholar
  11. 11.
    Dieterle F, Ross A, Schlotterbeck G, Senn H (2006) Metabolite projection analysis for fast identification of metabolites in metabonomics. Application in an amiodarone study. Anal Chem 78(11):3551–61PubMedCrossRefGoogle Scholar
  12. 12.
    Kettaneh N, Berglund A, Wold S (2005) PCA and PLS with very large data sets. Comput Stat Data Anal 48(1):69–85CrossRefGoogle Scholar
  13. 13.
    Trygg J, Holmes E, Lundstedt T (2007) Chemometrics in metabonomics. J Proteome Res 6(2):469–79PubMedCrossRefGoogle Scholar
  14. 14.
    Vaidyanathan S, Harrigan GG, Goodacre R (2005) Metabolome analyses: strategies for systems biology. Springer, BostonCrossRefGoogle Scholar
  15. 15.
    Sumner LW, Amberg A, Barrett D, Beger R, Beale MH, Daykin C, Fan TW-M, Fiehn O, Goodacre R, Griffin JL, Hardy N, Higashi RM, Kopka J, Lindon JC, Lane AN, Marriott P, Nicholls AW, Reily MD, Viant M (2007) Proposed minimum reporting standards for chemical analysis. Metabolomics 3:211–21PubMedCentralPubMedCrossRefGoogle Scholar
  16. 16.
    Castle AL, Fiehn O, Kaddurah-Daouk R, Lindon JC (2006) Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results. Brief Bioinform 7(2):159–65PubMedCrossRefGoogle Scholar
  17. 17.
    Sansone SA, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R, Kristal BS, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, Sumner LW, Taylor C, van der Werf M, van Ommen B, Fiehn O (2007) The metabolomics standards initiative. Nat Biotechnol 25(8):844–8CrossRefGoogle Scholar
  18. 18.
    Goodacre R, Broadhurst D, Smilde AK, Kristal BS, Baker JD, Beger R, Bessant C, Connor S, Calmani G, Craig A, Ebbels T, Kell DB, Manetti C, Newton J, Paternostro G, Somorjai R, Sjostrom M, Trygg J, Wulfert F (2007) Proposed minimum reporting standards for data analysis in metabolomics. Metabolomics 3(3):231–41CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Teresa Whei-Mei Fan
    • 1
    Email author
  • Andrew N. Lane
    • 2
  • Richard M. Higashi
    • 1
  1. 1.Department of Chemistry, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleUSA
  2. 2.Departments of Medicine and Chemistry, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleUSA

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