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Metabolomics

Metabolomics. ‘ Omics Family Tree. W. M. Claudino , et al., Journal of Clinical Oncology, 2007, 25 (19), pp. 2840-2846. Metabolomics mɪˈtabəlɒmɪks / Noun BIOCHEMISTRY noun: metabolomics The scientific study of the set of metabolites present within an organism, cell, or tissue .

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Metabolomics

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  1. Metabolomics

  2. ‘Omics Family Tree W. M. Claudino, et al., Journal of Clinical Oncology, 2007, 25(19), pp. 2840-2846

  3. Metabolomics mɪˈtabəlɒmɪks/ Noun BIOCHEMISTRY noun: metabolomics • The scientific study of the set of metabolites present within an organism, cell, or tissue. The Oxford Dictionary

  4. How are metabolites influenced? W. M. Claudino, et al., Journal of Clinical Oncology, 2007, 25(19), pp. 2840-2846

  5. Instrumental Analysis • Gas Chromatography Mass Spectrometry (GC-MS) • High Performance Liquid Chromatography (HPLC) • Nanostructure Initiator Mass Spectrometry (NIMS) • Secondary Ion Mass Spectrometry (SIMS) • Nuclear Magnetic Resonance (NMR)

  6. Image : www.metabolomics.biozentrum.uni-wuerzburg.de/research1/

  7. Metabolic Fingerprinting • Generally a no a priori approach • Diagnostic based upon correlation of metabolites • Qualitative analysis

  8. Metabolic Fingerprinting 600 MHz representative 1H NMR spectra of tissue samples. A normal control B stage I of rectal cancer C stage II of rectal cancer D stage III of rectal cancer E stage IV of rectal cancer. H. Wang, et al., Molecular Cancer, 2013, 12(121). DOI: 10.1186/1476-4598-12-121

  9. Principal Component Analysis Principal Component Analysis (PCA) scores plot showing discriminate metabolites from cancer tissues, versus normal controls H. Wang, et al., Molecular Cancer, 2013, 12(121). DOI: 10.1186/1476-4598-12-121

  10. Orthogonal Projections to Latent Structures What in X is related to Y – Predictive What in X is not related to Y – Orthogonal (J. Trygg 2010) Image: Positive region – Cancerous tissues Negative region – Normal tissues H. Wang, et al., Molecular Cancer, 2013, 12(121). DOI: 10.1186/1476-4598-12-121

  11. Statistical Validation of Multivariate Models R2 = Explained Variance Q2 = Predictable ability of the model H. Wang, et al., Molecular Cancer, 2013, 12(121). DOI: 10.1186/1476-4598-12-121

  12. Metabolite Screening and Targeted Analysis • Requires some prior knowledge • Identification of metabolites • Quantitative approach

  13. Metabolite Screening and Targeted Analysis Human Metabolome Database (www.hmdb.ca) Pubchem (http://pubchem.ncbi.nlm.nih.gov) Metabolights (www.ebi.ac.uk/metabolights) Kegg (www.genome.jp/kegg) Metlin (http://metlin.scripps.edu) Massbank (www.massbank.jp)

  14. Mestrelab : Mnova • Predicts NMR spectra of compounds

  15. Example http://www.frontiersin.org/Journal/10.3389/fncel.2013.00179/full http://www.hmdb.ca/metabolites/HMDB00190 Fetal Bovine Serum (FBS) - 1H NMR spectrum acquired on 300MHz Oxford Instrument – 04/02/2014

  16. Recommended Reading • D. I. Broadhurst and D. B. Kell, Metabolomics, 2007, 2(4), pp. 171-196. DOI: 10.1007-511306-006-0037-z • R. Goodacre, et al., Trends in Biotechnol., 2004, 22(5), pp. 245-252. • R. Zenobi, Science, 2013, 342, pp. 1201-1212. DOI: 10.1126/science.1243259 • N. V. Reo, Drug Chem. Toxicol., 2002, 25(4), pp. 375-382. • W. M. Claudino, et al., Journal of Clinical Oncology, 2007, 25(19), pp. 2840-2846. • H. Wang, et al., Molecular Cancer, 2013, 12(121). • D. L. Massart et al., Chemometrics : A Textbook, Elsevier, New York, 1988. • J. Trygg and S. Wold, J. Chemom., 2002, 16(3), pp. 119-128.

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