Skip to main content

Differential Metabolic Profiling for Biomarker Discovery

A mass spectrometric approach

  • Chapter
Metabolome Analyses: Strategies for Systems Biology

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Adam B-L, Vlahou A, Semmes OJ and Wright GL Jr. Proteomic approaches to biomarker discovery in prostate and bladder cancers. Proteomics, 1: 1264–1270 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Aharoni A, de Vos CHR, Verhoeven HA, Maliepaard CA, Kruppa G, Bino R and Goodenowe DB. Nontargeted metabolome analysis by use of Fourier transform ion cyclotron mass spectrometry. Omics, 6: 217–234 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Allen J, Davey HM, Broadhurst D, Heald JK, Rowland JJ, Oliver SG and Kell DB. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat. Biotechnol., 21: 692–696 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Anderle M, Roy S, Lin H, Becker C. Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum. Bioinformatics, 20: 3575–3582 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Beckonert O, Bollard ME, Ebbels TMD, Keun HC, Antti H, Holmes E, Lindon JC and Nicholson JK. NMR-based metabonomic toxicity classification: hierarchical cluster analysis and k-nearest-neighbour approaches. Anal. Chim. Acta, 490: 3–15 (2003).

    Article  CAS  Google Scholar 

  • Beecher CWW. The human metabolome, In Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis, Harrigan GG, Goodacre R. (Eds), Kluwer Publishers, New York, 311–319 (2003).

    Google Scholar 

  • Bischoff R and Luider TM. Methodological advances in the discovery of protein and peptide disease markers. J. Chromat. B, 803: 27–40 (2004).

    Article  CAS  Google Scholar 

  • Blair RC, Troendle JF, Beck RW. Control of familywise errors in multiple endpoint assessments via stepwise permutation tests. Stat. Med., 15: 1107–1121 (1996).

    Article  PubMed  CAS  Google Scholar 

  • Bonato PS. Recent advances in the determination of enantiomeric drugs and their metabolites in biological fluids by capillary electrophoresis-mediated microanalysis. Electrophoresis, 24: 4078–4094 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Brindle JT, Antti H, Holmes E, Tranter G, Nicholson JK, Bethell HWL, Clarke S, Schofield PM, McKilligin E, Mosedale DE and Grainger DJ. Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics. Nat. Medicine, 8: 1439–1445 (2002).

    Article  CAS  Google Scholar 

  • Diamandis EP. Mass spectrometry as a diagnostic and a cancer biomarker discovery tool. Mol. Cell. Proteomics, 3: 367–378 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Dow LK, Kalelkar S and Dow ER. Self-organizing maps for the analysis of NMR spectra. Drug Discov. Today: BIOSILICO, 2: 157–163 (2004).

    Article  CAS  Google Scholar 

  • Dumas M-E, Canlet C, Andre F, Vercauteren J and Paris A. Metabonomic assessment of physiological disruptions using 1H-13C HMBC-NMR spectroscopy combined with pattern recognition procedures performed on filtered variables. Anal. Chem., 74: 2261–2273 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Eisen MB, Spellman PT, Brown PO and Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 95: 14863–8 (1998).

    Article  PubMed  CAS  Google Scholar 

  • Fiehn O. Metabolomics — the link between genotypes and phenotypes. Plant Mol Biol., 48: 155–71 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Garrod S, Humpher E, Connor SC, Connelly JC, Spraul M, Nicholson JK and Holmes E. High-resolution 1H NMR and magic angle spinning NMR spectroscopic investigation of the biochemical effects of 2-bromoethanamine in intact renal and hepatic tissue. Mag. Reson. Medicine, 45: 781–790 (2001).

    Article  CAS  Google Scholar 

  • Glassbrook N and Ryals J. A systematic approach to biochemical profiling. Curr. Opin. Plant Biol., 4: 186–90 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Griffin JL, Walker LA, Shore RF and Nicholson JK. Metabolic profiling of chronic Cadmium exposure in the rat. Chem. Res. Toxicol., 14: 1428–1434 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Group BDW. Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clin. Pharmacol. Ther., 69: 89–95 (2001).

    Article  Google Scholar 

  • Harrigan GG, Goodacre R. (Eds) Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis, pp. 335 pp. Kluwer Publishers, New York (2003).

    Google Scholar 

  • Hastings CA, Norton SM and Roy S. New algorithms for processing and peak detection in liquid chromatography/mass spectrometry data, Rapid Commun. Mass Spectrom., 16: 462–7 (2002).

    Article  PubMed  CAS  Google Scholar 

  • He Q-Y and Chiu J-F. Proteomics in biomarker discovery and drug development. J. Cell. Biochem., 89: 868–886 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Hilsenbeck SG, Friedrichs WE, Schiff R, O’Connell P, Hansen RK, Osborne CK and Fuqua SA. Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J. Natl. Cancer Inst., 91: 453–9 (1999).

    Article  PubMed  CAS  Google Scholar 

  • Holm S. A simple sequentially rejective multiple test procedure. Scand. J. Statist., 6: 65–70 (1979).

    Google Scholar 

  • Horning EC and Horning MG. Human metabolic profiles obtained by gas chromatography and gas chromatography-mass spectrometry. Advan. Chromatogr. Proc. Int. Symp., 6th:226–43 (1970).

    Google Scholar 

  • Huck CW, Stecher G, Bakry R and Bonn GK. Recent progress in high-performance capillary bioseparations. Electrophoresis, 24: 3977–3997 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Idborg H, Edlund PO and Jacobsson SP. Multivariate approaches for efficient detection of potential metabolites from liquid chromatography/mass spectrometry data. Rapid Commun. Mass Spectrom., 18: 944–54 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Idborg-Bjorkman H, Edlund PO, Kvalheim OM, Schuppe-Koistinen I and Jacobsson SP. Screening of biomarkers in rat urine using LC/electrospray ionization-MS and two-way data analysis. Anal Chem., 75: 4784–92 (2003).

    Article  PubMed  Google Scholar 

  • Kaddurah-Daouk R, Beecher C, Kristal BS, Matson WR, Bogdanov M and Asa DJ. Bioanalytical advances for metabolomics and metabolic profiling. PharmaGenomics 4: 46–52 (2004).

    CAS  Google Scholar 

  • Kantor AB. Comprehensive phenotyping and biological marker discovery. Dis. Markers 18: 91–7 (2002).

    PubMed  CAS  Google Scholar 

  • Kantor AB, Wang W, Lin H, Govindarajan H, Anderle M, Perrone A and Becker C. Biomarker discovery by comprehensive phenotyping for autoimmune diseases. Clin. Immunol., 111: 186–195 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Krieg RC, Paweletz CP, Liotta LA and Petricoin EF. III. Clinical proteomics for cancer biomarker discovery and therapeutic targeting. Technol. Cancer Res. Treat., 1: 263–272 (2002).

    PubMed  CAS  Google Scholar 

  • Lenz EM, Wilson ID, Timbrell JA and Nicholson JK. A 1H NMR spectroscopic study of the biochemical effects of ifosfamide in the rat: evaluation of potential biomarkers. Biomarkers, 5: 424–435 (2000).

    Article  CAS  Google Scholar 

  • Lindon JC, Holmes E, Bollard ME, Stanley EG and Nicholson JK. Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis. Biomarkers, 9: 1–31 (2004a).

    Article  PubMed  CAS  Google Scholar 

  • Lindon JC, Holmes E and Nicholson JK. Metabonomics and its role in drug development and disease diagnosis. Expert Rev. Mol. Diagn., 4: 189–199 (2004b).

    Article  PubMed  CAS  Google Scholar 

  • Manne R and Grande BV. Resolution of two-way data from hyphenated chromatography by means of elementary matrix transformations. Chemomet. Ihtell. Lab. Syst., 50: 35–46 (2000).

    Article  CAS  Google Scholar 

  • McDonald WH and Yates JR 3rd Shotgun proteomics and biomarker discovery. Dis. Markers, 18: 99–105 (2002).

    PubMed  CAS  Google Scholar 

  • Minutti CZ, Lacey JM, Magera MJ, Hahn SH, McCann M, Schulze A, Cheillan D, Dorche C, Chace DH, Lymp JF, Zimmerman D, Rinaldo P and Matern D. Steroid profiling by tandem mass spectrometry improves the positive predictive value of newborn screening for congenital adrenal hyperplasia. J. Clin. Endocrin. Metabol., 89: 3687–3693 (2004).

    Article  CAS  Google Scholar 

  • Nicholson J, Lindon J, Scarfe G, Wilson I, Abou-Shakra F, Sage A, Harland G and Castro-Perez J. Quantification and identification of 2-bromo-4-trifluoromethylaniline metabolites in rat urine using HPLC-ICP-MS/TOF/MS. Adv. Mass Spectrom., 15: 659–661 (2001).

    CAS  Google Scholar 

  • Nicholson JK and Wilson ID. Opinion: Understanding ‘global’ systems biology: Metabonomics and the continuum of metabolism. Nat. Rev. Drug Discov., 2: 668–676 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Ott K-H, Aranibar N, Singh B and Stockton GW. Metabonomics classifies pathways affected by bioactive compounds. Artificial neural network classification of NMR spectra of plant extracts. Phytochemistry, 62: 971–985 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Pang JX, Ginanni N, Dongre AR, Hefta SA and Opiteck GJ. Biomarker discovery in urine by proteomics. J. Proteome Res., 1: 161–169 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Scarfe GB, Clayton E, Wilson ID and Nicholson JK. Identification and quantification of metabolites of 2,3,5,6-tetrafluoro-4-trifluoromethylaniline in rat urine using 19F nuclear magnetic resonance spectroscopy, high-performance liquid chromatography-nuclear magnetic resonance spectroscopy and high-performance liquid chromatography-mass spectrometry. J. Chromatog, B, 748: 311–319 (2000).

    CAS  Google Scholar 

  • Schlichtherle-Cerny H, Affolter M and Cerny C. Hydrophilic interaction liquid chromatography coupled to electrospray mass spectrometry of small polar compounds in food analysis. Anal. Chem., 75: 2349–54 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Shen H, Grung B, Kvalheim OM and Eide I. Automated curve resolution applied to data from multi-detection instruments. Anal. Chimic. Acta, 446: 313–328 (2001).

    CAS  Google Scholar 

  • Shoemaker JD and Elliott WH. Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease. J. Chromatography, 562: 125–38 (1991).

    CAS  Google Scholar 

  • Soga T, Ohashi Y, Ueno Y, Naraoka H, Tomita M and Nishioka T. Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J. Proteome Res., 2: 488–94 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Spraul M, Freund AS, Nast RE, Withers RS, Maas WE and Corcoran O. Advancing NMR sensitivity for LC-NMR-MS using a cryoflow probe: Application to the analysis of acetaminophen metabolites in urine. Anal. Chem., 75: 1536–1541 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Stobiecki M and Makkar HPS. Recent advances in analytical methods for identification and quantification of phenolic compounds. EAAP Publication 110 (Recent Advances of Research in Antinutritional Factors in Legume Seeds and Oilseeds): 11–28 (2004).

    CAS  Google Scholar 

  • Tolstikov VV and Fiehn O. Analysis of highly polar compounds of plant origin: Combination of hydrophilic interaction chromatography and electrospray ion trap mass spectrometry. Anal. Biochem., 301: 298–307 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Tugwood JD, Hollins LE and Cockerill MJ. Genomics and the search for novel biomarkers in toxicology. Biomarkers, 8: 79–92 (2003).

    Article  PubMed  CAS  Google Scholar 

  • van der Greef J, Stroobant P and van der Heijden R. The role of analytical sciences in medical systems biology. Curr. Opin. Chem. Biol., 8: 559–565 (2004).

    Article  PubMed  Google Scholar 

  • Vernon SD, Unger ER, Dimulescu IM, Rajeevan M and Reeves WC. Utility of the blood for gene expression profiling and biomarker discovery in chronic fatigue syndrome. Dis. Markers, 18: 193–199 (2002).

    PubMed  CAS  Google Scholar 

  • Viant MR, Rosenblum ES and Tieerdema RS. NMR-based metabolomics: A powerful approach for characterizing the effects of environmental stressors on organism health. Environ. Sci. Technol., 37: 4982–9 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Wang W, Zhou H, Lin H, Roy S, Shaler TA, Hill LR, Norton S, Kumar P, Anderle M and Becker CH. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 75: 4818–4826 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Warne MA, Lenz EM, Osborn D, Weeks JM and Nicholson JK. An NMR-based metabonomic investigation of the toxic effects of 3-trifluoromethyl-aniline on the earthworm Eisenia veneta. Biomarkers, 5: 56–72 (2000).

    Article  CAS  Google Scholar 

  • Waters NJ, Holmes E, Waterfield CJ, Farrant RD and Nicholson JK. NMR and pattern recognition studies on liver extracts and intact livers from rats treated with anaphthylisothiocyanate. Biochem.Pharmacol., 4: 67–77 (2002).

    Article  Google Scholar 

  • White CN, Chan DW and Zhang Z. Bioinformatics strategies for proteomic profiling. Clin. Biochem., 37: 636–41 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Whitehouse CM, Dreyer RN, Yamashita M and Fenn JB. Electrospray interface for liquid chromatographs and mass spectrometers. Anal. Chem., 57: 675–9 (1985).

    Article  PubMed  CAS  Google Scholar 

  • Wu CC and MacCoss MJ. Shotgun proteomics: tools for the analysis of complex biological systems. Curr. Opin. Mol. Ther., 4: 242–50 (2002).

    PubMed  CAS  Google Scholar 

  • Yamashita M and Fenn JB. Electrospray ion source. Another variation on the free-jet theme. J. Phys. Chem., 88: 4451–9 (1984).

    Article  CAS  Google Scholar 

  • Zhu W, Wang X, Ma Y, Rao M, Glimm J and Kovach JS. Detection of cancer-specific markers amid massive mass spectral data. Proc. Natl. Acad. Sci. USA, 100: 14666–71 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Zlatkis A and Liebich HM. Profile of volatile metabolites in human urine. Clin. Chem., 17: 592–4 (1971).

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer Science+Business Media, Inc.

About this chapter

Cite this chapter

Zhou, H., Kantor, A.B., Becker, C.H. (2005). Differential Metabolic Profiling for Biomarker Discovery. In: Vaidyanathan, S., Harrigan, G.G., Goodacre, R. (eds) Metabolome Analyses: Strategies for Systems Biology. Springer, Boston, MA. https://doi.org/10.1007/0-387-25240-1_9

Download citation

Publish with us

Policies and ethics