Advances of analysis technology and data processing in metabonomics study

Abstract

Abstract: Metabonomics takes great progress withthe development of analysis technology and biometrics. Asa new member of omicssciences, metabonomics hasshown potentials in drug development, screening of drugtoxicity, and disease diagnosis for its sensitive, rapid,quantitative, noninvasive, and systemic characteristics.The key aspects of metabonomics, including preparationof samples, analysis technology, principle of data pro-cessing, traectory of metabolome, identification of bio-markers and indexation of metabolic pathway are reviewed in this article. The advantages and disadvantages of sev-eral popular analysis technologies for metabonomics areevaluated. Also the development prospect of metabonom-ics is expected.

Key words: metabonomics, nuclear magnetic reso-nance, GC/MS, LC/MS, biomarkers, multivariate analy-sis, patterm recognition, metabolic pathway

CLC Number:

R969.1

REN Hong-can, WANG Cuang-ji, A Ji-ye, HAO Hai-ping, SUN Jian-guo, ZHA Wei-bin, YAN Bei. Advances of analysis technology and data processing in metabonomics study[J]. Chinese Journal of Clinical Pharmacology and Therapeutics, 2007, 12(12): 1332-1338.

References

[1] Nicholson JK, onnelly J, Lindon JC, el al. Metabonomics: aplatfom for sludying drug toxicity and gene function [J]. NatRev Drug Discov, 2002;1:153-161.
[2] 徐旻,林东海，刘昌孝，代谢组学研究现状与展望[J]. 2005;40:769-774.
[3] Oliver SG. Yeast as a navigational aid in genome analysis[J].Microbiology, 1997; 143: 1483-1487.
[4] Nicholson JK, Lindon JC, Holmes E. Metabonomics :under-standing the metabolic responses of living systems to pathophysi-ological stimuli via multivariate statistical analysis of biologicalNMR spectroscopic data[J]. Xenobiotica, 1999; 29: 1181-189.
[5] Dunn WB, Bailey NJ, Johnson HE. Measuring the metabo-lome: current analytical technologies[J]. Analyst, 2005; 130:606-625 .
[6] Fiehn O, Kloska S, Altmann T. Integrated studies on plant bi-ology using multiparallel techniques[J]. Curr Opin Botechnol, 2001;12:82-86.
[7] Plumb RS, Granger JH, Stumpf CL, et al. A rapid screeningapproach to metabonomics using UPLC and oa-TOF mass spec-trometry: application to age, gender and diumal variation innommal Zucker obese rats and black, white and nude mice[J] .Analyst, 2005; 130:844-849.
[8] Fiehn O, Kristal B, van OmmenB, el al, Establishing report-ing standards for metabolomic and metabonomic studies: a callfor participation[J]. Omics, 2006;10:158-163.
[9] Jenkins H, Hardy N, Beckmann M, el al. A proposed frame-work for the description of plant metabolomics experiments andtheir resuls[J]. Nat Biotechnol, 2004;22:1601-1606.
[10] AJ, Trygg J, GullbergJ, et al. Extraction and CC/MS analys-is of the human blood plasma metabolome[J]. Anal Chem,2005;77 :8086-8094.
[11] Koek MM, Muilwijk B, van der Werf MJ, et al. Microbialmetabolomics with gas chromatography/mass spectrometry[J].Anal Chem, 2006;78:1272-1281.
[12] Lindon JC, Nicholson JK, Holmes E, et al . Sunmary recom-mendations for standardization and reporting of metabolic analy-ses[J]. Nat Biotechnol, 2005 ;23:833-838.
[13] Allen J, Davey HM, Broadhurst D, et al. High-throughputclassification of yeast mutants for functional genomics usingmetabolic footprinting[J]. Nat Biotechnol, 2003; 21:692-696.
[14] Want EJ, O'Maille G, Smith CA, et al. Solvent-dependentmetabolite distribution, clustering, and protein extraction foserum profiling with mass spectrometry[J]. Anal Chem, 2006;78:743-752.
[15] Akira K, Imachi M, Hashimoto T. Investigations into biochemical changes of genetic hypertensive rats using IH nuclear mag-netic resond metabnomics [J]. Hypertens Res, 2005;28:425-430.
[16] 许国旺，杨军．代谢组学及其研究进展[J].色谱，2003;21 :316-320.
[17] 赵剑宇,颜贤忠基于核磁共振的代谢组学研究进展[J].国外医学药学分册，2004;31:308-312.
[18] Lenz EM, Wilson ID. Analytical strategies in metabonomics[J]. J Proteome Res, 2007 ;6:443-458.
[19] Boemsen ко, Gatzek s, Imbert c, el al. Controlled proteinprecipitation in combination with chip-based nanospray infusionmass spectrometry .An approach for metabolomics profiling ofplasma[J]. Anal Chem, 2005 ;77:7255-7264.
[20] Castrillo JI, Hayes A, MohammedS, el al. An optimized pru-tocol for metabolome analysis in yeast using direct infusion elec-trospray mass spectrometry [J]. Phytochemistry, 2003 ; 62: 929-937.
[21] Allen J, Davey HM , Broadhurst D,et al. High-throughputclassification of yeast mutants for functional genomics usingmetabolic footprintinglJ J. Nat Biotechnol, 2003; 21: 692-696.
[22] Scholz M, Gatzek s, Serling A, et al. Metabolite fingerprint-ing: detecting biological features by independentcomponentanalysis[J]. Bioinfomnatics, 2004 ;20: 24472454.
[23] Hirai MY, Yano M, Goodenowe DB, et al . Integration of tran-scriptomics and metabolomics for understanding of global re-sponses to nutritional stresses in Arabidopsis thaliana[J]. ProcNatl Acad Sci USA, 2004; 101: 10205-10210.
[24] Plumb RS, Sumpf CL, Corenstein Mv, et al. Metaboromics:the use of electrospray mass spectrometry coupled to reversed-phase liquid ehromratogruphy shkown polential for the screening ofrat rine in drug development(]. Rapid Cummun Mass Spec-trom, 20021 161 1991-1996.
[25] Wilson ID, Plumb R, Cranger J, et al. HPLC MS basedmethodl for the study of metalonomics[J, J Chromnatogr B An-alyt Technol Biomed Life Sci, 2005;817;67-76.
[26] Phuan-Tuan H, Kaskavelis L, Daykin CA, el al. Method de-velopment in high-performance liquid chromatography for high-throughput profiling and metabononic studies of biofluid samples[J]. J Chromatography B, 2003;789:283-301.
[27] Plumb RS, Johnson KA, RainvilleP, et al. úPLC/MS: a newapproach for generating molecular fragment information for bio-maker stru ture elucidation [J]. Rapid Commun Mass Spec-trom, 2006; 20:2234.
[28] Lafaye A, Junot c, Ramounet-Le GB, et al. Metabolite profil-ing in rat urine by liquid chromatographylelectrospray ion trapmass spectrometry: Application to the study of heavy metal tox-icity[J]. Rapid Commun Mass Speetrom, 2003; 17:2541-2549.
[29] Snbatine MS, Liu E, Morrow DA, et al. Metabolomic identifi-cation of novel biomarkers of myocardial ischemia[J]. Circula-tion, 2005;112:3868-3875.
[30] Raiville PD, Stunpf CL, Shockoor JP, et al. Novel applica-tion of reversed-phase UPLC-oaTOF-MS for lipid analysis incomplex biological mixtures: a now tool for lipidomics[J]. JProteome Res, 2007 ;6:552-SS8.
[31] Yin P, Zhao X, LiQ, el al. Metalonomics Study of Intestinal Fistulas Based on Ultraperfomance Liquid ChromatographyCoupled with Q-TOF Mass Spectromelry (UPLC/Q-TOF MS)[J]. J Proteome Res, 2006;5:2135-2143.
[32] Viant MR, Pincetich CA, Hinton DE, et al . Toxic actions ofdinoseb in medaka (Oryzias latipes) embryos as detemmined byin vivo 'p NMR, HPLC-UV and 'H NMR metabolomics J].Aquatic Toxicology , 2006; 76: 329-342.
[33] Lenz EM, Bright J, Knight R, et al . Cyclosporin A-inducedchanges in endogenous metabolites in rat urine: a metabonomicinvestigation using high field 'H NMR spectroscopy, HPLC-TOF/MS and chemometrics[J]. J Pharm Biomed Anal, 2005 ;35:599-608.
[34] Williams RE, Major H, Lock EA, et al. D-Serine-inducednephrotoxicity: a HPLC-TOF/MS-based metabonomics approach[J]. Toxicology, 2005;207:179-190.
[35] YangJ, ZhaoX, LiuX, et al. High Performance Liquid Chro-matography-Mass Spectrometry for Metabonomics: Potential Bio-markers for Acute Deterioration of Liver Function in ChronicHepatitis B[J]. J Proteome Res, 2006;5:554-561.
[36] Dettmer K, Aronov PA, Hammock BD.Mass spectrometry-based metabolomics[J]. Mass Spectrom Rev, 2007;26:51-78.
[37] Adahchour M, Brandt M, Baier HU. Comprehensive two-di-mensional gas chromatography coupled to a rapid-scanning qua-drupole mass spectrometer: principles and applications[J]. JChromatogr A, 2005; 1067:245-254.
[38] O'HaganS, Dunn WB, Knowles JD, et al. Closed-loop, mul-tiobjective optimization of two-dimensional gas chromatography/ma8s spertrometryfor serurI metabolomics J]. Anal Chem,2007;79:464-476.
[39] Kuhara T. Gas chromatographic-mass spectrometric urinarymetabolome analysis to study mutations of inbom errors of me-tabolism[J]. Mass Spectrom Rev, 2005;24:814-827.
[40] OhdoiC, Nyhan WL, Kuhara T. Chemical diagnosis of Lesch-Nyhan syndrome using gas chromatography-mass spectrometrydeltection[J]. J Chromatography B, 2003;792;123-130.
[41] Terabe S. Metabolome analysis by capillary electrophoresis-mass spectromelry[J]. J Chromatogr A, 2007; 1168: 237-246.
[42] Ramautar R, Jong GJ, Demirci A. Capillary electrophoresis inmetabolomics[J]. Trends Analyt Chem, 2006; 25:455-466.
[43] Reo NV. NMR-based metabolomics[J]. Drug Chem Toxicol,2002;25:375-382.
[44] Dumas M, Maibaum EC, Teague c, et al. Assessment of ana-lytical reproducibility of (1)H NMR spectroscopy based metab)-nomics for large-scale epidemiological research: the INTERMAP study[J]. Anal Chem, 2006 ;78:2199-2208.
[45] Sandusky P, Raftery D. Use of semiselective TOCSY and thepearson correlation for the metabonomic analysis of biofluid mix-tures: aplication to urine[J]. Anal Chem, 2005 ;77:7717-7723.
[46] Wind RA, Hu JZ, Majors PD. Slow-MAS NMR: A new techn-ology for in vivo metalolomic studies[J]. Drug Discov Today:Technol, 2005;2: 291-294.
[47] Clayton TA, Lindon JC, Cloarec 0, et al. Pharmaco-metabo-nomic phenolyping and personalized drug treatmen[J]. Nature,2006;440: 1073-1077.
[48] Lindon JC, Keun HC, Ebbels TM, et al. The consortium formetabonomic toxicology (COMET) : aims, activities and achie-vements[J]. Pharmacogenomics, 2005 ;6:691-699.
[49] Brindle JT, Henrik A, Elaine H, et al . Nature Medicine[J].Nat Med, 2002;8: 1439-1444.
[50] Bo llardME, Stanley EG, Lindon JC. NMR-based metabonomicapproaches for evaluating physiological influences on biofluidcomposition[J]. NMR Biomed, 2005;18: 143-162.
[51] Atherton HJ, Bailey NJ, Zhang W, et al. A combined IHNMRspectroscopy andmass spectrometry-based metabolomicstudy of the PPAR null mutant mouse defines profound systemicchanges in metabolism linked to the metabolic syndrome[J].Physiol Genomics, 2006;27: 178-186.
[52] Crockford DJ, Holmes E, Lindon JC, et al. Statistical het-erospectroscopy, an approach to the integrated analysis of NMRand UPLC-MS data sels: application in metabonomic toxicologystudies[J]. Anal Chem, 2006 ;78:363-371.
[53] Willians R, Lenz, EM, Wilson AJ, et al. A multi-analyticalplatform approach to the metabonomic analysis of plasma fromnormal and zucker (fa/fa) obxese rats[J]. Mol Biosyst, 2006;2: 74-183.
[54] Goodacre R J. Making sense of the metalolome using evolution-ary computation: seeing the wood with the trees [J]. Exp Bot,2005 ;56:245-254.
[55] Shulaev V. Metalolomics technology and bioinfonnatics[J].Brief Bioinforn, 2006;7:128-139.
[56] SmithCA, Want EJ, O'Maille G, et al. XCMS: processingmass spectrometry data for metabolite profiling using nonlinearpeak alignent, matching, and idenifiation[J], Anal Chem,2006;78:779-787.
[57] Eriksson L, Antti H, Gotfries J, et al . Using chemometrics fornavigating in the large data sets of genomics, proteomics, andmetabonomics(gpm)[J].Anal Bioanal Chem, 2004; 380:419-429.
[58] Trygg J, Holmes E, Lundstedt T. Chemometrics in Metabo-nomics[J]. J Proteome Res. 2007;6:469-479.
[59] Keun HC, Ebbels TM, Bollard ME, et al. Ceometric trajectoryanalysis of metabolic responses to toxicity can define treatmentspecific profiles[J]. Chem Res Toxicol, 2004;17:579-587.
[60] Williams RE, Lenz EM, Lowden JS, et al . The metabonomics ofaging and development in the rat: an investigation into the effectof age on the profile of endogenous metabolites in the urine ofmale rats using 'H NMR and HPLC-TOF MS[J]. Mol Biosyst,2005;1:166-175.
[61] Bollard ME, Keun HC, Beckonert 0, et al . Comparative meta-bonomics of differential hydrazine toxicity in the rat and mouse[J]. Toxicol Appl Pharmacol, 2005 ;204:135-I51.
[62] Styczynski MP, Moxley JF, Tong LV, et al. Systematic Identi-fication of Conserved Metabolites in GC/MS Data for Metabolo-mics and Biomarker Discovery[J]. Anal Chem, 2007;79:966-973.
[63] Schauer N, Seinhauser D, Strelkov s, et al. GC-MS librariesfor the rapid ident ifiation of metabklites in complex biologicalsamples[J]. FEBS Lett, 2005;579:1332-1337.
[64] Halket JM, Wateman D, Przyborowska AM, et al. Chemicalderivatization and mass spectral libraries in metabolic profilingby GC/MS and LC/MSMS[J]. J Exp Bot, 2005;56:219-243.
[65] Fridman E, PicherskyE.Metabolomics,genomics, pro-teomics, and the identification of enzymes and their substratesand prodlucts[J]. Curr Opin Plant Biol, 2005;8:242-248. .