Metabolomics technology and bioinformatics

Briefings in Bioinformatics

Volumn 7, Issue 2, 2006, Pages 128-139

  Shulaev, Vladimir ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

Bioinformatics; CE MS; GC MS; LC MS; Mass spectrometry; Metabolite profiling; Metabolomics

Indexed keywords

BIOINFORMATICS; CAPILLARY ELECTROPHORESIS; DATA ANALYSIS; FUNCTIONAL GENOMICS; GAS CHROMATOGRAPHY; INFORMATION PROCESSING; INFRARED SPECTROSCOPY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MEDICAL RESEARCH; MEDICAL TECHNOLOGY; METABOLITE; METABOLOMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; REVIEW; STATISTICAL ANALYSIS; SYSTEMS BIOLOGY; ANIMAL; BIOLOGY; BIOTECHNOLOGY; CELL FUNCTION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMAN; METABOLISM; METHODOLOGY; PHYSIOLOGY; PROTEOMICS; SIGNAL TRANSDUCTION;

PROTEOME;

ANIMALS; BIOTECHNOLOGY; CELL PHYSIOLOGY; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; METABOLISM; PROTEOME; PROTEOMICS; SIGNAL TRANSDUCTION;

EID: 33748468414     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbl012     Document Type: Review

References (147)

1. Oliver SG, Winson MK, Kell DB, et al. Systematic functional analysis of the yeast genome. Trends Biotechnol 1998;16:373-8.
2. Raamsdonk LM, Teusink B, Broadhurst D, et al. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol 2001;19:45-50.
3. Viant MR, Rosenblum ES, Tieerdema RS. NMR-based metabolomics: A powerful approach for characterizing the effects of environmental stressors on organism health. Environ Sci Technol 2003;37:4982-9.
4. Rizhsky L, Liang H, Shuman J, et al. When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. Plant Physiol 2004; 134:1683-96.
5. Catchpole GS, Beckmann M, Enot DP, et al. Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. PNAS 2005;102:14458-62.
6. Tweeddale H, Notley-McRobb L, Ferenci T. Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool ("metabolome") analysis. J Bacteriol 1998;180:5109-16.
7. Martins AM, Camacho D, Shuman J, et al. A systems biology study of two distinct growth phases of Saccharomyces cerevisiae cultures. Curr Genomics 2004;5: 649-63.
8. Nicholson JK, Lindon JC, Holmes E. 'Metabonomics': Understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 1999;29: 1181-9.
9. Watkins SM, German JB. Metabolomics and biochemical profiling in drug discovery and development. Curr Opin Mol Ther 2002;4:224-8.
10. German JB, Roberts MA, Fay L, et al. Metabolomics and individual metabolic assessment: The next great challenge for nutrition. J Nutr 2002;132:2486-7.
11. German JB, Roberts MA, Watkins SM. Genomics and metabolomics as markers for the interaction of diet and health: Lessons from lipids. J Nutr 2003;133:2078S-83S.
12. Watkins SM, Hammock BD, Newman JW, et al. Individual metabolism should guide agriculture toward foods for improved health and nutrition. Am J Clin Nutr 2001;74: 283-6.
13. Watkins SM, German JB. Toward the implementation of metabolomic assessments of human health and nutrition. Curr Opin Biotechnol 2002;13:512-6.
14. German JB, Roberts MA, Fay L, et al. Metabolomics and individual metabolic assessment: The next great challenge for nutrition. J Nutr 2002;132:2486-7.
15. Griffiths JR, Stubbs M. Opportunities for studying cancer by metabolomics: Preliminary observations on tumors deficient in hypoxia-inducible factor 1. Adv in Enzyme Regul 2003;43:67-76.
16. Watkins SM, Reifsnyder PR, Pan HJ, et al. Lipid metabolome-wide effects of the PPARgamma agonist rosiglitazone. J Lipid Res 2002;43:1809-17.
17. Fiehn O, Kopka J, Trethewey RN, et al. Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry. Anal Chem 2000;72: 3573-80.
18. Mendes P. Modeling large scale biological systems from functional genomic data: parameter estimation. In: Kitano H (ed). Foundations of Systems BioPogy. Cambridge, MA: MIT Press, 2001: pp. 163-86.
19. Weckwerth W, Loureiro ME, Wenzel K, et al. Differential metabolic networks unravel the effects of silent plant phenotypes. Proc Natl Acad Sci USA 2004;101:7809-14.
20. Kell DB, Mendes P. Snapshots of systems-metabolic control analysis and biotechnology in the post-genomic era. In: Cornish-Bowden A, Cardenas ML (eds). Technological and Medical Implications of Metabolic Control Analysis. Dordrecht: Kluwer Pcademic Publishers, 2000: pp. 3-25.
21. Phelps TJ, Palumbo AV, Beliaev AS. Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. Curr Opin Biotechnol 2002;13:20-4.
22. Theobald U, Mailinger W, Baltes M, et al. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 1. Experimental observations. Biotechnol Bioeng 1997;55: 305-16.
23. Buchholz A, Hurlebaus J, Wandrey C, et al. Metabolomics: Quantification of intracellular metabolite dynamics. Biomol Eng 2002;19:5-15.
24. Rizzi M, Baltes M, Theobald U, et al. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae.2. Mathematical model. Biotechnol Bioeng 1997;55:592-608.
25. Mendes P. Emerging bioinformatics for the metabolome. Brief Bioinform 2002;3:134-45.
26. Fiehn O. Metabolomics-the link between genotypes and phenotypes. Plant Mol Biol 2002;48:155-71.
27. Halket JM, Waterman D, Przyborowska AM, et al. Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/ MS. J Exp Bot 2005;56:219-43.
28. Allen J, Davey HM, Broadhurst D, et al. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 2003;21:692-6.
29. Florian CL, Preece NE, Bhakoo KK, et al. Characteristic metabolic profiles revealed by 1H NMR spectroscopy for three types of human brain and nervous system tumours. NMR Biomed 1995;8:253-64.
30. Florian CL, Preece NE, Bhakoo KK, et al. Cell type-specific fingerprinting of meningioma and meningeal cells by proton nuclear magnetic resonance spectroscopy. Cancer Res 1995;55:420-7.
31. Kim HK, Choi YH, Erkelens C, et al. Metabolic fingerprinting of Ephedra species using 1H-NMR spectroscopy and principal component analysis. Chem Pharm Bull 2005;53:105-9.
32. Choi HK, Choi YH, Verberne M, et al. Metabolic fingerprinting of wild type and transgenic tobacco plants by 1H NMR and multivariate analysis technique. Phytochemistry 2004;65:857-64.
33. Lamers RJ, Wessels EC, van de Sandt JJ, et al. A pilot study to investigate effects of inulin on Caco-2 cells through in vitro metabolic fingerprinting. J Nutr 2003;133:3080-4.
34. Johnson HE, Broadhurst D, Kell DB, et al. High-throughput metabolic fingerprinting of legume silage fermentations via Fourier transform infrared spectroscopy and chemometrics. Appl environ microbiol 2004;70:1583-92.
35. Gidman E, Goodacre R, Emmett B, et al. Investigating plant-plant interference by metabolic fingerprinting. Phytochemistry 2003;63:705-10.
36. Chung Y-L, Stubbs M, Griffiths JR. Metabolic profiling in tumors by in vivo and in vitro NMR spectroscopy. In: Harrigan GG, Goodacre R (eds). Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis. Boston, Dordrecht and London: Kluwer Academic Publishers, 2003: Pp. 83-94.
37. Fiehn O, Spranger J. Use of metabolomics to discover metabolic, patterns associated with human disease. In: Harrigan GG, Goodacre R (eds). Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis. Boston, Dordrecht and London: Kluwer Academic Publishers, 2003: Pp. 199-215.
38. Himmelreich U, Somorjai RL, Dolenko, B, et al. Rapid identification of Candida species by using nuclear magnetic resonance spectroscopy and a statistical classification strategy. Appl environ microbiol 2003;69:4566-74.
39. Jarvis RM, Goodacre R. Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data. Bioinformatics 2005;21:860-8.
40. Jonsson P, Gullberg J, Nordstrom A, et al. A strategy for identifying differences in large series of metabolomic samples analyzed by GC/MS. Anal Chem 2004;76:1738-45.
41. Kell DB. Metabolomics and machine learning: Explanatory analysis of complex metabolome data using genetic programming to produce simple, robust rules. Mol Biol Rep 2002;29:237-41.
42. Scholz M, Gatzek S, Sterling A, et al. Metabolite fingerprinting: detecting biological features by independent component analysis. Bioinformatics 2004;20:2447-54.
43. Hall R, Beale M, Fiehn O, et al. Plant metabolomics: The missing link in functional genomics strategies. Plant Cell 2002;14:1437-40.
44. Fiehm O. Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp Func Genom 2001;2:155-68.
45. Xing Li X, Brazhnik O, Kamal A, et al. Databases and visualization for metabolomics. In: Harrigan GG, Goodacre R (eds). Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis. Boston, Dordrecht and London: KluwerPAcademic Publishers, 2002: pp. 293-309.
46. Villas-Boas SG, Moxley JF, Akesson M, et al. High-throughput metabolic state analysis: The missing link in integrated functional genomics of yeasts. Biochem J 2005;388: 669-77.
47. Sumner LW, Mendes P, Dixon RA. Plant metabolomics: Large-scale phytochemistry in the functional genomics era. Phytochemistry 2003;62:817-36.
48. Roessner U, Wagner C, Kopka J, et al. Technical advance: Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J 2000;23: 131-42.
49. Fraser PD, Pinto ME, Holloway DE, et al. Technical advance: Application of high-performance liquid chromatography with photodiode array detection to the metabolic profiling of plant isoprenoids. Plant J 2000;24:551-8.
50. Huhman DV, Sumner LW. Metabolic profiling of saponins in Medicago sativa and Medicago truncatula using HPLC coupled to an electrospray ion-trap mass spectrometer. Phytochemistry 2002;59:347-60.
51. Tolstikov VV, Lommen A, Nakanishi K, et al. Monolithic silica-based capillary reversed-phase liquid chromatography/electrospray mass spectrometry for plant metabolomics. Anal Chem 2003;75:6737-40.
52. Soga T, Imaizumi M. Capillary electrophoresis method for the analysis of inorganic anions, organic acids, amino acids, nucleotides, carbohydrates and other anionic compounds. Electrophoresis 2001;22:3418-25.
53. Soga T, Ueno Y, Naraoka H, et al. Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. Anal Chem 2002;74:2233-9.
54. Soga T, Ohashi Y, Ueno Y, et al. Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J Proteome Res 2003;2:488-94.
55. Maharjan RP, Ferend T. Global metabolite analysis: The influence of extraction methodology on metabolome profiles of Escherichia coli. Anal Biochem 2003;313:145-54.
56. Villas-Boas SG, Hojer-Pedersen J, Akesson M, et al. Global metabolite analysis of yeast: Evaluation of sample preparation methods. Yeast 2005;22:1155-69.
57. Le GG, Colquhoun IJ, Davis AL, et al. Metabolite profiling of tomato (Lycopersicon esculentum) using 1H NMR spectroscopy as a tool to detect potential unintended effects following a genetic modification. J Agric Food Chem 2003;51: 2447-56.
58. Krishnan P, Kruger NJ, Ratcliffe RG. Metabolite finger-printing and profiling in plants using NMR. J Exp Bot 2005; 56:255-65.
59. Ratcliffe RG, Shachar-Hill Y. Probing plant metabolism with NMR. Annu Rev Plant Physiol Plant Mol Biol 2001;52: 499-526.
60. Griffin JL. Metabonomics: NMR spectroscopy and pattern recognition analysis of body fluids and tissues for characterisation of xenobiotic toxicity and disease diagnosis. Curr Opin Chem Biol 2003;7:648-54.
61. Glinski M, Weckwerth W. The role of mass spectrometry in plant systems biology. Mass Spectrom Rev 2006;25: 173-214.
62. Fiehn O, Kopka J, Dormann P, et al. Metabolite profiling for plant functional genomics. Nat Biotechnol 2000;18: 1157-61.
63. Gates SC, Sweeley CC, Krivit W, et al. Automated metabolic profiling of organic adds in human urine. II. Analysis of urine samples from "healthy" adults, sick children, and children with neuroblastoma. Clin Chem 1978;24:1680-9.
64. Gates SC, Dendramis N, Sweeley CC. Automated metabolic profiling of organic acids in human urine. I. Description of methods. Clin Chem 1978;24:1674-9.
65. Gates SC, Sweeley CC. Quantitative metabolic profiling based on gas chromatography. Clin Chem 1978;24:1663-73.
66. Little JL. Artifacts in trimethylsilyl derivatization reactions and ways to avoid them. J Chromatogr A 1999;844:1-22.
67. Maurer HH. Advances in analytical toxicology: The current role of liquid chromatography-mass spectrometry in drug quantification in blood and oral fluid. Anal Bioanal Chem 2005;381:110-8.
68. Maurer HH. Liquid chromatography-mass spectrometry in forensic and clinical toxicology. J Chromatogr B Biomed Sci Appl 1998;713:3-25.
69. Maurer HH, Peters FT. Toward high-throughput drug screening using mass spectrometry. Ther Drug Monit 2005; 27:686-8.
70. Bendahl L, Hansen SH, Gammelgaard B, et al. Hyphenation of ultra performance liquid chromatography (UPLC) with inductively coupled plasma mass spectrometry (ICP-MS) for fast analysis of bromine containing preservatives. J Pharm Biomed Anal 2006;40:648-52.
71. Castro-Perez J, Plumb R, Granger JH, et al. Increasing throughput and inforination content for in vitro drug metabolism experiments using ultra-performance liquid chromatography coupled to a quadrupole time-of-flight mass spectrometer. Rapid Commun Mass Spectrom 2005;19: 843-48.
72. Churchwell MI, Twaddle NC, Meeker LR, et al. Improving LC-MS sensitivity through increases in chromatographic performance: Comparisons of UPLC-ES/ MS/MS to HPLC-ES/MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2005;825:134-43.
73. Johnson KA, Plumb R. Investigating the human metabolism of acetaminophen using UPLC and exact mass oa-TOF MS. J Pharm Biomed Anal 2005;39:805-10.
74. Leandro CC, Hancock P, Fussell RJ, et al. Comparison of ultra-performance liquid chromatography and high-performance liquid chromatography for the determination of priority pesticides in baby foods by tandem quadrupole mass spectrometry. J Chromatogr A 2006;1103:94-101.
75. O'Connor D, Mortishire-Smith R, Morrison D, et al. Ultra-performance liquid chromatography coupled to time-of-flight mass spectrometry for robust, high-throughput quantitative analysis of an automated metabolic stability assay, with simultaneous determination of metabolic data. Rapid Commun Mass Spectrom 2006;20:851-7.
76. Plumb R, Castro-Perez J, Granger J, et al. Ultra-performance liquid chromatography coupled to quadrupole-orthogonal time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2004;18:2331-7.
77. Sherma J. UPLC: Ultra-performance liquid chromatography. J AOAC Int 2005;88:63A-7A.
78. Wilson ID, Nicholson JK, Castro-Perez J, et al. High resolution "ultra performance" liquid chromatography coupled to oa-TOF mass spectrometry as a tool for differential metabolic pathway profiling in functional genomic studies. J Proteome Res 2005;4:591-8.
79. Wilson ID, Plumb R, Granger J, et al. HPLC-MS-based methods for the study of metabonomics. J Chromatogr B Analyt Technol Biomed Life Sci 2005;817:67-76.
80. Wren SA. Peak capacity in gradient ultra performance liquid chromatography (UPLC). J Pharm Biomed Anal 2005; 38:337-43.
81. Yu K, Little D, Plumb R, et al. High-throughput quantification for a drug mixture in rat plasma - a comparison of ultra performance liquid chromatography/tandem mass spectrometry with high-performance liquid chromatography/tandem mass spectrometry. Rapid Commun Mass Spectrom 2006;20:544-52.
82. Tolstikov VV, Fiehn O. Analysis of highly polar compounds of plant origin: Combination of hydrophilic interaction chromatography and electrospray ion trap mass spectrometry. Anal Biochem 2002;301:298-307.
83. Terabe S, Markuszewski MJ, Inoue N, et al. Capillary electrophoretic techniques toward the metabolome analysis. Pure Appl Chem 2001;73:1563-72.
84. Perrett D, Ross G. Capillary electrophoresis - a powerful tool for biomedical analysis and research. TrAC, Trends Anal Chem 1992;11:156-63.
85. Perrett D, Alfrzema L, Hows M, et al. Capillary electrophoresis for small molecules and metabolites. Biochem Soc Trans 1997;25:273-8.
86. Perrett D. Capillary electrophoresis in clinical chemistry. Ann Clin Biochem 1999;36:133-50.
87. Kobayashi J, Shirao M, Nakazawa H. Simultaneous determination of anions and cations in mineral water by capillary electrophoresis with a chelating agent. J Liq Chromatogr RT 1998;21:1445-56.
88. Shirao M, Furuta R, Suzuki S, et al. Determination of organic-acids in urine by capillary zone electrophoresis. J Chromatogr A 1994;680:247-51.
89. Vorarat S, Aromdee C, Podokmai Y. Determination of alpha hydroxy acids in fruits by capillary electrophoresis. Anal Sciences 2002;18:893-6.
90. Soga T, Heiger DN. Amino acid analysis by capillary electrophoresis electrospray ionization mass spectrometry. Anal Chem 2000;72:1236-41.
91. Cohen AS, Terabe S, Smith JA, et al. High-performance capillary electrophoretic separation of bases, nucleosides, and oligonucleotides: retention manipulation via micellar solutions and metal additives. Anal Chem 1987;59: 1021-7.
92. Schreiner M, Razzazi E, Luf W. Determination of water-soluble vitamins in soft drinks and vitamin supplements using capillary electrophoresis. Nahrung-Food 2003;47: 243-7.
93. Carru C, Zinellu A, Galistu F, et al. Ultra rapid capillary electrophoresis method for total plasma thiols measurement. Clin Chem 2003;49:36.
94. Soga T, Heiger DN. Simultaneous determination of monosaccharides in glycoproteins by capillary electrophoresis. Anal Biochem 1998;261:73-8.
95. Perrett D, Birch A, Ross G. Capillary electrophoresis for peptides, including neuropeptides. Biochem Soc Transact 1994;22:127-31.
96. Britz-McKibbin P, Terabe S. High-sensitivity analyses of metabolites in biological samples by capillary electrophoresis using dynamic PH junction-sweeping. Chem Rec 2002; 2:397-404.
97. Tweeddale H, Notley-McRobb L, Ferenci T. Assessing the effect of reactive oxygen species on Escherichia coli using a metabolome approach. Redox Rep 1999;4:237-41.
98. Gamache PH, Meyer DF, Granger MC, et al. Metabolomic applications of electrochemistry/mass spectrometry. J Am Soc Mass Spectrom 2004;15:1717-26.
99. Kristal BS, Vigneau-Callahan K, Matson WR. Simultaneous analysis of multiple redox-active metabolites from biological matrices. Methods Mol Biol 2002;186: 185-94.
100. Shi H, Vigneau-Callahan KE, Shestopalov AI, et al. Characterization of diet-dependent metabolic serotypes: Primary validation of male and female serotypes in independent cohorts of rats. J Nutr 2002;132: 1039-46.
101. Thomas N, Goodacre R, Timmins EM, et al. Fourier transform infrared spectroscopy of follicular fluids from large and small antral follicles. Hum Reprod 2000;15: 1667-71.
102. Bochner BR, Gadzinski P, Panomitros E. Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res 2001;11:1246-55.
103. Mehrotra B, Mendes P. Bioinformatics approaches to integrate metabolomics and other systems biology data. In: Saito K, Dixon RA, Willmitzer L (eds). Plant Metabolomics; Vol. 57. Berlin, Heidelberg: Springer-Verlag, 2006: Pp. 105-15.
104. Halket JM, Przyborowska A, Stein SE, 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 1999;13:279-84.
105. Windig W, Phalp JM, Payne AW. A noise and background reduction methods for component detection in liquid chromatography/mass spectrometry. Anal Chem 1996;68:3602-6.
106. Fleming CM, Kowalski BR, Apffel A, et al. Windowed mass selection method: A new data processing algorithm for liquid chromatography-mass spectrometry data. J Chromatogr A 1999;849:71-85.
107. Duran AL, Yang J, Wang L, et al. Metabolomics spectral formatting, alignment and conversion tools (MSFACTs). Bioinformatics 2003;19:2283-93.
108. Windig W, Marchincin TF, Meyer GN. Determining sample differences in a sample series of complex liquid chromatography-diode array detector data using chemometrics. Appl Spectrosc 2003;57:1575-84.
109. Windig W, Antalek B, Lippert JL, et al. Combined use of conventional and second-derivative data in the SIMPLISMA self-modeling mixture analysis approach. Anal Chem 2002;74:1371-9.
110. Katajamaa M, Oresic M. Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics 2005;6:179.
111. Moulder R, Filen JJ, Salmi J, et al. A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments. Proteomics 2005;5:2748-60.
112. Katajamaa M, Miettinen J, Oresic M. MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 2006;22: 634-6.
113. Eisen MB, Spellman PT, Brown PO, et al. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998;95:14863-8.
114. Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 2000;97: 10101-6.
115. Tamayo P, Slonim D, Mesirov J, et al. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 1999;96:2907-12.
116. Churchill GA. Using ANOVA to analyze microarray data. Biotechniques 2004;37:173-5, 177.
117. Musumarra G, Barresi V, Condorelli DF, et al. A bioinformatic approach to the identification of candidate genes for the development of new cancer diagnostics. Biol Chem 2003;384:321-7.
118. Kohane IS, Kho AT, Butte AJ. Microarrays for integrative genomics. A Bradford Book. Pambridge: The MIT Press, 2003: p. 12.
119. Pena-Reyes CA, Sipper M. Evolutionary computation in medicine: An overview. Artif Intell Med 2000;19:1-23.
120. Goodacre R. Making sense of the metabolome using evolutionary computation: Seeing the wood with the trees. J Exper Botany 2005;56:245-54.
121. Shi H, Paolucci U, Vigneau-Callahan KE, et al. Development of biomarkers based on diet-dependent metabolic serotypes: Practical issues in development of expert system-based classification models in metabolomic studies. OMICS 2004;8:197-208.
122. Brazma A, Hingamp P, Quackenbush J, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001;29: 365-71.
123. Jenkins H, Hardy N, Beckmann M, et al. A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol 2004;22: 1601-6.
124. Binc RJ, Hall RD, Fiehn O, et al. Potential of metabolomics as a functional genomics tool. Trends Plant Sci 2004;9:418-25.
125. Lindon JC, Nicholson JK, Holmes E, et al. Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol 2005;23:833-8.
126. Castle AL, Fiehn O, Kaddurah-Daouk R, et al. Metabolomics standards workshop and the development of international standards for reporting metabolomics experimental results. Brief Bioinform 2006;7.
127. Wang J, Chen G. Microchip capillary electrophoresis with electrochemical detector for fast measurements of aromatic amino acids. Talanta 2003;60:1239-44.
128. Bilitewski U, Genrich M, Kadow S, et al. Biochemical analysis with microfluidic systems. Anal Bioanal Chem 2003; 377:556-69.
129. Figeys D, Gygi SP, McKinnon G, et al. An integrated microfluidics-tandem mass spectrometry system for automated protein analysis. Anal Chem 1998;70:3728-34.
130. Garcia CD, Henry CS. Direct determination of carbohydrates, amino acids, and antibiotics by microchip electrophoresis with pulsed amperometric detection. Anal Chem 2003;75:4778-83.
131. Dalluge J, Beens J, Brinkman UA. Comprehensive two-dimensional gas chromatography: A powerful and versatile analytical tool. J Chromatogr A 2003;1000:69-108.
132. Adahchour M, Jover E, Beens J, et al. Twin comprehensive two-dimensional gas chromatographic system: Concept and applications. J Chromatogr A 2005;1086:128-34.
133. Adahchour M, van Stee LL, Beens J, et al. Comprehensive two-dimensional, gas chromatography with time-of-flight mass spectrometric detection for the trace analysis of flavour compounds in food. J Chromatogr A 2003;1019: 157-72.
134. Adahchour M, Brandt M, Baier HU, et al. Comprehensive two-dimensional gas chromatography coupled to a rapid-scanning quadrupole mass spectrometer: Principles and applications. J Chromatogr A 2005;1067:245-54.
135. Evans CR, Jorgenson JW. Multidimensional LC-LC and LC-CE for high-resolution separations of biological molecules. Anal Bioanal Chem 2004;378:1952-61.
136. Kammerer B, Kahlich R, Ufer M, et al. Achiral-chiral LC/LC-MS/MS coupling for determination of chiral discrimination effects in phenprocoumon metabolism. Anal Biochem 2005;339:297-309.
137. Mondello L, Tranchida PQ, Stanek V, et al. Silver-ion reversed-phase comprehensive two-dimensional liquid chromatography combined with mass spectrometric detection in lipidic food analysis. J Chromatogr A 2005; 1086:91-8.
138. Sheldon EM. Development of a LC-LC-MS complete heart-cut approach for the characterization of pharmaceutical compounds using standard instrumentation. J Pharm Biomed Anal 2003;31:1153-66.
139. Stroink T, Ortiz MC, Bult A, et al. On-line multi-dimensional liquid chromatography and capillary electrophoresis systems for peptides and proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2005;817:49-66.
140. Bobzin SC, Yang S, Kasten TP. LC-NMR: A new tool to expedite the dereplication and identification of natural products. J Ind Microbiol Biotechnol 2000;25:342-5.
141. Burton KI, Everett JR, Newman MJ, et al. On-line liquid chromatography coupled with high field NMR and mass spectrometry (LC-NMR-MS): A new technique for drug metabolite structure elucidation. J Pharm Biomed Anal 1997; 15:1903-12.
142. Corcoran O, Spraul M. LC-NMR-MS in drug discovery. Drug Discov Today 2003;8:624-31.
143. Fritsche J, Angoelal R, Dachder M. On-line liquid-chromatography-nuclear magnetic resonance spectroscopy-mass spectrometry coupling for the separation and characterization of secoisolariciresinol diglucoside isomers in flaxseed. J Chromatogr A 2002;972: 195-203.
144. Holt RM, Newman MJ, Pullen FS, et al. High-performance liquid chromatography/NMR spectrometry/mass spectrometry: Further advances in hyphenated technology. J Mass Spectrom 1997;32:64-70.
145. Keifer PA. Flow NMR applications in combinatorial chemistry. Curr Opin Chem Biol 2003;7:388-94.
146. Spraul M, Freund AS, Nast RE, et al. Advancing NMR sensitivity for LC-NNM-MS using a cryoflow probe: Application to the analysis of acetaminophen metabolites in urine. Anal Chem 2003;75:1536-41.
147. Yang Z. Online hyphenated liquid chromatography-nuclear magnetic resonance spectroscopy-mass spectrometry for drug metabolite and nature product analysis. J Pharm Biomed Anal 2006;40:516-27.