Omics in Nutrition and Health Research

Nutrigenomics and Proteomics in Health and Disease: Food Factors and Gene Interactions

Volumn , Issue , 2009, Pages 11-29

  Affolter, Michael ^a   Raymond, Frédéric ^a   Kussmann, Martin ^a  

^a NESTLÉ RESEARCH CENTER   (Switzerland)

Author keywords

Absolute quantification (AQUA) of proteins peptides; Human genetic variation influencing nutrient bioavailability and bioefficacy; metabolomics technologies nuclear magnetic resonance (NMR) spectroscopy; Microarray based gene expression analysis mature genome wide profiling platform; Microarray based gene expression profiling; Microarray based transcriptomics in human nutritional intervention studies; Nature Methods mass spectrometry (MS) in proteomics; Nutrients and genome interaction; Omics in nutrition and health research; Proteomic technologies and applications

Indexed keywords

EID: 84889450222     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780813807263.ch2     Document Type: Chapter

References (172)

1. Adachi J, Kumar C, Zhang Y, Olsen JV, and Mann M. 2006. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol. 7(9): R80.
2. Aharoni A, Ric de Vos CH, Verhoeven HA, Maliepaard CA, Kruppa G, Bino R, and Goodenowe DB. 2002. Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry. OMICS. 6(3):217-234.
3. Anderson L and Hunter CL. 2006. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics. 5(4):573-588.
4. Anderson NL, Polanski M, Pieper R, Gatlin T, Tirumalai RS, Conrads TP, Veenstra TD, Adkins JN, Pounds JG, Fagan R, and Lobley A. 2004. The human plasma proteome: A nonredundant list developed by combination of four separate sources. Mol Cell Proteomics. 3(4):311-326.
5. Astle J, Ferguson JT, German JB, Harrigan GG, Kelleher NL, Kodadek T, Parks BA, Roth MJ, Singletary KW, Wenger CD, and Mahady GB. 2007. Characterization of proteomic and metabolomic responses to dietary factors and supplements. J Nutr. 137(12):2787-2793.
6. Astley SB and Elliott RM. 2007. The European Nutrigenomics Organisation: Linking genomics, nutrition and health research. J Sci Food Agr. 87(7):1180-1184.
7. Bains W. 1996. Company strategies for using bioinformatics. Trends Biotechnol. 14(8):312-317.
8. Bantscheff M, Schirle M, Sweetman G, Rick J, and Kuster B. 2007. Quantitative mass spectrometry in proteomics: A critical review. Anal Bioanal Chem. 389(4):1017-1031.
9. Barcelo-Batllori S, Andre M, Servis C, Levy N, Takikawa O, Michetti P, Reymond M, and Felley-Bosco E. 2002. Proteomic analysis of cytokine induced proteins in human intestinal epithelial cells: Implications for inflammatory bowel diseases. Proteomics. 2(5):551-560.
10. Barnes M, Freudenberg J, Thompson S, Aronow B, and Pavlidis P. 2005. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucl Acids Res. 33(18):5914-5923.
11. Barone AD, Beecher JE, Bury PA, Chen C, Doede T, Fidanza JA, and McGall GH. 2001. Photolithographic synthesis of high-density oligonucleotide probe arrays. Nucleosides Nucleotides Nucleic Acids. 20(4-7):525-531.
12. Beretta L. 2007. Proteomics from the clinical perspective: Many hopes and much debate. Nat Methods. 4(10):785-786.
13. Beynon RJ and Pratt JM. 2005. Metabolic labeling of proteins for proteomics. Mol Cell Proteomics. 4(7):857-872.
14. Bjorhall K, Miliotis T, and Davidsson P. 2005. Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics. 5(1):307-317.
15. Bosotti R, Locatelli G, Healy S, Scacheri E, Sartori L, Mercurio C, Calogero R, and Isacchi A. 2007. Cross platform microarray analysis for robust identification of differentially expressed genes. BMC Bioinformatics. 8(Suppl 1):S5.
16. Bowman MJ and Zaia J. 2007. Tags for the stable isotopic labeling of carbohydrates and quantitative analysis by mass spectrometry. Anal Chem. 79(15): 5777-5784.
17. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC et al. 2001. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 29(4): 365-371.
18. Breen FM, Plomin R, and Wardle J. 2006. Heritability of food preferences in young children. Physiol Behav. 88(4-5):443-447.
19. Breikers G, van Breda SG, Bouwman FG, van Herwijnen MH, Renes J, Mariman EC, Kleinjans JC, and van Delft JH. 2006. Potential protein markers for nutritional health effects on colorectal cancer in the mouse as revealed by proteomics analysis. Proteomics. 6(9):2844-2852.
20. Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O et al. 2007. A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol. 25(5):576-583.
21. Buchanan MV and Hettich RL. 1993. Fourier transform mass spectrometry of high-mass biomolecules. Anal Chem. 65(5):245A-259A.
22. Caspi A, Williams B, Kim-Cohen J, Craig IW, Milne BJ, Poulton R, Schalkwyk LC, Taylor A, Werts H, and Moffitt TE. 2007. Moderation of breastfeeding effects on the IQ by genetic variation in fatty acid metabolism. Proc Natl Acad Sci U S A. 104(47):18860-18865.
23. Colinge J, Masselot A, Cusin I, Mahe E, Niknejad A, Argoud-Puy G, Reffas S, Bederr N, Gleizes A, Rey PA, and Bougueleret L. 2004. High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics. 4(7):1977-1984.
24. Cornett DS, Reyzer ML, Chaurand P, and Caprioli RM. 2007. MALDI imaging mass spectrometry: Molecular snapshots of biochemical systems. Nat Methods. 4(10):828-833.
25. Davis CD and Milner J. 2004. Frontiers in nutrigenomics, proteomics, metabolomics and cancer prevention. Mutat Res. 551(1-2):51-64.
26. Davis CD and Milner JA. 2007. Biomarkers for diet and cancer prevention research: Potentials and challenges. Acta Pharmacol Sin. 28(9):1262-1273.
27. de Godoy LM, Olsen JV, de Souza GA, Li G, Mortensen P, and Mann M. 2006. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol. 7(6):R50.
28. Debey S, Schoenbeck U, Hellmich M, Gathof BS, Pillai R, Zander T, and Schultze JL. 2004. Comparison of different isolation techniques prior gene expression profiling of blood derived cells: Impact on physiological responses, on overall expression and the role of different cell types. Pharmacogenomics J. 4(3):193-207.
29. Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, and Aebersold R. 2006. The PeptideAtlas project. Nucleic Acids Res. 34(Database issue):D655-D658.
30. Dinkova-Kostova AT, Holtzclaw WD, Cole RN, Itoh K, Wakabayashi N, Katoh Y, Yamamoto M, and Talalay P. 2002. Direct evidence that sulfhydryl groups of Keap1 are the sensors regulating induction of phase 2 enzymes that protect against carcinogens and oxidants. Proc Natl Acad Sci U S A. 99(18): 11908-11913.
31. Doherty MK and Beynon RJ. 2006. Protein turnover on the scale of the proteome. Expert Rev Proteomics. 3(1):97-110.
32. Drewnowski A. 1997. Taste preferences and food intake. Annu Rev Nutr. 17:237-253.
33. Drewnowski A, Henderson SA, Levine A, and Hann C. 1999. Taste and food preferences as predictors of dietary practices in young women. Public Health Nutr. 2(4):513-519.
34. Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC et al. 2006a. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci U S A. 103(33):12511-12516.
35. Dumas ME, Maibaum EC, Teague C, Ueshima H, Zhou B, Lindon JC, Nicholson JK, Stamler J, Elliott P, Chan Q, and Holmes E. 2006b. Assessment of analytical reproducibility of 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: The INTERMAP Study. Anal Chem. 78(7):2199-2208.
36. Edvardsson U, von Lowenhielm HB, Panfilov O, Nystrom AC, Nilsson F, and Dahllof B. 2003. Hepatic protein expression of lean mice and obese diabetic mice treated with peroxisome proliferator-activated receptor activators. Proteomics. 3(4):468-478.
37. Fenn JB. 2003. Electrospray wings for molecular elephants (Nobel lecture). Angew Chem Int Ed Engl. 42(33):3871-3894.
38. Fiehn O, Kopka J, Dormann P, Altmann T, Trethewey RN, and Willmitzer L. 2000. Metabolite profiling for plant functional genomics. Nat Biotechnol. 18(11):1157-1161.
39. Field LA, Jordan RM, Hadix JA, Dunn MA, Shriver CD, Ellsworth RE, and Ellsworth DL. 2007. Functional identity of genes detectable in expression profiling assays following globin mRNA reduction of peripheral blood samples. Clin Biochem. 40(7):499-502.
40. Fong LY, Zhang L, Jiang Y, and Farber JL. 2005. Dietary zinc modulation of COX-2 expression and lingual and esophageal carcinogenesis in rats. J Natl Cancer Inst. 97(1):40-50.
41. Fuchs D, Erhard P, Rimbach G, Daniel H, and Wenzel U. 2005a. Genistein blocks homocysteine-induced alterations in the proteome of human endothelial cells. Proteomics. 5(11):2808-2818.
42. Fuchs D, Erhard P, Turner R, Rimbach G, Daniel H, and Wenzel U. 2005b. Genistein reverses changes of the proteome induced by oxidized-LDL in EA.hy 926 human endothelial cells. J Proteome Res. 4(2):369-376.
43. Fuchs D, Pascual-Teresa S, Rimbach G, Virgili F, Ambra R, Turner R, Daniel H, and Wenzel U. 2005c. Proteome analysis for identification of target proteins of genistein in primary human endothelial cells stressed with oxidized LDL or homocysteine. Eur J Nutr. 44(2):95-104.
44. Fuchs D, Vafeiadou K, Hall WL, Daniel H, Williams CM, Schroot JH, and Wenzel U. 2007. Proteomic biomarkers of peripheral blood mononuclear cells obtained from postmenopausal women undergoing an intervention with soy isoflavones. Am J Clin Nutr. 86(5):1369-1375.
45. Fuchs D, Winkelmann I, Johnson IT, Mariman E, Wenzel U, and Daniel H. 2005d. Proteomics in nutrition research: Principles, technologies and applications. Br J Nutr. 94(3):302-314.
46. Gavaghan CL, Holmes E, Lenz E, Wilson ID, and Nicholson JK. 2000. An NMR-based metabonomic approach to investigate the biochemical consequences of genetic strain differences: Application to the C57BL10J and Alpk:ApfCD mouse. FEBS Lett. 484(3):169-174.
47. Gelfi C, Vigano A, Ripamonti M, Pontoglio A, Begum S, Pellegrino MA, Grassi B, Bottinelli R, Wait R, and Cerretelli P. 2006. The human muscle proteome in aging. J Proteome Res. 5(6):1344-1353.
48. Gerber SA, Rush J, Stemman O, Kirschner MW, and Gygi SP. 2003. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A. 100(12):6940-6945.
49. German JB, Roberts MA, and Watkins SM. 2003. Genomics and metabolomics as markers for the interaction of diet and health: Lessons from lipids. J Nutr. 133(6 Suppl 1):2078S-2083S.
50. Giles J. 2005. Internet encyclopaedias go head to head. Nature. 438(7070):900-901.
51. Gingras AC, Gstaiger M, Raught B, and Aebersold R. 2007. Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol. 8(8):645-654.
52. Glassbrook N and Ryals, J. 2001. A systematic approach to biochemical profiling. Curr Opin Plant Biol. 4(3):186-190.
53. Gong Y, Li X, Yang B, Ying W, Li D, Zhang Y, Dai S, Cai Y, Wang J, He F, and Qian X. 2006. Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J Proteome Res. 5(6):1379-1387.
54. Gorg A, Weiss W, and Dunn MJ. 2004. Current two-dimensional electrophoresis technology for proteomics. Proteomics. 4(12):3665-3685.
55. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, and Aebersold R. 1999. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 17(10):994-999.
56. Hansen MB. 2003. The enteric nervous system I: Organisation and classification. Pharmacol Toxicol. 92(3):105-113.
57. Herzog A, Kindermann B, Doring F, Daniel H, and Wenzel U. 2004. Pleiotropic molecular effects of the pro-apoptotic dietary constituent flavone in human colon cancer cells identified by protein and mRNA expression profiling. Proteomics. 4(8):2455-2464.
58. Holmes E and Antti H. 2002. Chemometric contributions to the evolution of metabonomics: Mathematical solutions to characterising and interpreting complex biological NMR spectra. Analyst. 127(12):1549-1557.
59. Johnson A and Manor D. 2004. The transcriptional signature of vitamin E. Ann N Y Acad Sci. 1031:337-338.
60. Jones P, Cote RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, and Hermjakob H. 2008. PRIDE: New developments and new datasets. Nucleic Acids Res. 36(Database issue):D878-D883.
61. Joyce AR and Palsson BO. 2006. The model organism as a system: Integrating 'omics' data sets. Nat Rev Mol Cell Biol. 7(3):198-210.
62. Julka S and Regnier F. 2004. Quantification in proteomics through stable isotope coding: A review. J Proteome Res. 3(3):350-363.
63. Keun HC, Beckonert O, Griffin JL, Richter C, Moskau D, Lindon JC, and Nicholson JK. 2002. Cryogenic probe 13C NMR spectroscopy of urine for metabonomic studies. Anal Chem. 74(17): 4588-4593.
64. Khatri P and Draghici S. 2005. Ontological analysis of gene expression data: Current tools, limitations, and open problems. Bioinformatics. 21(18):3587-3595.
65. Kindermann B, Doring F, Fuchs D, Pfaffl MW, and Daniel H. 2005. Effects of increased cellular zinc levels on gene and protein expression in HT-29 cells. Biometals. 18(3):243-253.
66. Kitajka K, Sinclair AJ, Weisinger RS, Weisinger HS, Mathai M, Jayasooriya AP, Halver JE, and Puskas LG. 2004. Effects of dietary omega-3 polyunsaturated fatty acids on brain gene expression. Proc Natl Acad Sci U S A. 101(30): 10931-10936.
67. Knowles LM and Milner JA. 2003. Diallyl disulfide induces ERK phosphorylation and alters gene expression profiles in human colon tumor cells. J Nutr. 133(9):2901-2906.
68. Kocher T and Superti-Furga G. 2007. Mass spectrometry-based functional proteomics: From molecular machines to protein networks. Nat Methods. 4(10):807-815.
69. Kochhar S, Jacobs DM, Ramadan Z, Berruex F, Fuerholz A, and Fay LB. 2006. Probing gender-specific metabolism differences in humans by nuclear magnetic resonance-based metabonomics. Anal Biochem. 352(2):274-281.
70. Kolkman A, Dirksen EH, Slijper M, and Heck AJ. 2005. Double standards in quantitative proteomics: Direct comparative assessment of difference in gel electrophoresis and metabolic stable isotope labeling. Mol Cell Proteomics. 4(3):255-266.
71. Krijgsveld J, Ketting RF, Mahmoudi T, Johansen J, Artal-Sanz M, Verrijzer CP, Plasterk RH, and Heck AJ. 2003. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol. 21(8):927-931.
72. Kristiansen TZ, Bunkenborg J, Gronborg M, Molina H, Thuluvath PJ, Argani P, Goggins MG, Maitra A, and Pandey A. 2004. A proteomic analysis of human bile. Mol Cell Proteomics. 3(7):715-728.
73. Kuhn K, Baker SC, Chudin E, Lieu MH, Oeser S, Bennett H, Rigault P, Barker D, McDaniel TK, and Chee MS. 2004. A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res. 14(11):2347-2356.
74. Kussmann M and Affolter M. 2008. Proteomics and metabonomics routes towards obesity. In: Sorensen, CK (Ed), Obesity-Genomics and Postgenomics, Informa Health Care Inc., New York, pp 527-535.
75. Kussmann M and Blum S. 2007. OMICS-derived targets for inflammatory gut disorders: Opportunities for the development of nutrition related biomarkers. Endocr Metab Immune Disord Drug Targets. 7(4):271-287.
76. Kussmann M, Affolter M, and Fay LB. 2005. Proteomics in nutrition and health. Comb Chem High Throughput Screen. 8(8):679-696.
77. Kussmann M, Affolter M, Nagy K, Holst B, and Fay LB. 2007. Mass spectrometry in nutrition: Understanding dietary health effects at the molecular level. Mass Spectrom Rev. 26(6):727-750.
78. Lane MA, Roth GS, and Ingram DK. 2007. Caloric restriction mimetics: A novel approach for biogerontology. Methods Mol Biol. 371:143-149.
79. Lapillonne A, Clarke SD, and Heird WC. 2004. Polyunsaturated fatty acids and gene expression. Curr Opin Clin Nutr Metab Care. 7(2):151-156.
80. Lavine B and Workman JJ, Jr. 2004. Chemometrics. Anal Chem. 76(12):3365-3371.
81. Lee WN and Go VL. 2005. Nutrient-gene interaction: Tracer-based metabolomics. J Nutr. 135(12 Suppl): 3027S-3032S.
82. Lenaerts K, Bouwman FG, Lamers WH, Renes J, and Mariman EC. 2007. Comparative proteomic analysis of cell lines and scrapings of the human intestinal epithelium. BMC Genomics. 8:91.
83. Lenaerts K, Sokolovic M, Bouwman FG, Lamers WH, Mariman EC, and Renes J. 2006. Starvation induces phase-specific changes in the proteome of mouse small intestine. J Proteome Res. 5(9):2113-2122.
84. Lenz EM, Bright J, Wilson ID, Hughes A, Morrisson J, Lindberg H, and Lockton A. 2004. Metabonomics, dietary influences and cultural differences: A 1H NMR-based study of urine samples obtained from healthy British and Swedish subjects. J Pharm Biomed Anal. 36(4):841-849.
85. Lescuyer P, Hochstrasser D, and Rabilloud T. 2007. How shall we use the proteomics toolbox for biomarker discovery?. J Proteome Res. 6(9): 3371-3376.
86. Lindon JC, Holmes E, and Nicholson JK. 2001. Pattern recognition methods and applications in biomedical magnetic resonance. Progress Nucl Magn Reson Spectrosc. 39(1):1-40.
87. Lindon JC, Nicholson JK, Holmes E, Keun HC, Craig A, Pearce JT, Bruce SJ, Hardy N, Sansone SA, Antti H et al. 2005. Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol. 23(7):833-838.
88. Lopes LV, Marvin-Guy L, Fuerholz A, Affolter M, Ramadan Z, Kussmann M, Fay LB, and Bergonzelli GE. 2008. Maternal deprivation affects the neuromuscular protein profile of the rat colon in response to an acute stressor later in life. J Proteomics. 71(1):80-88.
89. Makarov A, Denisov E, Kholomeev A, Balschun W, Lange O, Strupat K, and Horning S. 2006. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal Chem. 78(7):2113-2120.
90. Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, and Aebersold R. 2007. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 25(1):125-131.
91. Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson ID, and Wang Y. 2007. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res. 6(2):546-551.
92. Marko-Varga G, Lindberg H, Lofdahl CG, Jonsson P, Hansson L, Dahlback M, Lindquist E, Johansson L, Foster M, and Fehniger TE. 2005. Discovery of biomarker candidates within disease by protein profiling: Principles and concepts. J Proteome Res. 4(4):1200-1212.
93. Martin FP, Dumas ME, Wang Y, Legido-Quigley C, Yap IK, Tang H, Zirah S, Murphy GM, Cloarec O, Lindon JC et al. 2007. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol. 3:112.
94. Marvin-Guy L, Lopes LV, Affolter M, Courtet-Compondu MC, Wagniere S, Bergonzelli GE, Fay LB, and Kussmann M. 2005. Proteomics of the rat gut: Analysis of the myenteric plexus-longitudinal muscle preparation. Proteomics. 5(10):2561-2569.
95. Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL et al. 2008. Human Proteinpedia enables sharing of human protein data. Nat Biotechnol. 26(2):164-167.
96. Matsuzaki K, Kato H, Sakai R, Toue S, Amao M, and Kimura T. 2005. Transcriptomics and metabolomics of dietary leucine excess. J Nutr. 135(6 Suppl): 1571S-1575S.
97. McCarroll SA and Altshuler DM. 2007. Copy-number variation and association studies of human disease. Nat Genet. 39(7 Suppl):S37-S42.
98. McClatchy DB, Dong MQ, Wu CC, Venable JD, and Yates JR, III. 2007. 15N metabolic labeling of mammalian tissue with slow protein turnover. J Proteome Res. 6(5):2005-2010.
99. McIver RT, Jr, Li Y, and Hunter RL. 1994. High-resolution laser desorption mass spectrometry of peptides and small proteins. Proc Natl Acad Sci U S A. 91(11):4801-4805.
100. McLoughlin P, Roengvoraphoj M, Gissel C, Hescheler J, Certa U, and Sachinidis A. 2004. Transcriptional responses to epigallocatechin-3 gallate in HT 29 colon carcinoma spheroids. Genes Cells. 9(7): 661-669.
101. Milner JA. 2006. Diet and cancer: Facts and controversies. Nutr Cancer. 56(2):216-224.
102. Mirzaei H, McBee J, Watts J, and Aebersold R. 2008. Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol Cell Proteomics. 7(4):813-823.
103. Mischak H, Apweiler R, Banks RE, Conaway M, Coon J, Dominiczak A, Ehrich JHH, Fliser D, Girolami M, Hermjakob H et al. 2007. Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clin Appl. 1(2):148-156.
104. Mitchell BL, Yasui Y, Lampe JW, Gafken PR, and Lampe PD. 2005. Evaluation of matrix-assisted laser desorption/ionization-time of flight mass spectrometry proteomic profiling: Identification of alpha 2-HS glycoprotein B-chain as a biomarker of diet. Proteomics. 5(8):2238-2246.
105. Motoyama A, Venable JD, Ruse CI, and Yates JR, III. 2006. Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. Anal Chem. 78(14): 5109-5118.
106. Mutch DM, Grigorov M, Berger A, Fay LB, Roberts MA, Watkins SM, Williamson G, and German JB. 2005. An integrative metabolism approach identifies stearoyl-CoA desaturase as a target for an arachidonate-enriched diet. FASEB J. 19(6):599-601.
107. Nandi A, Sprung R, Barma DK, Zhao Y, Kim SC, Falck JR, and Zhao Y. 2006. Global identification of O-GlcNAc-modified proteins. Anal Chem. 78(2): 452-458.
108. Nesvizhskii AI, Vitek O, and Aebersold R. 2007. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods. 4(10):787-797.
109. Nicholls AW, Mortishire-Smith RJ, and Nicholson JK. 2003. NMR spectroscopic-based metabonomic studies of urinary metabolite variation in acclimatizing germ-free rats. Chem Res Toxicol. 16(11):1395-1404.
110. Nicholson JK, Holmes E, Lindon JC, and Wilson ID. 2004. The challenges of modeling mammalian biocomplexity. Nat Biotechnol. 22(10):1268-1274.
111. Nicholson JK, Holmes E, and Wilson ID. 2005. Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol. 3(5):431-438.
112. Nicholson JK, Lindon JC, and Holmes E. 1999. 'Metabonomics': Understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica. 29(11):1181-1189.
113. Nicholson JK and Wilson ID. 1989. 1H NMR spectroscopy of biological fluids. Progress Nucl Magn Reson Spectrosc. 21:449-501.
114. Nicholson JK and Wilson ID. 2003. Opinion: Understanding 'global' systems biology: Metabonomics and the continuum of metabolism. Nat Rev Drug Discov. 2(8):668-676.
115. Nielsen ML, Savitski MM, and Zubarev RA. 2005. Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry. Mol Cell Proteomics. 4(6):835-845.
116. Nishikawa Y, Dmochowska B, Madaj J, Xue J, Guo Z, Satake M, Reddy DV, Rinaldi PL, and Monnier VM. 2003. Vitamin C metabolomic mapping in experimental diabetes with 6-deoxy-6-fluoro-ascorbic acid and high resolution 19F-nuclear magnetic resonance spectroscopy. Metabolism. 52(6):760-770.
117. Noguchi Y, Sakai R, and Kimura T. 2003. Metabolomics and its potential for assessment of adequacy and safety of amino acid intake. J Nutr. 133(6 Suppl 1):2097S-2100S.
118. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, and Ahn NG. 2005. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics. 4(10):1487-1502.
119. Ono M, Shitashige M, Honda K, Isobe T, Kuwabara H, Matsuzuki H, Hirohashi S, and Yamada T. 2006. Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol Cell Proteomics. 5(7):1338-1347.
120. Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P et al. 2007. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 25(8):894-898.
121. Ovstebo R, Lande K, Kierulf P, and Haug KB. 2007. Quantification of relative changes in specific mRNAs from frozen whole blood-methodological considerations and clinical implications. Clin Chem Lab Med. 45(2):171-176.
122. Panchaud A, Hansson J, Affolter M, Bel RR, Piu S, Moreillon P, and Kussmann M. 2008. ANIBAL-Stable-isotope-based quantitative proteomics by ANIline and Benzoic acid labeling of amino and carboxylic groups. Mol Cell Proteomics. 7(4): 800-812.
123. Perkins DN, Pappin DJ, Creasy DM, and Cottrell JS. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 20(18):3551-3567.
124. Raymond F, Metairon S, Borner R, Hofmann M, and Kussmann M. 2006. Automated target preparation for microarray-based gene expression analysis. Anal Chem. 78(18):6299-6305.
125. Reinders J and Sickmann A. 2005. State-of-the-art in phosphoproteomics. Proteomics. 5(16):4052-4061.
126. Rezzi S, Ramadan Z, Fay LB, and Kochhar S. 2007a. Nutritional metabonomics: Applications and perspectives. J Proteome Res. 6(2):513-525.
127. Rezzi S, Ramadan Z, Martin FP, Fay LB, van Bladeren P, Lindon JC, Nicholson JK, and Kochhar S. 2007b. Human metabolic phenotypes link directly to specific dietary preferences in healthy individuals. J Proteome Res. 6(11):4469-4477.
128. Righetti PG, Boschetti E, Lomas L, and Citterio A. 2006. Protein Equalizer Technology: The quest for a "democratic proteome." Proteomics. 6(14): 3980-3992.
129. Robertson DG. 2005. Metabonomics in toxicology: A review. Toxicol Sci. 85(2):809-822.
130. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S et al. 2004. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics. 3(12):1154-1169.
131. Scholten A, Poh MK, van Veen TA, van Breukelen B, Vos MA, and Heck AJ. 2006. Analysis of the cGMP/cAMP interactome using a chemical proteomics approach in mammalian heart tissue validates sphingosine kinase type 1-interacting protein as a genuine and highly abundant AKAP. J Proteome Res. 5(6):1435-1447.
132. Schrattenholz A and Groebe K. 2007. What does it need to be a biomarker? Relationships between resolution, differential quantification and statistical validation of protein surrogate biomarkers. Electrophoresis. 28(12):1970-1979.
133. Sellers KF, Miecznikowski J, Viswanathan S, Minden JS, and Eddy WF. 2007. Lights, Camera, Action! systematic variation in 2-D difference gel electrophoresis images. Electrophoresis. 28(18):3324-3332.
134. Selman C, Kerrison ND, Cooray A, Piper MD, Lingard SJ, Barton RH, Schuster EF, Blanc E, Gems D, Nicholson JK, Thornton JM, Partridge L, and Withers DJ. 2006. Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice. Physiol Genomics. 27(3):187-200.
135. Shelling AN and Ferguson LR. 2007. Genetic variation in human disease and a new role for copy number variants. Mutat Res. 622(1-2):33-41.
136. Shockcor JP and Holmes E. 2002. Metabonomic applications in toxicity screening and disease diagnosis. Curr Top Med Chem. 2(1):35-51.
137. Siuti N and Kelleher NL. 2007. Decoding protein modifications using top-down mass spectrometry. Nat Methods. 4(10):817-821.
138. Solanky KS, Bailey NJ, Beckwith-Hall BM, Davis A, Bingham S, Holmes E, Nicholson JK, and Cassidy A. 2003a. Application of biofluid 1H nuclear magnetic resonance-based metabonomic techniques for the analysis of the biochemical effects of dietary isoflavones on human plasma profile. Anal Biochem. 323(2):197-204.
139. Solanky KS, Bailey NJ, Holmes E, Lindon JC, Davis AL, Mulder TP, Van Duynhoven JP, and Nicholson JK. 2003b. NMR-based metabonomic studies on the biochemical effects of epicatechin in the rat. J Agric Food Chem. 51(14):4139-4145.
140. Staab CA, Ceder R, Jagerbrink T, Nilsson JA, Roberg K, Jornvall H, Hoog JO, and Grafstrom RC. 2007. Bioinformatics processing of protein and transcript profiles of normal and transformed cell lines indicates functional impairment of transcriptional regulators in buccal carcinoma. J Proteome Res. 6(9):3705-3717.
141. Stella C, Beckwith-Hall B, Cloarec O, Holmes E, Lindon JC, Powell J, van der Ouderaa F, Bingham S, Cross AJ, and Nicholson JK. 2006. Susceptibility of human metabolic phenotypes to dietary modulation. J Proteome Res. 5(10):2780-2788.
142. Stierum R, Burgemeister R, van Helvoort A, Peijnenburg A, Schutze K, Seidelin M, Vang O, and van Ommen B. 2001. Functional food ingredients against colorectal cancer. An example project integrating functional genomics, nutrition and health. Nutr Metab Cardiovasc Dis. 11(4 Suppl): 94-98.
143. Stoyanova R, Nicholson JK, Lindon JC, and Brown TR. 2004. Sample classification based on Bayesian spectral decomposition of metabonomic NMR data sets. Anal Chem. 76(13):3666-3674.
144. Sun B, Ranish JA, Utleg AG, White JT, Yan X, Lin B, and Hood L. 2007. Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics. Mol Cell Proteomics. 6(1):141-149.
145. Tan S, Seow TK, Liang RC, Koh S, Lee CP, Chung MC, and Hooi SC. 2002. Proteome analysis of butyrate-treated human colon cancer cells (HT-29). Int J Cancer. 98(4):523-531.
146. Tanaka K. 2003. The origin of macromolecule ionization by laser irradiation (Nobel lecture). Angew Chem Int Ed Engl. 42(33):3860-3870.
147. Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW et al. 2007. The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 25(8):887-893.
148. Tom Dieck H, Doring F, Fuchs D, Roth HP, and Daniel H. 2005. Transcriptome and proteome analysis identifies the pathways that increase hepatic lipid accumulation in zinc-deficient rats. J Nutr. 135(2): 199-205.
149. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, and Davison M. 2001. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics. 1(3):377-396.
150. Trygg J and Wold S. 2002. Orthogonal projections to latent structures (O-PLS). J Chemometrics. 16(3): 119-128.
151. Urfer W, Grzegorczyk M, and Jung K. 2006. Statistics for proteomics: A review of tools for analyzing experimental data. Proteomics. 6(Suppl 2):48-55.
152. Vittal R, Selvanayagam ZE, Sun Y, Hong J, Liu F, Chin KV, and Yang CS. 2004. Gene expression changes induced by green tea polyphenol (-)-epigallocatechin-3-gallate in human bronchial epithelial 21BES cells analyzed by DNA microarray. Mol Cancer Ther. 3(9):1091-1099.
153. Vitzthum F, Behrens F, Anderson NL, and Shaw JH. 2005. Proteomics: From basic research to diagnostic application. A review of requirements & needs. J Proteome Res. 4(4):1086-1097.
154. Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, and Burlingame AL. 2006. O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry. Mol Cell Proteomics. 5(5):923-934.
155. Walsh MC, Brennan L, Malthouse JP, Roche HM, and Gibney MJ. 2006. Effect of acute dietary standardization on the urinary, plasma, and salivary metabolomic profiles of healthy humans. Am J Clin Nutr. 84(3):531-539.
156. Wang J, Li D, Dangott LJ, and Wu G. 2006a. Proteomics and its role in nutrition research. J Nutr. 136(7):1759-1762.
157. Wang Y, Holmes E, Tang H, Lindon JC, Sprenger N, Turini ME, Bergonzelli G, Fay LB, Kochhar S, and Nicholson JK. 2006b. Experimental metabonomic model of dietary variation and stress interactions. J Proteome Res. 5(7):1535-1542.
158. Wang Y, Lawler D, Larson B, Ramadan Z, Kochhar S, Holmes E, and Nicholson JK. 2007. Metabonomic investigations of aging and caloric restriction in a life-long dog study. J Proteome Res. 6(5): 1846-1854.
159. Waterland RA and Jirtle RL. 2003. Transposable elements: Targets for early nutritional effects on epigenetic gene regulation. Mol Cell Biol. 23(15): 5293-5300.
160. Watkins SM and German JB. 2002. Toward the implementation of metabolomic assessments of human health and nutrition. Curr Opin Biotechnol. 13(5):512-516.
161. Watkins SM, Zhu X, and Zeisel SH. 2003. Phosphatidylethanolamine-N-methyltransferase activity and dietary choline regulate liver-plasma lipid flux and essential fatty acid metabolism in mice. J Nutr. 133(11):3386-3391.
162. Watson AD. 2006. Thematic review series: Systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: A global approach to lipid analysis in biological systems. J Lipid Res. 47(10): 2101-2111.
163. Weniger M, Engelmann JC, and Schultz J. 2007. Genome Expression Pathway Analysis Tool-analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context. BMC Bioinformatics. 8:179.
164. Whitfield PD, German AJ, and Noble PJ. 2004. Metabolomics: An emerging post-genomic tool for nutrition. Br J Nutr. 92(4):549-555.
165. Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, and Williams KL. 1996. Progress with proteome projects: Why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev. 13:19-50.
166. Williams RE, Lenz EM, Lowden JS, Rantalainen M, and Wilson ID. 2005. The metabonomics of aging and development in the rat: An investigation into the effect of age on the profile of endogenous metabolites in the urine of male rats using 1H NMR and HPLC-TOF MS. Mol Biosyst. 1(2):166-175.
167. Wolber PK, Collins PJ, Lucas AB, De Witte A, and Shannon KW. 2006. The Agilent in situ-synthesized microarray platform. Methods Enzymol. 410:28-57.
168. Wood JD, Alpers DH, and Andrews PL. 1999. Fundamentals of neurogastroenterology. Gut. 45(Suppl 2):116-1116.
169. Wu CC and MacCoss MJ. 2002. Shotgun proteomics: Tools for the analysis of complex biological systems. Curr Opin Mol Ther. 4(3):242-250.
170. Wu WW, Wang G, Baek SJ, and Shen RF. 2006. Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gelor LC-MALDI TOF/TOF. J Proteome Res. 5(3): 651-658.
171. Yates JR, III, Eng JK, McCormack AL, and Schieltz D. 1995. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem. 67(8):1426-1436.
172. Yi M, Horton JD, Cohen JC, Hobbs HH, and Stephens RM. 2006. WholePathwayScope: A comprehensive pathway-based analysis tool for high-throughput data. BMC Bioinformatics. 7:30.