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Nutrition
Volume 25, Issue 11
, Pages 1085-1093
, November 2009
Proteomics at the center of nutrigenomics: Comprehensive molecular understanding of dietary health effects
References
- . Mass spectrometry in nutrition: understanding dietary health effects at the molecular level. Mass Spectrom Rev. 2007;26:727–750
- . OMICS-driven biomarker discovery in nutrition and health. J Biotechnol. 2006;124:758–787
- . Nutrigenomics and personalized nutrition: science and concept. Pers Med. 2008;5:447–455
- . Nutritional genomics. Annu Rev Genomics Hum Genet. 2004;5:71–118
- . Nutrigenomics research for personalized nutrition and medicine. Curr Opin Biotechnol. 2008;19:110–120
- . Personalizing foods: is genotype necessary?. Curr Opin Biotechnol. 2008;19:121–128
- . Nutri-epigenomics: lifelong remodelling of our epigenomes by nutritional and metabolic factors and beyond. Clin Chem Lab Med. 2007;45:321–327
- . [Nutritionnal epigenomics: consequences of unbalanced diets on epigenetics processes of programming during lifespan and between generations]. Ann Endocrinol (Paris). 2005;66(pt 3):2S19–228
- . Proteomic methods in nutrition. Curr Opin Clin Nutr Metab Care. 2006;9:575–583
- . Proteomics in nutrition and health. Comb Chem High Throughput Screen. 2005;8:679–696
- . Editorial overview. Curr Opin Biotechnol. 2008;19:63–65
- . Profiling techniques in nutrition and health research. Curr Opin Biotechnol. 2008;19:83–99
- . Electrospray wings for molecular elephants (Nobel lecture). Angew Chem Int Ed Engl. 2003;42:3871–3894
- . The origin of macromolecule ionization by laser irradiation (Nobel lecture). Angew Chem Int Ed Engl. 2003;42:3860–3870
- . Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal Chem. 2006;78:2113–2120
- . Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry. Mol Cell Proteomics. 2005;4:835–845
- . Utilizing human blood plasma for proteomic biomarker discovery. J Proteome Res. 2005;4:1073–1085
- Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J Proteome Res. 2006;5:1379–1387
- . Analytical strategies for phosphoproteomics. Proteomics. 2009;9:1451–1468
- . Glycoprotein enrichment through lectin affinity techniques. Methods Mol Biol. 2008;424:373–396
- Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol. 2009;27:378–386
- . Lights, camera, action! Systematic variation in 2-D difference gel electrophoresis images. Electrophoresis. 2007;28:3324–3332
- . The continuing evolution of shotgun proteomics. Drug Discov Today. 2005;10:719–725
- . Quantitative mass spectrometry as a tool for nutritional proteomics. Am J Clin Nutr. 2008;88:597–604
- . ANIBAL, stable isotope-based quantitative proteomics by aniline and benzoic acid labeling of amino and carboxylic groups. Mol Cell Proteomics. 2008;7:800–812
- . Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999;17:994–999
- Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics. 2004;3:1154–1169
- Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem. 2003;75:1895–1904
- . Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol. 2006;7:R50
- . An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res. 2008;7:51–61
- . Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments. Brief Bioinform. 2008;9:156–165
- . Isotope dilution strategies for absolute quantitative proteomics. J Proteomics. 2009;Article in press; doi:10.1016/j.jprot.2009.03.007
- . Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A. 2003;100:6940–6945
- . Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat Protoc. 2006;1:1029–1043
- . Protein standard absolute quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks. Proteomics. 2008;8:4633–4636
- Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 2007;25:125–131
- . Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol. 2008;4:222
- . Current affairs in quantitative targeted proteomics: multiple reaction monitoring–mass spectrometry. Brief Funct Genomic Proteomic. 2009;8:145–157
- . Targeted proteomic strategy for clinical biomarker discovery. Mol Oncol. 2009;3:33–44
- A human proteome detection and quantitation project. Mol Cell Proteomics. 2009;8:883–886
- . Accuracy requirements for peptide characterization by monoisotopic molecular mass measurements. Anal Chem. 1996;68:4060–4063
- . Utility of accurate mass tags for proteome-wide protein identification. Anal Chem. 2000;72:3349–3354
- . Peptide mass fingerprinting using MALDI-TOF mass spectrometry. Methods Mol Biol. 1997;64:165–173
- . Prestructured MALDI-MS sample supports. Anal Chem. 2000;72:3436–3442
- . Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem. 1994;33:4390–4399
- . An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom. 1994;5:976–989
- . Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 1999;20:3551–3567
- . Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem. 2002;74:5383–5392
- . A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 2003;75:4646–4658
- . Statistics for proteomics: a review of tools for analyzing experimental data. Proteomics. 2006;6:48–55
- . Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007;4:207–214
- 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. 2007;6:3705–3717
- . Proteomics in nutrition research: principles, technologies and applications. Br J Nutr. 2005;94:302–314
- . OMICS-derived targets for inflammatory gut disorders: opportunities for the development of nutrition related biomarkers. Endocr Metab Immune Disord Drug Targets. 2007;7:271–287
- . Proteomics and metabonomics routes towards obesity. In: Sorensen T, Clément K editor. Obesity—genomics and postgenomics. New York: Informa Health Care; 2008;p. 527–536
- . The human peripheral blood mononuclear cell proteome responds to a dietary flaxseed-intervention and proteins identified suggest a protective effect in atherosclerosis. Proteomics. 2007;7:3278–3288
- Potential protein markers for nutritional health effects on colorectal cancer in the mouse as revealed by proteomics analysis. Proteomics. 2006;6:2844–2852
- . Transcriptome and proteome analysis identifies the pathways that increase hepatic lipid accumulation in zinc-deficient rats. J Nutr. 2005;135:199–205
- . The enteric nervous system I: organisation and classification. Pharmacol Toxicol. 2003;92:105–113
- Proteomics of the rat gut: analysis of the myenteric plexus-longitudinal muscle preparation. Proteomics. 2005;5:2561–2569
- Maternal deprivation affects the neuromuscular protein profile of the rat colon in response to an acute stressor later in life. J Proteomics. 2008;71:80–88
- Proteomic analysis of cytokine-induced proteins in human intestinal epithelial cells: implications for inflammatory bowel diseases. Proteomics. 2002;2:551–560
- . Fundamentals of neurogastroenterology. Gut. 1999;45(suppl 2):II6–II16
- . Temporal proteomic analysis of intestine developing necrotizing enterocolitis following enteral formula feeding to preterm pigs. J Proteome Res. 2009;8:72–81
- Functional food ingredients against colorectal cancer. An example project integrating functional genomics, nutrition and health. Nutr Metab Cardiovasc Dis. 2001;11(suppl):94–98
- . Proteome analysis of butyrate-treated human colon cancer cells (HT-29). Int J Cancer. 2002;98:523–531
- . Pleiotropic molecular effects of the pro-apoptotic dietary constituent flavone in human colon cancer cells identified by protein and mRNA expression profiling. Proteomics. 2004;4:2455–2464
- . The dietary bioflavonoid, quercetin, selectively induces apoptosis of prostate cancer cells by down-regulating the expression of heat shock protein 90. Prostate. 2008;68:1773–1789
- . Dietary zinc modulation of COX-2 expression and lingual and esophageal carcinogenesis in rats. J Natl Cancer Inst. 2005;97:40–50
- . Proteomic analysis of fructose-induced fatty liver in hamsters. Metabolism. 2008;57:1115–1124
- . Frontiers in nutrigenomics, proteomics, metabolomics and cancer prevention. Mutat Res. 2004;551:51–64
- . Diallyl disulfide induces ERK phosphorylation and alters gene expression profiles in human colon tumor cells. J Nutr. 2003;133:2901–2906
- 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 USA. 2002;99:11908–11913
- . Experimental and computational approaches to quantitative proteomics: status quo and outlook. J Proteomics. 2008;71:19–33
- . Proteomic analysis of human very low-density lipoprotein by two-dimensional gel electrophoresis and MALDI-TOF/TOF. Proteomics. 2007;7:143–154
- Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol. 2007;25:1035–1044
- Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 2007;25:125–131
- . Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics. 2006;5:573–588
- . Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov. 2002;1:153–161
- . Protein turnover on the scale of the proteome. Expert Rev Proteomics. 2006;3:97–110
- . G protein polymorphisms in hypertension, atherosclerosis, and diabetes. Annu Rev Med. 2005;56:17–28
- . Genetic and genomic insights into the molecular basis of atherosclerosis. Cell Metab. 2007;6:164–179
- G-protein beta 3 subunit 825 CC genotype is associated with unexplained (functional) dyspepsia. Gastroenterology. 2004;126:971–979
- Quantitative proteomic analysis of post-translational modifications of human histones. Mol Cell Proteomics. 2006;5:1314–1325
- . Characterization of histone H2A and H2B variants and their post-translational modifications by mass spectrometry. Mol Cell Proteomics. 2006;5:541–552
PII: S0899-9007(09)00244-5
doi: 10.1016/j.nut.2009.05.022
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Nutrition
Volume 25, Issue 11
, Pages 1085-1093
, November 2009
