Hostname: page-component-848d4c4894-4rdrl Total loading time: 0 Render date: 2024-06-13T12:21:45.609Z Has data issue: false hasContentIssue false
  • English
  • Français

Proteomics in nutrition research: principles, technologies and applications

Published online by Cambridge University Press:  08 March 2007

Dagmar Fuchs ,
Isabel Winkelmann ,
Ian T. Johnson ,
Edwin Mariman ,
Uwe Wenzel  and
Hannelore Daniel
Dagmar Fuchs
Affiliation:
Molecular Nutrition Unit, Technical University of Munich, Am Forum 5, D-85 350 Freising-Weihenstephan, Germany
Isabel Winkelmann
Affiliation:
Molecular Nutrition Unit, Technical University of Munich, Am Forum 5, D-85 350 Freising-Weihenstephan, Germany
Ian T. Johnson
Affiliation:
Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
Edwin Mariman
Affiliation:
NUTRIM, University of Maastricht, PO Box 616, 6200 MD Maastricht, The Netherlands
Uwe Wenzel
Affiliation:
Molecular Nutrition Unit, Technical University of Munich, Am Forum 5, D-85 350 Freising-Weihenstephan, Germany
Hannelore Daniel*
Affiliation:
Molecular Nutrition Unit, Technical University of Munich, Am Forum 5, D-85 350 Freising-Weihenstephan, Germany
*
*Corresponding author: Professor Hannelore Daniel, fax +49 8161 71 3999, email daniel@wzw.tum.de
Rights & Permissions [Opens in a new window]

Abstract

Core share and HTML view are not available for this content. However, as you have access to this content, a full PDF is available via the ‘Save PDF’ action button.

The global profiling of the whole protein complement of the genome expressed in a particular cell or organ, or in plasma or serum, makes it possible to identify biomarkers that respond to alterations in diet or to treatment, and that may have predictive value for the modelling of biological processes. Proteomics has not yet been applied on a large scale in nutritional studies, yet it has advantages over transcriptome profiling techniques in that it directly assesses the entities that carry out the biological functions. The present review summarizes the different approaches in proteomics research, with special emphasis on the current technical ‘workhorses’: two-dimensional (2D)-PAGE with immobilized pH gradients and protein identification by MS. Using a work-flow approach, we provide information and advice on sample handling and preparation, protein solubilization and pre-fractionation, protein separation by 2D-PAGE, detection and quantification via computer-assisted analysis of gels, and protein identification and characterization techniques by means of MS. Examples from nutritional studies employing proteomics are provided to demonstrate not only the advantages but also the limitations of current proteome analysis platforms.

Keywords

ProteomicsTwo-dimensional gel electrophoresisMass spectrometryPrinciplesExamples
Type
Horizons in Nutritional Science
Information
British Journal of Nutrition , Volume 94 , Issue 3 , September 2005 , pp. 302 - 314
Copyright
Copyright © The Nutrition Society 2005

References

Alba, FJ, Bermudez, A, Bartolome, S & Daban, JR (1996) Detection of five nanograms of protein by two-minute Nile red staining of unfixed SDS gels. Biotechniques 21, 625–626.CrossRefGoogle ScholarPubMed
Barry, RC, Alsaker, BL, Robison-Cox, JF & Dratz, EA (2003) Quantitative evaluation of sample application methods for semipreparative separations of basic proteins by two-dimensional gel electrophoresis. Electrophoresis 24, 3390–3404.CrossRefGoogle ScholarPubMed
Beranova-Giorgianni, S (2003) Proteome analysis by two-dimensional gel electrophoresis and mass spectrometry: strength and limitations. TrAC 22, 273–281.Google Scholar
Bjellqvist, B, Ek, K, Righetti, PG, Gianazza, E, Gorg, A, Westermeier, R & Postel, W (1982) Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods 6, 317–339.CrossRefGoogle ScholarPubMed
Bouwman, F, Renes, J & Mariman, E (2004) A combination of protein profiling and isotopomer analysis using matrix-assisted laser desorption/ionization-time of flight mass spectrometry reveals an active metabolism of the extracellular matrix of 3T3-L1 adipocytes. Proteomics 4, 3855–3863.CrossRefGoogle ScholarPubMed
Bruker Daltonik GmbH (2002) MALDI Mass Spectrometry. Leipzig: Bruker Daltonik GmbH.Google Scholar
Carboni, L, Piubelli, C, Righetti, PG, Jansson, B & Domenici, E (2002) Proteomic analysis of rat brain tissue: comparison of protocols for two-dimensional gel electrophoresis analysis based on different solubilizing agents. Electrophoresis 23, 4132–4141.CrossRefGoogle ScholarPubMed
Chamrad, DC, Koerting, G, Gobom, J, Thiele, H, Klose, J, Meyer, HE & Blueggel, M (2003) Interpretation of mass spectrometry data for high-throughput proteomics. Anal Bioanal Chem 376, 1014–1022.CrossRefGoogle ScholarPubMed
Chaurand, P, Luetzenkirchen, F & Spengler, B (1999) Peptide and protein identification by matrix-assisted laser desorption ionization (MALDI) and MALDI–post-source decay time-of-flight mass spectrometry. J Am Soc Mass Spectrom 10, 91–103.CrossRefGoogle ScholarPubMed
Choi, BK, Cho, YM, Bae, SH, Zoubaulis, CC & Paik, YK (2003) Single-step perfusion chromatography with a throughput potential for enhanced peptide detection by matrix-assisted laser desorption/ionization–mass spectrometry. Proteomics 3, 1955–1961.CrossRefGoogle ScholarPubMed
Chrambach, A, Reisfeld, RA, Wyckoff, M & Zaccari, J (1967) A procedure for rapid and sensitive staining of protein fractionated by polyacrylamide gel electrophoresis. Anal Biochem 20, 150–154.CrossRefGoogle ScholarPubMed
Conrads, TP, Anderson, GA, Veenstra, TD, Pasa-Tolic, L & Smith, RD (2000) Utility of accurate mass tags for proteome-wide protein identification. Anal Chem 72, 3349–3354.CrossRefGoogle ScholarPubMed
Corthals, GL, Molloy, MP, Herbert, BR, Williams, KL & Gooley, AA (1997) Prefractionation of protein samples prior to two-dimensional electrophoresis. Electrophoresis 18, 317–323.CrossRefGoogle ScholarPubMed
Craven, RA, Totty, N, Harnden, P, Selby, PJ & Banks, RE (2002) Laser capture microdissection and two-dimensional polyacrylamide gel electrophoresis: evaluation of tissue preparation and sample limitations. Am J Pathol 160, 815–822.CrossRefGoogle ScholarPubMed
Dowsey, AW, Dunn, MJ & Yang, GZ (2003) The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics 3, 1567–1596.CrossRefGoogle ScholarPubMed
Dunn, MJ & Gorg, A (2001) Two-dimensional polyacrylamide gel electrophoresis for proteome analysis. In Proteomics from Protein Sequence to Function, 1st ed. pp. 45–47 [Pennington, SR and Dunn, MJ, editors]. Oxford: Bios.Google Scholar
Fels, LM, Buschmann, T, Meuer, J, Reymond, MA, Lamer, S, Rocken, C & Ebert, MP (2003) Proteome analysis for the identification of tumor-associated biomarkers in gastrointestinal cancer. Dig Dis 21, 292–298.CrossRefGoogle ScholarPubMed
Friedman, DB, Hill, S, Keller, JW, Merchant, NB, Levy, SE, Coffey, RJ & Caprioli, RM (2004) Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 4, 793–811.CrossRefGoogle ScholarPubMed
Fuchs, D, De Pascual-Teresa, S, Rimbach, G, Virgili, F, Ambra, R, Turner, R, Daniel, H & Wenzel, U (2005a) Proteome analysis for identification of target proteins of genistein in primary human endothelial cells stressed with oxidized LDL or homocysteine. Eur J Nutr 44, 95–104.CrossRefGoogle ScholarPubMed
Fuchs, D, Erhard, P, Turner, R, Rimbach, G, Daniel, H & Wenzel, U (2005b) Genistein reverses changes of the proteome induced by ox-LDL in EA.hy 926 endothelial cells. J Proteome Res 4, 369–376.CrossRefGoogle Scholar
Fuchs, D, Erhard, P, Rimbach, G, Daniel, H & Wenzel, U (2005c) Genistein blocks alterations of the proteome induced by homocysteine in endothelial cells. Proteomics (In the Press).CrossRefGoogle ScholarPubMed
Fuller, AP, Palmer-Toy, D, Erlander, MG & Sgroi, DC (2003) Laser capture microdissection and advanced molecular analysis of human breast cancer. J Mammary Gland Biol Neoplasia 8, 335–345.CrossRefGoogle ScholarPubMed
Garrels, JI (1979) Two dimensional gel electrophoresis and computer analysis of proteins synthesized by clonal cell lines. J Biol Chem 254, 7961–7977.CrossRefGoogle ScholarPubMed
Gelfi, C, Morelli, A, Rovida, E & Righetti, PG (1986) pH measurements in ultranarrow immobilized pH gradients. J Biochem Biophys Methods 13, 113–124.CrossRefGoogle ScholarPubMed
Gianazza, E, Veber, D, Eberini, I, Buccellato, FR, Mutti, E, Sironi, L & Scalabrino, G (2003) Cobalamin (vitamin B 12 )-deficiency-induced changes in the proteome of rat cerebrospinal fluid. Biochem J 374, 239–246.CrossRefGoogle ScholarPubMed
Gobom, J, Nordhoff, E, Mirgorodskaya, E, Ekman, R & Roepstorff, P (1999) Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry. J Mass Spectrom 34, 105–116.3.0.CO;2-4>CrossRefGoogle ScholarPubMed
Gobom, J, Schuerenberg, M, Mueller, M, Theiss, D, Lehrach, H & Nordhoff, E (2001) α-Cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics. Anal Chem 3, 434–438.CrossRefGoogle Scholar
Gohlke, RS (1959) Time-of-flight mass spectrometry and gas–liquid partition chromatography. Anal Chem 31, 535–541.CrossRefGoogle Scholar
Gorg, A, Boguth, G, Drews, O, Kopf, A, Luck, C, Reid, G & Weiss, W (2003) Two-dimensional Electrophoresis with Immobilized pH Gradients for Proteome Analysis, A Laboratory Manual. Munich: Technical University of Munich http://www.weihenstephan.de/blm/degGoogle Scholar
Gorg, A, Boguth, G, Obermaier, C & Weiss, W (1998) Two-dimensional electrophoresis of proteins in an immobilized pH 4–12 gradient. Electrophoresis 19, 1516–1519.CrossRefGoogle Scholar
Gorg, A, Obermaier, C, Boguth, G, Csordas, A, Diaz, JJ & Madjar, JJ (1997) Very alkaline immobilized pH gradients for two-dimensional electrophoresis of ribosomal and nuclear proteins. Electrophoresis 18, 328–337.Google Scholar
Gorg, A, Obermaier, C, Boguth, G, Harder, A, Scheibe, B, Wildgruber, R & Weiss, W (2000) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21, 1037–1053.3.0.CO;2-V>CrossRefGoogle ScholarPubMed
Gorg, A, Postel, W & Gunther, S (1988) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 9, 531–546.CrossRefGoogle ScholarPubMed
Gorg, A, Postel, W, Westermeier, R, Gianazza, E & Righetti, PG (1980) Gel gradient electrophoresis, isoelectric focusing and two-dimensional techniques in horizontal, ultrathin polyacrylamide layers. J Biochem Biophys Methods 3, 273–284.CrossRefGoogle ScholarPubMed
Hamdan, M, Galvani, M & Righetti, PG (2001) Monitoring 2-D gel-induced modifications of proteins by MALDI-TOF mass spectrometry. Mass Spectrom Rev 20, 121–141.CrossRefGoogle ScholarPubMed
Herbert, B (1999) Advances in protein solubilisation for two-dimensional electrophoresis. Electrophoresis 20, 660–666.3.0.CO;2-Q>CrossRefGoogle ScholarPubMed
Herzog, A, Kindermann, B, Doring, F, Daniel, H & Wenzel, U (2004a) Pleiotropic molecular effects of the pro-apoptotic dietary constituent flavone in human colon cancer cells identified by protein and mRNA expression profiling. Proteomics 4, 2455–2464.CrossRefGoogle ScholarPubMed
Herzog, A, Kuntz, S, Daniel, H & Wenzel, U (2004b) Identification of biomarkers for the initiation of apoptosis in human preneoplastic colonocytes by proteome analysis. Int J Cancer 109, 220–229.CrossRefGoogle ScholarPubMed
Hoving, S, Gerrits, B, Voshol, H, Muller, D, Roberts, RC & Van Oostrum, J (2002) Preparative two-dimensional gel electrophoresis at alkaline pH using narrow range immobilized pH gradients. Proteomics 2, 127–134.3.0.CO;2-Y>CrossRefGoogle ScholarPubMed
Huber, LA, Pfaller, K & Vietor, I (2003) Organelle proteomics: implications for subcellular fractionation in proteomics. Circ Res 92, 962–968.CrossRefGoogle ScholarPubMed
Jain, KK (2004) Role of pharmacoproteomics in the development of personalized medicine. Pharmacogenomics 5, 331–336.Google Scholar
Jespersen, S, Niessen, WM, Tjaden, UR, van der Greef, J (1998) Basic matrices in the analysis of non-covalent complexes by matrix-assisted laser desorption/ionization mass spectrometry. J Mass Spectrom 33, 1088–1093.3.0.CO;2-8>CrossRefGoogle ScholarPubMed
Johnson, T, Bergquist, J, Ekman, R, Nordhoff, E, Schurenberg, M, Kloppel, KD, Muller, M, Lehrach, H & Gobom, J (2001) A CE–MALDI interface based on the use of prestructured sample supports. Anal Chem 73, 1670–1675.CrossRefGoogle ScholarPubMed
Joo, WA, Lee, DY & Kim, CW (2003) Development of an effective sample preparation method for the proteome analysis of body fluids using 2-D gel electrophoresis. Biosci Biotechnol Biochem 67, 1574–1577.CrossRefGoogle ScholarPubMed
Karas, M & Hillenkamp, F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 Daltons. Anal Chem 60, 2299–2301.CrossRefGoogle ScholarPubMed
Laemmli, UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685.Google Scholar
Linke, T, Ross, AC & Harrison, EH (2004) Profiling of rat plasma by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, a novel tool for biomarker discovery in nutrition research. J Chromatogr A 1043, 65–71.CrossRefGoogle ScholarPubMed
Loo, JA & Muenster, H (1999) Magnetic sector-ion trap mass spectrometry with electrospray ionization for high sensitivity peptide sequencing. Rapid Commun Mass Spectrom 13, 54–60.3.0.CO;2-Y>CrossRefGoogle ScholarPubMed
Lopez, MF, Berggren, K, Chernokalskaya, E, Lazarev, A, Robinson, M & Patton, WF (2000) A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling. Electrophoresis 21, 3673–3683.3.0.CO;2-M>CrossRefGoogle ScholarPubMed
Mariani, SM (2003) Clinical proteomics: new promises for early cancer detection. MedGenMed 5, 23.Google ScholarPubMed
Marvin, LF, Roberts, MA & Fay, LB (2003) Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in clinical chemistry. Clin Chim Acta 337, 11–21.CrossRefGoogle ScholarPubMed
Park, JY, Seong, JK & Paik, YK (2004) Proteomic analysis of diet-induced hypercholesterolemic mice. Proteomics 4, 514–523.CrossRefGoogle ScholarPubMed
Patton, WF (2002) Detection technologies in proteome analysis. J Chromatogr B Analyt Technol Biomed Life Sci 771, 3–31.CrossRefGoogle ScholarPubMed
Pennigton, SR & Dunn, MJ (2001) Proteomics from protein sequence to function. Oxford, UK: B105.Google Scholar
Petricoin, EF, Zoon, KC, Kohn, EC, Barrett, JC & Liotta, LA (2002) Clinical proteomics: translating benchside promise into bedside reality. Nat Rev Drug Discov 1, 683–695.Google Scholar
Phelan, ML & Nock, S (2003) Generation of bioreagents for protein chips. Proteomics 3, 2123–2134.CrossRefGoogle ScholarPubMed
Pieper, R, Su, Q, Gatlin, CL, Huang, ST, Anderson, NL & Steiner, S (2003) Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome. Proteomics 3, 422–432.Google Scholar
Plymoth, A, Lofdahl, CG, Ekberg-Jansson, A, Dahlback, M, Lindberg, H, Fehniger, TE & Marko-Varga, G (2003) Human bronchoalveolar lavage: biofluid analysis with special emphasis on sample preparation. Proteomics 3, 962–972.CrossRefGoogle ScholarPubMed
Polednak, AP & Frome, EL (1981) Mortality among men employed between 1943 and 1947 at a uranium-processing plant. J Occup Med 23, 169–178.Google Scholar
Quadroni, M & James, P (1999) Proteomics and automation. Electrophoresis 20, 664–677.3.0.CO;2-A>CrossRefGoogle ScholarPubMed
Rabilloud, T, Valette, C & Lawrence, JJ (1994) Sample application by in-gel rehydration improves the resolution of two-dimensional electrophoresis with immobilized pH gradients in the first dimension. Electrophoresis 15, 1552–1558.CrossRefGoogle ScholarPubMed
Rai, AJ & Chan, DW (2004) Cancer proteomics: serum diagnostics for tumor marker discovery. Ann N Y Acad Sci 1022, 286–294.CrossRefGoogle ScholarPubMed
Rehm, H (2002) Der Experimentator: Proteinbiochemie/Proteomics. Stuttgart: Spektrum Akademischer Verlag.Google Scholar
Rekhter, MD & Chen, J (2001) Molecular analysis of complex tissues is facilitated by laser capture microdissection: critical role of upstream tissue processing. Cell Biochem Biophys 35, 103–113.CrossRefGoogle ScholarPubMed
Scheele, GA (1975) Two-dimensional gel analysis of soluble proteins. Charaterization of guinea pig exocrine pancreatic proteins. J Biol Chem 250, 5375–5385.CrossRefGoogle ScholarPubMed
Shaw, MM & Riederer, BM (2003) Sample preparation for two-dimensional gel electrophoresis. Proteomics 3, 1408–1417.CrossRefGoogle ScholarPubMed
Shevchenko, A, Wilm, M, Vorm, O & Mann, M (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68, 850–858.CrossRefGoogle ScholarPubMed
Sigma-Aldrich (2005) Peptide analysis: MALDI-MS. http://www.sigmaaldrich.com/Brands/Fluka_Riedel_Home/Bioscience/Peptide_Analysis/MALDI_Mass.htmlGoogle Scholar
Steinberg, TH, Haugland, RP & Singer, VL (1996) Applications of SYPRO orange and SYPRO red protein gel stains. Anal Biochem 239, 238–245.Google Scholar
Stephens, WE (1946) A pulsed mass spectrometer with time dispersion. Phys Rev 69, 691.Google Scholar
Tanaka, K, Waki, H, Ido, Y, Akita, S, Yoshida, Y & Yoshida, T (1988) Protein and polymer analyses up to m / z 100,000 by laser ionization time of flight mass spectrometry. Rapid Commun Mass Spectrom 2, 151–153.CrossRefGoogle Scholar
Thongboonkerd, V, Klein, E & Klein, JB (2004) Sample preparation for 2-D proteomic analysis. Contrib Nephrol 141, 11–24.CrossRefGoogle ScholarPubMed
tom Dieck, H, Doring, F, Fuchs, D, Roth, HP & Daniel, H (2005) Transcriptome and proteome analysis identifies the pathways that increase hepatic lipid accumulation in zinc-deficient rats. J Nutr 135, 199–205.CrossRefGoogle ScholarPubMed
Tonge, R, Shaw, J, Middleton, B, Rowlinson, R, Rayner, S, Young, J, Pognan, F, Hawkins, E, Currie, I & Davison, M (2001) Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 1, 377–396.3.0.CO;2-6>CrossRefGoogle Scholar
Trayhurn, P (2000) Proteomics and nutrition – a science for the first decade of the new millennium. Br J Nutr 83, 1–2.CrossRefGoogle ScholarPubMed
Unlu, M, Morgan, ME & Minden, JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071–2077.CrossRefGoogle ScholarPubMed
Vuadens, F, Gasparini, D, Deon, C, Sanchez, JC, Hochstrasser, DF, Schneider, P & Tissot, JD (2002) Identification of specific proteins in different lymphocyte populations by proteomic tools. Proteomics 2, 105–111.3.0.CO;2-F>CrossRefGoogle ScholarPubMed
Washburn, MP & Yates, JR 3rd (2000) Analysis of the microbial proteome. Curr Opin Microbiol 3, 292–297.Google Scholar
Weiss, W, Postel, W & Gorg, A (1992) Application of sequential extraction procedures and glycoprotein blotting for the characterization of the 2-D polypeptide patterns of barley seed proteins. Electrophoresis 13, 770–773.CrossRefGoogle ScholarPubMed
Weiss, W, Vogelmeier, C & Gorg, A (1993) Electrophoretic characterization of wheat grain allergens from different cultivars involved in bakers’ asthma. Electrophoresis 14, 805–816.CrossRefGoogle ScholarPubMed
Wenzel, U, Herzog, A, Kuntz, S & Daniel, H (2004) Protein expression profiling identifies molecular targets of quercetin as a major dietary flavonoid in human colon cancer cells. Proteomics 4, 2160–2174.Google Scholar
Westermeier, R (2001) Electrophoresis in Practice, 3rd ed. Weinheim: Wiley-VCH.Google Scholar
Wildgruber, R, Harder, A, Obermaier, C, Boguth, G, Weiss, W, Fey, SJ, Larsen, PM & Gorg, A (2000) Towards higher resolution: two-dimensional electrophoresis of Saccharomyces cerevisiae proteins using overlapping narrow immobilized pH gradients. Electrophoresis 21, 2610–2616.3.0.CO;2-H>CrossRefGoogle ScholarPubMed
Wilkins, MR, Sanchez, JC, Gooley, AA, Appel, RD, Humphery-Smith, I, Hochstrasser, DF & 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.CrossRefGoogle ScholarPubMed
Wirth, PJ & Romano, A (1995) Staining methods in gel electrophoresis, including the use of multiple detection methods. J Chromatogr A 698, 123–143.CrossRefGoogle ScholarPubMed
Zhan, X & Desiderio, DM (2003) Differences in the spatial and quantitative reproducibility between two second-dimensional gel electrophoresis systems. Electrophoresis 24, 1834–1846.CrossRefGoogle ScholarPubMed