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Proteome Analysis

  • Matthew J. Powell
  • Aaron T. Timperman
Part of the Methods in Molecular Biology™ book series (MIMB, volume 251)

Abstract

A major goal of proteomics is qualitative and quantitative analysis of all the proteins expressed in a cell, tissue, or organism. Changes in protein expression owing to a stimulus or condition are measured in a systematic manner, and are used to elucidate mechanisms of cell function and signaling. A strength of proteomics is that a “shot-gun” approach requiring no prior knowledge of the system is often used and does not assume a model prior to data collection. Therefore, proteomics provides the ability to deal with the complexity of biological systems with minimal experimental bias. The complexity of biological systems arises from the numerous parallel signaling pathways that interact with each other. The ability to monitor many proteins simultaneously yields a global view of protein expression and posttranslation modifications, which is much more informative than monitoring a few proteins. Methods that follow a few proteins and assume a model are more likely to miss interactions and yield biased results.

Keywords

Electrospray Ionization Tandem Mass Spectrometry Laser Desorption Ionization Mass Spectrometry Heptafluorobutyric Acid Capillary HPLC Amino Acid Sequence Information 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Kuster, B., Mortensen, P., and Mann, M. (1999) in Proc. 47th ASMS Conf. Mass Spectrom. and Allied Top., Dallas, TX, p. 1897.Google Scholar
  2. 2.
    Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, p. 1720–1730.PubMedGoogle Scholar
  3. 3.
    Tew, K. D. (1996) Glutathione-associated enzymes in the human cell lines of the National Cancer Institute Drug Screening Program. Mol. Pharmacol. 50, p. 149–159.PubMedGoogle Scholar
  4. 4.
    Boucherie, H., Sagliocco, F., Joubert, R., Maillet, I., Labarre, J., and Perrot, M. (1996) Two-dimensional gel protein database of Saccharomyces cerevisiae. Electrophoresis 17, 1683–1699.PubMedCrossRefGoogle Scholar
  5. 5.
    Ducret, A., Van Oostveen, I., Eng, J. K., Yates, J. R., and Aebersold, R. (1998) High throughput protein characterization by automated reverse-phase chromatography electrospray tandem mass spectrometry. Protein Sci. 7, p. 706–719.PubMedCrossRefGoogle Scholar
  6. 6.
    Garrels, J. I., Futcher, B., Kobayshi, R., et al. (1994) Protein Identifications for a Saccharomyces cerevisiae protein database. Electrophoresis 15, 1466–1486.PubMedCrossRefGoogle Scholar
  7. 7.
    Gygi, S. P., Corthals, G. L., Zhang, Y, Rochon, Y, and Aebersold, R. (2000) Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. in Proc. Nat. Acad. Sci. USA 97, p. 9390–9395.PubMedCrossRefGoogle Scholar
  8. 8.
    Shevchenko, A. O., Jensen, O. N., Podtelejnikov, A. V., et al. (1996) Linking genome and proteome by mass sepctrometry: large scale identification of yeast proteins from two-dimensional gels. Proc. Nat. Acad. Sci. USA 93, p. 14,440–14,445.PubMedCrossRefGoogle Scholar
  9. 9.
    Wilkins, M. R., Gasteiger, E., Sanchez, J.-C, Bairoch, A., and Hochstrasser, D. F (1998) Two-dimensional gel electrophoresis for proteome projects. The effects of protein hydrophobicity and copy number. Electrophoresis 19, 1501–1505.PubMedCrossRefGoogle Scholar
  10. 10.
    Yates, J. R. 3rd, Speicher, S., Griffin, P. R; Hunkapiller, T (1993) Peptide mass maps: a highly informative approach to protein identification. Anal. Biochem. 214, p. 397–408.PubMedCrossRefGoogle Scholar
  11. 11.
    Henzel, W. J. B., Todd, M., Stults, J. T, Wong, S. C., Grimley, C., and Watanabe, C. (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Nat. Acad. Sci. USA 90, p. 5011–5015.PubMedCrossRefGoogle Scholar
  12. 12.
    James, P., Manfredo, Q., Carafoli, E., and Gonnet, G. (1993) Protein identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 195, p. 58–64.PubMedCrossRefGoogle Scholar
  13. 13.
    Pappin, D. J. C., Hojrup, P., and Bleasby, A. J. (1993) Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 3, p. 327–332.PubMedCrossRefGoogle Scholar
  14. 14.
    Hunt, D. F. Y., Shabanowitz, J., Winston, S., and Hauer, C. R. (1986) Protein sequencing by tandem mass spectrometry. Proc. Nat. Acad. Sci. USA 83, p. 6233–6237.PubMedCrossRefGoogle Scholar
  15. 15.
    Loboda, A. V., Krutchinsky, A. N., Bromirski, M., Ens, W., and Standing, K. G. (2000) A tandem quadrapole/time-of-flight mass spectrometer with a matrix-assisted laser desorption/ionization source: design and performance. Rap. Commun. Mass Spectrometry 14, p. 1047–1057.CrossRefGoogle Scholar
  16. 16.
    Shevchenko, A., Loboda, A., Ens, W., and Standing, K. G. (2000) MALDI quadrupole time-of-flight mass spectrometry: A powerful tool for proteomic research. Anal. Chem. 72, p. 2132–2141.PubMedCrossRefGoogle Scholar
  17. 17.
    Fenn, J. B. M., Meng, C. K., Wong, S. F., and Whitehouse, C. M. (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246, p. 64–71.PubMedCrossRefGoogle Scholar
  18. 18.
    Wilm, M. and Mann, M. (1996) Analytical properties of the nanoelectrospray ion source. Anal. Chem. 68, p. 1–8.PubMedCrossRefGoogle Scholar
  19. 19.
    Deterding, L. J. M., Arthur, M., Tomer, Kenneth, B., and Jorgenson, J. W. (1991) Nanoscale separations combined with tandem mass spectrometry. J. Chromatogr. 554, p. 73–82.Google Scholar
  20. 20.
    Hail, M., Lewis, S., and Jardine, I. (1990) Detection and sequence analysis of tryptic peptides by microcolumn liquid chromatography-tandem mass spectrometry using an electrospray interface. J. Microcolumn Sep. 2, p. 285–292.CrossRefGoogle Scholar
  21. 21.
    Huang, E. C. and Henion, J. D. (1991) Packed-capillary liquid chromatography/ion-spray tandem mass spectrometry determination of biomolecules. Anal. Chem. 63, p. 732–739.CrossRefGoogle Scholar
  22. 22.
    Hunt, D. F., Alexander, J. E., McCormack, A. L., et al. (1990) Mass spectrometric methods for protein and peptide sequence analysis, in Pap. Annu. Symp. Protein Soc, 4th, Villafranca, J. J., ed., Academic, New York, p. 441–454.Google Scholar
  23. 23.
    Griffin, P. R., Coffman, J. A., Hood, L. E., and Yates, J. R. III (1991) Structural analysis of proteins by capillary HPLC electrospray tandem mass spec. Int. J. Mass Spectrom. Ion Processes 111, p. 131–149.CrossRefGoogle Scholar
  24. 24.
    Gygi, S. P., Han, D. K. M., Gingras, A. C, Sonenberg, N., and Aebersold, R. (1999) Protein analysis by mass spectrometry and sequence database searching: Tools for cancer research in the post-genomic era. Electrophoresis 20, p. 310–319.PubMedCrossRefGoogle Scholar
  25. 25.
    Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal. Chem. 68, p. 850–858.PubMedCrossRefGoogle Scholar
  26. 26.
    Cortes, H. J., Pfeiffer, C. D., Richter, B. E., and Stevens, T S. (1987) Porous ceramic bed supports for fused silica packed capillary columns used in liquid chromatography. J. HRC&CC 10, p. 446–448.CrossRefGoogle Scholar
  27. 27.
    Kennedy, R. T and Jorgenson, J. W. (1989) Preparation and evaluation of packed capillary liquid chromatography columns with inner diameters from 20 to 50 micrometers Anal. Chem. 61, p. 1128–1135.CrossRefGoogle Scholar
  28. 28.
    Yates, J. R. (1998) Database searching using mass spectrometry data. Electrophoresis 19, p. 893–900.PubMedCrossRefGoogle Scholar
  29. 29.
    Snyder, L. R., Stadalius, M. A., and Quarry, M. A. (1983) Gradient elution in reversed-phase HPLC separation of macromolecules. Anal. Chem. 55, p. 1412A.CrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2004

Authors and Affiliations

  • Matthew J. Powell
    • 1
  • Aaron T. Timperman
    • 1
  1. 1.Department of ChemistryWest Virginia UniversityMorgantown

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