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Proteomics

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Handbook of Industrial Cell Culture

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Abstract

With the recent completion and publication of the first-pass sequence of the human genome (1,2), scientific attention has been refocused on the roles of these genes, particularly the roles and functions of the products of these genes, the proteins. The study of the gene products or proteins of a cell or tissue or organism is now being referred to as the study of proteomics.

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References

  1. Venter, J. C., Adams, M. D., Myers, E. W. et al (2001) The sequence of the human genome. Science 291, 1304–1351.

    Article  CAS  Google Scholar 

  2. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.

    Article  Google Scholar 

  3. Wasinger, V. C., Cordwell, S. J., Cerpa-Poljak, A., Yan, J. X., Gooley, A. A., Wilkins, M. R., et al. (1995) Progress with gene-product map** of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16, 1090–1094.

    Article  CAS  Google Scholar 

  4. Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., et al. (1996) Life with 6000 genes. Science 274, 546–567.

    Article  CAS  Google Scholar 

  5. Yarema, K. J. and Bertozzi, C. R. (2001) Characterizing glycosylation pathways. Genome Biology 2, reviews 0004.1–0004.10.

    Google Scholar 

  6. Hubbard, S. R. and Till, J. H. (2000) Protein tyrosine kinase structure and function. Annu. Rev. Biochem. 69, 373–398.

    Article  CAS  Google Scholar 

  7. O’Reilly, D. R., Miller, L. K., and Luckow, V. A. (1992) in, Baculovirus Expression Vectors: A Laboratory Manual, W.H. Freeman and Company, New York, p. 216.

    Google Scholar 

  8. Pandey, A. and Mann, M. (2000) Proteomics to study genes and genomes. Nature 405, 837–846.

    Article  CAS  Google Scholar 

  9. Fields, S. (2001) Proteomics: proteomics in genomeland. Science 291, 1221–1224.

    Article  CAS  Google Scholar 

  10. Blackstock, W. (2000) in Proteomics: A Trends Guide, (Blackstock, W. and Mann, M., eds.), Elsevier Science, London, pp. 12–17.

    Google Scholar 

  11. Griffin, T. J. and Aebersold, R. (2001) Advances in proteome analysis by mass spectrometry. J. Biol. Chem. 276, 45497–45500.

    Article  CAS  Google Scholar 

  12. Mann, M., Hendrickson, R. C., and Pandey, A. (2001) Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70, 437–473.

    Article  CAS  Google Scholar 

  13. Green, R. and Noller, H. F. (1997) Ribosomes and translation. Annu. Rev. Biochem. 66, 679–716.

    Article  CAS  Google Scholar 

  14. Pandey, A., Fernandez, M. M., Steen, H., Blagoev, B., Nielsen, M. M., Roche, S., et al. (2000) Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways. J. Biol. Chem. 275, 38633–38639.

    Article  CAS  Google Scholar 

  15. Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R., Mann, M., and Lodish, H. F. (2000) Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proc. Natl. Acad. Sci. USA 97, 179–184.

    Article  CAS  Google Scholar 

  16. Neubauer, G., King, A., Rappsilber, J., Calvio, C., Watson, M., Ajuh, P., et al. (1998) Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nat. Genet. 20, 5–6.

    Article  Google Scholar 

  17. Voges, D., Zwickl, P., and Baumeister, W. (1999) The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu. Rev. Biochem. 68, 1015–1068.

    Article  CAS  Google Scholar 

  18. Miyamoto, S., Teramoto, H. Coso, O. A., Gutkind, J. S., Burbelo, P. D., Akiyama, S. K., et al. (1995) Integrin function: Molecular hierarchies of cytoskeletal and signaling molecules. J. Cell Biol. 131, 791–805.

    Article  CAS  Google Scholar 

  19. Barth, A. I. M., Näthke, I. S., and Nelson, W. J. (1997) Cadherins, catenins and APC protein: interplay between cytoskeletal complexes and signaling pathways. Curr. Op. Cell Biol. 9, 683–690.

    Article  CAS  Google Scholar 

  20. Wilm, M., Shevchenko, A., Houthaeve, T., Breit, S., Schweigerer, L., Fotsis, T., et al (1996) Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379, 466–469.

    Article  CAS  Google Scholar 

  21. Hale, J. E., Butler, J. P., Knierman, M. D., and Becker, G. W. (2000) Increased sensitivity of tryptic peptide detection by MALDI-TOF mass spectrometry is achieved by conversion of lysine to homoarginine. Anal. Biochem. 287, 110–117.

    Article  CAS  Google Scholar 

  22. Krishnan, S., Hale, J. E., and Becker, G. W. (2001) Proteomics: chromatographic fractionation prior to 2-dimensional polyacrylamide gel electrophoresis for enrichment of low abundance proteins facilitating identification by mass spectrometric methods, in: Enzyme Technology for Pharmaceutical and Biotechnological Applications, (Kirst, H. A., Yeh, W. K., and Zmijewski, M. J., eds.), Marcel Dekker, Inc., New York, NY, pp. 575–596.

    Google Scholar 

  23. Klose, J. (1975) Protein map** by combined iso electric focusing and electrophoresis of mouse tissues a novel approach to testing for induced point mutations in mammals. Humangenetik 26, 231–243.

    CAS  Google Scholar 

  24. O’Farrell, P. H. (1975) High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007–4021.

    Google Scholar 

  25. Righetti, P. G. (1990) Immobilized pH gradients: theory and methodology, in: Laboratory Techniques in Biochemistry and Molecular Biology, vol. 20. (Burdon, R. H. and van Knippenberg, P. H., eds.), Elsevier Biomedical Press, Amsterdam, The Netherlands.

    Google Scholar 

  26. Righetti, P. G. and Bossi, A. (1997) Isoelectric focusing in immobilized pH gradients: an update. J. Chromatogr. B 699, 77–89.

    Article  CAS  Google Scholar 

  27. Gorg, A., Obermaier, C., Boguth, G., Csordas, A., Diaz, J.-J., and Madjar, J.-J. (1997) Very alkaline immobilized pH gradients for two-dimensional electrophoresis of ribosomal and nuclear proteins. Electrophoresis 18, 328–337.

    Article  CAS  Google Scholar 

  28. Valdes, I., Pitarch, A., Gil, C., Bermudez, A., Llorente, M., Nombela, C., et al. (2000) Novel procedure for the identification of proteins by mass fingerprinting combining two-dimensional electrophoresis with fluorescent SYPRO red staining. J. Mass Spectrom. 35, 672–682.

    Article  CAS  Google Scholar 

  29. Righetti, P. G., Castagna, A., and Herbert, B. (2001) Prefractionation techniques in proteome analysis. Anal. Chem. 73, 320A–326A.

    Article  Google Scholar 

  30. Rachez, C., Lemon, B. D., Suldan, Z., Bromleigh, V., Gamble, M., Naar, A.M., et al. (1999) Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex. Nature 398, 824–828.

    Article  CAS  Google Scholar 

  31. Husi, H., Ward, M. A., Choudhary, J. S., Blackstock, W. P., and Grant, S. G. (2000) Proteomic analysis of NMDA receptor-adhesion protein signaling complexes. Nature Neuroscience 3, 661–669.

    Article  CAS  Google Scholar 

  32. Carr, S. A., Hemling, M. E., Bean, M. F., and Roberts, G. D. (1991) Integration of mass spectrometry in analytical biotechnology. Anal. Chem. 63, 2802–2824.

    Article  CAS  Google Scholar 

  33. McCormack, A. L., Schieltz, D. M., Goode, B., Yang, S., Barnes, G., Drubin, D., et al. (1997) Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. Anal. Chem. 69, 767–776.

    Article  CAS  Google Scholar 

  34. Washburn, M. P., Wolters, D., and Yates, J. R. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242–247.

    Article  CAS  Google Scholar 

  35. Moore, R. E., Licklider, L., Schumann, D., and Lee, T. D. (1998) A microscale electrospray interface incorporating a monolithic, poly(styrene-divinylbenzene) support for on-line liquid chromatography/tandem mass spectrometry analysis of peptides and proteins. Anal. Chem. 70, 4879–4884.

    Article  CAS  Google Scholar 

  36. Poon, R. Y. and Hunt, T. (1994) Reversible immunoprecipitation using histidine- or glutathione S-transferase-tagged staphylococcal protein A. Anal. Biochem. 218, 26–33.

    Article  CAS  Google Scholar 

  37. Hopp, T. P., Prickett, K. S., Price, U., Libby, R. T., March, C. J., Cerretti, P., et al. (1988). A short polypeptide marker sequence useful for recombinant protein identification and purification. Biotechnol. (NY) 6, 1205–1210.

    Google Scholar 

  38. Jensen, O. N., Podtelejnikov, A., and Mann, M. (1996) Delayed extraction improves specificity in database searches by matrix-assisted laser desorption/ionization peptide maps. Rapid Commun. Mass Spectrom. 10, 1371–1378.

    Article  CAS  Google Scholar 

  39. Zhang, W. and Chait, B. T. (2000) ProFound: an expert system for protein identification using mass spectrometric peptide map** information. Anal. Chem. 72, 2482–2489.

    Article  CAS  Google Scholar 

  40. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567.

    Article  CAS  Google Scholar 

  41. Clauser, K. R., Baker, P. R., and Burlingame, A. L. (1999) Role of accurate mass measurement (+/-10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871–2882.

    Article  CAS  Google Scholar 

  42. Krause, E., Wenschuh, H., Jungblut, P.R. (1999) The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins. Anal. Chem. 71, 4160–4165.

    Article  CAS  Google Scholar 

  43. Ducret, A., Van Oostveen, I., Eng, J. K., Yates, J. R. 3rd, and Aebersold, R. (1998) High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry. Protein Sci. 7, 706–719.

    Article  CAS  Google Scholar 

  44. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., et al. (1999) Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17, 676–682.

    Article  CAS  Google Scholar 

  45. Beavis, R. C. and Fenyö, D. (2000) Database searching with mass spectrometric information, in: Proteomics: A Trends Guide (Mann, M. and Blackstock W., eds), Elsevier Science, New York, pp. 23–27.

    Google Scholar 

  46. Washburn, M. P., Wolters, D., and Yates, J. R. 3rd. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242–247.

    Article  CAS  Google Scholar 

  47. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994–999.

    Article  CAS  Google Scholar 

  48. Shen, Y., Zhao, R., Belov, M. E., Conrads, T. P., Anderson, G. A., Tang, K., et al. (2001) Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics. Anal. Chem. 73, 1766–1775.

    Article  CAS  Google Scholar 

  49. Edman, P. (1950) Method for the determination of the amino acid sequence in peptides. Acta Chem. Scand. 4, 283–293.

    Article  CAS  Google Scholar 

  50. Hewick, R. M., Hunkapiller, M.W., Hood, L.E., and Dreyer, W.J. (1981) A gas-liquid solid phase peptide and protein sequenator. J. Biol. Chem. 256 , 7990–7997.

    CAS  Google Scholar 

  51. Matsudaira, P. (1987) Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J. Biol. Chem. 262, 10,035–10,038.

    Google Scholar 

  52. Rich, R. L. and Myszka, D. G. (2000) Advances in surface plasmon resonance biosensor analysis. Curr. Opin. Biotechnol. 11, 54–61.

    Article  CAS  Google Scholar 

  53. Fitz, L. J., Morris, J. C., Towler, P., Long, A., Burgess, P., Greco, R., et al. (1997) Characterization of murine Flt4 ligand/VEGF-C. Oncogene 15, 613–618.

    Article  CAS  Google Scholar 

  54. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627.

    CAS  Google Scholar 

  55. Fields, S. and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature 340, 245–246.

    Article  CAS  Google Scholar 

  56. Regnier, F. E., Riggs, L., Zhang, R., **ong, L., Liu, P., Chakraborty, A., et al (2002) Comparative proteomics based on stable isotope labeling and affinity selection. J. Mass Spectrom. 37, 133–145.

    Article  CAS  Google Scholar 

  57. Davies, H., Lomas, L., and Austen, B. (1999) Profiling of amyloid beta peptide variants using SELDI Protein Chip arrays. Biotechniques 27, 1258–1261.

    CAS  Google Scholar 

  58. Frears, E. R., Stephens, D. J., Walters, C. E., Davies, H., and Austen, B. M. (1999) The role of cholesterol in the biosynthesis of beta-amyloid. Neuroreport10, 1699–1705.

    Article  CAS  Google Scholar 

  59. Senior, K. (1999). Fingerprinting disease with protein chip arrays. Mol. Med. Today 5, 326–327.

    Article  CAS  Google Scholar 

  60. MacBeath, G. and Schreiber, S. L. (2000) Printing proteins as microarrays for high-throughput function determination. Science 289, 1760–1763.

    CAS  Google Scholar 

  61. Arenkov, P., Kukhtin, A., Gemmell, A., Voloshchuk, S., Chupeeva, V., and Mirzabekov, A. (2000) Protein microchips: use for immunoassay and enzymatic reactions. Anal. Biochem. 278, 123–131.

    Article  CAS  Google Scholar 

  62. Zhu, H., Klemic, J. F., Chang, S., Bertone, P., Casamayor, A., Klemic, K. G., et al. (2000) Analysis of yeast protein kinases using protein chips. Nat. Genet. 26, 283–289.

    Article  CAS  Google Scholar 

  63. Lazar, I. M., Ramsey, R. S., Jacobson, S. C., Foote, R. S., and Ramsey, J. M. (2000) Novel microfabricated device for electrokinetically induced pressure flow and electrospray ionization mass spectrometry. J. Chromatogr. A 892, 195–201.

    Article  CAS  Google Scholar 

  64. Wachs, T. and Henion, J. (2001) Electrospray device for coupling microscale separations and other miniaturized devices with electrospray mass spectrometry. Anal. Chem. 73, 632–638.

    Article  CAS  Google Scholar 

  65. Li, J., Wang, C., Kelly, J. F., Harrison, D. J., and Thibault, P. (2000) Rapid and sensitive separation of trace level protein digests using microfabricated devices coupled to a quadrupole-time-of-flight mass spectrometer. Electrophoresis 21, 198–210.

    Article  CAS  Google Scholar 

  66. Medzihradszky, K. F., Campbell, J. M., Baldwin, M. A., Falick, A. M., Juhasz, P., Vestal, M. L., et al. (2000) The characteristics of peptide collision-induced dissociation using a highperformance MALDI-TOF/TOF tandem mass spectrometer. Anal. Chem. 72, 552–558.

    Article  CAS  Google Scholar 

  67. Laiko, V. V., Baldwin, M. A., and Burlingame, A. L. (2000) Atmospheric pressure matrixassisted laser desorption/ionization mass spectrometry. Anal. Chem. 72, 652–657.

    Article  CAS  Google Scholar 

  68. Laiko, V. V., Moyer, S. C., and Cotter, R. J. (2000) Atmospheric pressure MALDI/ion trap mass spectrometry. Anal. Chem. 72, 5239–5243.

    Article  CAS  Google Scholar 

  69. Meng, F., Cargile, B. J., Miller, L. M., Forbes, A. J., Johnson, J. R., and Kelleher, N. L. (2001) Informatics and multiplexing of intact protein identification in bacteria and the Archaea. Nat. Biotechnol. 19, 952–957.

    Article  CAS  Google Scholar 

  70. Horn, D. M., Zubarev, R. A., and McLafferty, F. W. (2000) Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc. Natl. Acad. Sci. USA 97, 10,313–10,317.

    Article  Google Scholar 

  71. Richardson, F. C., Strom, S. C., Copple, D. M., Bendele, R. A., Probst, G. S., and Anderson, L. (1993) Comparisons of protein changes in human and rodent hepatocytes induced by the ratspecific carcinogen, methapyrilene. Electrophoresis 14, 157–161.

    Article  CAS  Google Scholar 

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Authors
  1. Gerald W. Becker
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  2. Michael D. Knierman
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  3. Pavel Shiyanov
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  4. John E. Hale
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Editors and Affiliations

  1. Eli Lilly and Company, Indianapolis, IN, USA

    Victor A. Vinci PhD

  2. Dow AgroSciences, Indianapolis, IN, USA

    Sarad R. Parekh PhD

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Becker, G.W., Knierman, M.D., Shiyanov, P., Hale, J.E. (2003). Proteomics. In: Vinci, V.A., Parekh, S.R. (eds) Handbook of Industrial Cell Culture. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59259-346-0_14

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  • DOI: https://doi.org/10.1007/978-1-59259-346-0_14

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61737-315-2

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