Proteomics: Evolution of the technology

BioTechniques

Volumn 35, Issue 3, 2003, Pages 440-444

  Patterson, Scott D ^a  

^a Farmal Biomedicines   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; PROTEOME;

ANALYTIC METHOD; BIOTECHNOLOGICAL PROCEDURES; DISEASE MARKER; DRUG EFFICACY; DRUG TARGETING; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW;

EID: 0043192615     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/03353ap01     Document Type: Review

References (45)

1. Thornton, J. 2001. Structural genomics takes off, Trends Biochem. Sci. 26:88-89.
2. Marte, B. (Ed.) 2003. Nature insight: proteomics. Nature 422 (Suppl.): 191-237.
3. Patterson, S.D. and R.H. Aebersold. 2003. Proteomics: the first decade and beyond. Nat. Genet. 33:311-323.
4. Klose, J. 1975. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues: a novel approach to testing for induced point mutations in mammals. Humangenetik 26:231-243.
5. O'Farrell, P.H. 1975. High resolution two-dimensional gel electrophoresis of proteins. J. Biol. Chem. 250:4007-4021.
6. Scheele, G.A. 1975. Two-dimensional gel analysis of soluble proteins. Characterization of guinea pig exocrine pancreatic proteins. J. Biol. Chem. 250:5375-5385.
7. Celis, J.E. and R. Bravo. 1984. Synthesis of the nuclear protein cyclin in growing, senescent and morphologically transformed human skin fibroblasts. FEBS Lett. 165:21-25.
8. Mathews, M.B., R.M. Bernstein, B.R. Franza, Jr., and J.I. Garrels. 1984. Identity of the proliferating cell nuclear antigen and cyclin. Nature 309:374-376.
9. Rauscher, F.J., III, D.R. Cohen, T. Curran, T.J. Bos, P.K. Vogt, D. Bohmann, R. Tjian, and B.R. Franza, Jr. 1988. Fos-associated protein p39 is the product of the jun proto-oncogene. Science 240:1010-1016.
10. Wilkins, M.R., J.-C. Sanchez, A.A. Gooley, R.D. Appel, I. Humphery-Smith, D.F. Hochstrasser, and K.L. Williams. 1995. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotech. Gen. Eng. Rev. 13:19-50.
11. Tucker, C.L., J.F. Gera, and P. Uetz. 2001. Towards an understanding of complex protein networks. Trends Cell Biol. 11:102-106.
12. Ullrich, B., Y.A. Ushkaryov, and T.C. Sudhof. 1995. Cartography of neurexins: more than 1000 isoforms generated by alternative splicing and expressed in distinct subsets of neurons. Neuron 14:497-507.
13. Endo, T., D. Groth, S.B. Prusiner, and A. Kobata. 1989. Diversity of oligosaccharide structures linked to asparagines of the scrapie prion protein. Biochemistry 28:8380-8388.
14. Klose, J. 1999. Genotypes and phenotypes. Electrophoresis 20:643-652.
15. Lee, S.J., S. Evers, D. Roeder, A.E Parlow, J. Risteli, L. Risteli, Y.C. Lee, T. Feiziet al. 2002. Mannose receptor-mediated regulation of serum glycoprotein homeostasis. Science 295:1898-1901.
16. Houry, W.A., D. Frishman, C. Eckerskorn, F. Lottspeich, and F.U. Hartl. 1999. Identification of in vivo substrates of the chaperonin GroEL. Nature 402:147-154.
17. Kelleher, N.L., H.Y. Lin, G.A. Valaskovic, D.J. Aaserud, E.K. Fridriksson, and F.W. McLafferty. 1999. Top down versus bottom up protein characterization by tandem high resolution mass spectrometry. J. Am. Chem. Soc. 121:806-812.
18. Appella, E., E.A. Padlan, and D.E Hunt. 1995. Analysis of the structure of naturally processed peptides bound by class I and class II major histocompatibility complex molecules. EXS 73:105-119.
19. Patterson, S.D. 1998. Using MS fragment-ion data to identify proteins from large sequence databases, p. 127-135. In L.M. Savage (Ed.), Proteomics, Integrating Protein-based Tools and Applications for Drug Discovery. International Business Communications, Southborough, MA.
20. Yates, J.R., III, A.L. McCormack, D. Schieltz, E. Carmack, and A. Link. 1997. Direct analysis of protein mixtures by tandem mass spectrometry. J. Prot. Chem. 16:495-497.
21. Gygi, S.P., B. Rist, S.A. Gerber, F. Turecek, M.H. Gelb, and R. Aebersold. 1999. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17:994-999.
22. De Leenheer, A.P. and L.M. Thienpont. 1992. Application of isotope dilution-mass spectrometry in clinical chemistry, pharmacokinetics, and toxicology. Mass Spectrom. Rev. 11:249-307.
23. Spahr, C.S., S.A. Susin, E.J. Bures, J.H. Robinson, M.T. Davis, M.D. McGinley, G. Kroemer, and S.D. Patterson. 2000. Simplification of complex peptide mixtures for proteomic analysis: reversible biotinylation of cysteinyl peptides. Electrophoresis 21:1635-1650.
24. Ficarro, S.B., M.L. McCleland, P.T. Stukenberg, D.J. Burke, M.M. Ross, J. Shabanowitz, D.F. Hunt, and F.M. White. 2002. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20:301-305.
25. Kaji, H., H. Saito, Y. Yamauchi, T. Shinkawa, M. Taoka, J. Hirabayashi, K. Kasai, N. Takahashi, et al. 2003. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat. Biotechnol. 21:667-672.
26. Zhang, H., X.J. Li, D.B. Martin, and R. Aebersold. 2003. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol, 21:660-666.
27. Gerber, S.A., J. Rush, O. Stemman, M.W. Kirschner, and S.P. Gygi. 2003. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 100:6940-6945.
28. Ayad, N.G., S. Rankin, M. Murakami, J. Jebanathirajah, S. Gygi, and M.W. Kirschner. 2003. Tome-1, a trigger of mitotic entry, is degraded during G1 via the APC. Cell 113:101-113.
29. Aebersold, R. 2003. Constellations in a cellular universe. Nature 422:115-116.
30. Mintz, P.J., S.D. Patterson, A.E Neuwald, C.S. Spahr, and D.L. Spector. 1999. Purification and biochemical characterization of interchromatin granule clusters. EMBO J. 18:4308-4320.
31. Rout, M.P., J.D. Aitchison, A. Suprapto, K. Hjertaas, Y. Zhao, and B.T. Chait. 2000. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148:635-651.
32. Patterson, S.D., C.S. Spahr, E. Daugas, S.A. Susin, T. Irinopoulou, C. Koehler, and G. Kroemer. 2000. Mass spectrometric identification of proteins released from mitochondria undergoing permeability transition. Cell Death Diff. 7:137-144.
33. Liu, Y., M.P. Patricelli, and B.F. Cravatt. 1999. Activity-based protein profiling: the serine hydrolases. Proc. Natl. Acad. Sci. USA 96:14694-14699.
34. Caprioli, R.M., T.B. Farmer, and J. Gile. 1997. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal. Chem. 69:4751-4760.
35. Ideker, T., V. Thorsson, J.A. Ranish, R. Christmas, J. Buhler, J.K. Eng, R. Bumgarner, D.R. Goodlett, et al. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292:929-934.
36. Adam, B.L., Y. Qu, J.W. Davis, M.D. Ward, M.A. Clements, L.H. Cazares, O.J. Semmes, P.F. Schellhammer, et al. 2002. Serum protein finger-printing coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res. 62:3609-3614.
37. Petricoin, E.F., G.B. Mills, E.C. Kohn, and L.A. Liotta. 2002. Proteomic patterns in serum and identification of ovarian cancer. Lancet 360:170-171.
38. Schweitzer, B., S. Roberts, B. Grimwade, W. Shao, M. Wang, Q. Fu, Q. Shu, I. Laroche, et al. 2002. Multiplexed protein profiling on microarrays by rolling-circle amplification. Nat. Biotechnol. 20:359-365.
39. Borrebaeck, C.A.K. and C. Wingren (Eds.) 2002. High-throughput proteomics: Protein arrays. BioTechniques 33 (Suppl.):4-69.
40. Scrivener, E., R. Barry, A. Platt, R. Calvert, G. Masih, P. Hextall, M. Soloviev, and J. Terrett. 2003. Peptidomics: a new approach to affinity protein microarrays. Proteomics 3:122-128.
41. Leung, D., C. Hardouin, D.L. Boger, and B.F. Cravatt. 2003. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nat. Biotechnol. 21:687-691.
42. Gavin, A.C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J.M. Rick, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147.
43. Ho, Y., A. Gruhler, A. Heilbut, G.D. Bader, L. Moore, S.L. Adams, A. Millar, P. Taylor, et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183.
44. Patterson, S.D. 2003. Data analysis - the Achilles heel of proteomics. Nat. Biotechnology 21:221-222.
45. Ryan, T.E. and S.D. Patterson. 2002. Proteomics: drug target discovery on an industrial scale. Trends Biotechnol. 20:S45-S51.