Implications of New Proteomics Strategies for Biology and Medicine

Journal of Proteome Research

Volumn 3, Issue 2, 2004, Pages 253-260

  Domon, Bruno ^a   Broder, Samuel ^a  

^a CELERA GENOMICS   (United States)

Author keywords

Functional proteomics; Mass spectrometry; Medicine; Oncology; Quantitative proteomics; Structural proteomics

Indexed keywords

BIOLOGICAL MARKER; CELL SURFACE PROTEIN;

CANCER; DRUG TARGETING; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN TARGETING; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW;

BIOLOGICAL MARKERS; BIOLOGY; CHROMATOGRAPHY, LIQUID; HUMANS; MASS SPECTROMETRY; MEDICINE; MODELS, CHEMICAL; MOLECULAR BIOLOGY; NEOPLASMS; PROTEOME; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 6344221680     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr034082c     Document Type: Review

References (23)

1. Subramanian, G.; Adams, M. D.; Venter, J. C.; Broder, S. Implications of the human genome for understanding human biology and medicine. JAMA 2001, 286, 2296-2307.
2. Henzel, W. J.; Billeci, T. M.; Stults, J. T.; Wong, S. C.; Grimley, C.; Watanabe, C. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 5011-5015.
3. Karas, M.; Hillenkamp, F. Laser desorption ionization of proteins with molecular masses exceeding 10 000 Daltons. Anal. Chem. 1988, 60, 2299-2301.
4. Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246, 64-71.
5. Wilm, M.; Mann, M. Analytical properties of the nanoelectrospray ion source. Anal. Chem. 1996, 68, 1-8.
6. Aebersold, R.; Goodlett, D. R. Mass spectrometry in proteomics. Chem. Rev. 2001, 101, 269-295.
7. MacCoss, M. J.; McDonald, W. H.; Saraf, A.; Sadygov, R.; Clark, J. M.; Tasto, J. J.; Gould, K. L.; Wolters, D.; Washburn, M.; Weiss, A.; et al. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 7900-7905.
8. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
9. Petricoin, E. F.; Ardekani, A. M.; Hitt, B. A.; Levine, P. J.; Fusaro, V. A.; Steinberg, S. M.; Mills, G. B.; Simone, C.; Fishman, D. A.; Kohn, E. C.; et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002, 359, 572-577.
10. Xu, B. J.; Caprioli, R. M.; Sanders, M. E.; Jensen, R. A. Direct analysis of laser capture microdissected cells by MALDI mass spectrometry. J. Am. Soc. Mass. Spectrom. 2002, 13, 1292-1297.
11. Meng, F.; Cargile, B. J.; Patrie, S. M.; Jeffrey, R.; Johnson, J. S.; Shaun, M.; McLoughlin, S. M.; Kelleher, N. L. Processing Complex Mixtures of Intact Proteins for Direct Analysis by Mass Spectrometry. Anal. Chem. 2002, 74, 2923-2929.
12. McLachlin, D. T.; Chait, B. T. Analysis of phosphorylated proteins and peptides by mass spectrometry. Curr. Opin. Chem. Biol. 2001, 5, 591-602.
13. Mann, M.; Ong, S. E.; Gronborg, M.; Steen, H.; Jensen, O. N.; Pandey, A. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol. 2002, 20, 261-8.
14. Ficarro, S. B.; McCleland, M. L.; Stukenberg, P. T.; Burke, D. J.; Ross, M. M.; Shabanowitz, J.; Hunt, D. F.; White, F. M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 2002, 20, 301-305.
15. Dwek, M. V.; Ross, H. A.; Leathem, A. J. Proteome and glycosylation mapping identifies post-translational modifications associated with aggressive breast cancer. Proteomics 2001, 1, 756-762.
16. Regnier, F. E.; Riggs, L.; Zhang, R.; Xiong, L.; Liu, P.; Chakraborty, A.; Seeley, E.; Sioma, C.; Thompson, R. A. Comparative proteomics based on stable isotope labeling and affinity selection. J. Mass Spectrom. 2002, 37,: 133-145.
17. Zhang, H.; Li, X. J.; Martin, D. B.; Aebersold, R. Identification and quantification of N-glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotech. 2003, 21, 660-666
18. Flory, M. R.; Griffin, T. J.; Martin, D.; Aebersold, R. Advances in quantitative proteomics using stable isotope tags. Trends Biotechnol. 2002, 20(12 Suppl): S23-9.
19. Adam, G. C.; Sorensen, E. J.; Cravatt, B. F. Chemical strategies for functional proteomics. Mol. Cell Proteomics 2002, 1, 781-790.
20. Lo, L. C.; Pang, T. L.; Kuo, C. H.; Chiang, Y. L.; Wang, H. Y.; Lin, J. J. Design and Synthesis of Class-Selective Activity Probes for Protein Tyrosine Phosphatases. J. Proteome Res. 2002, 1: 35-40.
21. Gavin, A. C.; et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415, 141-7.
22. Rappsilber, J.; Siniossoglou, S.; Hurt, E. C.; Mann, M. A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry. Anal. Chem. 2000, 72, 267-75.
23. Baerga-Ortiz, A.; Hughes, C. A.; Mandell, J. G.; Komives, E. A. Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Sci. 2002, 11, 1300-8.