The dynamics of the proteome: Strategies for measuring protein turnover on a proteome-wide scale

Briefings in Functional Genomics and Proteomics

Volumn 3, Issue 4, 2005, Pages 382-390

  Beynon, Robert J ^a  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

Author keywords

Protein turnover; Proteome dynamics; Proteomics; Stable isotope labelling

Indexed keywords

PROTEOME;

CELL CULTURE; CELLULAR DISTRIBUTION; IMMUNOPRECIPITATION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NONHUMAN; PROTEIN LOCALIZATION; PROTEIN METABOLISM; PROTEIN SYNTHESIS; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; STEADY STATE;

ANIMALS; CELLS, CULTURED; CHICKENS; GENETIC TECHNIQUES; KINETICS; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEINS; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; TIME FACTORS;

EID: 16344363793     PISSN: 14739550     EISSN: None     Source Type: Journal    
DOI: 10.1093/bfgp/3.4.382     Document Type: Review

References (22)

1. Izzotti, A. M., Bagnasco, C., Cartiglia, M. et al. (2004), 'Proteomic analysis as related to transcriptome data in the lung of chromium(VI)-treated rats', Int. J. Oncol., Vol. 24, pp. 1513-1522.
2. Yoon, S. H., Han, M. J., Lee, S. Y. et al. (2003), 'Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture', Biotechnol. Bioeng., Vol. 81, pp. 753-767.
3. Gerner, C. S., Vejda, D., Gelbmann, E. et al. (2002), 'Concomitant determination of absolute values of cellular protein amounts, synthesis rates, and turnover rates by quantitative proteome profiling', Mol. Cell. Proteomics, Vol. 1, pp. 528-537.
4. Waterlow, J. C., Garlick, P. J. and Millward, D.J. (1978), 'Protein Turnover in Mammalian Tissues and in the Whole Body', Elsevier-North Holland, Amsterdam, Netherlands.
5. Wickner, S., Maurizi, M. R. and Gottesman, S. (1999), 'Posttranslational quality control: Folding, refolding, and degrading proteins', Science, Vol. 286, pp. 1888-1893.
6. Gottesman, S. (2003), 'Proteolysis in bacterial regulatory circuits', Annu. Rev. Cell Dev. Biol., Vol. 19, pp. 565-587.
7. Hilt, W. (2004), 'Targets of programmed destruction: A primer to regulatory proteolysis in yeast', Cell. Mol. Life Sci., Vol. 61, pp. 1615-1632.
8. Gygi, S. P., Rist, B., Gerber, S. A. et al. (1999), 'Quantitative analysis of complex protein mixtures using isotope-coded affinity tags', Nat. Biotechnol., Vol. 17, pp. 994-999.
9. Ross, P. L., Huang, Y. N., Marchese, J. et al. (2004), 'Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents', Mol. Cell. Proteomics, Vol. 3, pp. 1154-1169.
10. Heller, M., Mattou, H., Menzel, C. and Yao, X. (2003), 'Trypsin catalyzed 16O-to-18O exchange for comparative proteomics: Tandem mass spectrometry comparison using MALDI-TOF, ESI-QTOF, and ESI-ion trap mass spectrometers', J. Am. Soc. Mass Spectrom., Vol. 14, pp. 704-718.
11. Blagoev, B., Ong, S . E., Kratchmarova, I. and Mann, M. (2004), 'Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics', Nat. Biotechnol., Vol. 22, pp. 1139-1145.
12. Blagoev, B., Kratchmarova, I., Ong, S. E. et al. (2003), 'A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling', Nat. Biotechnol., Vol. 21, pp. 315-318.
13. Everley, P. A., Krijgsveld, J., Zetter, B. R. and Gygi, S. P. (2004), 'Quantitative cancer proteomics: Stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research', Mol. Cell. Proteomics, Vol. 3, pp. 729-735.
14. Ong, S. E., Blagoev, B., Kratchmarova, I. et al. (2002), 'Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics', Mol. Cell. Proteomics, Vol. 1, pp. 376-386.
15. Cargile, B. J., Bundy, J. L., Grunden, A. M. and Stephenson Jr., J. L. (2004), 'Synthesis/degradation ratio mass spectrometry for measuring relative dynamic protein turnover', Anal. Chem., Vol. 76, pp. 86-97.
16. Beynon, R. J. and Pratt, J. M. (2005), 'Metabolic labelling of proteins for proteomics', Mol. Cell. Proteomics (in press).
17. Pratt, J. M., Petty, J., Riba-Garcia, I. et al. (2002), 'Dynamics of protein turnover, a missing dimension in proteomics', Mol. Cell. Proteomics, Vol. 1, pp. 579-591.
18. Doherty, M. K., Whitehead, C., McCormack, H. et al. (2005), 'Proteome dynamics in complex organisms: Using stable isotopes to monitor individual protein turnover rates', Proteomics (in press).
19. Papageorgopoulos, C. K., Caldwell, H., Schweingrubber, R. A. et al. (2002), 'Measuring synthesis rates of muscle creatine kinase and myosin with stable isotopes and mass spectrometry', Anal. Biochem. Vol. 309, pp. 1-10.
20. Hellerstein, M. K. (2003), 'In vivo measurement of fluxes through metabolic pathways: the missing link in functional genomics and pharmaceutical research', Annu. Rev. Nutr., Vol. 23, pp. 379-402.
21. Hellerstein, M. K. (2004), 'New stable isotope-mass spectrometric techniques for measuring fluxes through intact metabolic pathways in mammalian systems: Introduction of moving pictures into functional genomics and biochemical phenotyping', Metab. Eng., Vol. 6, pp. 85-100,
22. Pratt, J. M., Robertson, D. H., Gaskell, S. J. et al. (2002), 'Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting', Proteomics, Vol. 2, pp. 157-163.