Measuring proteome dynamics in Vivo: As easy as adding water?

Molecular and Cellular Proteomics

Volumn 8, Issue 12, 2009, Pages 2653-2663

  Rachdaoui, Nadia ^a,b   Austin, Leanne ^a   Kramer, Eric ^a   Previs, Michael J ^b   Anderson, Vernon E ^a   Kasumov, Takhar ^c   Previs, Stephen F ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF VERMONT   (United States)

^c LERNER RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALBUMIN; DEUTERIUM OXIDE; OXYGEN 18; PROTEOME; UNCLASSIFIED DRUG; WATER; WATER O 18;

AMINO ACID ANALYSIS; ANIMAL EXPERIMENT; ARTICLE; GENE EXPRESSION; IN VIVO STUDY; ISOTOPE LABELING; MALE; MASS SPECTROMETRY; MOLECULAR DYNAMICS; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN SYNTHESIS; PROTEOMICS;

ALBUMINS; AMINO ACID SEQUENCE; ANIMALS; DEUTERIUM; ISOTOPE LABELING; MALE; MICE; MICE, INBRED C57BL; MOLECULAR SEQUENCE DATA; OXYGEN ISOTOPES; PEPTIDES; PROTEOME; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TIME FACTORS; TRYPSIN; WATER;

MUS;

EID: 75149158422     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M900026-MCP200     Document Type: Article

References (48)

1. Anderson, N. L., Polanski, M., Pieper, R., Gatlin, T., Tirumalai, R. S., Conrads, T. P., Veenstra, T. D., Adkins, J. N., Pounds, J. G., Fagan, R., and Lobley, A. (2004) The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol. Cell. Proteomics 3, 311-326
2. Beynon, R. J., and Pratt, J. M. (2005) Metabolic labeling of proteins for proteomics. Mol. Cell. Proteomics 4, 857-872
3. Pratt, J. M., Petty, J., Riba-Garcia, I., Robertson, D. H., Gaskell, S. J., Oliver, S. G., and Beynon, R. J. (2002) Dynamics of protein turnover, a missing dimension in proteomics. Mol. Cell. Proteomics 1, 579-591
4. Andersen, J. S., Lam, Y. W., Leung, A. K., Ong, S. E., Lyon, C. E., Lamond, A. I., and Mann, M. (2005) Nucleolar proteome dynamics. Nature 433, 77-83
5. Jahoor, F., and Jackson, A. A. (1982) Hepatic function in rats with dietary-induced fatty liver, as measured by the uptake of indocyanine green. Br. J. Nutr. 47, 391-397
6. Wolfe, R. R., and Chinkes, D. L. (2004) Isotope Tracers in Metabolic Re search: Principles and Practice of Kinetic Analyses, Wiley-Liss, New York
7. van Eijk, H. M., and Deutz, N. E. (2003) Plasma protein synthesis measurements using a proteomics strategy. J Nutr. 133, 2084S-2089S
8. Whitelegge, J. P., Katz, J. E., Pihakari, K. A., Hale, R., Aguilera, R., Gómez, S. M., Faull, K. F., Vavilin, D., and Vermaas, W. (2004) Subtle modification of isotope ratio proteomics; an integrated strategy for expression proteomics. Phytochemistry 65, 1507-1515
9. Ussing, H. H. (1941) The rate of protein renewal in mice and rats studied by means of heavy hydrogen. Acta Physiol. Scand. 2, 209-221
10. 2O to study the influence of feeding on protein synthesis: effect of isotope equilibration in vivo vs. in cell culture. Am. J. Physiol. Endocrinol. Metab. 288, E1277-E1283
11. 2O: application to patients with end-stage renal disease. Am. J. Physiol. Endocrinol. Metab. 286, E665-E672
12. Busch, R., Kim, Y. K., Neese, R. A., Schade-Serin, V., Collins, M., Awada, M., Gardner, J. L., Beysen, C., Marino, M. E., Misell, L M., and Hellerstein, M. K. (2006) Measurement of protein turnover rates by heavy water labeling of nonessential amino acids. Biochim. Biophys. Acta 1760, 730-744
13. Belloto, E., Diraison, F., Basset, A., Allain, G., Abdallah, P., and Beylot, M. (2007) Determination of protein replacement rates by deuterated water validation of underlying assumptions. Am. J. Physiol. Endocrinol. Metab. 292, E1340-E1347
14. 2 production and the tissue-specific dynamics of lipid and protein in vivo. Am. J. Physiol. Endocrinol. Metab. 290, E1048-E1056
15. Anderson, S. R., Gilge, D. A., Steiber, A. L., and Previs, S. F. (2008) Diet-induced obesity alters protein synthesis: tissue-specific effects in fasted vs. fed mice. Metab. Clin. Exp. 57, 347-354
16. 16O measurements. Anal. Biochem. 367, 28-39
17. Wang, B., Sun, G., Anderson, D. R., Jia, M., Previs, S., and Anderson, V. E. (2007) lsotopologue distributions of peptide product ions by tandem mass spectrometry: quantitation of low levels of deuterium incorporation. Anal. Biochem. 367, 40-48
18. Borek, E., Ponticorvo, L., and Rittenberg, D. (1958) Protein turnover in micro-organisms. Proc. Natl. Acad. Sci. U.S.A. 44, 369-374
19. Bemlohr, R. W. (1972) Oxygen probes of protein turnover, amino acid transport, and protein synthesis in Bacillus licheniformis. J. Biol. Chem. 247, 4893-4899
20. 18O-labelled leucine and phenylalanine to measure protein turnover in muscle cell cultures and possible futile cycling during aminoacylation. Biochem. J. 294, 427-433
21. Bemlohr, R. W., and Webster, G. C. (1958) Transfer of oxygen-18 during amino acid activation. Arch. Biochem. Biophys. 73, 276-278
22. Brunengraber, D. Z., McCabe, B. J., Kasumov, T., Alexander, J. C., Chandramouli, V., and Previs, S. F. (2003) Influence of diet on the modeling of adipose tissue triglycerides during growth. Am. J. Physiol. Endocrinol. Metab. 285, E917-E925
23. McCabe, B. J., and Previs, S. F. (2004) Using isotope tracers to study metabolism: application in mouse models. Metab. Eng. 6, 25-35
24. 2H labeling of water: application for measuring body composition in mice. Anal. Biochem. 350, 171-176
25. 3]acetone and gas chromatography-mass spectrometry. Anal. Biochem. 258, 315-321
26. Brunengraber, D. Z., McCabe, B. J., Katanik, J., and Previs, S. F. (2002) Gas chromatography-mass spectrometry assay of the (18)O-enrichment of water as trimethyl phosphate. Anal. Biochem. 306, 278-282
27. 15N enrichment in multiple amino acids and urea in a single analysis by gas chromatography/mass spectrometry. Biol. Mass. Spectrom. 22, 518-523
28. Gehrke, C. W., and Leimer, K. (1970) Effect of solvents on derivatization using bis(trimethylsilyl)trifluoracetamide. J. Chromatogr. 53, 201-208
29. Gehrke, C. W., and Leimer, K. (1971) Trimethylsilylation of amino acids: derivatization and chromatography. J. Chromatogr. 57, 219-238
30. Toffolo, G., Foster, D. M., and Cobelli, C. (1993) Estimation of protein fractional synthetic rate from tracer data. Am. J. Physiol. Endocrinol. Metab. 264, E128-E135
31. Sechi, S. (2007) Quantitative Proteomics by Mass Spectrometry, Humana Press, Totowa, NJ
32. Sun, G., Wang, B., Previs, S. F., and Anderson, V. E. (2004) Simultaneous determination of multiple protein synthesis rates by in vivo deuterium labeling. J. Am. Soc. Mass Spectrom. 15, 92S
33. Xiao, G. G., Garg, M., Um, S., Wong, D., Go, V. L., and Lee, W. N. (2008) Determination of protein synthesis in vivo using labeling from deuterated water and analysis of MALDI-TOF spectrum. J. Appl. Physiol. 104, 828-836
34. Fahey, A. J., and Messenger, S. (2001) lsotopic ratio measurements by time-of-flight secondary ion mass spectrometry. Int. J. Mass Spectrom. 208, 227-242
35. Previs, S. F., Gilge, D. A., and Rachdaoui, N. (2007) Protein and amino acid kinetics, in Clinical Diabetes Research: Methods and Techniques (Roden, M., ed) pp. 169-187, J. Wiley and Sons, West Sussex, UK
36. Cabrai, C. B., Bullock, K. H., Bischoff, D. J., Tompkins, R. G., Yu, Y. M., and Kelleher, J. K. (2008) Estimating glutathione synthesis with deuterated water: a model for peptide biosynthesis. Anal. Biochem. 379, 40-44
37. Commerford, S. L., Carsten, A. L., and Cronkite, E. P. (1983) The distribution of tritium among the amino acids of proteins obtained from mice exposed to tritiated water. Radiat. Res. 94, 151-155
38. MacCoss, M. J., Wu, C. C, Matthews, D. E., and Yates, J. R., 3rd (2005) Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides. Anal. Chem. 77, 7646-7653
39. 13C]leucine infusion in man: a method for measuring human intracellular leucine tracer enrichment. Metabolism 31, 1105-1112
40. Yang, R. D., Matthews, D. E., Bier, D. M., Lo, C., and Young, V. R. (1984) Alanine kinetics in humans: influence of different isotopic tracers. Am. J. Physiol. Endocrinol. Metab. 247, E634-E638
41. Murphy, R. C., and Clay, K. L. (1990) Preparation of labeled molecules by exchange with oxygen-18 water. Methods Enzymol. 193, 338-348
42. Murphy, R. C., and Clay, K. L. (1979) Synthesis and back exchange of 18O labeled amino acids for use as internal standards with mass spectrometry. Biomed. Mass Spectrom. 6, 309-314
43. Krüger, M., Moser, M., Ussar, S., Thievessen, I., Luber, C. A., Forner, F., Schmidt, S., Zanivan, S., Fässler, R., and Mann, M. (2008) SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134, 353-364
44. Doherty, M. K., Hammond, D. E., Clague, M. J., Gaskell, S. J., and Beynon, R. J. (2009) Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. J. Proteome Res. 8, 104-112
45. Previs, M. J., VanBuren, P., Begin, K. J., Vigoreaux, J. O., LeWinter, M. M., and Matthews, D. E. (2008) Quantification of protein phosphorylation by liquid chromatography-mass spectrometry. Anal. Chem. 80, 5864-5872
46. Ong, S. E., Foster, L. J., and Mann, M. (2003) Mass spectrometric-based approaches in quantitative proteomics. Methods 29, 124-130
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
48. MacCoss, M. J., and Matthews, D. E. (2005) Quantitative MS for proteomics: teaching a new dog old tricks. Anal. Chem. 77, 294A-302A