Protein quantitation using isotope-assisted mass spectrometry

Annual Review of Biophysics

Volumn 39, Issue 1, 2010, Pages 291-308

  Kline, Kelli G ^a   Sussman, Michael R ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Metabolic labeling; Proteomics; Quantitation; Stable isotopes

Indexed keywords

ISOTOPE; PROTEOME; STABLE ISOTOPE; TRANSCRIPTOME;

DERIVATIZATION; IN VITRO STUDY; ISOTOPE LABELING; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METABOLOME; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN SYNTHESIS; QUANTITATIVE ANALYSIS; REVIEW;

ANIMALS; HUMANS; ISOTOPE LABELING; MASS SPECTROMETRY; PROTEINS; PROTEOMICS;

MAMMALIA;

EID: 77952930004     PISSN: 1936122X     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.093008.131339     Document Type: Review

References (52)

1. Arnott D, Kishiyama A, Luis EA, Ludlum SG, Marsters JC Jr, Stults JT. 2002. Selective detection of membrane proteins without antibodies: a mass spectrometric version of the Western blot. Mol. Cell Proteomics 1:148-156
2. Bantscheff M, Eberhard D, Abraham Y, Bastuck S, Boesche M, et al. 2007. Quantitative chemical pro-teomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol. 25:1035-1044
3. Barnidge DR, Dratz EA, Martin T, Bonilla LE, Moran LB, Lindall A. 2003. Absolute quantification of the G protein-coupled receptor rhodopsin by LC/MS/MS using proteolysis product peptides and synthetic peptide standards. Anal. Chem. 75:445-451
4. Barnidge DR, Goodmanson MK, Klee GG, Muddiman DC. 2004. Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-MS/MS using protein cleavage and isotope dilution mass spectrometry. J. Proteome Res. 3:644-652
5. Cox B, Kislinger T, Emili A 2005. Integrating gene and protein expression data: pattern analysis and profile mining. Methods 35:303-314
6. Doherty MK, Hammond DE, Clague MJ, Gaskell SJ, Beynon RJ. 2009. Turnoverofthe human proteome: determination of protein intracellular stability by dynamic SILAC. J. Proteome Res. 8:104-112
7. Doherty MK, WhiteheadC, McCormackH, Gaskell SJ, Beynon RJ. 2005. Proteome dynamicsincomplex organisms: using stable isotopes to monitor individual protein turnover rates. Proteomics 5:522-533
8. Domon B, Aebersold R 2006. Mass spectrometry and protein analysis. Science 312:212-217
9. Edlund O, Bowers L, Henion J, Covey TR. 1989. Rapid determination of methandrostenolone in equine urine by isotope dilution liquid chromatography-tandem mass spectrometry. J. Chromatogr. 497:49-57
10. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. 2003. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 100:6940-6945
11. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, et al 2003. Global analysis of protein expression in yeast. Nature 425:737-741
12. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. 1999. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17:994-999
13. Gygi SP, Rochon Y, Franza BR, Aebersold R. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19:1720-1730
14. Hekmat O, He S, Warren RA, Withers SG. 2008. A mechanism-based ICAT strategy for comparing relative expression and activity levels of glycosidases in biological systems. J. Proteome Res. 7:3282-3292
15. Hunt DF, Yates JR 3rd, Shabanowitz J, Winston S, Hauer CR. 1986. Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 83:6233-6237
16. Huttlin EL, Chen X, Barrett-Wilt GA, Hegeman A, Halberg RB, et al. 2009. Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotope dilution. Proc. Natl. Acad. Sci. USA 106:17235-17240
17. Huttlin EL, Hegeman AD, Harms AC, Sussman MR. 2007. Comparison of full versus partial metabolic labeling for quantitative proteomics analysis in Arabidopsis thaliana. Mol. Cell Proteomics 6:860-881
18. Jiang H, English AM. 2002. Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine. J. Proteome Res. 1:345-350
19. Kirkpatrick DS, Gerber SA, Gygi SP 2005. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35:265-273
20. Krijgsveld J, Ketting RF, Mahmoudi T, Johansen J, Artal-Sanz M, et al. 2003. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat. Biotechnol. 21:927-931
21. Kushner DJ, Baker A, Dunstall TG. 1999. Pharmacological uses and perspectives of heavy water and deuterated compounds. Can. J. Physiol. Pharmacol. 77:79-88
22. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, et al. 1999. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17:676-682
23. Mann M. 2006. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol. 7:952-958
24. Meselson M, Stahl FW. 1958. The replication of DNA in Escherichia coli. Proc. Natl. Acad. Sci. USA 44:671-682
25. Muck WM, Henion JD. 1990. High-performance liquid chromatography/tandem mass spectrometry: its use for the identification of stanozolol and its major metabolites in human and equine urine. Biomed. Environ. Mass Spectrom. 19:37-51
26. Nelson CJ, Hegeman AD, Harms AC, Sussman MR. 2006. A quantitative analysis of Arabidopsis plasma membrane using trypsin-catalyzed (18)O labeling. Mol. Cell Proteomics 5:1382-1395
27. Nelson CJ, Huttlin EL, Hegeman AD, Harms AC, Sussman MR. 2007. Implications of 15 N-metabolic labeling for automated peptide identification in Arabidopsis thaliana. Proteomics 7:1279-1292
28. Nie L, Wu G, Zhang W. 2006. Correlation of mRNA expression and protein abundance affected by multiple sequence features relatedtotranslational efficiency inDesulfovibrio vulgaris: a quantitative analysis. Genetics 174:2229-2243
29. Ong SE, Mann M. 2006. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat. Prot. 1:2650-2660
30. Ong SE, Schenone M, Margolin AA, Li X, Do K, et al. 2009. Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc. Natl. Acad. Sci. USA 106:4617-4622
31. Pan C, Olsen JV, Daub H, Mann M. 2009. Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics. Mol. Cell Proteomics 8:2796-2808
32. Pascal LE, True LD, Campbell DS, Deutsch EW, Risk M, et al. 2008. Correlation of mRNA and protein levels: cell type-specific gene expression of cluster designation antigens in the prostate. BMC Genomics 9:246-259
33. Pittendrigh CS, Caldarola PC, Cosbey ES. 1973. A differential effect of heavy water on temperature-dependent and temperature-compensated aspects of circadian system of Drosophila pseudoobscura. Proc. Natl. Acad. Sci. USA 70:2037-2041
34. Pratt JM, Petty J, Riba-Garcia I, Robertson DH, Gaskell SJ, et al. 2002. Dynamics of protein turnover, a missing dimension in proteomics. Mol. Cell Proteomics 1:579-591
35. Reinl T, Nimtz M, Hundertmark C, Johl T, Kéri G, et al. 2009. Quantitative phosphokinome analysis of the Met pathway activated by the invasin internalin B from Listeria monocytogenes. Mol. Cell Proteomics 8:2778-2795
36. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, et al. 2004. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 3:1154-1169
37. Sabree Z, Rondon M, Handelsman J. 2009. Metagenomics. In Encyclopedia of Microbiology, ed. M Schaechter, 3:622-632 Oxford: Elsevier
38. Schwanhausser B, Gossen M, Dittmar G, Selbach M. 2009. Global analysis of cellular protein translation by pulsed SILAC. Proteomics 9:205-209
39. Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N 2008. Widespread changes in protein synthesis induced by microRNAs. Nature 455:58-63
40. Smolka MB, Zhou H, Purkayastha S, Aebersold R. 2001. Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal. Biochem. 297:25-31
41. Steen H, Mann M. 2004. The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 5:699-711
42. Taylor RL, Grebe SK, Singh RJ. 2004. Quantitative, highly sensitive liquid chromatography-tandem mass spectrometry method for detection of synthetic corticosteroids. Clin. Chem. 50:2345-2352
43. Wang YK, Ma Z, Quinn DF, Fu EW. 2002. Inverse 15 N-metabolic labeling/mass spectrometry for comparative proteomics and rapid identification of protein markers/targets. Rapid Commun. Mass Spectrom. 16:1389-1397 (Pubitemid 34760677)
44. Washburn MP, Ulaszek R, Deciu C, Schieltz DM, Yates JR 3rd. 2002. Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal. Chem. 74:1650-1657
45. Whitelegge JP, Katz JE, Pihakari KA, Hale R, Aguilera R, et al. 2004. Subtle modification of isotope ratio proteomics; an integrated strategy for expression proteomics. Phytochemistry 65:1507-1515
46. Wu CC, MacCoss MJ, Howell KE, Matthews DE, Yates JR 3rd. 2004. Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal. Chem. 76:4951-4959
47. Ye X, Luke B, Andresson T, Blonder J. 2009. 18 O stable isotope labeling in MS-based proteomics. Brief Funct. Genomic Proteomic 8:136-144
48. Zhang H, Li XJ, Martin DB, Aebersold R. 2003. Identification and quantification of N-linked glycopro-teins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21:660-666
49. Zhang R, Sioma CS, Thompson RA, Xiong L, Regnier FE. 2002. Controlling deuterium isotope effects in comparative proteomics. Anal. Chem. 74:3662-3669 (Pubitemid 34855856)
50. Zhou H, Watts JD, Aebersold R. 2001. A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 19:375-378
51. Zhu H, Pan S, Gu S, Bradbury EM, Chen X. 2002. Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom. 16:2115-2123
52. Zuo X, Echan L, Hembach P, Tang HY, Speicher KD, et al 2001. Towards global analysis of mammalian proteomes using sample prefractionation prior to narrow pH range two-dimensional gels and using one-dimensional gels for insoluble and large proteins. Electrophoresis 22:1603-1615