Isotope dilution strategies for absolute quantitative proteomics

Journal of Proteomics

Volumn 72, Issue 5, 2009, Pages 740-749

  Brun, Virginie ^a,b,c   Masselon, Christophe ^a,b,c   Garin, Jérôme ^a,b,c   Dupuis, Alain ^a,b,c  

^a CEA GRENOBLE   (France)

^b INSERM   (France)

^c UNIV GRENOBLE ALPES   (France)

Author keywords

AQUA; Mass spectrometry; Proteomics; PSAQ; QconCAT; Quantification

Indexed keywords

BIOLOGICAL MARKER; PEPTIDE;

HUMAN; ISOTOPE DILUTION ASSAY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUALITY CONTROL; QUANTITATIVE ANALYSIS; REVIEW;

ANIMALS; BIOLOGICAL MARKERS; CHEMISTRY TECHNIQUES, ANALYTICAL; HUMANS; ISOTOPE LABELING; ISOTOPES; MASS SPECTROMETRY; PEPTIDES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 67649511917     PISSN: 18743919     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jprot.2009.03.007     Document Type: Review

References (59)

1. Ong S.E., and Mann M. Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 1 (2005) 252-262
2. Bantscheff M., Schirle M., Sweetman G., Rick J., and Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 389 (2007) 1017-1031
3. Iliuk A., Galan J., and Tao W.A. Playing tag with quantitative proteomics. Anal Bioanal Chem 393 (2009) 503-513
4. Pan S., Aebersold R., Chen R., Rush J., Goodlett D.R., McIntosh M.W., et al. Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res 8 (2009) 787-797
5. Viswanathan C.T., Bansal S., Booth B., DeStefano A.J., Rose M.J., Sailstad J., et al. Quantitative bioanalytical methods validation and implementation: best practices for chromatographic and ligand binding assays. Pharm Res 24 (2007) 1962-1973
6. Beynon R.J., Doherty M.K., Pratt J.M., and Gaskell S.J. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat Methods 2 (2005) 587-589
7. Brun V., Dupuis A., Adrait A., Marcellin M., Thomas D., Court M., et al. Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol Cell Proteomics 6 (2007) 2139-2149
8. Anderson NL, Anderson NG, Pearson TW, Borchers CH, Paulovich AG, Patterson SD, Gillette M, Aebersold R, Carr SA. A human proteome detection and quantitation project: hPDQ. Mol Cell Proteomics 2009;in press.
9. Huerta-Fontela M., Galceran M.T., and Ventura F. Ultraperformance liquid chromatography-tandem mass spectrometry analysis of stimulatory drugs of abuse in wastewater and surface waters. Anal Chem 79 (2007) 3821-3829
10. Tai S.S., and Welch M.J. Development and evaluation of a candidate reference method for the determination of total cortisol in human serum using isotope dilution liquid chromatography/mass spectrometry and liquid chromatography/tandem mass spectrometry. Anal Chem 76 (2004) 1008-1014
11. Stocklin R., Vu L., Vadas L., Cerini F., Kippen A.D., Offord R.E., et al. A stable isotope dilution assay for the in vivo determination of insulin levels in humans by mass spectrometry. Diabetes 46 (1997) 44-50
12. Kippen A.D., Cerini F., Vadas L., Stocklin R., Vu L., Offord R.E., et al. Development of an isotope dilution assay for precise determination of insulin, C-peptide, and proinsulin levels in non-diabetic and type II diabetic individuals with comparison to immunoassay. J Biol Chem 272 (1997) 12513-12522
13. Mallick P., Schirle M., Chen S.S., Flory M.R., Lee H., Martin D., et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol 25 (2007) 125-131
14. Ferrarello C., Encinar J., Centineo G., Alonso J., de la Campa M., and Sanz-Medel A. Comparison of three different ICP-MS instruments in the study of cadmium speciation in rabbit liver metallothionein-1 using reversed-phase HPLC and post-column isotope dilution analysis. J Anal At Spectrom 17 (2002) 1024-1029
15. Polatajko A., Encinar J., Schaumloffel D., and Szpunar J. Quantification of a selenium-containing protein in yeast extract via an accurate determination of a tryptic peptide by species-specific isotope dilution capillary HPLC-ICP MS. Chem Anal (Warsaw) 50 (2005) 265-278
16. Busto M.E., Montes-Bayon M., and Sanz-Medel A. Accurate determination of human serum transferrin isoforms: exploring metal-specific isotope dilution analysis as a quantitative proteomic tool. Anal Chem 78 (2006) 8218-8226
17. Sanz-Medel A. Heteroatom(isotope)-tagged proteomics via ICP-MS: screening and quantification of proteins and their post-translational modifications. Anal Bioanal Chem 391 (2008) 885-894
18. Sanz-Medel A., Montes-Bayon M., del Rosario Fernandez de la Campa M., Encinar J.R., and Bettmer J. Elemental mass spectrometry for quantitative proteomics. Anal Bioanal Chem 390 (2008) 3-16
19. Zhang G., and Neubert T.A. Automated comparative proteomics based on multiplex tandem mass spectrometry and stable isotope labeling. Mol Cell Proteomics 5 (2006) 401-411
20. Lange V., Picotti P., Domon B., and Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 4 (2008) 222
21. Stahl-Zeng J., Lange V., Ossola R., Eckhardt K., Krek W., Aebersold R., et al. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics 6 (2007) 1809-1817
22. Malmstrom J., Lee H., and Aebersold R. Advances in proteomic workflows for systems biology. Curr Opin Biotechnol 18 (2007) 378-384
23. Rifai N., Gillette M.A., and Carr S.A. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol 24 (2006) 971-983
24. Vipond C., Suker J., Jones C., Tang C., Feavers I.M., and Wheeler J.X. Proteomic analysis of a meningococcal outer membrane vesicle vaccine prepared from the group B strain NZ98/254. Proteomics 6 (2006) 3400-3413
25. Heudi O., Barteau S., Zimmer D., Schmidt J., Bill K., Lehmann N., et al. Towards absolute quantification of therapeutic monoclonal antibody in serum by LC-MS/MS using isotope-labeled antibody standard and protein cleavage isotope dilution mass spectrometry. Anal Chem 80 (2008) 4200-4207
26. Dubois M., Becher F., Herbet A., and Ezan E. Immuno-mass spectrometry assay of EPI-HNE4, a recombinant protein inhibitor of human elastase. Rapid Commun Mass Spectrom 21 (2007) 352-358
27. Dubois M., Fenaille F., Clement G., Lechmann M., Tabet J.C., Ezan E., et al. Immunopurification and mass spectrometric quantification of the active form of a chimeric therapeutic antibody in human serum. Anal Chem 80 (2008) 1737-1745
28. Careri M., Costa A., Elviri L., Lagos J.B., Mangia A., Terenghi M., et al. Use of specific peptide biomarkers for quantitative confirmation of hidden allergenic peanut proteins Ara h 2 and Ara h 3/4 for food control by liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem 389 (2007) 1901-1907
29. Dupuis A., Hennekinne J.A., Garin J., and Brun V. Protein Standard Absolute Quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks. Proteomics 8 (2008) 4633-4636
30. Thevis M., Thomas A., and Schanzer W. Mass spectrometric determination of insulins and their degradation products in sports drug testing. Mass Spectrom Rev 27 (2008) 35-50
31. Kirsch S., Widart J., Louette J., Focant J.F., and De Pauw E. Development of an absolute quantification method targeting growth hormone biomarkers using liquid chromatography coupled to isotope dilution mass spectrometry. J Chromatogr A 1153 (2007) 300-306
32. Gerber S.A., Rush J., Stemman O., Kirschner M.W., and Gygi S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 100 (2003) 6940-6945
33. Barr J.R., Maggio V.L., Patterson Jr. D.G., Cooper G.R., Henderson L.O., Turner W.E., et al. Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. Clin Chem 42 (1996) 1676-1682
34. Stemmann O., Zou H., Gerber S.A., Gygi S.P., and Kirschner M.W. Dual inhibition of sister chromatid separation at metaphase. Cell 107 (2001) 715-726
35. Cheng D., Hoogenraad C.C., Rush J., Ramm E., Schlager M.A., Duong D.M., et al. Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol Cell Proteomics 5 (2006) 1158-1170
36. Bondar O.P., Barnidge D.R., Klee E.W., Davis B.J., and Klee G.G. LC-MS/MS quantification of Zn-alpha2 glycoprotein: a potential serum biomarker for prostate cancer. Clin Chem 53 (2007) 673-678
37. Kirkpatrick D.S., Gerber S.A., and Gygi S.P. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35 (2005) 265-273
38. Havlis J., and Shevchenko A. Absolute quantification of proteins in solutions and in polyacrylamide gels by mass spectrometry. Anal Chem 76 (2004) 3029-3036
39. Arsene C.G., Ohlendorf R., Burkitt W., Pritchard C., Henrion A., O'Connor G., et al. Protein quantification by isotope dilution mass spectrometry of proteolytic fragments: cleavage rate and accuracy. Anal Chem 80 (2008) 4154-4160
40. Mirzaei H., McBee J., Watts J., and Aebersold R. Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol Cell Proteomics 7 (2008) 813-823
41. Burkitt W.I., Pritchard C., Arsene C., Henrion A., Bunk D., and O'Connor G. Toward Systeme International d'Unite-traceable protein quantification: from amino acids to proteins. Anal Biochem 376 (2008) 242-251
42. Anderson N.L., Anderson N.G., Haines L.R., Hardie D.B., Olafson R.W., and Pearson T.W. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards And Capture By Anti-Peptide Antibodies (SISCAPA). J Proteome Res 3 (2004) 235-244
43. Mayya V., Rezual K., Wu L., Fong M.B., and Han D.K. Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: determination of inhibitory phosphorylation status of cyclin-dependent kinases. Mol Cell Proteomics 5 (2006) 1146-1157
44. Pratt J.M., Simpson D.M., Doherty M.K., Rivers J., Gaskell S.J., and Beynon R.J. Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat Protoc 1 (2006) 1029-1043
45. Rivers J., Simpson D.M., Robertson D.H., Gaskell S.J., and Beynon R.J. Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT. Mol Cell Proteomics 6 (2007) 1416-1427
46. Anderson L., and Hunter C.L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 5 (2006) 573-588
47. Kito K., Ota K., Fujita T., and Ito T. A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes. J Proteome Res 6 (2007) 792-800
48. Nanavati D., Gucek M., Milne J.L., Subramaniam S., and Markey S.P. Stoichiometry and absolute quantification of proteins with mass spectrometry using fluorescent and isotope-labeled concatenated peptide standards. Mol Cell Proteomics 7 (2008) 442-447
49. Eyers C.E., Simpson D.M., Wong S.C., Beynon R.J., and Gaskell S.J. QCAL-a novel standard for assessing instrument conditions for proteome analysis. J Am Soc Mass Spectrom 19 (2008) 1275-1280
50. Fang X., and Zhang W.W. Affinity separation and enrichment methods in proteomic analysis. J Proteomics 71 (2008) 284-303
51. Picotti P., Aebersold R., and Domon B. The implications of proteolytic background for shotgun proteomics. Mol Cell Proteomics 6 (2007) 1589-1598
52. Janecki D.J., Bemis K.G., Tegeler T.J., Sanghani P.C., Zhai L., Hurley T.D., et al. A multiple reaction monitoring method for absolute quantification of the human liver alcohol dehydrogenase ADH1C1 isoenzyme. Anal Biochem 369 (2007) 18-26
53. Dinges M.M., Orwin P.M., and Schlievert P.M. Exotoxins of Staphylococcus aureus. Clin Microbiol Rev 13 (2000) 16-34
54. Hanke S., Besir H., Oesterhelt D., and Mann M. Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. J Proteome Res 7 (2008) 1118-1130
55. Lescuyer P., Hochstrasser D., and Rabilloud T. How shall we use the proteomics toolbox for biomarker discovery?. J Proteome Res 6 (2007) 3371-3376
56. Graslund S., Nordlund P., Weigelt J., Hallberg B.M., Bray J., Gileadi O., et al. Protein production and purification. Nat Methods 5 (2008) 135-146
57. Goshima N., Kawamura Y., Fukumoto A., Miura A., Honma R., Satoh R., et al. Human protein factory for converting the transcriptome into an in vitro-expressed proteome. Nat Methods 5 (2008) 1011-1017
58. Good D.M., Thongboonkerd V., Novak J., Bascands J.L., Schanstra J.P., Coon J.J., et al. Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future. J Proteome Res 6 (2007) 4549-4555
59. Hober S., and Uhlen M. Human protein atlas and the use of microarray technologies. Curr Opin Biotechnol 19 (2008) 30-35