Stable isotopic labeling and mass spectrometry as a means to determine differences in protein expression

TrAC - Trends in Analytical Chemistry

Volumn 22, Issue 5, 2003, Pages 282-290

  Goodlett, David R ^a   Yi, Eugene C ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; DNA SEQUENCES; GENES; MASS SPECTROMETRY; PHYSIOLOGY;

PROTEOMICS;

PROTEINS;

CARBON 13; CARBON 14; COMPLEMENTARY DNA; DEUTERIUM; HYDROGEN; MESSENGER RNA; PROTEIN;

BIOINFORMATICS; CELL GROWTH; DATA BASE; DNA MICROARRAY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ION EXCHANGE CHROMATOGRAPHY; ISOTOPE LABELING; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN METHYLATION; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; WESTERN BLOTTING;

EID: 0038401326     PISSN: 01659936     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0165-9936(03)00505-3     Document Type: Review

References (56)

1. Haynes P.A., Gygi S.P., Figeys D., Aebersold R. Electrophoresis. 19:1998;1862.
2. Aebersold R., Goodlett D.R. Chem. Rev. 101:2001;269.
3. Forbes A.J., Mazur M.T., Patel H.M., Walsh C.T., Kelleher N.L. Proteomics. 1:2001;927.
4. O'Farrell P.H. J. Biol. Chem. 250:1975;4007.
5. Klose J. Humangenetik. 26:1975;231.
6. Shevchenko A., Jensen O.N., Podtelejnikov A.V., Sagliocco F., Wilm M., Vorm O., Mortensen P., Shevchenko A., Boucherie H., Mann M. Proc. Natl. Acad. Sci. U.S.A. 93:1996;14440.
7. Futcher B. Methods Cell Sci. 21:1999;79.
8. Perrot M., Sagliocco F., Mini T., Monribot C., Schneider U., Shevchenko A., Mann M., Jeno P., Boucherie H. Electrophoresis. 20:1999;2280.
9. Gygi S.P., Rochon Y., Franza B., Aebersold R. Mol. Cell. Biol. 19:1999;1729.
10. Link A.J., Eng J., Schieltz D.M., Carmack E., Mize G.J., Morris D.R., Garvik B.M., Yates J.R. III Nat. Biotechnol. 17:1999;676.
11. Washburn M.P., Yates J.R. Curr. Opin. Microbiol. 3:2000;292.
12. Tong W., Link A., Eng J.K., Yates J.R. III Anal. Chem. 71:1999;2270.
13. Jensen P.K., Pasa-Tolic L., Peden K.K., Martinovic S., Lipton M.S., Anderson G.A., Tolic N., Wong K.K., Smith R.D. Electrophoresis. 21:2000;1372.
14. Opiteck G.J., Jorgenson J.W. Anal. Chem. 69:1997;2283.
15. Opiteck G.J., Lewis K.C., Jorgenson J.W., Anderegg R.J. Anal. Chem. 69:1997;1518.
16. Yi E.C., Marelli M., Lee H., Purvine S.O., Aebersold R., Aitchison J.D., Goodlett D.R. Electrophoresis. 23:2002;3205.
17. Oda Y., Huang K., Cross F.R., Cowburn D., Chait B.T. Proc. Natl. Acad. Sci. U.S.A. 96:1999;6591.
18. Munchbach M., Quadroni M., Miotto G., James P. Anal. Chem. 72:2000;4047.
19. Crowther J., Adusumalli V., Mukherjee T., Jordan K., Abuaf P., Corkum N., Goldstein G., Tolan J. Anal. Chem. 66:1994;2356.
20. Adusumalli V., Corkum N., Jacala A., Mukherjee T., Goodlett D., Crowther J., McConnell I., Goldstein G. Biopharm. Drug Dispos. 17:1996;25.
21. De Leenheer A.P., Thienpont L.M. Mass Spectrom. Rev. 11:1992;249.
22. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Nat. Biotech. 17:1999;994.
23. Pasa-Tolic L., Jensen P.K., Anderson G.A., Lipton M.S., Peden K.K., Martinovic S., Tolic N., Bruce J.E., Smith R.D. J. Am. Chem. Soc. 121:1999;7949.
24. Zhu H., Snyder M. Curr. Opin. Chem. Biol. 5:2001;40.
25. Zhu H., Bilgin M., Bangham R., Hall D., Casamayor A., Bertone P., Lan N., Jansen R., Bidlingmaier S., Houfek T., Mitchell T., Miller P., Dean R.A., Gerstein M., Snyder M. Science. 293:2001;2101.
26. DeRisi J.L., Iyer V.R., Brown P.O. Science. 278:1997;680.
27. Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., Hood L. Science. 292:2001;929.
28. Marshall A.G., Hendrickson C.L., Jackson G.S. Mass Spectrom. Rev. 17:1998;1.
29. Martinovic S., Veenstra T.D., Anderson G.A., Pasa-Tolic L., Smith R.D. J. Mass Spectrom. 37:2002;99.
30. Conrads T.P., Alving K., Veenstra T.D., Belov M.E., Anderson G.A., Anderson D.J., Lipton M.S., Pasa-Tolic L., Udseth H.R., Chrisler W.B., Thrall B.D., Smith R.D. Anal. Chem. 73:2001;2132.
31. Griffin T.J., Gygi S.P., Rist B., Aebersold R., Loboda A., Jilkine A., Ens W., Standing K.G. Anal. Chem. 73:2001;978.
32. Griffin T.J., Han D.K., Gygi S.P., Rist B., Lee H., Aebersold R., Parker K.C. J. Am. Soc. Mass Spectrom. 12:2001;1238.
33. Han D.K., Eng J., Zhou H., Aebersold R. Nat. Biotech. 19:2001;946.
34. Goodlett D.R., Keller A., Watts J.D., Newitt R., Yi E.C., Purvine S., von Haller P.D., Eng J.K., Aebersold R., Kolker E. Rapid Commun. Mass Spectrom. 14:2001;1214.
35. Cagney G., Emili A. Nat. Biotechnol. 20:2002;163.
36. Yao X., Freas A., Ramirez J., Demirev P.A., Fenselau C. Anal. Chem. 73:2001;2836.
37. Moseley M.A. Trends Biotechnol. 19(10 Suppl.):2001;S10.
38. Regnier F.E., Riggs L., Zhang R., Xiong L., Liu P., Chakraborty A., Seeley E., Sioma C., Thompson R.A. J. Mass Spectrom. 37:2002;133.
39. Kindy J.M., Taraszka J.A., Regnier F.E., Clemmer D.E. Anal. Chem. 74:2002;950.
40. Stahl N., Baldwin M.A., Teplow D.B., Hood L., Gibson B.W., Burlingame A.L., Prusiner S.B. Biochem. 32:1993;1991.
41. Danèík V., Addona T.A., Clauser K.R., Vath J.E., Pevzner P.A. J. Comput. Biol. 6:1999;327.
42. Hunt D.F., Yates J.R. III, Shabanowitz J., Winston S., Hauer C.R. Proc. Natl. Acad. Sci. U.S.A. 83:1986;6233.
43. Wilm M., Neubauer G., Taylor L., Shevchenko A., Bachi A. De novo sequencing of proteins with mass spectrometry using the differential scanning technique. Kamp R.M., Kyriakidis D., Choli-Papadopoulou T. Proteome and Protein Analysis. 1999;65-80 Springer-Verlag, Berlin and Heidelberg, Germany.
44. Moore R.E., Young M.K., Lee T.D. J. Am. Soc. Mass Spectrom. 11:2000;422.
45. th ASMS Conference, Session ThPG, Slot 148, 2001. (http://www.inmerge.com/asms01pdf/a011844.pdf).
46. Moore R.E., Young M.K., Lee T.D. J. Am. Soc. Mass Spectrom. 13:2002;378.
47. Katze M.G., Kwieciszewski B., Goodlett D.R., Blakely C.M., Nedderman P., Tan S.-L., Aebersold R. Virology. 278:2000;501.
48. Sechi S., Chait B.T. Anal. Chem. 70:1998;5150.
49. Goodlett D.R., Bruce J.E., Anderson G.A., Rist B., Pasa-Tolic L., Fiehn O., Smith R.D., Aebersold R. Anal. Chem. 72:2000;1112.
50. Stewart I.I., Thomson T., Figeys D. Rapid Commun. Mass Spectrom. 15:2001;2456.
51. J.A. Ranish, E.C. Yi, D.M. Leslie, S.O. Purvine, D.R. Goodlett, J. Eng, R. Aebersold, Nat. Genetics 33 (2003) 349.
52. Weckwerth W., Willmitzer L., Fiehn O. Rapid Commun. Mass Spectrom. 14:2000;1677.
53. Goshe M.B., Veenstra T.D., Panisko E.A., Conrads T.P., Angell N.H., Smith R.D. Anal. Chem. 74:2002;607.
54. Zhou H., Watts J.D., Aebersold R. Nat. Biotechnol. 19:2001;375.
55. Oda Y., Nagasu T., Chait B.T. Nat. Biotechnol. 19:2001;379.
56. Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:2002;301.