Protein identification using sequential ion/ion reactions and tandem mass spectrometry

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 27, 2005, Pages 9463-9468

  Coon, Joshua J ^a,e   Ueberheide, Beatrix ^a   Syka, John E P ^a,b   Dryhurst, Deanna D ^c   Ausio, Juan ^c   Shabanowitz, Jeffrey ^a   Hunt, Donald F ^a,d  

^a UNIVERSITY OF VIRGINIA   (United States)

^b Thermo Fisher Scientific   (United States)

^c UNIVERSITY OF VICTORIA   (Canada)

^d UNIVERSITY OF VIRGINIA   (United States)

^e UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Electron transfer dissociation; Fragmentation; Ion trap; Ion ion reactions; Top down

Indexed keywords

BENZOIC ACID; CARBOXYLIC ACID; CYTOCHROME C; FLUORANTHENE; HISTONE H2A; HISTONE H3; POLYCYCLIC AROMATIC HYDROCARBON; UBIQUITIN;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHEMICAL BOND; CONTROLLED STUDY; DISSOCIATION; ELECTRON TRANSPORT; ELECTROSPRAY; GAS; HELA CELL; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN CELL; ION TRAP MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROCESSING; TANDEM MASS SPECTROMETRY;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DATABASES, GENETIC; FLUORENES; HISTONES; PROTEIN PROCESSING, POST-TRANSLATIONAL; SEQUENCE ANALYSIS, PROTEIN; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

EID: 22144482323     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0503189102     Document Type: Article

References (44)

1. Delahunty, C. & Yates, J. R. (2005) Methods 35, 248-255.
2. Godovac-Zimmermann, J. & Brown, L. R. (2001) Mass Spectrom. Rev. 20, 1-57.
3. Kelleher, N. L. (2004) Anal. Chem. 76, 196a-203a.
4. Johnson, J. M., Castle, J., Garrett-Engele, P., Kan, Z. Y., Loerch, P. M., Armour, C. D., Santos, R., Schadt, E. E., Stoughton, R. & Shoemaker, D. D. (2003) Science 302, 2141-2144.
5. Stamm, S., Ben-Ari, S., Rafalska, I., Tang, Y. S., Zhang, Z. Y., Toiber, D., Thanaraj, T. A. & Soreq, H. (2005) Gene 344, 1-20.
6. Resch, A., Xing, Y., Modrek, B., Gorlick, M., Riley, R. & Lee, C. (2004) J. Proteome Res. 3, 76-83.
7. Godovac-Zimmermann, J., Kleiner, O., Brown, L. R. & Drukier, A. K. (2005) Proteomics 5, 699-709.
8. Ge, Y., ElNaggar, M., Sze, S. K., Bin Oh, H., Begley, T. P., McLafferty, F. W., Boshoff, H. & Barry, C. E. (2003) J. Am. Soc. Mass Spectrom. 14, 253-261.
9. Sze, S. K, Ge, Y., Oh, H. & McLafferty, F. W. (2002) Proc. Natl. Acad. Sci. USA 99, 1774-1779.
10. Ge, Y., Lawhorn, B. G., ElNaggar, M., Strauss, E., Park, J. H., Begley, T. P. & McLafferty, F. W. (2002) J. Am. Chem. Soc. 124, 672-678.
11. Forbes, A. J., Patrie, S. M., Taylor, G. K., Kim, Y. B., Jiang, L. H. & Kelleher, N. L. (2004) Proc. Natl. Acad. Sci. USA 101, 2678-2683.
12. Du, Y., Meng, F. Y., Patrie, S. M., Miller, L. M. & Kelleher, N. L. (2004) J. Proteome Res. 3, 801-806.
13. Amunugama, R., Hogan, J. M., Newton, K. A. & McLuckey, S. A. (2004) Anal. Chem. 76, 720-727.
14. Hogan, J. M., Pitteri, S. J. & McLuckey, S. A. (2003) Anal. Chem. 75, 6509-6516.
15. Reid, G. E. & McLuckey, S. A. (2002) J. Mass Spectrom. 37, 663-675.
16. Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J. & Hunt, D. F. (2004) Proc. Natl. Acad. Sci. USA 101, 9528-9533.
17. Coon, J. J., Syka, J. E. P., Schwartz, J. C., Shabanowitz, J. & Hunt, D. F. (2004) Int. J. Mass Spectrom. 236, 33-42.
18. Coon, J. J., Syka, J. E. P., Shabanowitz, J. & Hunt, D. F. (2005) BioTechniques 38, 519-523.
19. Stephenson, J. L. & McLuckey, S. A. (1998) Anal. Chem. 70, 3533-3544.
20. McLuckey, S. A. & Stephenson, J. L. (1998) Mass Spectrom. Rev. 17, 369-407.
21. Loo, R. R. O., Winger, B. E. & Smith, R. D. (1994) J. Am. Soc. Mass Spectrom. 5, 1064-1071.
22. Loo, R. R. O. & Smith, R. D. (1995) J. Mass Spectrom. 30, 339-347.
23. Stephenson, J. L. & McLuckey, S. A. (1996) Anal. Chem. 68, 4026-4032.
24. Stephenson, J. L., VanBerkel, G. J. & McLuckey, S. A. (1997) J. Am. Soc. Mass Spectrum. 8, 637-644.
25. McLuckey, S. A., Stephenson, J. L. & Asano, K. G. (1998) Anal. Chem. 70, 1198-1202.
26. Scalf, M., Westphall, M. S., Krause, J., Kaufman, S. L. & Smith, L. M. (1999) Science 283, 194-197.
27. Scalf, M., Westphall, M. S. & Smith, L. M. (2000) Anal. Chem. 12, 52-60.
28. Reid, G. E., Shang, H., Hogan, J. M., Lee, G. U. & McLuckey, S. A. (2002) J. Am. Chem. Soc. 124, 7353-7362.
29. He, M. & McLuckey, S. A. (2004) J. Mass Spectrom. 39, 1231-1259.
30. Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. (1997) Nature 389, 251-260.
31. Barber, C. M., Turner, F. B., Wang, Y. M., Hagstrom, K., Taverna, S. D., Mollah, S., Ueberheide, B., Meyer, B. J., Hunt, D. F., Cheung, P. & Allis, C. D. (2004) Chromosoma 112, 360-371.
32. Syka, J. E. P., Marto, J. A., Bai, D. L., Horning, S., Senko, M. W., Schwartz, J. C., Ueberheide, B., Garcia, B., Busby, S., Muratore, T., et al. (2004) J. Proteome Res. 3, 621-626.
33. Dryhurst, D., Thambirajah, A. A. & Ausio, J. (2004) Biochem. Cell Biol. 82, 490-497.
34. Martin, S. E., Shabanowitz, J., Hunt, D. F. & Marto, J. A. (2000) Anal. Chem. 12, 4266-4274.
35. Horn, D. M., Breuker, K., Frank, A. J. & McLafferty, F. W. (2001) J. Am. Chem. Soc. 123, 9792-9799.
36. Oh, H., Breuker, K., Sze, S. K, Ge, Y., Carpenter, B. K. & McLafferty, F. W. (2002) Proc. Natl. Acad. Sci. USA 99, 15863-15868.
37. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990) J. Mol. Biol. 215, 403-410.
38. Ausio, J. & Abbott, D. W. (2002) Biochemistry 41, 5945-5949.
39. Santisteban, M. S., Kalashnikova, T. & Smith, M. M. (2000) Cell 103, 411-422.
40. Dhillon, N. & Kamakaka, R. T. (2000) Mol. Cell 6, 769-780.
41. Fan, J. Y., Rangasamy, D., Luger, K. & Tremethick, D. J. (2004) Mol. Cell 16, 655-661.
42. Fischle, W., Wang, Y. M. & Allis, C. D. (2003) Nature 425, 475-479.
43. Eng, J. K., Mccormack, A. L. & Yates, J. R. (1994) J. Am. Soc. Mass Spectrom. 5, 976-989.
44. Mortz, E., O'Connor, P. B., Roepstorff, P., Kelleher, N. L., Wood, T. D., McLafferty, F. W. & Mann, M. (1996) Proc. Natl. Acad. Sci. USA 93, 8264-8267.