Automatic validation of phosphopeptide identifications from tandem mass spectra

Analytical Chemistry

Volumn 79, Issue 4, 2007, Pages 1301-1310

  Lu, Bingwen ^a   Ruse, Cristian ^a   Xu, Tao ^a   Park, Sung Kyu ^a   Yates III, John ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATABASE SYSTEMS; IDENTIFICATION (CONTROL SYSTEMS); LEARNING SYSTEMS; MASS SPECTROMETRY; STATISTICAL METHODS;

DATA SETS; PHOSPHOPEPTIDES; PHOSPHORYLATION; SUPPORT VECTOR MACHINE (SVM);

PROTEINS;

PHOSPHOPEPTIDE; PHOSPHOSERINE; PHOSPHOTHREONINE; SYNTHETIC PEPTIDE;

ALGORITHM; ANIMAL TISSUE; ARTICLE; AUTOMATION; BRAIN TISSUE; HELA CELL; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN CELL; ION TRAP MASS SPECTROMETRY; MASS SPECTROMETER; MASS SPECTROMETRY; MEDICAL TECHNOLOGY; MULTIPLE DIMENSIONAL PROTEIN IDENTIFICATION TECHNOLOGY; NONHUMAN; PEPTIDE ANALYSIS; PROTEIN ANALYSIS; PROTEIN PHOSPHORYLATION; RAT; TANDEM MASS SPECTROMETRY;

ALGORITHMS; ANIMALS; BRAIN; DATABASES, PROTEIN; HELA CELLS; HUMANS; PHOSPHOPEPTIDES; RATS; SENSITIVITY AND SPECIFICITY; TANDEM MASS SPECTROMETRY;

EID: 33847194634     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac061334v     Document Type: Article

References (36)

1. Johnson, S. A.; Hunter, T. Nat. Methods 2005, 2, 17-25.
2. Steen, H.; Kuster; B.; Fernandez, M.; Pandey, A.; Mann, M. J. Biol. Chem. 2002, 277, 1031-1039.
3. Rush, J.; Moritz, A.; Lee, K. A.; Guo, A.; Goss, V. L.; Spek, E. J.; Zhang, H.; Zha, X. M.; Polakiewicz, R. D.; Comb, M. J. Nat. Biotechnol. 2005, 23, 94-101.
4. 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. 2002, 20, 301-305.
5. Brill, L. M.; Salomon, A. R.; Ficarro, S. B.; Mukherji, M.; Stettler-Gill, M.; Peters, E. C. Anal. Chem. 2004, 76, 2763-2772.
6. Oda, Y.; Nagasu, T.; Chait, B. T. Nat. Biotechnol. 2001, 19, 379-382.
7. Beausoleil, S. A.; Jedrychowski, M.; Schwartz, D.; Elias, J. E.; Villen, J.; Li, J.; Cohn, M. A.; Cantley, L. C.; Gygi, S. P. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 12130-12135.
8. Pinkse, M. W.; Uitto, P. M.; Hilhorst, M. J.; Ooms, B.; Heck, A. J. Anal Chem. 2004, 76, 3935-3943.
9. Mann, M.; Jensen, O. N. Nat. Biotechnol. 2003, 21, 255-261.
10. Cantin, G. T.; Yates, J. R., III. J. Chromatogr., A 2004, 1053, 7-14.
11. Garcia, B. A.; Shabanowitz, J.; Hunt, D. F. Methods 2005, 35, 256-264.
12. Jensen, O. N. Curr. Opin. Chem. Biol. 2004, 8, 33-41.
13. DeGnore, J. P.; Qin, J. J. Am. Soc. Mass Spectrom. 1998, 9, 1175-1188.
14. Zubarev, R. A.; Kelleher, N. L.; McLafferty, F. W. J. Am. Chem. Soc. 1998, 120, 3265-3266.
15. Cooper, H. J.; Hakansson, K.; Marshall, A. G. Mass Spectrom. Rev. 2005, 24, 201-222.
16. Syka, J. E.; Coon, J. J.; Schroeder, M. J.; Shabanowitz, J.; Hunt, D. F. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9528-9533.
17. Hartmer, R.; Lubeck, M.; Baessmann, C.; Brekenfeld, A. 54th ASMS Conference on Mass Spectrometry; American Society for Mass Spectrometry: Santa Fe, NM, 2006.
18. Kocher, T.; Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A. J. Proteome Res. 2006, 5, 659-668.
19. Anderson, D. C.; Li, W.; Payan, D. G.; Noble, W. S. J. Proteome Res. 2003, 2, 137-146.
20. Klammer, A. A.; Wu, C. C.; Maccoss, M. J.; Noble, W. S. Proc. IEEE Comput. Syst. Bioinf. Conf. 2005, 175-185.
21. Zhang, X.; Lu, X.; Shi, Q.; Xu, X. Q.; Leung, H. C.; Harris, L. N.; Iglehart, J. D.; Miron, A.; Liu, J. S.; Wong, W. H. BMC Bioinf. 2006, 7, 197.
22. McDonald, W. H.; Tabb, D. L.; Sadygov, R. G.; MacCoss, M. J.; Venable, J.; Graumann, J.; Johnson, J. R.; Cociorva, D.; Yates, J. R., III. Rapid Commun. Mass Spectrom. 2004, 18, 2162-2168.
23. Bern, M.; Goldberg, D.; McDonald, W. H.; Yates, J. R. III. Bioinformatics 2004, 20 (Suppl. 1), 149-154.
24. Eng, J.; McCormack, A.; Yates, J. R., III. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
25. Cociorva, D.; Tao, X.; Yates, J. R., III. 54th ASMS Conference on Mass Spectrometry; American Society for Mass Spectrometry: Santa Fe, NM, 2006.
26. Vapnik, V. The Nature of Statistical Learning Theory, Springer Press: New York, 1995.
27. Vapnik, V. Statistical Learning Theory; Wiley Press: New York, 1998.
28. Cristianini, N.; Shawe-Taylor, J. An introduction to support vector machines and other kernel-based learning methods; Cambridge University Press: Cambridg, U.K., 2000.
29. Chang, C. C.; Lin, C. J. LIBSVM: a library for support vector machines. National Taiwan University, 2001: software available at http://www.csie.ntu.edu. tw/~cjlin/libsvm.
30. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. J. Proteome Res. 2003, 2, 43-50.
31. Moore, R. E.; Young, M. K.; Lee, T. D. J. Am. Soc. Mass Spectrom. 2002, 13, 378-86.
32. Wu, C. C.; MacCoss, M. J.; Howell, K. E.; Yates, J. R., III. Nat. Biotechnol. 2003, 21, 532-8.
33. Venable, J. D.; Yates, J. R., III. Anal. Chem. 2004, 76, 2928-37.
34. Geer, L. Y.; Markey, S. P.; Kowalak, J. A.; Wagner, L.; Xu, M.; Maynard, D. M.; Yang, X.; Shi, W.; Bryant, S. H. J. Proteome Res. 2004, 3, 958-964.
35. Beausoleil, S. A.; Villen, J.; Gerber, S. A.; Rush, J.; Gygi, S. P. Nat. Biotechnol. 2006, 24, 1285-92.
36. Olsen, J. V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P.; Mann, M. Cell 2006, 127, 635-648.