Similarity among tandem mass spectra from proteomic experiments: Detection, significance, and utility

Analytical Chemistry

Volumn 75, Issue 10, 2003, Pages 2470-2477

  Tabb, David L ^a,b   MacCoss, Michael J ^a   Wu, Christine C ^a   Anderson, Scott D ^a   Yates III, John R ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; CHEMICAL MODIFICATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; SEPARATION;

SPECTRAL SIMILARITY;

PROTEINS;

ACCURACY; ALGORITHM; ANIMAL TISSUE; ARTICLE; COMPARATIVE STUDY; COMPLEX FORMATION; CONTROLLED STUDY; LIQUID CHROMATOGRAPHY; NONHUMAN; PEPTIDE ANALYSIS; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN PROCESSING; PROTEOMICS; RAT; SEPARATION TECHNIQUE; TANDEM MASS SPECTROMETRY;

ALGORITHMS; ANIMALS; HIPPOCAMPUS; MASS SPECTROMETRY; PEPTIDE FRAGMENTS; PROTEOME; PROTEOMICS; RATS;

EID: 0037953090     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac026424o     Document Type: Article

References (25)

1. Lipton, M. S.; Paša-Tolić, L.; Anderson, G. A.; Anderson, D. J.; Auberry, D. L.; Battista, J. R.; Daly, M. J.; Fredrickson, J.; Hixson, K. K.; Kostandarithes, H.; Masselon, C.; Markillie, L. M.; Moore, R. J.; Romine, M. F.; Shen, Y.; Stritmatter, E.; Tolić; Udseth, H. R.; Venkateswaran, A.; Wong, K.-K.; Zhao, R.; Smith, R. D. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11049-11054.
2. Koller, A.; Washburn, M. P.; Lange, B. M.; Andon, N. L.; Deciu, C.; Haynes, P. A.; Hayes, L.; Schieltz, D.; Ulaszek, R.; Wei, J.; Wolters, D.; Yates, J. R., 3rd. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11969-11974.
3. Washburn, M. P.; Wolters, D.; Yates, J. R., 3rd. Nat. Biotechnol. 2001, 19, 242-247.
4. Florens, L.; Washburn, M. P.; Raine, J. D.; Anthony, R. M.; Grainger, M.; Haynes, J. D.; Moch, J. K.; Muster, N.; Sacci, J. B.; Tabb, D. L.; Witney, A. A.; Wolters, D.; Wu, Y.; Gardner, M. J.; Holder, A. A.; Sinden, R. E.; Yates, J. R.; Carucci, D. J. Nature 2002, 419, 520-526.
5. VerBerkmoes, N. C.; Bundy, J. L.; Hauser, L.; Asano, K. G.; Razumovskaya, J.; Larimer, F.; Hettich, R. L.; Stephenson, J. L., Jr. J. Proteome Res. 2002, 1, 239-252.
6. Thermo Finnigan. Product Support Bulletin 105. http://www.thermofinnigan.com.
7. Eng, J. K.; McCormack, A. L.; Yates, J. R., III. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
8. ExtractMS. http://fields.scripps.edu/sequest/extractms.html.
9. Sadygov, R. G.; Eng, J.; Durr, E.; Saraf, A.; McDonald, H.; MacCoss, M. J.; Yates, J. R., 3rd. J. Proteome Res. 2002, 1, 211-215.
10. Stein, S. E.; Scott, D. R. J. Am. Soc. Mass Spectrom. 1994, 5, 859-866.
11. Gan, F.; Yang, J.-H.; Liang, Y.-Z. Anal. Sci. 2001, 17, 635-638.
12. Wan, K. X.; Vidavsky, I.; Gross, M. L. J. Am. Soc. Mass Spectrom. 2002, 13, 85-88.
13. Yates, J. R., 3rd; Morgan S. F.; Gatlin, C. L.; Griffin, P. R.; Eng, J. K. Anal. Chem. 1998, 70, 3557-3565.
14. Hansen, B. T.; Jones, J. A.; Mason, D. E.; Liebler, D. C. Anal. Chem. 2001, 73, 1676-1683.
15. Canettieri, G.; Morantte, I.; Guzmán, E.; Asahara, H.; Herzig, S.; Anderson, S. D.; Yates, J. R., 3rd; Montminy, M. Nat. Struct. Biol. 2003, 10, 175-181.
16. Mitchison Lab Protocols. http://mitchison.med.harvard.edu/protocols/tubprep.html.
17. Wu, C. C.; MacCoss, M. J.; Howell, K. E.; Yates, J. R., 3rd. Nat. Biotechnol., in press.
18. McDonald, W. H.; Ohi, R.; Miyamoto, D. T.; Mitchison, T. J.; Yates, J. R., 3rd. Int. J. Mass Spectrom. 2002, 219, 245-251.
19. MacCoss, M. J.; Wu, C. C.; Yates, J. R., 3rd. Anal. Chem. 2002, 74, 5593-5599.
20. National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/.
21. Tabb, D. L.; McDonald, W. H.; Yates, J. R., 3rd. J. Proteome Res. 2002, 1, 21-26.
22. SEQUEST Unified File Format. http://fields.scripps.edu/sequest/SQTFormat.html.
23. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. J. Proteome Res. 2003, 2, 43-50.
24. Wolters, D. A.; Washburn, M. P.; Yates, J. R., III. Anal. Chem. 2001, 73, 5683-5690.
25. Pevzner, P. A.; Dancik, V.; Tang, C. L. J. Comput. Biol. 2000, 7, 777-787.