SLoMo: Automated site localization of modifications from ETD/ECD mass spectra

Journal of Proteome Research

Volumn 8, Issue 4, 2009, Pages 1965-1971

  Bailey, Christopher M ^a   Sweet, Steve M M ^a   Cunningham, Debbie L ^a   Zeller, Martin ^b   Heath, John K ^a   Cooper, Helen J ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^b THERMO FISHER SCIENTIFIC   (Germany)

Author keywords

Ascore; Bioinformatics; Mass spectrometry; Phosphopeptide; Phosphoproteomics; Phosphorylation; Post translational modifications; Site localization

Indexed keywords

PEPTIDE LIBRARY; PHOSPHOPEPTIDE;

ALGORITHM; ANALYTIC METHOD; ANIMAL CELL; ARTICLE; AUTOMATION; DISSOCIATION; ELECTRON CAPTURE DETECTION; ELECTRON TRANSPORT; MASS SPECTROMETRY; MOUSE; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN MODIFICATION;

ALGORITHMS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; SEQUENCE ANALYSIS, PROTEIN;

EID: 65249185673     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800917p     Document Type: Article

References (22)

1. Mann, M.; Ong, S. E.; Gronborg, M.; Steen, H.; Jensen, O. N.; Pandey, A. Trends Biotechnol. 2002, 20, 261-8.
2. Gruhler, A.; Olsen, J. V.; Mohammed, S.; Mortensen, P.; Faergeman, N. J.; Mann, M.; Jensen, O. N. Mol. Cell. Proteomics 2005, 4, 310-27.
3. 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, 301-5.
4. Molina, H.; Horn, D. M.; Tang, N.; Mathivanan, S.; Pandey, A. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 2199-204.
5. Chi, A.; Huttenhower, C.; Geer, L. Y.; Coon, J. J.; Syka, J. E.; Bai, D. L.; Shabanowitz, J.; Burke, D. J.; Troyanskaya, O. G.; Hunt, D. F. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 2193-8.
6. Beausoleil, S. A.; Villen, J.; Gerber, S. A.; Rush, J.; Gygi, S. P. Nat. Biotechnol. 2006, 24, 1285-92.
7. Olsen, J. V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P.; Mann, M. cell 2006, 127, 635-48.
8. Ruttenberg, B. E.; Pisitkun, T.; Knepper, M. A.; Hoffert, J. D. J. Proteome Res. 2008, 7, 3054-9.
9. Wan, Y.; Cripps, D.; Thomas, S.; Campbell, P.; Ambulos, N.; Chen, T.; Yang, A. J. Proteome Res. 2008, 7, 2803-2811.
10. Syka, J. E.; Coon, J. J.; Schroeder, M. J.; Shabanowitz, J.; Hunt, D. F. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9528-33.
11. Zubarev, R. A.; Kelleher, N. L.; McLafferty, F. W. J. Am. Chem. Soc. 1998, 120, 3265-3266.
12. Sweet, S. M. M.; Bailey, C. M.; Cunningham, D. L.; Heath, J. K.; Cooper, H. J. Mol. Cell. Proteomics, in press; DOI: 10.1074/mcp.M800451-MCP200.
13. Sweet, S. M.; Cooper, H. J. Expert Rev. Proteomics 2007, 4, 149-59.
14. Keller, A.; Eng, J.; Zhang, N.; Li, X. J.; Aebersold, R. Mol. Syst. Biol. 2005, 1, 2005-0017.
15. Creasy, D. M.; Cottrell, J. S. Proteomics 2004, 4, 1534-6.
16. Cooper, H. J.; Hudgins, R. R.; Hakansson, K.; Marshall, A. G. Int. J. Mass Spectrom. 2003, 228, 723-728.
17. 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, 958-64.
18. Larsen, M. R.; Thingholm, T. E.; Jensen, O. N.; Roepstorff, P.; Jorgensen, T. J. Mol. Cell. Proteomics 2005, 4, 873-86.
19. Akbarzadeh, S.; Wheldon, L. M.; Sweet, S. M.; Talma, S.; Marda-kheh, F. K.; Heath, J. K. PLoS ONE 2008, 3, e1873.
20. Sweet, S. M.; Mardakheh, F. K.; Ryan, K. J.; Langton, A. J.; Heath, J. K.; Cooper, H. J. Anal. Chem. 2008, 80, 6650-7.
21. Eng, J. K.; McCormack, A. L.; Yates, J. R. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
22. Savitski, M. M.; Kjeldsen, F.; Nielsen, M. L.; Zubarev, R. A. J. Am. Soc. Mass Spectrom. 2007, 18, 113-20.