A tandem orthogonal proteolysis strategy for high-content chemical proteomics

Journal of the American Chemical Society

Volumn 127, Issue 28, 2005, Pages 10018-10019

  Speers, Anna E ^a   Cravatt, Benjamin F ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; IONIZATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PROTEIN DEGRADATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEOMICS; TECHNIQUE; THEORETICAL STUDY;

AMINO ACID SEQUENCE; ANIMALS; ENZYMES; MOLECULAR PROBE TECHNIQUES; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEOMICS; TRYPSIN;

EID: 22244445882     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0532842     Document Type: Article

References (25)

1. Patterson, S. D.; Aebersold, R. Nat. Genet. 2003, 33, 311-323.
2. Corthals, G. L.; Wasinger, V. C.; Hochstrasser, D. F.; Sanchez, J. C. Electrophoresis 2000, 21, 1104-1115.
3. (a) Speers, A. E.; Cravatt, B. F. Chembiochem 2004, 5, 41-47.
4. (b) Liu, Y.; Patricelli, M. P.; Cravatt, B. F. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14694-14699.
5. Jessani, N.; Liu, Y.; Humphrey, M.; Cravatt, B. F. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 10335-10340.
6. (a) Zhou, H.; Watts, J. D.; Aebersold, R. Nat. Biotechnol. 2001, 19, 375-378.
7. (b) Oda, Y.; Nagasu, T.; Chait, B. T. Nat. Biotechnol. 2001, 19, 379-382.
8. (c) Vocadlo, D. J.; Hang, H. C.; Kim, E. J.; Hanover, J. A.; Bertozzi, C. R. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 9116-9121.
9. (d) Tai, H.-C.; Khidekel, N.; Ficarro, S. B.; Peters, E. C.; Hsieh-Wilson, L. C. J. Am. Chem. Soc. 2004, 126, 10500-10501.
10. Hansen, K. C.; Schmitt-Ulms, G.; Chalkely, R. J.; Hirsch, J., Baldwin, M. A.; Burlingame, A. L. Mol. Cell. Proteomics 2003, 2, 299-314.
11. (a) Adam, G. C.; Burbaum, J.; Kozarich, J. W.; Patricelli, M. P.; Cravatt, B. F. J. Am. Chem. Soc. 2004, 126, 1363-1368.
12. (b) Adam, G. C.; Sorensen, E. J.; Cravatt, B. F. Nat. Biotechnol. 2002, 20, 805-809.
13. (a) Speers, A. E.; Adam, G. C.; Cravatt, B. F. J. Am. Chem. Soc. 2003, 125, 4686-4687.
14. (b) Speers, A. E.; Cravatt, B. F. Chem. Biol. 2004, 11, 535-546.
15. Dougherty, W. G.; Cary, S. M.; Parks, T. D. Virology 1989, 171, 356-364.
16. Multi-dimensional Protein Identification Technology; Washburn, M. P.; Wolters, D.; Yates, J. R. Nat. Biotechnol. 2001, 19, 242-247.
17. 2 spectra against a mouse protein database. For TEV data, a differential modification of 435.3 was assigned to C, D, E, and Y, which were the primary residues modified by PS≡=.
18. For proteins to be scored as correct assignments, they needed to be detected in all three tryptic data sets and in at least two of the three TEV data sets (at least four spectra/peptide). See also Supporting Information.
19. Djordjevic, S.; Pace, C. P.; Stankovich, M. T.; Kim, J.-J. P. Biochemistry 1995, 34, 2163-2171.
20. Foster, C. E.; Bianchet, M. A.; Talalay, P.; Zhao, Q.; Amzel, L. M. Biochemistry 1999, 38, 9881-9886.
21. Kil, I. S.; Park, J. W. J. Biol. Chem. 2005, 280, 10846-10854.
22. MacCoss, M. J.; Wu, C. C.; Yates, J. R. Anal. Chem. 2002, 74, 5593-5599.
23. Consistent with this premise, many of these proteins were found in control enrichments in which PS≡ was not added to the proteome.
24. Gysi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Nat. Biotechnol. 1999, 17, 994-999.
25. Liu, H.; Sadygov, R. G.; Yates, J. R. Anal. Chem. 2004, 76, 4193-4201.