Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway

Journal of Proteome Research

Volumn 5, Issue 1, 2006, Pages 127-134

  Cantin, Greg T ^a   Venable, John D ^a   Cociorva, Daniel ^a   Yates III, John R ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Apoptosis; IMAC; Isoelectric focusing; Metabolic labeling; Phosphoproteome; PKA; TNF

Indexed keywords

TUMOR NECROSIS FACTOR;

AMINO ACID SEQUENCE; APOPTOSIS; ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; HUMAN; HUMAN CELL; IMMOBILIZED METAL AFFINITY CHROMATOGRAPHY; ISOELECTRIC FOCUSING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PHOSPHORYLATION; PROTEOMICS; QUANTITATIVE ANALYSIS; QUANTITATIVE PHOSPHOPROTEOMIC ANALYSIS;

CHROMATOGRAPHY, AFFINITY; CHROMATOGRAPHY, LIQUID; HELA CELLS; HUMANS; ISOELECTRIC FOCUSING; ISOTOPE LABELING; MASS SPECTROMETRY; NITROGEN ISOTOPES; PEPTIDE FRAGMENTS; PHOSPHOPEPTIDES; PHOSPHOPROTEINS; PHOSPHORYLATION; PROTEOME; PROTEOMICS; TUMOR NECROSIS FACTOR-ALPHA;

EID: 30744432140     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr050270m     Document Type: Article

References (43)

1. Hunter, T. Cell 2000, 100, 113-127.
2. Yates, J. R., 3rd; Eng, J. K.; McCormack, A. L.; Schieltz, D. Anal. Chem. 1995, 67, 1426-1436.
3. Mann, M.; Ong, S. E.; Gronborg, M.; Steen, H.; Jensen, O. N.; Pandey, A. Trends Biotechnol. 2002, 20, 261-268.
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. 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.
6. Gruhler, A.; Olsen, J. V.; Mohammed, S.; Mortensen, P.; Faergeman, N. J.; Mann, M.; Jensen, O. N. Mol. Cell. Proteomics 2005, 4, 310-327.
7. Annan, R. S.; Huddleston, M. J.; Verma, R.; Deshaies, R. J.; Carr, S. A. Anal. Chem. 2001, 73, 393-404.
8. McLachlin, D. T.; Chait, B. T. Curr. Opin. Chem. Biol. 2001, 5, 591-602.
9. DeGnore, J. P.; Qin, J. J. Am. Soc. Mass. Spectrom. 1998, 9, 1175-1188.
10. Syka, J. E.; Coon, J. J.; Schroeder, M. J.; Shabanowitz, J.; Hunt, D. F. Proc. Natl. Acad. Sci. USA 2004, 101, 9528-9533.
11. Peters, E. C.; Brock, A.; Ficarro, S. B. Mini. Rev. Med. Chem. 2004, 4, 313-324.
12. Loyet, K. M.; Stults, J. T.; Arnott, D. Mol. Cell Proteomics 2005, 4, 235-245.
13. DiDonato, J. A.; Hayakawa, M.; Rothwarf, D. M.; Zandi, E.; Karin, M. Nature 1997, 388, 548-554.
14. Van Antwerp, D. J.; Martin, S. J.; Kafri, T.; Green, D. R.; Verma, I. M. Science 1998, 274, 787-789.
15. Chen, G.; Goeddel, D. V. Science 2002, 296, 1634-1635.
16. Mercurio, F.; Murray, B. W.; Shevchenko, A.; Bennett, B. L.; Young, D. B.; Li, J. W.; Pascual, G.; Motiwala, A.; Zhu, H.; Mann, M.; Manning, A. M. Mol. Cell Biol. 1999, 19, 1526-1538.
17. McDonald, W. H.; Ohi, R.; Miyamoto, D. T.; Mitchison, T. J.; Yates, J. R., 3rd Int. J. Mass. Spec. 2002, 219, 245-251.
18. Washburn, M. P.; Wolters, D.; Yates, J. R., 3rd Nat. Biotechnol. 2001, 19, 242-247.
19. Eng, J. K.; McCormack, A. L.; Yates, J. R., 3rd J. Am. Soc. Mass. Spectrom. 1994, 5, 976-989.
20. Tabb, D. L.; McDonald, W. H.; Yates, J. R., 3rd J. Proteome Res. 2002, 1, 21-26.
21. Bern, M.; Goldberg, D.; McDonald, W. H.; Yates, J. R., 3rd Bioinformatics 2004, 20 Suppl. 1, 149-154.
22. MacCoss, M. J.; Wu, C. C.; Liu, H.; Sadygov, R.; Yates, J. R., 3rd Anal. Chem. 2003, 75, 6912-6921.
23. Zuo, X.; Speicher, D. W. Anal. Biochem. 2000, 284, 266-278.
24. Halligan, B. D.; Ruotti, V.; Jin, W.; Laffoon, S.; Twigger, S. N.; Dratz, E. A. Nucleic Acids Res. 2004, 32, W638-644.
25. Cauthron, R. D.; Carter, K. B.; Liauw, S.; Steinberg, R. A. Mol. Cell Biol. 1998, 18, 1416-1423.
26. Butt, E.; Immler, D.; Meyer, H. E.; Kotlyarov, A.; Laass, K.; Gaestel, M. J. Biol. Chem. 2001, 276, 7108-7113.
27. Varticovski, L.; Chahwala, S. B.; Whitman, M.; Cantley, L.; Schindler, D.; Chow, E. P.; Sinclair, L. K.; Pepinsky, R. B. Biochemistry 1988, 27, 3682-3690.
28. Bruce, J. I.; Yule, D. I.; Shuttleworth, T. J. J. Biol. Chem. 2002, 277, 48172-48181.
29. Zhong, H.; SuYang, H.; Erdjument-Bromage, H.; Tempst, P.; Ghosh, S. Cell 1997, 89, 413-424.
30. Hayden, M. S.; Ghosh, S. Genes Dev. 2004, 18, 2195-2224.
31. Piller, V.; Piller, F.; Fukuda, M. J. Biol. Chem. 1989, 264, 18824-18831.
32. Woo, M. S.; Ohta, Y.; Rabinovitz, I.; Stossel, T. P.; Blenis, J. Mol. Cell Biol. 2004, 24, 3025-3035.
33. Deiss, L. P.; Feinstein, E.; Berissi, H.; Cohen, O.; Kimchi, A. Genes Dev. 1995, 9, 15-30.
34. Kasof, G. M.; Goyal, L.; White, E. Mol. Cell Biol. 1999, 19, 4390-4404.
35. Boyd, J. M.; Malstrom, S.; Subramanian, T.; Venkatesh, L. K.; Schaeper, U.; Elangovan, B.; D'Sa-Eipper, C.; Chinnadurai, G. Cell 1994, 79, 341-351.
36. Bokoch, G. M. Cell Death Differ. 1998, 5, 637-645.
37. Henis-Korenblit, S.; Shani, G.; Sines, T.; Marash, L.; Shohat, G.; Kimchi, A. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5400-5405.
38. McCarthy, J. V.; Ni, J.; Dixit, V. M. J. Biol. Chem. 1998, 273, 16968-16975.
39. Gatti, A.; Huang, Z.; Tuazon, P. T.; Traugh, J. A. J. Biol. Chem. 1999, 274, 8022-8028.
40. Posewitz, M. C.; Tempst, P. Anal. Chem. 1999, 71, 2883-2892.
41. Nuhse, T. S.; Stensballe, A.; Jensen, O. N.; Peck, S. C. Mol. Cell Proteomics 2003, 2, 1234-1243.
42. Essader, A. S.; Cargile, B. J.; Bundy, J. L.; Stephenson, J. L., Jr. Proteomics 2005, 5, 24-34.
43. Moritz, R. L.; Ji, H.; Schutz, F.; Connolly, L. M.; Kapp, E. A.; Speed, T. P.; Simpson, R. J. Anal. Chem. 2004, 76, 4811-4824.