Proteomic identification and analysis of K63-linked ubiquitin conjugates

Analytical Chemistry

Volumn 84, Issue 22, 2012, Pages 10121-10128

  Cannon, Joe ^a   Nakasone, Mark ^a,b   Fushman, David ^a,b   Fenselau, Catherine ^a  

^a University of Maryland   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACID HYDROLYSIS; ASPARTATE RESIDUE; CELLULAR SIGNALS; CLEAVAGE PATTERNS; COVALENT ATTACHMENT; EUKARYOTIC CELLS; FRAGMENTATION PATTERNS; IMMUNOPRECIPITATIONS; POLYUBIQUITIN; POST-TRANSLATIONAL MODIFICATIONS; PROTEOMIC IDENTIFICATION; SUBSTRATE PROTEINS; UBIQUITIN; UBIQUITINATION;

CHEMICAL ANALYSIS; DIMERS; HYDROLYSIS; MASS SPECTROMETRY; ORGANIC POLYMERS; PEPTIDES;

PROTEOLYSIS;

LYSINE; UBIQUITIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; IMMUNOPRECIPITATION; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN SECONDARY STRUCTURE; PROTEOMICS; UBIQUITINATION;

AMINO ACID SEQUENCE; IMMUNOPRECIPITATION; LYSINE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; UBIQUITIN; UBIQUITINATION;

EID: 84869392554     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac302675y     Document Type: Article

References (28)

1. Kerscher, O.; Felberbaum, R.; Hochstrasser, M. Annu. Rev. Cell Dev. Biol. 2006, 22, 159-180
2. Pickart, C. M.; Fushman, D. Curr. Opin. Chem. Biol. 2004, 8, 610-616
3. Peng, J.; Schwartz, D.; Elias, J. E.; Thoreen, C. C.; Cheng, D.; Marsischky, G.; Roelofs, J.; Finley, D.; Gygi, S. P. Nat. Biotechnol. 2003, 21, 921-926
4. Wagner, S. A.; Beli, P.; Weinert, B. T.; Nielsen, M. L.; Cox, J. R.; Mann, M.; Choudhary, C. Mol. Cell. Proteomics 2011, 10, 1074-1086
5. Xu, P.; Peng, J. Anal. Chem. 2008, 80, 3438-3444
6. Strachan, J.; Roach, L.; Sokratous, K.; Tooth, D.; Long, J.; Garner, T. P.; Searle, M. S.; Oldham, N. J.; Layfield, R. J. Proteome Res. 2012, 11, 1969-1980
7. Xu, P.; Duong, D. M.; Seyfried, N. T.; Cheng, D.; Xie, Y.; Robert, J.; Rush, J.; Hochstrasser, M.; Finley, D.; Peng, J. Cell 2009, 137, 133-145
8. Ziv, I.; Matiuhin, Y.; Kirkpatrick, D. S.; Erpapazoglou, Z.; Leon, S.; Pantazopoulou, M.; Kin, W.; Gygi, S. P.; Haguenauer-Tsapis, R.; Reis, N.; Glickman, M. N.; Kleifeld, O. Mol. Cell. Proteomics 2011, 10, M111.009753
9. Kratsova-Ivantsiv, Y.; Ciechanover, A. J. Cell Sci. 2012, 125, 539-548
10. Pickart, C. M.; Raasi, S. Methods Enzymol. 2005, 399, 21-36
11. Johnston, S. C.; Riddle, S. M.; Cohen, R. E.; Hill, C. P. EMBO J. 1999, 18, 3877-3887
12. Datta, A. B.; Hura, G. L.; Wolberger, C. J. Mol. Biol. 2009, 392, 1117-1124
13. Dong, K. C.; Helgason, E.; Yu, C.; Phu, L.; Arnott, D. P.; Bosanac, I.; Compana, D. M.; Huang, O. W.; Fedorova, A. V.; Kirkpatrick, D. S.; Hymowitz, S. G.; Dueber, E. C. Structure 2011, 19, 1053-1063
14. Cannon, J. Asp-Selective Acid Hydrolysis for Proteomics. Ph.D. Dissertation, University of Maryland, College Park, College Park, MD, 20742.
15. Swatkoski, S.; Gutierrez, P.; Wynne, C.; Petrov, A.; Dinman, J. D.; Edwards, N.; Fenselau, C. J. Proteome Res. 2008, 7, 579-586
16. Cannon, J.; Lohnes, K.; Wynne, C.; Wang, Y.; Edwards, N.; Fenselau, C. J. Proteome Res. 2010, 9, 3886-3890
17. Inglis, A. S. Methods Enzymol. 1983, 91, 324-332
18. Li, A.; Sowder, R. C.; Henderson, L. E.; Moore, S. P.; Garfinkel, D. J.; Fisher, R. J. Anal. Chem. 2001, 73, 5395-5402
19. Cornilescu, G.; Marquardt, J. L.; Ottiger, M.; Bax, A. J. Am. Chem. Soc. 1998, 120, 6836-6837
20. Vijay-Kumar, S.; Bugg, C. E.; Cook, W. J. J. Mol. Biol. 1987, 194, 531-544
21. Tjandra, N.; Feller, S. E.; Pastor, R. W.; Bax, A. J. Am. Chem. Soc. 1987, 117, 12562-12566
22. Ibarra-Molero, B.; Loladze, V. V.; Makhatadze, G. I.; Sanchez-Ruiz, J. M. Biochemistry 1999, 38, 8138-8149
23. Cannon, J. R.; Fenselau, C. In Proteomic and Metabolomic Approaches to Biomarker Discovery; Vennstra, T. D.; Issaq, H. J., Eds.; Elsevier: Chennai, India, 2013.
24. Warren, M. R.; Parker, C. E.; Mocanu, V.; Klapper, D.; Borchers, C. H. Rapid Commun. Mass Spectrom. 2005, 19, 429-437
25. Newton, K.; Matsumoto, M. L.; Wertz, I. E.; Kirkpatrick, D. S.; Lill, J. R.; Tan, J.; Dugger, D.; Gordon, N.; Sidhu, S. S.; Fellouse, F. A.; Komives, L.; French, D. M.; Ferrando, R. E.; Lam, C.; Compaan, D.; Yu, C.; Bosanac, I.; Hymowitz, S. G.; Kelley, R. F.; Dixit, V. M. Cell 2008, 134, 668-678
26. Saville, M. K.; Sparks, A.; Xirodimas, D. P.; Wardrop, J.; Stevenson, L. F.; Bourdon, J. C.; Woods, Y. L.; Lane, D. P. J. Biol. Chem. 2004, 279, 42169-42181
27. Mirzaei, H.; Rogers, R. S.; Grimes, B.; Eng, J.; Aderem, A.; Aebersold, R. Mol. Syst. 2010, 6, 2004-2014
28. Kim, H. T.; Kim, K. P.; Lledias, F.; Kisselev, A. F.; Scaglione, K. M.; Skowyra, D.; Gygi, S. P.; Goldberg, A. L. J. Biol. Chem. 2007, 282, 17375-17386