Large-scale identification of ubiquitination sites by mass spectrometry

Nature Protocols

Volumn 8, Issue 10, 2013, Pages 1950-1960

  Udeshi, Namrata D ^a   Mertins, Philipp ^a   Svinkina, Tanya ^a   Carr, Steven A ^a  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ISOTOPE; LYSINE EPSILON GLYCYLGLYCINE; POLYPEPTIDE; UNCLASSIFIED DRUG;

ANTIBODY SPECIFICITY; ARTICLE; CELL FRACTIONATION; CELL LABELING; CELL PH; CLINICAL PROTOCOL; CROSS LINKING; CYTOLYSIS; IMMOBILIZATION; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR DYNAMICS; PEPTIDE ANALYSIS; PH MEASUREMENT; PRIORITY JOURNAL; PROTEIN PURIFICATION; PROTEOMICS; QUANTITATIVE ANALYSIS; REVERSED PHASE LIQUID CHROMATOGRAPHY; SIGNAL TRANSDUCTION; TANDEM MASS SPECTROMETRY; UBIQUITINATION; WORKFLOW;

CELLS, CULTURED; CHEMICAL FRACTIONATION; CHROMATOGRAPHY, REVERSE-PHASE; MASS SPECTROMETRY; UBIQUITIN; UBIQUITINATION;

EID: 84885012783     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2013.120     Document Type: Article

References (25)

1. Ye, Y. & Rape, M. Building ubiquitin chains: E2 enzymes at work. Nat. Rev. Mol. Cell Biol. 10, 755-764 (2009
2. Dikic, I., Wakatsuki, S. & Walters, K.J. Ubiquitin-binding domains-from structures to functions. Nat. Rev. Mol. Cell Biol. 10, 659-671 (2009
3. Peng, J. et al. A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21, 921-926 (2003
4. Danielsen, J.M.R. et al. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Mol. Cell Proteomics 10, M110.003590 (2010
5. Udeshi, N.D. et al. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol. Cell Proteomics 11, 148-159 (2012
6. Udeshi, N.D. et al. Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments. Mol. Cell Proteomics 12, 825-831 (2013
7. Kim, W. et al. Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol. Cell 44, 325-340 (2011
8. Xu, G., Paige, J.S. & Jaffrey, S.R. Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat. Biotechnol. 28, 868-873 (2010
9. Ong, S-E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 1, 376-386 (2002
10. Wagner, S.A. et al. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol. Cell Proteomics 10, M111.013284 (2011
11. Emanuele, M.J. et al. Global identification of modular cullin-RING ligase substrates. Cell 147, 459-474 (2011
12. Sarraf, S.A. et al. Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization. Nature (2013
13. Wagner, S.A. et al. Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues. Mol. Cell Proteomics 11, 1578-1585 (2012
14. Mertins, P. et al. Integrated proteomic analysis of post-translational modifications by serial enrichment. Nat. Methods 10, 634-637 (2013
15. James, G.T. Inactivation of the protease inhibitor phenylmethylsulfonyl fluoride in buffers. Anal. Biochem. 86, 574-579 (1978
16. Meng, L. et al. Epoxomicin, a potent and selective proteasome inhibitor, exhibits in vivo anti-inflammatory activity. Proc. Natl. Acad. Sci. USA 96, 10403-10408 (1999
17. Harper, J.W. & Tan, M-K.M. Understanding cullin-RING E3 biology through proteomics-based substrate identification. Mol. Cell Proteomics 11, 1541-1550 (2012
18. Ong, S.E. & Mann, M. Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Methods Mol. Biol. 359, 37-52 (2007
19. Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896-1906 (2007
20. Glatter, T. et al. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J Proteome Res. 11, 5145-5156 (2012
21. Villén, J. & Gygi, S.P. The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat. Protoc. 3, 1630-1638 (2008
22. Wang, Y. et al. Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 11, 2019-2026 (2011
23. Yang, F., Shen, Y., Camp, D.G. II & Smith, R.D. High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis. Expert Rev. Proteomics 9, 129-134 (2012
24. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b-range mass accuracies and proteome-wide protein quantification. Nat. Biotech. 26, 1367-1372 (2008
25. Cox, J. et al. Andromeda: A peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805 (2011