ETD Outperforms CID and HCD in the Analysis of the Ubiquitylated Proteome

Journal of the American Society for Mass Spectrometry

Volumn 26, Issue 9, 2015, Pages 1580-1587

  Porras Yakushi, Tanya R ^a   Sweredoski, Michael J ^a   Hess, Sonja ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Collisional induced dissociation; Electron transfer dissociation; K GG antibody; Mass spectrometry; Proteomics; Ubiquitin; Ubiquitylation

Indexed keywords

DECISION TREES; ELECTRON TRANSITIONS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PROTEINS; SPECTROMETRY;

COLLISIONAL-INDUCED DISSOCIATIONS; ELECTRON TRANSFER DISSOCIATION; PROTEOMICS; UBIQUITIN; UBIQUITYLATION;

DISSOCIATION;

N ETHYLMALEIMIDE; PROTEOME; SYNTHETIC PEPTIDE; UBIQUITINATED PROTEIN;

ALKYLATION; ARTICLE; COLLISIONAL INDUCED DISSOCIATION; CONTROLLED STUDY; CROSS LINKING; DISSOCIATION; ELECTRON TRANSFER DISSOCIATION; FUNGUS GROWTH; HIGHER ENERGY COLLISION DISSOCIATION; NONHUMAN; PROTEIN ANALYSIS; PROTEOMICS; SACCHAROMYCES CEREVISIAE; UBIQUITINATION; CHEMISTRY; MASS SPECTROMETRY; PROCEDURES; PROTEIN DATABASE;

DATABASES, PROTEIN; MASS SPECTROMETRY; PROTEOME; UBIQUITINATED PROTEINS;

EID: 84938787732     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-015-1168-0     Document Type: Article

References (34)

1. Porras-Yakushi, T.R., Hess, S.: Recent advances in defining the ubiquitylome. Expert Rev. Proteomics 11, 477-490 (2014)
2. Low, T.Y., Magliozzi, R., Guardavaccaro, D., Heck, A.J.R.: Unraveling the ubiquitin-regulated signaling networks by mass spectrometry-based proteomics. Proteomics 13, 526-537 (2013)
3. Sylvestersen, K.B., Young, C., Nielsen, M.L.: Advances in characterizing ubiquitylation sites by mass spectrometry. Curr. Opin. Chem. Biol. 17, 49-58 (2013)
4. Anania, V.G., Pham, V.C., Huang, X., Masselot, A., Lill, J.R., Kirkpatrick, D.S.: Peptide level immunoaffinity enrichment enhances ubiquitination site identification on individual proteins. Mol. Cell. Probes 13, 145-156 (2014)
5. Polge, C., Uttenweiler-Joseph, S., Leulmi, R., Heng, A.-E., Burlet-Schiltz, O., Attaix, D., Taillandier, D.: Deciphering the ubiquitin proteome: limits and advantages of high throughput global affinity purification-mass spectrometry approaches. Int. J. Biochem. Cell Biol. 45, 2136-2146 (2013)
6. Xu, G., Jaffrey, S.R.: Comprehensive profiling of protein ubiquitination for drug discovery. Curr. Pharm. Des. 19, 3315-3328 (2013)
7. Warren, M.R.E., Parker, C.E., Mocanu, V., Klapper, D., Borchers, C.H.: Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination. Rapid Commun. Mass Spectrom. 19, 429-437 (2005)
8. Peng, J., Schwartz, D., Elias, J.E., Thoreen, C.C., Cheng, D., Marsischky, G., Roelofs, J., Finley, D., Gygi, S.P.: A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21, 921-926 (2003)
9. Udeshi, N.D., Svinkina, T., Mertins, P., Kuhn, E., Mani, D.R., Qiao, J.W., Carr, S.A.: Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000 s of ubiquitination sites in single proteomics experiments. Mol. Cell. Proteomics 12, 825-831 (2013)
10. Udeshi, N.D., Mertins, P., Svinkina, T., Carr, S.A.: Large-scale identification of ubiquitination sites by mass spectrometry. Nat. Protoc. 8, 1950-1960 (2013)
11. Udeshi, N.D., Mani, D.R., Eisenhaure, T., Mertins, P., Jaffe, J.D., Clauser, K.R., Hacohen, N., Carr, S.A.: Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol. Cell. Proteomics 11, 148-159 (2012)
12. Starita, L.M., Lo, R.S., Eng, J.K., von Haller, P.D., Fields, S.: Sites of ubiquitin attachment in Saccharomyces cerevisiae. Proteomics 12, 236-240 (2012)
13. Bustos, D., Bakalarski, C.E., Yang, Y., Peng, J., Kirkpatrick, D.S.: Characterizing ubiquitination sites by peptide-based immunoaffinity enrichment. Mol. Cell. Proteomics 11, 1529-1540 (2012)
14. Iesmantavicius, V., Weinert, B.T., Choudhary, C.: Convergence of ubiquitylation and phosphorylation signaling in rapamycin-treated yeast cells. Mol. Cell. Proteomics 13, 1979-1992 (2014)
15. Kim, D.-Y., Scalf, M., Smith, L.M., Vierstra, R.D.: Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis. Plant Cell 25, 1523-1540 (2013)
16. Cannon, J., Nakasone, M., Fushman, D., Fenselau, C.: Proteomic identification and analysis of K63-linked ubiquitin conjugates. Anal. Chem. 84, 10121-10128 (2012)
17. Stes, E., Laga, M., Walton, A., Samyn, N., Timmerman, E., De Smet, I., Goormachtig, S., Gevaert, K.: A COFRADIC protocol to study protein ubiquitination. J. Proteome Res. 13, 3107-3113 (2014)
18. Cooper, H.J., Heath, J.K., Jaffray, E., Hay, R.T., Lam, T.T., Marshall, A.G.: Identification of sites of ubiquitination in proteins: a Fourier transform ion cyclotron resonance mass spectrometry approach. Anal. Chem. 76, 6982-6988 (2004)
19. Mikesh, L.M., Ueberheide, B., Chi, A., Coon, J.J., Syka, J.E.P., Shabanowitz, J., Hunt, D.F.: The utility of ETD mass spectrometry in proteomic analysis. Biochim. Biophys. Acta 1764, 1811-1822 (2006)
20. Sobott, F., Watt, S.J., Smith, J., Edelmann, M.J., Kramer, H.B., Kessler, B.M.: Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination. J. Am. Soc. Mass Spectrom. 20, 1652-1659 (2009)
21. Sarbu, M., Ghiulai, R.M., Zamfir, A.D.: Recent developments and applications of electron transfer dissociation mass spectrometry in proteomics. Amino Acids 46, 1625-1634 (2014)
22. Jufvas, A., Strålfors, P., Vener, A.V.: Histone variants and their post-translational modifications in primary human fat cells. PLoS One 6, e15960 (2011)
23. Boja, E.S., Fales, H.M.: Overalkylation of a protein digest with iodoacetamide. Anal. Chem. 73, 3576-3582 (2001)
24. Nielsen, M.L., Vermeulen, M., Bonaldi, T., Cox, J., Moroder, L., Mann, M.: Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nat. Methods 5, 459-460 (2008)
25. Kalli, A., Smith, G.T., Sweredoski, M.J., Hess, S.: Evaluation and optimization of mass spectrometric settings during data-depndent acquisition mode: focus on LTQ-Orbitrap mass analyzers. J. Proteome Res. 12, 3071-3086 (2013)
26. Swaney, D.L., McAlister, G.C., Coon, J.J.: Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat. Methods 5, 959-964 (2008)
27. Cox, J., Mann, M.: MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372 (2008)
28. Cox, J., Neuhauser, N., Michalski, A., Scheltema, R.A., Olsen, J.V., Mann, M.: Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805 (2011)
29. Neuhauser, N., Michalski, A., Cox, J., Mann, M.: Expert system for computer-assisted annotation of MS/MS spectra. Mol. Cell. Proteomics 11, 1500-1509 (2012)
30. Elias, J.E., Gygi, S.P.: Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol. Biol. 604, 55-71 (2010)
31. Krzywinski, M., Altman, N.: Points of view: designing comparative experiments. Nat. Methods 11, 597-598 (2014)
32. MacLean, B., Tomazela, D.M., Shulman, N., Chambers, M., Finney, G.L., Frewen, B., Kern, R., Tabb, D.L., Liebler, D.C., MacCoss, M.J.: Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966-968 (2010)
33. Sweredoski, M.J., Smith, G.T., Kalli, A., Graham, R.L.J., Hess, S.: LogViewer: A software tool to visualize quality control parameters to optimize proteomics experiments using Orbitrap and LTQ-FT mass spectrometers. J. Biomol. Tech. 22, 122-126 (2011)
34. Kirkpatrick, D.S., Denison, C., Gygi, S.P.: Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat. Cell Biol. 7, 750-757 (2005)