Analysis of ubiquitinated proteome by quantitative mass spectrometry

Methods in Molecular Biology

Volumn 893, Issue , 2012, Pages 417-429

  Na, Chan Hyun ^a   Peng, Junmin ^a  

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

Author keywords

Mass spectrometry; Proteomics; SILAC; Ubiquitin

Indexed keywords

AMINO ACID; PEPTIDE FRAGMENT; PROTEOME; SACCHAROMYCES CEREVISIAE PROTEIN; TRYPSIN; UBIQUITINATED PROTEIN;

AFFINITY CHROMATOGRAPHY; ARTICLE; CHEMISTRY; ION EXCHANGE CHROMATOGRAPHY; ISOLATION AND PURIFICATION; ISOTOPE LABELING; METABOLISM; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN DEGRADATION; PROTEIN PROCESSING; SACCHAROMYCES CEREVISIAE; TANDEM MASS SPECTROMETRY; UBIQUITINATION;

AMINO ACIDS; CHROMATOGRAPHY, AFFINITY; CHROMATOGRAPHY, ION EXCHANGE; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ISOTOPE LABELING; PEPTIDE FRAGMENTS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOLYSIS; PROTEOME; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TANDEM MASS SPECTROMETRY; TRYPSIN; UBIQUITINATED PROTEINS; UBIQUITINATION;

EUKARYOTA;

EID: 84864131300     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-885-6_26     Document Type: Article

References (49)

1. Semple CA (2003) The comparative proteomics of ubiquitination in mouse. Genome Res 13:1389-1394
2. Schwartz AL, Ciechanover A (2009) Targeting proteins for destruction by the ubiquitin system: Implications for human pathobiology. Annu Rev Pharmacol Toxicol 49: 73-96
3. Finley D (2009) Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu Rev Biochem 78:477-513
4. Peng J, Schwartz D, Elias JE et al (2003) A proteomics approach to understanding protein ubiquitination. Nat Biotechnol 21: 921-926
5. Iwai K, Tokunaga F (2009) Linear polyubiquitination: A new regulator of NF-kappaB activation. EMBO Rep 10:706-713
6. Pickart CM, Fushman D (2004) Polyubiquitin chains: Polymeric protein signals. Curr Opin Chem Biol 8:610-616
7. Mukhopadhyay D, Riezman H (2007) Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science 315:201-205
8. Xu P, Duong DM, Seyfried NT et al (2009) Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137:133-145
9. Jin L, Williamson A, Banerjee S et al (2008) Mechanism of ubiquitin-chain formation by the human anaphase-promoting complex. Cell 133:653-665
10. Bhoj VG, Chen ZJ (2009) Ubiquitylation in innate and adaptive immunity. Nature 458: 430-437
11. Hochstrasser M (2009) Origin and function of ubiquitin-like proteins. Nature 458:422-429
12. Darwin KH (2009) Prokaryotic ubiquitin-like protein (Pup), proteasomes and pathogenesis. Nat Rev Microbiol 7:485-491
13. Kirkpatrick DS, Denison C, Gygi SP (2005) Weighing in on ubiquitin: The expanding role of mass-spectrometry-based proteomics. Nat Cell Biol 7:750-757
14. Xu P, Peng J (2006) Dissecting the ubiquitin pathway by mass spectrometry. Biochim Biophys Acta 1764:1940-1947
15. Wang X, Guerrero C, Kaiser P et al (2007) Proteomics of proteasome complexes and ubiquitinated proteins. Expert Rev Proteomics 4:649-665
16. Cravatt BF, Simon GM, Yates JR III (2007) The biological impact of mass-spectrometrybased proteomics. Nature 450:991-1000
17. Gstaiger M, Aebersold R (2009) Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet 10:617-627
18. Choudhary C, Mann M (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol 11: 427-439
19. Peng J (2008) Evaluation of proteomic strategies for analyzing ubiquitinated proteins. BMB Rep 41:177-183
20. Peng J, Cheng D (2005) Proteomic analysis of ubiquitin conjugates in yeast. Methods Enzymol 399:367-381
21. Tagwerker C, Flick K, Cui M et al (2006) A tandem af finity tag for two-step purification under fully denaturing conditions: Application in ubiquitin pro filing and protein complex identification combined with in vivo crosslinking. Mol Cell Proteomics 5:737-748
22. Meierhofer D, Wang X, Huang L et al (2008) Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. J Proteome Res 7:4566-4576
23. Matsumoto M, Hatakeyama S, Oyamada K et al (2005) Large-scale analysis of the human ubiquitin-related proteome. Proteomics 5: 4145-4151
24. Vasilescu J, Smith JC, Ethier M et al (2005) Proteomic analysis of ubiquitinated proteins from human MCF-7 breast cancer cells by immunoaf finity purification and mass spectrometry. J Proteome Res 4:2192-2200
25. Newton K, Matsumoto ML, Wertz IE et al (2008) Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies. Cell 134:668-678
26. Lay field R, Tooth D, Landon M et al (2001) Purification of poly-ubiquitinated proteins by S5a-af finity chromatography. Proteomics 1:773-777
27. Weekes J, Morrison K, Mullen A et al (2003) Hyperubiquitination of proteins in dilated cardiomyopathy. Proteomics 3:208-216
28. Maor R, Jones A, Nuhse TS et al (2007) Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants. Mol Cell Proteomics 6:601-610
29. Bennett EJ, Shaler TA, Woodman B et al (2007) Global changes to the ubiquitin system in Huntington's disease. Nature 448:704-708
30. Hjerpe R, Aillet F, Lopitz-Otsoa F et al (2009) Ef ficient protection and isolation of ubiquitylated proteins using tandem ubiquitin-binding entities. EMBO Rep 10:1250-1258
31. Peng J, Gygi SP (2001) Proteomics: The move to mixtures. J Mass Spectrom 36:1083-1091
32. Marotti LA Jr, Newitt R, Wang Y et al (2002) Direct identification of a G protein ubiquitination site by mass spectrometry. Biochemistry 41:5067-5074
33. Seyfried NT, Xu P, Duong DM et al (2008) Systematic approach for validating the ubiquitinated proteome. Anal Chem 80:4161-4169
34. Mayor T, Graumann J, Bryan J et al (2007) Quantitative pro filing of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire in fl uenced by the Rpn10 receptor pathway. Mol Cell Proteomics 6:1885-1895
35. Xu P, Duong DM, Peng J (2009) Systematical optimization of reverse-phase chromatography for shotgun proteomics. J Proteome Res 8:3944-3950
36. Eng J, McCormack AL, Yates JR 3rd (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976-989
37. Peng J, Elias JE, Thoreen CC et al (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J Proteome Res 2:43-50
38. Elias JE, Gygi SP (2007) Target-decoy search strategy for increased con fidence in large-scale protein identifications by mass spectrometry. Nat Methods 4:207-214
39. Seyfried NT, Gozal YM, Dammer EB et al (2010) Multiplex SILAC analysis of a cellular TDP-43 proteinopathy model reveals protein inclusions associated with SUMOylation and diverse polyubiquitin chains. Mol Cell Proteomics 9:705-718
40. Shevchenko A, Wilm M, Vorm O et al (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68:850-858
41. De Godoy LM, Olsen JV, Cox J et al (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455:1251-1254
42. Sury MD, Chen JX, Selbach M (2010) The SILAC fl y allows for accurate protein quantification in vivo. Mol Cell Proteomics 9(10):2173-2178
43. Kruger M, Moser M, Ussar S et al (2008) SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134:353-364
44. Nielsen ML, Vermeulen M, Bonaldi T et al (2008) Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nat Methods 5:459-460
45. Xu P, Cheng D, Duong DM et al (2006) A proteomic strategy for quantifying polyubiquitin chain topologies. Israel J Chem 46:171-182
46. Golebiowski F, Matic I, Tatham MH et al (2009) System-wide changes to SUMO modifications in response to heat shock. Sci Signal 2:ra24
47. Xu G, Paige JS, Jaffrey SR (2010) Global analysis of lysine ubiquitination by ubiquitin remnant immunoaf finity pro filing. Nat Biotechnol 28:868-873
48. Ross PL, Huang YN, Marchese JN et al (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3:1154-1169
49. Kirkpatrick DS, Hathaway NA, Hanna J et al (2006) Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology. Nat Cell Biol 8:700-710