Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics

Abstract

Mass-spectrometry-based proteomics has become an essential tool for the qualitative and quantitative analysis of cellular systems. The biochemical complexity and functional diversity of the ubiquitin system are well suited to proteomic studies. This review summarizes advances involving the identification of ubiquitinated proteins, the elucidation of ubiquitin-modification sites and the determination of polyubiquitin chain linkages, as well as offering a perspective on the application of emerging technologies for mechanistic and functional studies of protein ubiquitination.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Mechanisms of protein modification by ubiquitin and Ubl proteins.
Figure 2: Overview of shotgun sequencing from complex mixtures by mass spectrometry.
Figure 3: Quantitative profiling of ubiquitinated proteins using stable isotopes.
Figure 4: Detecting unique diglycine (–GG) signature peptides for each polyubiquitin chain linkage.

Similar content being viewed by others

References

  1. Hershko, A. & Ciechanover, A. The ubiquitin system. Annu. Rev. Biochem. 67, 425–479 (1998).

    Article  CAS  PubMed  Google Scholar 

  2. Pickart, C. M. Mechanisms underlying ubiquitination. Nature Rev. Mol. Cell Biol. 70, 503–533 (2001).

    CAS  Google Scholar 

  3. Finley, D., Ciechanover, A. & Varshavsky, A. Ubiquitin as a central cellular regulator. Cell 116, S29–32 (2004).

    Article  CAS  PubMed  Google Scholar 

  4. Ciechanover, A., Heller, H., Elias, S., Haas, A. L. & Hershko, A. ATP-dependent conjugation of reticulocyte proteins with the polypeptide required for protein degradation. Proc. Natl Acad. Sci. USA 77, 1365–1368 (1980).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Hershko, A., Ciechanover, A., Heller, H., Haas, A. L. & Rose, I. A. Proposed role of ATP in protein breakdown: conjugation of protein with multiple chains of the polypeptide of ATP-dependent proteolysis. Proc. Natl Acad. Sci. USA 77, 1783–1786 (1980).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Finley, D., Ciechanover, A. & Varshavsky, A. Thermolability of ubiquitin-activating enzyme from the mammalian cell cycle mutant ts85. Cell 37, 43–55 (1984).

    Article  CAS  PubMed  Google Scholar 

  7. Ciechanover, A., Finley, D. & Varshavsky, A. Ubiquitin dependence of selective protein degradation demonstrated in the mammalian cell cycle mutant ts85. Cell 37, 57–66 (1984).

    Article  CAS  PubMed  Google Scholar 

  8. Johnson, E. S. Protein modification by SUMO. Annu. Rev. Biochem. 73, 355–382 (2004).

    Article  CAS  PubMed  Google Scholar 

  9. Ritchie, K. J. & Zhang, D. E. ISG15: the immunological kin of ubiquitin. Semin. Cell Dev. Biol. 15, 237–246 (2004).

    Article  CAS  PubMed  Google Scholar 

  10. Chiba, T. & Tanaka, K. Cullin-based ubiquitin ligase and its control by NEDD8-conjugating system. Curr. Protein Pept. Sci. 5, 177–184 (2004).

    Article  CAS  PubMed  Google Scholar 

  11. Pan, Z. Q., Kentsis, A., Dias, D. C., Yamoah, K. & Wu, K. Nedd8 on cullin: building an expressway to protein destruction. Oncogene 23, 1985–1997 (2004).

    Article  CAS  PubMed  Google Scholar 

  12. Wolters, D. A., Washburn, M. P. & Yates, J. R. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683–5690 (2001).

    Article  CAS  PubMed  Google Scholar 

  13. Eng, J., McCormack, A. L. & Yates, J. R., III 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 (1994).

    Article  CAS  PubMed  Google Scholar 

  14. Perkins, D. N., Pappin, D. J., Creasy, D. M. & Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567 (1999).

    Article  CAS  PubMed  Google Scholar 

  15. Lasonder, E. et al. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419, 537–542 (2002).

    Article  CAS  PubMed  Google Scholar 

  16. Everley, P. A., Krijgsveld, J., Zetter, B. R. & Gygi, S. P. Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol. Cell Proteomics 3, 729–735 (2004).

    Article  CAS  PubMed  Google Scholar 

  17. Florens, L. et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520–526 (2002).

    Article  CAS  PubMed  Google Scholar 

  18. Peng, J. et al. A proteomics approach to understanding protein ubiquitination. Nature Biotech. 21, 921–926 (2003).

    Article  CAS  Google Scholar 

  19. Washburn, M. P., Wolters, D. & Yates, J. R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol. 19, 242–247 (2001).

    Article  CAS  Google Scholar 

  20. Hitchcock, A. L., Auld, K., Gygi, S. P. & Silver, P. A. A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery. Proc. Natl Acad. Sci. USA 100, 12735–12740 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Mayor, T., Russell-Lipford, J., Graumann, J., Smith, G. T. & Deshaies, R. J. Analysis of poly-ubiquitin conjugates reveals that the Rpn10 substrate receptor contributes to the turnover of multiple proteasome targets. Mol. Cell. Proteomics 4, 741–751 (2005).

    Article  CAS  PubMed  Google Scholar 

  22. Zhou, W., Ryan, J. J. & Zhou, H. Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses. J. Biol. Chem. 279, 32262–32268 (2004).

    Article  CAS  PubMed  Google Scholar 

  23. Wohlschlegel, J. A., Johnson, E. S., Reed, S. I. & Yates J. R. Global analysis of protein sumoylation in Saccharomyces cerevisiae. J. Biol. Chem. 279, 45662–45668 (2004).

    Article  CAS  PubMed  Google Scholar 

  24. Denison, C. et al. Proteomic insights into protein sumoylation. Mol. Cell. Proteomics 4, 246–254 (2005).

    Article  CAS  PubMed  Google Scholar 

  25. Hannich, J. T. et al. Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J. Biol. Chem. 280, 4102–4110 (2005).

    Article  CAS  PubMed  Google Scholar 

  26. Panse, V. G., Hardeland, U., Werner, T., Kuster, B. & Hurt, E. A proteome-wide approach identifies sumoylated substrate proteins in yeast. J. Biol. Chem. 279, 41346–41351 (2004).

    Article  CAS  PubMed  Google Scholar 

  27. Kirkpatrick, D. S., Weldon, S. F., Tsaprailis, G., Liebler, D. C. & Gandolfi, A. J. Proteomic identification of ubiquitinated proteins from human cells expressing His-tagged ubiquitin. Proteomics 5, 2104–2111 (2005).

    Article  CAS  PubMed  Google Scholar 

  28. Vertegaal, A. C. et al. A proteomic study of SUMO-2 target proteins. J. Biol. Chem. 279, 33791–33798 (2004).

    Article  CAS  PubMed  Google Scholar 

  29. Manza, L. L. et al. Global shifts in protein sumoylation in response to electrophile and oxidative stress. Chem. Res. Tox. 17, 1706–1715 (2004).

    Article  CAS  Google Scholar 

  30. Zhao, Y., Kwon, S. W., Anselmo, A., Kaur, K. & White, M. A. Broad spectrum identification of cellular small ubiquitin-related modifier (SUMO) substrate proteins. J. Biol. Chem. 279, 20999–21002 (2004).

    Article  CAS  PubMed  Google Scholar 

  31. Rosas-Acosta, G., Russell, W. K., Deyrieux, A., Russell, D. H. & Wilson, V. G. A universal strategy for proteomic studies of SUMO and other ubiquitin-like modifiers. Mol. Cell. Proteomics 4, 56–72 (2005).

    Article  CAS  PubMed  Google Scholar 

  32. Tsirigotis, M. et al. Analysis of ubiquitination in vivo using a transgenic mouse model. Biotechniques 31, 120–130 (2001).

    Article  CAS  PubMed  Google Scholar 

  33. Finley, D. et al. Inhibition of proteolysis and cell cycle progression in a multiubiquitination-deficient yeast mutant. Mol. Cell Biol. 14, 5501–5509 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Weekes, J. et al. Hyperubiquitination of proteins in dilated cardiomyopathy. Proteomics 3, 208–216 (2003).

    Article  CAS  PubMed  Google Scholar 

  35. Gururaja, T., Li, W., Noble, W. S., Payan, D. G. & Anderson, D. C. Multiple functional categories of proteins identified in an in vitro cellular ubiquitin affinity extract using shotgun peptide sequencing. J. Prot. Res. 2, 394–404 (2003).

    Article  CAS  Google Scholar 

  36. Li, T. et al. Sumoylation of heterogeneous ribonucleoproteins, zinc finger proteins, and nuclear pore complex proteins: a proteomic analysis. Proc. Natl Acad. Sci. USA 101, 8551–8556 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Gocke, C. B., Yu, H. & Kang, J. Systematic identification and analysis of mammalian small ubiquitin-like modifier substrates. J. Biol. Chem. 280, 5004–5012 (2005).

    Article  CAS  PubMed  Google Scholar 

  38. Sato, K. et al. Nucleophosmin/B23 is a candidate substrate for the BRCA1-BARD1 ubiquitin ligase. J. Biol. Chem. 279, 30919–30922 (2004).

    Article  CAS  PubMed  Google Scholar 

  39. Starita, L. M. et al. BRCA1-dependent ubiquitination of gamma-tubulin regulates centrosome number. Mol. Cell. Biol. 24, 8457–8466 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Chang, T. L., Cubillos, F. F., Kakhniashvili, D. G. & Goodman, S. R. Ankyrin is a target of spectrin's E2/E3 ubiquitin-conjugating/ligating activity. Cell. Mol. Biol. 50, 59–66 (2004).

    CAS  PubMed  Google Scholar 

  41. Chung, D. L. et al. In vitro modification of centromere protein CENP-C fragments by small ubiquitin-like modifier (SUMO) protein: definitive identification of the modification sites by tandem mass spectrometry analysis of isopeptides. J. Biol. Chem. 279, 39653–39662 (2004).

    Article  CAS  PubMed  Google Scholar 

  42. Schirmer, E. C., Florens, L., Guan, T., Yates, J. R. & Gerace, L. Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science 301, 1380–1382 (2003).

    Article  CAS  PubMed  Google Scholar 

  43. Oda, Y., Huang, K., Cross, F. R., Cowburn, D. & Chait, B. T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl Acad. Sci. USA 96, 6591–6596 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. 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).

    Article  CAS  PubMed  Google Scholar 

  45. Andersen, J. S. et al. Nucleolar proteome dynamics. Nature 433, 77–83 (2005).

    Article  CAS  PubMed  Google Scholar 

  46. Gygi, S. P. et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotech. 17, 994–999 (1999).

    Article  CAS  Google Scholar 

  47. Wykoff, D. D. & O'Shea, E. K. Identification of sumoylated proteins by systematic immunoprecipitation of the budding yeast proteome. Mol. Cell. Proteomics 4, 73–83 (2005).

    Article  CAS  PubMed  Google Scholar 

  48. Zachariae, W. et al. Mass spectrometric analysis of the anaphase-promoting complex from yeast: identification of a subunit related to cullins. Science 279, 1216–1219 (1998).

    Article  CAS  PubMed  Google Scholar 

  49. Yoon, H. J. et al. Proteomics analysis identifies new components of the fission and budding yeast anaphase-promoting complexes. Curr. Biol. 12, 2048–2054 (2002).

    Article  CAS  PubMed  Google Scholar 

  50. Seol, J. H. et al. Cdc53/cullin and the essential Hrt1 RING-H2 subunit of SCF define a ubiquitin ligase module that activates the E2 enzyme Cdc34. Genes Dev. 13, 1614–1626 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Seol, J. H., Shevchenko, A. & Deshaies, R. J. Skp1 forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly. Nature Cell Biol. 3, 384–391 (2001).

    Article  CAS  PubMed  Google Scholar 

  52. Li, M. et al. Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature 416, 648–653 (2002).

    Article  CAS  PubMed  Google Scholar 

  53. Rajendra, R. et al. Topors functions as an E3 ubiquitin ligase with specific E2 enzymes and ubiquitinates p53. J. Biol. Chem. 279, 36440–36444 (2004).

    Article  CAS  PubMed  Google Scholar 

  54. Harada, J. N., Shevchenko, A., Pallas, D. C. & Berk, A. J. Analysis of the adenovirus E1B-55K-anchored proteome reveals its link to ubiquitination machinery. J. Virol. 76, 9194–9206 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Yaron, A. et al. Identification of the receptor component of the IκB α-ubiquitin ligase. Nature 396, 590–594 (1998).

    Article  CAS  PubMed  Google Scholar 

  56. Liu, Z., Oughtred, R. & Wing, S. S. Characterization of E3Histone, a novel testis ubiquitin protein ligase which ubiquitinates histones. Mol. Cell. Biol. 25, 2819–2831 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Wang, H. et al. Role of histone H2A ubiquitination in Polycomb silencing. Nature 431, 873–878 (2004).

    Article  CAS  PubMed  Google Scholar 

  58. Wertz, I. E. et al. Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase. Science 303, 1371–1374 (2004).

    Article  CAS  PubMed  Google Scholar 

  59. Feshchenko, E. A. et al. TULA: an SH3- and UBA-containing protein that binds to c-Cbl and ubiquitin. Oncogene 23, 4690–4706 (2004).

    Article  CAS  PubMed  Google Scholar 

  60. Verma, R. et al. Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol. Cell. Biol. 11, 3425–3439 (2000).

    Article  CAS  Google Scholar 

  61. Verma, R. et al. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 298, 611–615 (2002).

    Article  CAS  PubMed  Google Scholar 

  62. Borodovsky, A. et al. Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family. Chem. Biol. 9, 1149–1159 (2002).

    Article  CAS  PubMed  Google Scholar 

  63. Ovaa, H. et al. Activity-based ubiquitin-specific protease (USP) profiling of virus-infected and malignant human cells. Proc. Natl Acad. Sci. USA 101, 2253–2258 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Hemelaar, J. et al. Chemistry-based functional proteomics: mechanism-based activity-profiling tools for ubiquitin and ubiquitin-like specific proteases. J. Prot. Res. 3, 268–276 (2004).

    Article  CAS  Google Scholar 

  65. Hemelaar, J. et al. Specific and covalent targeting of conjugating and deconjugating enzymes of ubiquitin-like proteins. Mol. Cell. Biol. 24, 84–95 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Mann, M. & Jensen, O. N. Proteomic analysis of post-translational modifications. Nature Biotechnol. 21, 255–261 (2003).

    Article  CAS  Google Scholar 

  67. Chen, W. G. & White, F. M. Proteomic analysis of cellular signaling. Expert Rev. Proteomics 1, 89–100 (2004).

    Article  Google Scholar 

  68. Ficarro, S. B. et al. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nature Biotechnol. 20, 301–305 (2002).

    Article  CAS  Google Scholar 

  69. Beausoleil, S. A. et al. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl Acad. Sci. USA 101, 12130–12135 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Rush, J. et al. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nature Biotechnol. 23, 94–101 (2005).

    Article  CAS  Google Scholar 

  71. Marotti L. A. Jr, Newitt, R., Wang, Y., Aebersold, R. & Dohlman, H. G. Direct identification of a G protein ubiquitination site by mass spectrometry. Biochem. 41, 5067–5074 (2002).

    Article  CAS  Google Scholar 

  72. Coulombe, P., Rodier, G., Bonneil, E., Thibault, P. & Meloche, S. N-Terminal ubiquitination of extracellular signal-regulated kinase 3 and p21 directs their degradation by the proteasome. Mol. Cell. Biol. 24, 6140–6150 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Flick, K. et al. Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain. Nature Cell Biol. 6, 634–641 (2004).

    Article  CAS  PubMed  Google Scholar 

  74. Lee, J. S., Hong, U. S., Lee, T. H., Yoon, S. K. & Yoon, J. B. Mass spectrometry analysis of tumor necrosis factor receptor-associated factor 1 ubiquitinatin mediated by cellular inhibitor of apoptosis 2. Proteomics 4, 3376–3382 (2004).

    Article  CAS  PubMed  Google Scholar 

  75. Moren, A. et al. Differential ubiquitination defines the functional status of the tumor suppressor Smad4. J. Biol. Chem. 278, 33571–33582 (2003).

    Article  CAS  PubMed  Google Scholar 

  76. Petroski, M. D. & Deshaies, R. J. Context of multiubiquitin chain attachment influences the rate of Sic1 degradation. Mol. Cell 11, 1435–1444 (2003).

    Article  CAS  PubMed  Google Scholar 

  77. Terrell, J., Shih, S., Dunn, R. & Hicke, L. A function for monoubiquitination in the internalization of a G protein-coupled receptor. Mol. Cell 1, 193–202 (1998).

    Article  CAS  PubMed  Google Scholar 

  78. Cooper, H. J. et al. Identification of sites of ubiquitination in proteins: a fourier transform ion cyclotron resonance mass spectrometry approach. Anal. Chem. 76, 6982–6988 (2004).

    Article  CAS  PubMed  Google Scholar 

  79. Warren, M. R., 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).

    Article  CAS  PubMed  Google Scholar 

  80. Wang, D. & Cotter, R. J. Approach for determining protein ubiquitination sites by MALDI-TOF mass spectrometry. Anal. Chem. 77, 1458–1466 (2005).

    Article  CAS  PubMed  Google Scholar 

  81. Brittain, S. M., Ficarro, S. B., Brock, A. & Peters, E. C. Enrichment and analysis of peptide subsets using fluorous affinity tags and mass spectrometry. Nature Biotechnol. 23, 463–468 (2005).

    Article  CAS  Google Scholar 

  82. Pickart, C. M. & Fushman, D. Polyubiquitin chains: polymeric protein signals. Curr. Opin. Chem. Biol. 8, 610–616 (2004).

    Article  CAS  PubMed  Google Scholar 

  83. Chau, V. et al. A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein. Science 243, 1576–1583 (1989).

    Article  CAS  PubMed  Google Scholar 

  84. Spence, J., Sadis, S., Haas, A. L. & Finley, D. A ubiquitin mutant with specific defects in DNA repair and multiubiquitination. Mol. Cell. Biol. 15, 1265–1273 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Thrower, J. S., Hoffman, L., Rechsteiner, M. & Pickart, C. M. Recognition of the polyubiquitin proteolytic signal. EMBO J. 19, 94–102 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Hofmann, R. M. & Pickart, C. M. In vitro assembly and recognition of Lys-63 polyubiquitin chains. J. Biol. Chem. 276, 27936–27943 (2001).

    Article  CAS  PubMed  Google Scholar 

  87. Mastrandrea, L. D., You, J., Niles, E. G. & Pickart, C. M. E2/E3-mediated assembly of lysine 29-linked polyubiquitin chains. J. Biol. Chem. 274, 27299–27306 (1999).

    Article  CAS  PubMed  Google Scholar 

  88. Takada, K., Hibi, N., Tsukada, Y., Shibasaki, T. & Ohkawa, K. Ability of ubiquitin radioimmunoassay to discriminate between monoubiquitin and multi-ubiquitin chains. Biochim. Biophys. Acta 1290, 282–288 (1996).

    Article  PubMed  Google Scholar 

  89. Takada, K. et al. Immunoassay for the quantification of intracellular multi-ubiquitin chains. Eur. J. Biochem. 233, 42–47 (1995).

    Article  CAS  PubMed  Google Scholar 

  90. Haglund, K. et al. Multiple monoubiquitination of RTKs is sufficient for their endocytosis and degradation. Nature Cell Biol. 5, 461–466 (2003).

    Article  CAS  PubMed  Google Scholar 

  91. Saeki, Y., Tayama, Y., Toh-e, A. & Yokosawa, H. Definitive evidence for Ufd2-catalyzed elongation of the ubiquitin chain through Lys48 linkage. Biochem. Biophys. Res. Commun. 320, 840–845 (2004).

    Article  CAS  PubMed  Google Scholar 

  92. Wu-Baer, F., Lagrazon, K., Yuan, W. & Baer, R. The BRCA1/BARD1 heterodimer assembles polyubiquitin chains through an unconventional linkage involving lysine residue K6 of ubiquitin. J. Biol. Chem. 278, 34743–34746 (2003).

    Article  CAS  PubMed  Google Scholar 

  93. Nishikawa, H. et al. Mass spectrometric and mutational analyses reveal Lys6-linked polyubiquitin chains catalyzed by BRCA1–BAR1 ubiquitin ligase. J. Biol. Chem. 279, 3916–3924 (2004).

    Article  CAS  PubMed  Google Scholar 

  94. Shang, F. et al. Lys-6-modified ubiquitin inhibits ubiquitin-dependent protein degradation. J. Biol. Chem. 280, 20365–20374 (2005).

    Article  CAS  PubMed  Google Scholar 

  95. Russell, N. S. & Wilkinson, K. D. Identification of a novel 29-linked polyubiquitin binding protein, Ufd3, using polyubiquitin chain analogues, Biochemistry. Biochemistry 43, 4844–4854 (2004).

    Article  CAS  PubMed  Google Scholar 

  96. Kirkpatrick, D. S., Gerber, S. A. & Gygi, S. P. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35, 265–273 (2005).

    Article  CAS  PubMed  Google Scholar 

  97. Li, M. et al. Mono- versus polyubiquitination: differential control of p53 fate by mdm2. Science 302, 1972–1975 (2003).

    Article  CAS  PubMed  Google Scholar 

  98. Richly, H. et al. A series of ubiquitin binding factors Cdc48/p97 to substrate multiubiquitylation and proteasomal targeting. Cell 120, 73–84 (2005).

    Article  CAS  PubMed  Google Scholar 

  99. Verma, R., Oania, R., Graumann, J. & Deshaies, R. J. Multiubiquitin chain receptors define a layer of substrate selectivity in the ubiquitin-proteasome system. Cell 118, 99–110 (2004).

    Article  CAS  PubMed  Google Scholar 

  100. Verma, R. et al. Ubistatins inhibit proteasome-dependent degradation by binding the ubiquitin chain. Science 306, 117–120 (2004).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

Work in the laboratory of S.P.G. is supported by National Institutes of Health grants HG00041 and GM67945.

Author information

Authors and Affiliations

Authors

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kirkpatrick, D., Denison, C. & Gygi, S. Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol 7, 750–757 (2005). https://doi.org/10.1038/ncb0805-750

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/ncb0805-750

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing