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Deciphering Tissue-Specific Ubiquitylation by Mass Spectrometry

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Ubiquitin Family Modifiers and the Proteasome

Part of the book series: Methods in Molecular Biology ((MIMB,volume 832))

Abstract

Protein ubiquitylation is a highly conserved, central mechanism to regulate cellular events in all eukaryotes, such as proteasomal degradation, protein trafficking, DNA repair, synaptic plasticity, and immune response. The consequence of protein ubiquitylation is modulated by the structure of ubiquitin (Ub) moiety attached on the substrates, including ubiquitin monomer and diverse polyubiquitin chains with different linkages (N-terminus, K6, K11, K27, K29, K33, K48, and K63). The development of ubiquitin-enrichment strategies coupled with sensitive mass spectrometry enables direct analysis of ubiquitylated proteins in cells, providing an invaluable tool for ubiquitin research. In this chapter, we describe recent technology updates for analyzing tissue-specific ubiquitin conjugates in transgenic models, as well as targeted proteomics methods for quantifying different polyubiquitin chain linkages in any type of ­samples, including human tissues.

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Acknowledgments

This work was partially supported by the National Institutes of Health grant (RR025822) and the American Cancer Society grant (RSG-09-181). UM is an Ikerbasque Research Professor.

Author information

Authors and Affiliations

  1. Ikerbasque, Basque Foundation for Science, Bilbao, Spain

    Ugo Mayor

  2. CIC bioGUNE, Technology Park of Bizkaia, Derio, Spain

    Ugo Mayor

  3. Department of Structural Biology, St. Jude Proteomics Facility, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105-3678, USA

    Junmin Peng

Authors
  1. Ugo Mayor
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  2. Junmin Peng
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Corresponding author

Correspondence to Junmin Peng .

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Editors and Affiliations

  1. Institut für Genetik, Universität Köln, Zülpicher Str. 47, Köln, 50674, Germany

    R. Jürgen Dohmen

  2. Fak. Biologie, Universität Konstanz, Konstanz, 78457, Germany

    Martin Scheffner

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Mayor, U., Peng, J. (2012). Deciphering Tissue-Specific Ubiquitylation by Mass Spectrometry. In: Dohmen, R., Scheffner, M. (eds) Ubiquitin Family Modifiers and the Proteasome. Methods in Molecular Biology, vol 832. Humana Press. https://doi.org/10.1007/978-1-61779-474-2_3

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  • DOI: https://doi.org/10.1007/978-1-61779-474-2_3

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-473-5

  • Online ISBN: 978-1-61779-474-2

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