Interpreting the Language of Polyubiquitin with Linkage-Specific Antibodies and Mass Spectrometry

  • Marissa L. MatsumotoEmail author
  • Erick R. Castellanos
  • Yi Jimmy Zeng
  • Donald S. KirkpatrickEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1844)


Posttranslational modification of cellular proteins by ubiquitin serves a variety of functions. Among the multitude of ubiquitin substrates, ubiquitin itself is the most prevalent. For many years, the direct detection of polyubiquitin chains attached to cellular substrates was not practical, with cell biologists relegated to indirect approaches involving site-directed mutagenesis or in vitro biochemistry. Recent advances in two technologies—polyubiquitin linkage-specific antibodies and mass spectrometry proteomics, have overcome that limitation. Using one or both of these, the direct analysis of polyubiquitin chain linkages on cellular substrate proteins may be performed. This paper describes the complimentary nature of linkage-specific antibodies and mass spectrometry proteomics for the characterization of complex ubiquitin signals using lessons learned in early development of both technologies.

Key words

Ubiquitin Polyubiquitin chains Linkage-specific antibodies Mass spectrometry Ub-AQUA 



All authors are employees of Genentech Inc. and shareholders of the Roche group.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Structural BiologyGenentech, Inc.South San FranciscoUSA
  2. 2.Department of Microchemistry, Proteomics and LipidomicsGenentech, Inc.South San FranciscoUSA

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