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Mol Cell Proteomics. 2013 Dec;12(12):3521-31. doi: 10.1074/mcp.R113.029744. Epub 2013 May 23.

Using the ubiquitin-modified proteome to monitor protein homeostasis function.

Author information

1
Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093.

Abstract

The ubiquitin system is essential for the maintenance of proper protein homeostasis function across eukaryotic species. Although the general enzymatic architecture for adding and removing ubiquitin from substrates is well defined, methods for the comprehensive investigation of cellular ubiquitylation targets have just started to emerge. Recent advances in ubiquitin-modified peptide enrichment have greatly increased the number of identified endogenous ubiquitylation targets, as well as the number of sites of ubiquitin attachment within these substrates. Herein we evaluate current strategies using mass-spectrometry-based proteomics to characterize ubiquitin and ubiquitin-like modifications. Using existing data, we describe the characteristics of the ubiquitin-modified proteome and discuss strategies for the biological interpretation of existing and future ubiquitin-based proteomic studies.

PMID:
23704779
PMCID:
PMC3861705
DOI:
10.1074/mcp.R113.029744
[Indexed for MEDLINE]
Free PMC Article

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