The data described here provide the first large-scale analysis of lysine 63 (K63)-linked polyubiquitin targets. Protein ubiquitination is a prominent post-translational modification, and a variety of ubiquitin chains exists, serving a multitude of functions . The chains differ by the lysine residue by which the ubiquitin monomers are linked. We used yeast Saccharomyces cerevisiae subjected to oxidative stress as a model to study K63 ubiquitination. K63 ubiquitinated targets were pulled-down by the K63-TUBE system (Tandem Ubiquitin Binding Entities) and analyzed by SILAC-based mass spectrometry . The data are associated to the research article 'K63 polyubiquitination is a new modulator of the oxidative stress response' . The mass spectrometry and the analysis dataset have been deposited to the ProteomeXchange Consortium (. http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000960.
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