20S and 26S Proteasome-binding proteins of the rabbit brain: a proteomic dataset

Fractions of 26S and 20S proteasomes isolated from the rabbit brain by the method of salt fractionation (salt-induced precipitation) contain intrinsic proteasome proteins responsible for assembly of the core particle and regulatory particle of proteasome and also proteasome-binding proteins. These proteasome-binding proteins include components of the ubiquitin-proteasome system, some ubiquitinated proteins, as well as cytoskeleton components, protective proteins, regulators of gene expression, cell division, and differentiation, and multifunctional proteins (mainly, glycolytic enzymes: glyceraldehyde-3-phosphate dehydrogenase (GAPDH), aldolase, pyruvate kinase, etc.). The multifunctional proteins are also known as “moonlighting proteins” are involved in various (regulatory) processes in the cell and this suggests that they represent important components of the proteasome interactome rather than contaminants of the 26S and 20S proteasome fractions.

Data obtained by high-resolution mass spectrometry in Ubiquitine-tag triggered MS3-mode with synchronous fragment ions selection, and nano-flow liquid chromatography (see "Steps to reproduce for details). The presented dataset comprised of two subsets: (1) Data of proteomes obtained for each animal under the study; these data are in Excel format and contain necessary information about proteins, peptides, fragments, and their abundance, and other related meta-data. Data contained specific modifications identified in peptides by the PSMs. (2) Combined data for the complete cohort of animals with protein distribution.

Both subsets also contain information about semi-quantitative protein representation estimated by the NSAF algorithm in the Search GUI/Peptide Shaker search engine.