Aging and diet alter the protein ubiquitylation landscape in the mouse brain

The datasets were generated primarily using mass spectrometry and RNA sequencing techniques. For ubiquitylation, acetylation, and phosphorylation analyses, tissues or cells were lysed, and proteins were extracted. Post-translational modifications were enriched using specific antibodies or affinity-based methods, and the modified peptides were analyzed by mass spectrometry to identify and quantify the modifications. Whole proteome analyses involved extracting total proteins, digesting them into peptides using enzymes like trypsin, and analyzing them by mass spectrometry to determine overall protein expression levels. RNA-Seq data were obtained by extracting RNA, converting it into complementary DNA (cDNA), and sequencing it to quantify gene expression. For AQUA-PRM ubiquitin chain analysis, synthetic peptides specific to ubiquitin chain linkages were used as standards, and parallel reaction monitoring (PRM) mass spectrometry was employed to quantify the abundance of different ubiquitin chain types.