Fig. 6 |. Integrating ubiquitin proteomics, WCP and RNA-seq data reveals a prevalence of non-degradative ubiquitylation.

a, Numbers of predicted degradative (gray) and non-degradative (red) ubiquitylation events for all proteins exhibiting basal (left) or TCR-induced (right) ubiquitylation in CD4⁺ T cells rested or restimulated for 4 h with CD3 + CD28 antibody-coated beads (3:1 cell/bead ratio). TCR-induced ubiquitylation produces a significantly higher proportion of non-degradative ubiquitylation events compared with basal ubiquitylation (P < 0.006) according to a two-tailed two-proportion test. b, Relative abundance of ubiquitin lysine peptides identified in the ubiquitin proteome of resting CD4⁺ T cells. Relative abundance is represented by the z-score of the peptide abundance quantified by mass spectrometry intensity values. c, The log₂ fold change in abundance of ubiquitin lysine peptides identified in the ubiquitin proteome during TCR stimulation. b,c, Relative abundance and log₂ fold changes are averaged for two di-glycine immunoprecipitation mass spectrometry experiments, as described in a.