YFP-PML WT, A216T, and L217F show differential ubiquitination at the site level. (A) Schematic presentation of PML sequence with sites of lysine modifications indicated. Ubiquitination sites are shown by circles, with size approximating to peptide intensity. Paler circles were not detected in WT-PML purifications. (B) Aggregated ubiquitin-PML peptide intensity data for each GlyGly-K peptide identified in each YFP-PML purification. (C) Schematic presentation of SUMO sequences with sites of lysine ubiquitination indicated as described for A. (D) Aggregated ubiquitin-SUMO peptide intensity data for each GlyGly-K peptide identified in experimental condition. (E) Schematic presentation of ubiquitin sequence with ubiquitination sites of ubiquitination shown as described for A. (F) Aggregated ubiquitin–ubiquitin peptide intensity data for each GlyGly-K peptide identified in each YFP-PML purification. (G) Charts of average intensity (columns) and SEM (bars) for the GlyGly-K peptides diagnostic of ubiquitin–ubiquitin modifications at the indicated sites (number of purifications, n = 4). (H)t test summary for the pairwise comparisons indicated for each ubiquitin–ubiquitin modification. Welch’s correction was applied for heteroskedastic data. Red entries are P < 0.05. Number of different peptides used for each site is indicated as evidence count.