YFP-PML WT, A216T, and L217F show differential SUMOylation at the site level. Data derived from the proteomics experiment detailed in Fig. S1. (A) Principal component analysis based on all modified and unmodified peptides detected from SUMO1, SUMO2, SUMO3, ubiquitin, and PML. (B) Relative protein intensity for SUMO1, SUMO2+3, ubiquitin, and PML in the purifications. Protein intensities are the sum of all unmodified peptide intensities and are a proxy for protein abundance. SUMO2+3 is the sum of the intensities all peptides derived from both paralogs. Number of replicates n = 4, and significance was determined by unpaired t tests with Welch’s correction where necessary. (C) Schematic presentation of PML with sites of lysine modifications indicated relative to PML domains. SUMO1 and SUMO2/3 modifications are shown as circles, with size approximating to peptide intensity. (D) Aggregated SUMO1-PML peptide intensity data for each branched peptide identified in each YFP-PML purification. (E) Aggregated SUMO2/3-PML peptide intensity data for each branched peptide identified in each YFP-PML purification. (F–H) Schematic presentation of SUMO1, SUMO2, and SUMO3 sequences with sites of lysine modifications indicated. SUMO1 and SUMO2/3 sites are shown by circles, with size approximating to peptide intensity. Paler circles were not detected in WT-PML purifications. (G and H) Aggregated peptide intensity data for each branched peptide for SUMO1 (G) or SUMO2/3 (H) conjugated to an acceptor SUMO molecule.