Datasets of the proteome-wide profiling of native SUMO post-translational modifications in HCT and HELA cells using a novel method to isolate modified peptides through a diglycyl lysine remnant, as previously used for proteome-wide ubiquitin profiling. Includes ID experiments for the identification of SUMO modification sites, quantification of the effects of proteome inhibition by MG132 using K8 SILAC methods, and side-by-side identification of ubiquitin and sumoylation modification sites.