ATO is a therapeutic agents used to treat APL, a disease caused by a chromosomal translocation of the RARα gene that can occur reciprocally with the PML gene. The mechanisms through which ATO function and how increased levels of ATO adversely affect the cell are not fully characterized though they involve the SUMOylation, the ubiquitylation and the degradation of the PML/RARα oncoprotein through the PML moiety. Changes in protein SUMOylation, phosphorylation and ubiquitylation were profiled using large-scale proteomic workflows on HEK293 cells following exposure to typical (1 μM) or elevated (10 μM) ATO for 4h to understand the mechanism that underlies the cytotoxicity induced with important ATO levels. Our analyses revealed that 88 proteins displayed divergent SUMOylation with elevated ATO compared to the lower dose, where the latter caused changes in SUMOylation of 4 proteins, including PML. Some of these differing SUMOylation events occurred on known substrates of caspase-3. A similar phenomenon was observed in the phosphoproteomic studies, where 48 proteins were specifically regulated with elevated ATO levels, while low ATO doses barely altered the phosphoproteome. Elevated levels of ATO cause the erroneous SUMOylation and phosphorylation of a vast amount of substrates, which may be responsible for its cytotoxic effects.