This proteomics dataset was generated to study the changes in SUMO site abundances between control cells and Interferon-alpha treated cells using SILAC. Cells were first fractionated into the cytoplasmic and nuclear fractions. SUMOylated proteins were then purified from these extracts by Ni-NTA via the 6xHIS tag on the SUMO3 construct. The proteins were then digested with trypsin and the peptides desalted on HLB cartridges. The SUMOylated peptides, which harbor an NQTGG remnant after tryptic digestion, were enriched with our anti-NQTGG antibody. The resulting peptides were injected on the orbitrap fusion instrument. The .raw files were analyzed with maxqunt.