Covalent protein modification by sumoylation (i.e., addition of small ubiquitin-like modifiers [SUMOs]) regulates a broad spectrum of critical functions in eukaryotic cells; however, usually ≤1% of a given protein is modified as a result of the highly dynamic nature of sumoylation. As such, capturing and identifying sumoylated proteins are both important in biological studies and very challenging tasks. Here we report a tailored purification protocol that includes rapid and complete cell disruption, coupled to highly stringent isolation of sumoylated proteins. Proteins purified using this protocol are compatible with common downstream applications such as western and mass spectrometry analyses. This protocol will work equally well to study other key covalent modifiers such as ubiquitin and Ned8.