Modification of proteins by covalent attachment of ubiquitin and the ubiquitin-like modifier SUMO are widespread regulatory events of all eukaryotic cells. SUMOylation has received much attention, because several identified targets play prominent roles, in particular, in cell signaling, gene expression, and DNA repair. Notably, only a very small fraction of a substrate is usually SUMOylated at steady-state levels, which could be because modification is reversible and transient. Because of the low level of modification, SUMOylated proteins are often overlooked or sometimes misinterpreted as a less important fraction of a protein pool. Here we discuss procedures that can circumvent identification problems and describe methods for their verification.