Alterations of the ubiquitin proteasome system (UPS) contribute to the progression of many diseases, such as cancer, neurodegenerative
diseases, immunological disorders, and inflammation. Pharmacologic inhibition of specific ubiquitin regulatory enzymes and
ubiquitination events is an important challenge in drug discovery. Identifying the substrates of the various enzymes that participate in the
UPS is needed to determine which enzymes are potential drug candidates. Additionally, identifying the ubiquitination events regulated by
pharmacological drugs can potentially discover new applications. In this review we describe mass spectrometry-based proteomic approaches
for the identification of ubiquitinated proteins and their modification sites on a proteome-wide scale, focusing on the ubiquitin
remnant profiling, a newly developed ubiquitination profiling technique. We then discuss the application of this approach for the profiling
of ubiquitination events regulated by cell signaling pathways and explore its future applications for drug discovery in the UPS.