Targeted Protein Degradation harnesses the cell’s natural protein degradation machinery, usually the ubiquitin proteasome system (UPS), to degrade a certain protein of interest. For a protein to be efficiently degraded using the UPS, it must be modified by ubiquitin conjugation. Ubiquitination of a target protein involves a number of enzymes such as E1, E2 and E3 ligase, in which the E3 ligase is responsible for determining substrate specificity. At Plexium, we develop monovalent degraders that enable ubiquitin tagging of a target protein by bringing together the protein of interest and its corresponding E3 ligase. The ubiquitin protein is then directed to the 26S proteasome for degradation. In TPD programs, monovalent degraders are usually validated using Global Proteome Analysis using quantitative proteomics and the most commonly isobaric mass tagging using TMT. In this study, we evaluate the use of Data Independent Acquisition (DIA) for the analysis of protein degradation vs. traditional TMT workflows…