Caspase-6 plays a role in neurodegenerative disorders like Alzheimer's and Parkinson's disease. A deeper understanding of caspase-6 regulation through characterization of its post-translational modifications (PTMs) could contribute to the prevention and treatment of these diseases. To monitor PTMs on caspase-6 and potentially discover novel PTM sites, we sought to develop an immunoprecipitation (IP) workflow, compatible with bottom-up mass spectrometry analysis, to enrich endogenous caspase-6 and its proteoforms. To enable effective mass spectrometry analysis of caspase-6 and its proteoforms, we aimed to minimize contamination of the protein enrichment caused by non-specific protein binding and reagent antibody contamination. We were especially interested in potential regulation at the ₄₂RRR₄₄ exosite previously identified by the Hardy Lab, and designed the workflow to be compatible with PTM discovery in this region on the protein. We also designed the workflow to optimize the amount of antibody used per IP reaction. The IP conditions were optimized using expression lysates from caspase-6-transformed BL-21 bacterial cells. SDS-PAGE and Western Blot analysis were performed to confirm efficient capture of recombinant caspase-6 from the BL-21 lysate and to validate the IP method for its application on a variety of human cell lines. Standard bottom-up sample processing methods, using acid-labile detergent, were used to convert captured caspase-6 from Jurkat cells into corresponding peptides for mass spectrometry (LC-MS/MS) characterization for PTM characterization. This work was performed to establish a foundation for future IP-based PTM discovery experiments for other caspase proteins in the Hardy Lab.