AAF-CMK trifluoroacetate salt is primarily used in biochemical research as a potent and irreversible inhibitor of serine proteases. Its application is significant in studying enzyme mechanisms, particularly in understanding the role of proteases in various biological processes. Researchers utilize this compound to block protease activity, allowing them to investigate the effects of protease inhibition on cellular functions and pathways. It is also employed in the development of therapeutic strategies targeting protease-related diseases, such as cancer, inflammation, and viral infections. Additionally, AAF-CMK trifluoroacetate salt is used in protein studies to prevent unwanted proteolysis during protein purification and analysis, ensuring the integrity of protein samples.