Phenylmethanesulfonyl fluoride is primarily used as a serine protease inhibitor in biochemical and molecular biology research. It effectively blocks the activity of enzymes like trypsin, chymotrypsin, and thrombin, making it valuable in protein purification and enzyme studies. Additionally, it is employed to prevent protein degradation during cell lysis, ensuring the integrity of samples for analysis. Its application extends to studying protease-dependent pathways and mechanisms in various biological systems.