Chemical Proteomics Probes: Classification, Applications, and Future Perspectives in Proteome-Wide Studies

Chemical proteomics probes serve as critical tools for investigating small molecule-protein interactions within complex biological systems. Traditionally, they are categorized into covalent probes and photoaffinity probes. They facilitate drug target discovery, targeted ligand screening, dynamic evaluation of enzyme activities in disease contexts, protein modification mapping, and bridging proteomics with other omics platforms. Despite their significant utility, challenges remain in probe design optimization, reduction of non-specific interactions, and expansion of targetable proteomic landscapes. Future research efforts are expected to focus on the development of novel probes, the integration of chemical proteomics with structural biology and artificial intelligence, and the advancement of clinical applications. These innovations will deepen our understanding of protein functions and support the advancement of precision medicine. In this review, we summarize the classification and fundamental principles of chemical proteomics probes and provide an in-depth discussion of their diverse applications.