Proteome-Wide Binding Affinity Profiling

Selective interactions between ligands and protein targets are fundamental to normal biological processes and drug action, and the strength of these interactions is a key metric that defines their functions and disease relevance. Recently introduced methods couple ligand-protein interactions to mass spectrometry-proteomic readouts, enabling the measurement of proteome-wide binding affinity profiles. Here, we review the state of affinity profiling technology, focusing on three key approaches: (a) protein stability-based methods, which detect ligand-induced stabilization against thermal or chemical denaturation; (b) proteolytic resistance-based methods, which infer protein binding through altered susceptibility to enzymatic digestion; and (c) methods that use derivatized probes to capture and enrich ligand-protein complexes.