Expanding the Reach of Membrane Protein–Ligand Interaction Studies Through the Integration of Mass Spectrometry and Membrane Mimetics

Mass spectrometry (MS) offers robust, label-free approaches for characterizing ligand-protein interactions through two main strategies: affinity-based and stability-based assays. However, their application to membrane proteins (MPs)-a major class of drug targets-has been limited by challenges such as structural complexity, low native expression, incomplete trypsin digestion, and poor compatibility with detergent-based MS protocols. Recent progress has advanced the field along two complementary fronts. First, innovations in MS methodology, including native MS, nativeomics, solution-phase thermochemistry, and ion mobility-mass spectrometry (IM-MS), have improved the ability to preserve intact assemblies, capture co-bound lipids and ligands, and resolve conformational and energetic landscapes of MPs. Second, advances in MP solubilization and stabilization, through tailored detergent architectures, MS-compatible detergents, and membrane mimetic (MM) systems-such as nanodiscs, peptidiscs, and styrene-maleic acid (SMA) polymers-have created more native-like environments that maintain functional conformations and ligand-binding sites, enabling integration of MPs into high-throughput MS platforms for ligand screening. This review outlines key affinity- and stability-based MS approaches for MPs and highlights how advances in MS methodology and solubilization strategies are extending their scope, positioning MS and MM as an increasingly powerful platform for high-throughput discovery of MP-ligand interactions.