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

Abstract

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.