Application of mass spectrometry techniques for analysis of higher order structure of proteins

Abstract

Determining the higher order structure (HOS) of proteins and protein complexes is central to understanding their functions, dynamics, and interactions. Traditional structural biology approaches, such as X-ray crystallography and nuclear magnetic resonance, provide high-resolution snapshots but often require large amounts of homogeneous samples and may miss dynamic or heterogeneous states. Mass spectrometry (MS) has become an indispensable tool for sensitive and rapid analysis of intact proteins and assemblies under native or near-native conditions. This review discusses the major MS-based strategies for probing HOS. Native mass spectrometry (nMS) preserves non-covalent interactions and exhibits characteristic charge-state distributions that report on folding, while native top-down fragmentation and ion mobility spectrometry provide sequence-specific and conformation-specific information. Hydrogen–deuterium exchange MS measures backbone amide exchange rates to map regions of solvent accessibility, ligand binding, and allosteric regulation in solution. Covalent labeling MS irreversibly modifies solvent-accessible side chains, allowing epitope mapping and detection of subtle conformational changes, while fast photochemical oxidation of proteins offers microsecond snapshots of transient structures. Chemical cross-linking MS applies bifunctional reagents to capture proximity between residues or subunits, providing distance restraints for integrative modeling and proteome-wide interaction mapping. We outline recent advances in instrumentation, software, labeling chemistry and in-cell techniques across these modalities, and we illustrate their applications to characterizing membrane proteins, large assemblies, therapeutic antibodies, intrinsically disordered proteins, and protein–ligand complexes. Together, these tools offer complementary insights into HOS that are reshaping structural biology, biopharmaceutical development and mechanistic studies.