Advances in mass spectrometry-based epitope mapping of protein therapeutics

Monoclonal antibody (mAb) has grown to be the major asset in protein therapeutics market since its initial introduction in 1980s. To identify a suitable mAb as a drug candidate for development requires deep understanding of disease biology and attribute sciences, including epitope-paratope binding recognition. Mass spectrometry (MS) has become a critical technology platform in epitope mapping. MS-based approaches utilize chemical labeling to assess the changes of solvent accessibilities during binding interactions, and the labeling can be either reversible or irreversible. Reversible labeling is represented by hydrogen/deuterium exchange (HDX), which probes the changes via exchange between backbone amide hydrogen and deuterium in the solvent. Irreversible labeling targets amino acid residue side chains and involves chemical based labeling such as glycine ethyl ester labeling, radical based labeling such as fast photochemical oxidation of proteins (FPOP), and chemical cross-linking. All these methods have been developed extensively for characterization of binding interface within an immunocomplex. This review covers the fundamentals of these different MS-based methods and highlights recent case studies to illustrate unique capabilities of MS-based approaches in epitope mapping of protein therapeutics.