As the pharmaceutical industry moves towards larger protein-based therapeutics over chemically synthesized small molecules, there are increasing demands for parallel advancement in the technologies used for quality control of these biologically-derived products (biopharmaceuticals). This work describes the implementation of mass spectrometry (MS)-based methods in three areas where MS is well-positioned to fulfill unmet analytical needs. First, time-resolved electrospray ionization hydrogen-deuterium exchange (TRESI-HDX) and ion mobility spectroscopy (IMS)-MS were used to study conformational dynamics in transient Cytochrome c-lipid interactions. MS was also implemented for proteomic characterization of in-process and purified samples from acellular Pertussis vaccines. Further development of a targeted MS method is described for quantitation of two residual protein toxins, adenylase cyclase toxin (ACT) and dermoneucrotic toxin (DNT), and a glycopeptide, tracheal cytotoxin (TCT), from Bordetella pertussis. Collectively, the results highlight advancement in the application of structural and quantitative proteomics for more effective characterization of next generation biopharmaceuticals
