Development of LC-MS methods for AAV capsid protein quantification and host cell protein profiling

Accurate quantification and characterization of recombinant adeno-associated virus (rAAV) capsid proteins are critical for evaluating product quality and safety, ensuring batch consistency, and informing process development of their manufacture. The capsid consists of three proteins derived from the same gene, and while the mean capsid stoichiometry is nominally 1:1:10 (VP1:VP2:VP3), capsids with different stoichiometries exist. Recent studies show that variations in the capsid stoichiometry can impact vector infectivity. Here, a mass spectrometry (MS)-based method was developed to quantify VP1, VP2, and VP3 in rAAV9 capsids and determine stoichiometry. Additionally, the methodology delivers precise measurement of total capsid content and provides a greater depth of information than traditional ELISA capsid titer measurements. The method could be further refined as a reference method to standardize measurements and assign values to reference materials. Host cell proteins consistent with other findings reported in the literature were also identified and reported. The consistent detection of these host cell proteins across different studies highlights their potential relevance to gene therapy products and the importance of their monitoring. Our report exhibits the utility of MS for precise rAAV characterization and presents the first approach to using MS for the standardized measurement of rAAV across different drug products.