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Adeno-associated virus (AAV) has been widely used in gene therapy applications. To fully realize the potential of AAV vectors, reliable and efficient analytical technologies have become increasingly relevant and urgent to help establish a structure-function relationship, guide the development of manufacturing process, and assess the quality of clinical materials. In this talk, we will highlight the novel LC/MS workflows that are developed for structural characterization of recombinant AAV vectors, including capsid protein identification and PTM analysis.