Using AAV2 as a test case, separation of all three full length VPs was performed using HILIC separation and difluoroacetic acid (DFA) as a mobile phase additive. Peptide mapping was performed for in-depth PTM analysis and for confirmation of PTMs detected during full-length VP analysis. This workflow was then applied to the development of a platform using GMP compliant software, capable of rapidly performing AAV serotype identification and then performing PTM characterization on a selected serotype if desired. Such a platform provides quick and reliable serotype identification using a single universal processing method and enables PTM monitoring for product quality, all while capable of being performed within a regulatory setting.