In this study we demonstrate how the microchip ZipChip CE-MS platform can be utilized for rapid indepth characterization of AAV serotypes, with runs performed in as little as 5 minutes. We first optimized the platform, demonstrating that low levels of DMSO (4%), improve platform sensitivity and component detection. A LoD study was then performed showing the sensitivity of the ZipChip platform, as all VP proteoforms were detected when as little as 2.64 × 10 6 particles (≈26.4 picograms) were injected. We then compared the analysis of empty and full capsid for serotypes AAV6, AAV8, and AAV9. In doing so we illustrated how the ZipChip platform can determine the presence of HCPs and other cellular contaminants and differentiate them from VP proteoforms.