Here we describe how the microchip ZipChip CE-MS platform can be utilized for the rapid characterization of AAV capsid proteins. We outline the steps taken to maximize detection of low abundant proteoforms and discuss how the use of low levels of dimethyl sulfoxide (DMSO) in the background electrolyte solution (BGE) improves VP detection and identification. A limit of detection (LoD) study was then performed to demonstrate how ZipChip CE-MS is a powerful platform even at low sample concentrations. Finally, we apply the ZipChip platform to the analysis of empty and full capsids from multiple serotypes to illustrate that it can, not only perform AAV serotype identification, but also the detection of VP variants and fragments, as well as proteoforms containing PTMs that can impact product efficacy and safety.