Analytical regulatory requirements for AAV-based gene therapies are currently not well established. However, monitoring protein and ssDNA heterogeneity for AAV may help define regulated analytics and accelerate AAV clinical and process development. Considerations in developing analytics for AAV include low concentrations, limited quantities, and large analyte masses that challenge commercially available analytical techniques. Here, we present methods for LC-TOF-MS analysis of both trypsin digested AAV5 and intact capsid proteins of several AAV serotypes. We also demonstrate the utility of charge-detection MS (CDMS) to analyze ssDNA isolated from AAV9 by anion-exchange chromatography (AEC). Additionally, CDMS, AEC, and size-exclusion chromatography measurements of the level of AAV8 without its targeted complement ssDNA are compared.