As discussed in Section 3.3, the set of peaks in the AAV8E samples migrating from ≈3.2-3.8 min corresponds to the VPs, while the set of peaks migrating from ≈2.8-3.2 min are HCPs and other cellular contaminants from the density gradient centrifugation process used to purify full AAVs. These additional proteins are not seen during the analysis of full AAVs. As expected, the intensity and total area of the AAV8E VP peaks in the electropherograms decreases as the concentration of Vps injected decreases. The MS signal intensity extracted from the total area of the VP peaks also decreases as the amount of injected Vps decreases (Figure ). Plotting both the electropherographic area of the VP peaks and the extracted MS spectra signal intensity against the amount of Vps injected, illustrates their correlation (Supplementary Figure (Figure )). Interestingly, for both peak area and MS signal intensity their relationships are not linear but follow more of a polynomial trend. We saw that the steepest rate of decrease in both MS signal intensity and peak area occurs from an injection of 2.20 × 10 were confidently detected at this concentration. However, such quantities would not be sufficient to differentiate between modified serotypes where modifications occur in the protein sequences unique to VP2 or VP1.