Throughout the optimization process, we have solely worked with empty AAVs, but the ZipChip CE-MS platform is also highly adept at analysing full AAV capsids. Here, we analysed empty and full capsids from the same batch process for serotypes AAV6, AAV8, and AAV9 respectively. Immediately, differences could be observed in the generated data (Figure ). As expected, the electropherograms of the full capsids only contain one set of peaks, detected between 3.2-3.8 min, corresponding to the presence of the capsid proteins. However, the empty capsids contain an additional second set of peaks detected between 2.8-3.2 min. Given that this set of peaks is not seen in the full capsids, it is thought that they correspond to the presence of host cell proteins (HCPs) or other cellular contaminants in the sample. According to the supplier, the empty and full capsids were separated using caesium chloride (CsCI) gradient density ultracentrifugation (), which serves to purify the full capsids . It is likely that no consideration was made to separate the empty capsids from other cellular contaminants generated during production, resulting in their presence in the empty samples, but not the full samples. Data processing supports this assumption as all the unknown components detected between 2.8-3.2 min in the empty capsids, are not seen in the full capsids (Table ). Furthermore, HCP analysis of the empty and full capsids shows significantly lower levels of HCPs detected in the full samples compared to the empty samples (data not shown, manuscript in preparation), illustrating that many of them were removed from the full capsids during the empty / full separation process. HCPs and other cellular contaminants were not necessarily confined to detection from 2.8-3.2 min.