To better understand host cell protein (HCP) retention in adeno-associated virus (AAV) downstream processes, sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) was used to quantitatively profile residual HCPs for four AAV serotypes (2, 5, 8, and 9) produced with HEK293 cells and purified using POROS™ CaptureSelect™ AAVX affinity chromatography.