Peptide mapping LC-MS analysis was performed following the procedure described in Guapo et al. . The resulting peptides from Section 2.5 were separated using a Thermo Scientific Easy-Spray PepMap RSLC C18 column, 2 µm, 75 µm × 50 cm (Thermo Fisher, Sunnyvale, CA, USA). Dried digested samples were reconstituted in 0.1% FA in water to a final concentration of 100 ng µL -1 , with 200 ng (2 µL) of digested AAV2 sample then injected onto the column. Injections were performed in technical triplicate. Peptide separation was performed using a linear gradient from 2 % B to 40 % B over 105 min, followed by an increase to 60 % B over 5 min. The column was then washed by increasing the percentage of B to 80 % over 0.1 min followed by an isocratic hold for 9.9 min. Mobile phase B was then decreased to 2 % over 0.1 min and then increased back to 80 % over 4.9 min, followed by a 5 min isocratic hold. The column was then re-equilibrated by decreasing mobile phase B to 2 % over 0.1 min and then performing an isocratic hold for 19.9 min. The flow rate was kept constant at 250 nL.min -1 and the column temperature was maintained at 45°C. Mobile phase A was UHPLC-MS grade water containing 0.1 % (v v -1 ) FA and mobile phase B was Optima™ LC-MS grade ACN containing 0.1 % (v v -1 ) FA.