The synthesis is carried out in HCl solution using APS or FeCl3 as the oxidant/catalyst. Both reactions give ES form PANI (half reduced and half oxidized), and should be doped with H+ and the counter ion to the doped site is Cl-.
However, depending on the catalyst, APS would produce SO42- counter ion, and FeCl3 would cause Fe2+ or Fe3+ doping of PANI. This products of catalyst would affect the vibration model of PANI (both Q and B structures), resulting in different IR peak positions. From my previous experience, the PANI need to be washed extensively with ammonia, then DI water and ethanol to dedope the strcture. Then you can dope it again using acid as you like.