Fragment ions in both the PepScore and Ascore steps have been limited to charge 1. This works against charge 3 and up peptides in CID and HCD fragmentation spectra since there are fragment ions which are never used. This PR will attempt to address this problem, by allowing the user to specify the max fragment charge state that they want to use.
Fragment ions in both the PepScore and Ascore steps have been limited to charge 1. This works against charge 3 and up peptides in CID and HCD fragmentation spectra since there are fragment ions which are never used. This PR will attempt to address this problem, by allowing the user to specify the max fragment charge state that they want to use.