We perform many limited proteolysis experiments that rely on broad-spectrum proteases followed by a tryptic work-up. It would be nice to see a specific option for these searches.
Semi-enzymatic - where peptides are first generated between specific cleave_at sites & then all possible peptides between min_len and max_len betweencleave_at sites are also generated (accounting for missed cleavages). This is technically covered by the non-enzymatic option, but many peptides that would not be generated by the experiment would be searched.
cleave_at="?KR" could be the notation for a semi-tryptic. We will try and do a PR on our attempt at this.
We perform many limited proteolysis experiments that rely on broad-spectrum proteases followed by a tryptic work-up. It would be nice to see a specific option for these searches.
Semi-enzymatic - where peptides are first generated between specific
cleave_atsites & then all possible peptides betweenmin_lenandmax_lenbetweencleave_atsites are also generated (accounting for missed cleavages). This is technically covered by the non-enzymatic option, but many peptides that would not be generated by the experiment would be searched.cleave_at="?KR"could be the notation for a semi-tryptic. We will try and do a PR on our attempt at this.Nice tool!