I ended up making the following patches for my purposes (getting everything
consistent as possible within our CPFP pipeline for the enzymes and search
engines I'm using there). Not sure whether any of these changes would be
useful in general.
ProteolyticEnzymeFactory.cxx
58c58
< , {"chymotrypsin", "true", NULL, "YWFL|P|false|"}
// original
---
> , {"chymotrypsin", "true", NULL, "FLWY|P|false|"}
// original
60,61c60,61
< , {"cnbr", "true", NULL, "M|P|false|"}
// original
< , {"elastase", "true", NULL, "GVLIA|P|false|"}
// original
---
> , {"cnbr", "true", NULL, "M||false|"}
// original
> , {"elastase", "true", NULL, "AGILV|P|false|"}
// original
63,64c63,64
< , {"gluc|glu_c", "true", NULL, "DE|P|false|"}
// original
< , {"gluc_bicarb", "true", NULL, "E|P|false|"}
// original
---
> , {"gluc|glu_c|v8-de", "true", NULL, "DE|P|false|"}
// original
> , {"gluc_bicarb|v8-e", "true", NULL, "E|P|false|"}
// original
73c73
< , {"protein_endopeptidase", "true", NULL, "P|-|false|"}
// original
---
> , {"proline_endopeptidase", "true", NULL, "P|-|false|"}
// original
TandemParamsParser.cxx
138c138
< addEnzyme("chymotrypsin", "[FLMWY]|{P}");
---
> addEnzyme("chymotrypsin", "[FLWY]|{P}");
141c141
< addEnzyme("cnbr", "[M]|{P}");
---
> addEnzyme("cnbr", "[M]|[X]");
153c153
< addEnzyme("protein_endopeptidase", "[P]|[X]");
---
> addEnzyme("proline_endopeptidase", "[P]|[X]"
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