Doh - I just noticed that in ProteolyticEnzymeFactory.cxx the
enterSpecificity definitions are not being used - so I guess the issue is
just Tandem2XML vs the enzyme catalog definitions.
On Wednesday, August 21, 2013 3:10:26 PM UTC-5, Dave Trudgian wrote:
>
> Hi,
>
> I've been running into some issues with non-tryptic searches using
> multiple enzymes and TPP 4.6.3. It appears that some of the problems are
> due to inconsistent enzyme specificity definitions in the different tools.
>
> E.g. for chymotrypsin:
>
> In Tandem2XML the specificity is defined with addEnzyme("chymotrypsin",
> "[FLMWY]|{P}");
>
> In ProteolyticEnzymeFactory.cxx the catalog entry is {"chymotrypsin",
> "true", NULL, "YWFL|P|false|"}
> ...but the getProteolyticEnzyme function uses
> enz->enterSpecificity("YWFM", "P", False, min_spacing_);
>
> I'm going to make everything consistent on my install here, and wondered
> if this would be useful to contribute to the main TPP trunk?
>
> It does depend on picking a single chymotrypsin specificity though - have
> no idea which is most appropriate?!
>
> DT
>
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