For additional enzyme specificities there's a page on the SPCTools Wiki hidden away that I've used as guidance a couple of times. The enzyme definition needs to be added to the code for the converters etc.:
http://tools.proteomecenter.org/wiki/index.php?title=Custom_digest_site However, I don't believe it's possible to represent (RK not before P) or (K) in the code. Instead a semi-tryptic, or a strict-trypsin (RK) search might be the best choice? You could edit the tandem output to one of these TPP-recognized enzymes, so it will go through Tandem2XML. DT On Tuesday, July 2, 2013 10:45:38 AM UTC-5, Gautam Saxena wrote: > > An X!Tandem file that has been successfully searched with two enzymes > (trypsin and endo-lys C --> [RK]|{P},[K]|[X]) will not get converted by the > Tandem2XML TPP program. This program return the error: > > ERROR: Unsupported search enzyme. > > Use one of the following cleavage site specifications: > > argc - [R]|{P} > > aspn - [X]|[D] > > chymotrypsin - [FMWY]|{P} > > clostripain - [R]|[X] > > cnbr - [M]|{P} > > elastase - [AGILV]|{P} > > formicacid - [D]|{P} > > gluc - [DE]|{P} > > gluc_bicarb - [E]|{P} > > iodosobenzoate - [W]|[X] > > lysc - [K]|{P} > > lysc-p - [K]|[X] > > lysn - [X]|[K] > > lysn_promisc - [X]|[AKRS] > > nonspecific - [X]|[X] > > pepsina - [FL]|[X] > > protein_endopeptidase - [P]|[X] > > staph_protease - [E]|[X] > > tca - [FMWY]|{P},[KR]|{P},[X]|[D] > > trypsin - [KR]|{P} > > trypsin/cnbr - [KR]|{P},[M]|{P} > > trypsin_gluc - [DEKR]|{P} > > > Is there any solution or workaround to this problem? (This question > appears similar to this other post which appears unresolved: > > https://groups.google.com/forum/#!searchin/spctools-discuss/unsupported$20search$20enzyme/spctools-discuss/EFbKPHxVTcU/bBYaOCnHHX4J > ) > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
