Hi,
We have "TPP v4.3 JETSTREAM rev 1" (installed using TPP installer), and
would like to add Mascot "TrypChymo" enzyme to Mascot2XML
I have downloaded the source code and able to build it using MinGW (MSys)...
But, when I try to convert dat to pepXML... I get error
These are the steps I followed :
Step 1) As a test I changed
...\trans_proteomic_pipeline\src\Enzyme\ProteolyticEnzyme\ProteolyticEnzymeFactory\ProteolyticEnzymeFactory.cxx
char *enzymes[] = {
...
, {"tryp_chymo", "true", NULL, "KR|P|false|,YWFM|P|false|"}
// added
....
else if(strcmp(name, "tryp_chymo") == 0) {//added 2011-12-20 for TrypChymo
test
enz = new ProteolyticEnzyme(name, fidelity, True, NULL);
enz->enterSpecificity("KR", "P", False, min_spacing_);
enz->enterSpecificity("YWFM", "P", False, min_spacing_);
enz->fixSpecificity();
}
.........
Step 2) Executed "make" command from MSys shell.
Step 3) Copied compiled Mascot2XML.exe to C:\Inetpub\tpp-bin
Step 4) Error while converting dat to pepXML
"OUTPUT>A stored as 71.0371OUTPUT>B stored as 114.535OUTPUT>C stored as
160.031OUTPUT>D stored as 115.027OUTPUT>E stored as 129.043OUTPUT>F stored
as 147.068OUTPUT>G stored as 57.0215OUTPUT>H stored as 137.059OUTPUT>I
stored as 113.084OUTPUT>J stored as 0OUTPUT>K stored as 128.095OUTPUT>L
stored as 113.084OUTPUT>M stored as 131.04OUTPUT>N stored as
114.043OUTPUT>O stored as 0OUTPUT>P stored as 97.0528OUTPUT>Q stored as
128.059OUTPUT>R stored as 156.101OUTPUT>S stored as 87.032OUTPUT>T stored
as 101.048OUTPUT>U stored as 150.954OUTPUT>V stored as 99.0684OUTPUT>W
stored as 186.079OUTPUT>X stored as 111OUTPUT>Y stored as 163.063OUTPUT>Z
stored as 128.551OUTPUT>c stored as 17.0027OUTPUT>n stored as
1.00782OUTPUT>variable modification 1, delta mass 15.9949 for Oxidation
(M):OUTPUT> residues: MOUTPUT> nterm: 0OUTPUT> cterm: 0OUTPUT> protterm:
0OUTPUT>
ERROR>tryp_chymo : cut(KR) nocuts(P) sense(C)ERROR> : cut(YWFM) nocuts(P)
sense(C)"
*Question :*
a) Is this the right way to add "TrypChymo" enzyme to Mascot2XML.exe
b) Is there any other file I need to change apart from
"ProteolyticEnzymeFactory.cxx"
Please suggest.
Thanks
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