Hi Rachel,
xinteract option -eS applied strict trypsin rules.
Here are all the rules. I got them by running InteractParser on the
commandline with no options.
trypsin : cut(KR) nocuts(P) sense(C)
stricttrypsin : cut(KR) sense(C)
argc : cut(R) nocuts(P) sense(C)
aspn : cut(D) sense(N)
chymotrypsin : cut(FLWY) nocuts(P) sense(C)
clostripain : cut(R) nocuts(-) sense(C)
cnbr : cut(M) sense(C)
elastase : cut(AGILV) nocuts(P) sense(C)
formicacid : cut(D) nocuts(P) sense(C)
gluc : cut(DE) nocuts(P) sense(C)
gluc_bicarb : cut(E) nocuts(P) sense(C)
iodosobenzoate : cut(W) nocuts(-) sense(C)
lysc : cut(K) nocuts(P) sense(C)
lysc-p : cut(K) sense(C)
lysn : cut(K) sense(N)
lysn_promisc : cut(KR) sense(N)
ralphtrypsin : cut(KRST) nocuts(P) sense(C)
nonspecific : cut() sense(C)
pepsina : cut(FL) nocuts(-) sense(C)
proline_endopeptidase : cut(P) nocuts(-) sense(C)
staph_protease : cut(E) nocuts(-) sense(C)
tca : cut(KR) nocuts(P) sense(C)
: cut(YWFM) nocuts(P) sense(C)
: cut(D) sense(N)
trypsin/cnbr : cut(KR) nocuts(P) sense(C)
: cut(M) nocuts(P) sense(C)
trypsin_gluc : cut(DEKR) nocuts(P) sense(C)
trypsin_k : cut(K) nocuts(P) sense(C)
trypsin_r : cut(R) nocuts(P) sense(C)
thermolysin : cut(ALIVFM) nocuts(DE) sense(N)
Here are the xinteract option to set *most* of the above enzymes rules:
-eX [specify sample enzyme]
-eT [specify sample enzyme = Trypsin]
-eS [specify sample enzyme = StrictTrypsin]
-eC [specify sample enzyme = Chymotrypsin]
-eR [specify sample enzyme = RalphTrypsin]
-eA [specify sample enzyme = AspN]
-eG [specify sample enzyme = GluC]
-eB [specify sample enzyme = GluC Bicarb]
-eM [specify sample enzyme = CNBr]
-eD [specify sample enzyme = Trypsin/CNBr]
-e3 [specify sample enzyme = Chymotrypsin/AspN/Trypsin]
-eE [specify sample enzyme = Elastase]
-eK [specify sample enzyme = LysC / Trypsin_K (cuts
after K not before P)]
-eL [specify sample enzyme = LysN (cuts before K)]
-eP [specify sample enzyme = LysN Promisc (cuts before
KASR)]
-eN [specify sample enzyme = Nonspecific or None]
Cheers,
-David
On Thu, Apr 3, 2014 at 1:52 AM, Rachel <[email protected]> wrote:
> Hi,
>
> Does anyone know whether TPPv4.7 can handle search outputs with tryspin/P
> digestion? I did not found such option in xinteract. And my test shows
> ProteinProphet can not work.
>
> Thanks
> Rachel
>
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