Hi Zsuzsi, Could you try renaming your enzyme, "trypsin_gluc" ? I think that is the secret enzyme name that PeptideProphet recognizes for that enzyme combination. Sorry for the trouble, I'll have dig through the code to see who is at fault (Kojak or PeptideProphet) for not properly interpreting the enzyme combination.
As for the bioRxiv publication, I'm not sure if anyone on that author list tried to contact us, so it seems there is an error or exaggeration in that statement... We appreciate you made the effort. Cheers, Mike On Tue, Sep 10, 2019 at 7:30 AM nzsuzsanna <[email protected]> wrote: > Hi, > I tried to analyze my DSS and DMTMM cross-linking data using Kojak and > PeptideProphet. > Kojak run properly, however Peptideprophet claims for Trypsin GluC > digestion, which is not defined. Kojak could handle it. > Why does PeptideProphet need the enzyme info at all? > > Is this possible to define for PeptideProphet the TryGluC "enzyme"? i > could not find it in the > I read in the bioRxiv Mendes et al publication 'An integrated workflow for > cross-linking/mass spectrometry" , that ".....we and the developers of > these tools could not pair Kojak with PeptideProphet for sequential > digestion." > > Thanks for answers in advance. > > best > > Zsuzsi > > -- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/b99a0ebf-2552-4622-ad8b-68d92f91fac7%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/b99a0ebf-2552-4622-ad8b-68d92f91fac7%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CANMWFMN_DpnVbjv2x8MXKCGkQd2G6GOfCMEhBcPvmyRCYC6oxA%40mail.gmail.com.
