Hi Mike, many thanks for your prompt answer. I tried and indeed if I defined my sequential digest in Kojak as you suggeste as "trypsin_gluc", then the PeptideProphet can analyze the pep.xml file. Many thanks.
Zsuzsi Am Mittwoch, 11. September 2019 01:57:20 UTC+2 schrieb Michael Hoopmann: > > 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] > <javascript:>> 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] <javascript:>. >> 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/3f98271f-f03b-4e31-9068-64622f9ec4d2%40googlegroups.com.
