Please find the links to the files below: https://drive.google.com/open?id=1bO2E0duY8gr3UCoMRClKhKlEBiLqG88D https://drive.google.com/open?id=15BKZkfBfPsMROSvrxBOK9XtCivHG7nHk
Am Freitag, 13. September 2019 16:27:47 UTC+2 schrieb David Shteynberg: > > It would be very helpful to see your Kojak pepxml results. > > Thanks, > David > > > On Fri, Sep 13, 2019, 12:01 AM Thomas Gossenreiter <[email protected] > <javascript:>> wrote: > >> Hi David, >> >> thanks for your quick response. Here is the link to the zipped pep.xml >> files. Is this enough or do you also need the pep.xmls from the kojak >> search? >> >> https://drive.google.com/open?id=1zKW0JVfVL_LME0gmt_L6AI7j8AymUmD1 >> >> >> Am Donnerstag, 12. September 2019 18:02:07 UTC+2 schrieb David Shteynberg: >>> >>> Hi Thomas, >>> >>> I am not sure what is happening but if you could provide the dataset >>> files for the two search results I can investigate. PeptideProphet does >>> calculate different models for the different crosslink types. >>> >>> Thanks, >>> -David >>> >>> On Thu, Sep 12, 2019 at 8:59 AM Thomas Gossenreiter < >>> [email protected]> wrote: >>> >>>> Hi, >>>> >>>> I have used Kojak 1.6.1 in the TPP pipeline and got some strange >>>> results (very similar ms2 spectra from one peptide with similar Kojak >>>> scores got very different probabilities when running peptide prophet). I >>>> have plotted the Kojak score vs. the peptide prophet probability for >>>> target >>>> and decoy hits and there is hardly any correlation between the kojak score >>>> and the probability. >>>> >>>> I have repeated the search Kojak version that comes along with TPP >>>> (1.5.5) using the same settings except for the top_count parameter. I >>>> think >>>> this looks how it should, except for the cross-links which are scored very >>>> well by Kojak but get a bad peptide prophet probability. Is this the case >>>> when one peptide has a very good Kojak sub score and the other one a very >>>> bad score? >>>> >>>> Does version 1.6.1 work for you or do you have any idea what is >>>> happening here? I attached a ppt file with the figures. >>>> >>>> I also got a general questions: Is peptide prophet calculating FDRs >>>> separately for cross-linked, loop-linked and normal peptides? >>>> >>>> Kind regards, >>>> Thomas >>>> >>>> >>>> >>>> >>>> -- >>>> 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/12f12195-f115-41e5-a196-b53e18e170df%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/spctools-discuss/12f12195-f115-41e5-a196-b53e18e170df%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] <javascript:>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/abe43fc7-eb03-4411-a6ac-c5ca4a5c326a%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/abe43fc7-eb03-4411-a6ac-c5ca4a5c326a%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/71e9da68-1b77-4913-b2f0-049275e04709%40googlegroups.com.
