Hi Thomas, Sorry for the slow response, but HUPO is over now. I'll help take a look and find the problem. Cheers, Mike
On Sun, Sep 15, 2019 at 11:56 PM Thomas Gossenreiter < thomas.gossenrei...@gmail.com> wrote: > 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 < >> thomas.go...@gmail.com> 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 < >>>> thomas.go...@gmail.com> 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 spctools...@googlegroups.com. >>>>> 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 spctools...@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/71e9da68-1b77-4913-b2f0-049275e04709%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/71e9da68-1b77-4913-b2f0-049275e04709%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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CANMWFMNVu2gfVxcUq_Pbttrx7WZOJHCsOtk6VOZb-H6THUtLTA%40mail.gmail.com.
