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] <javascript:>> 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] <javascript:>. >> 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]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/abe43fc7-eb03-4411-a6ac-c5ca4a5c326a%40googlegroups.com.
