Hi Thomas, The tables for each type of linked peptide is in the pepXML file (near the top of the file), listed separately for each type of link.
Thanks, -David On Thu, Sep 19, 2019 at 2:54 AM Thomas Gossenreiter < [email protected]> wrote: > Dear all, > > I would like to filter my Kojak cross-linking data at a defined FDR. > Actually I would like to apply a separate FDR for loop-links, cross-links > and non-linked peptides. > > So I am wondering if I can use the Error Table provided by the > PeptideProphet results to get the minimum probability to apply a certain > FDR on my dataset? Or doesn't this work for a dataset containing mixed > peptide species? > > Best 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/f3dffce4-ac1a-4512-92af-9ef459e8bbd3%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/f3dffce4-ac1a-4512-92af-9ef459e8bbd3%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/CAGJJY%3D-RsP_WO15wA5D9%3Dt%3DzzAH%2B5uBTDiNWbvn%3D-umXa3tnqA%40mail.gmail.com.
