Hi Lindsey, PeptideProphet will generate a separate FDR prediction table for each type of Kojak result it analysed, and all three should be in the pepXML file. The three types of Kojak hits are unlinked "n/a", self-linked "loop" and cross-linked "xl". PeptideProphet generates a separate model for each type of Kojak result.
Thanks for your question! -David On Wed, Sep 16, 2020 at 12:22 PM Lindsey Ulmer <ulmerlindse...@gmail.com> wrote: > Hi, > > I'm trying to determine the FDR of crosslinked products from a Kojak and > PeptideProphet analysis. There is a second plot in the Predicted > Sensitivity and Error Rate chart, which I'm assuming is for the crosslinked > products, but I'm having trouble determining which of the error tables > correspond to crosslinked results. I've attached a link to the > corresponding pepxml below. > > > https://drive.google.com/file/d/1hadnfjsFVCTMVqirdcC2jCeEuUvzVjAt/view?usp=sharing > > Thanks! > Lindsey > > -- > 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/1352899f-62a4-43fa-8ff1-0d6809251e9dn%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/1352899f-62a4-43fa-8ff1-0d6809251e9dn%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/CAGJJY%3D8fCBMQWB1tSp2vv1D%2Bc1uUxWYn2aQMsLpScy-jBaiS2g%40mail.gmail.com.
