Thanks! I do have less error tables than I would expect. When I ran PeptideProphet, I received the warning: "Mixture model quality test failed for charge (1+)" for multiple charge states. Would that warning account for the missing error tables?
On Wed, Sep 16, 2020 at 1:34 PM 'David Shteynberg' via spctools-discuss < spctools-discuss@googlegroups.com> wrote: > 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 > <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8fCBMQWB1tSp2vv1D%2Bc1uUxWYn2aQMsLpScy-jBaiS2g%40mail.gmail.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/CAJqN02SjRuo5v9W%3DzmMN__bkL88jr8u%2B%2B9pEPLWY6L1Ggv%3DOpw%40mail.gmail.com.
