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' v
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
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
corre
