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'
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
