As Natalie suggested, Analysis.yep indicates the Bruker/Agilent YEP
format which ProteoWizard reads with CompassXtract. Msconvert will
automatically detect the format of the .d directory and use the
appropriate reader. Keep in mind the CompassXtract interface (which
supports Bruker FID/BAF and
Hi Christian,
The problem is here:
WARNING: Inspect only support semi-parametric PeptideProphet
modelling, which relies on a DECOY search.
You need to include Decoy sequences (with a decoy tag) in the protein
database you are searching and specify this to PeptideProphet. If you
are using
