Concerning my previous post about "lost" peptides in  the TPP (X!
Tandem/Peptide+ProteinProphet, v4.2)

Checking "Force the fitting of the mixture model (bypass automatic
mixture model checks)" indeed significantly increases the number of
assigned peptides to a  protein and therefore the sequence coverage.

Now also the peptides assigned to a protein by OMSSA are  included

Regards, Robert

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