Hi David,
Thanks for the response. The release notes are helpful. And no, I
haven't noticed increased decoy hits w/ higher prob...but then again I
haven't really looked.
In addition to the release notes, is there any documentation about
which features from Alexey's papers have made it into the
Hi John,
Yes, the semi-supervised and semi-paramteric features from Alexey's
papers are implemented. Specifying a decoy tag to PeptideProphet
makes it semi-supervised and selecting the non-parametric model makes
it semi-parametric; the one remaining parameter in the distributions
is the
