PeptideProphet and Decoys

[rprambo]

Hi Everyone,

I am using X!Tandem as my search engine and would like to know WHEN
and HOW to include the decoy database? I used the TPP utility to
generate the decoy and concatenated that to my regular fasta database.

Do I start the search over with the combined database and then run
PeptideProphet with the box checked "Use decoy hits to pin down the
negative distribution"?

Any advice on the correct work flow would be greatly appreciated.

Thanks,

RPR