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 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
