PEAKS supports FDR estimation on inChorus results. To make this work on Mascot results, there are a few extra steps to follow.
PEAKS uses Decoy-Fusion method for FDR estimation. The first step is to create a decoy-fusion database. Go to PEAKS database configuration dialog. Select the FASTA database you want to search against. Then click the "Export Decoy DB" button. A decoy-fusion FASTA file will be generated.
The second step is to configure the decoy-fusion FASTA file into Mascot. This is very straightforward in Mascot 2.4 as the parsing rule of PEAKS decoy-fusion method can be automatically detected.
After the decoy-fusion database is up and running on Mascot server, the last step is to make sure that the "Search decoy database from PEAKS" option is selected in the search dialog.
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