The Protein FDR field in the Protein Output section of a workflow containing a Byonic search has three options:
- 1% FDR (or 20 reverse count)
- 2% FDR (or 50 reverse count)
- No cuts
The selection of one of these options defines how many target and decoy proteins will be displayed in the resulting protein list. After a Byonic search, identified peptides are assigned to proteins based on the rules of parsimony and, from which, a protein score is calculated. Similar to peptide-level FDR (false discovery rate), proteins are ranked by score and a protein FDR is calculated based on the following formula:
FDR = Number of decoy proteins / Number of target proteins
The first option, 1% FDR (or 20 reverse count), cuts the protein list after either 1% FDR is reached, or the number of decoys is 20. Between these two options the one that leads to a more conservative cutoff will be enforced.
The picture below shows an example where the cut was done at the count of 20 decoy proteins although the 1% FDR threshold was not reached.
In the second example, the cut is done at 1% FDR at the highest-ranking protein and the number of decoy proteins is 15.
The option 2% FDR (or 50 reverse count) cuts the protein list accordingly when 2% FDR is reached, or the number of decoy proteins is 50.