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 more protein hits will be enforced.
The picture below shows an example where the cut was done at 1% FDR decoy proteins although the total number of decoys is higher than 20.
In the second example, the cut is done at total number of 20 decoy protein, although an FDR higher than 1% was reached at a lower ranking protein.
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.
Literature:
https://pubmed.ncbi.nlm.nih.gov/12883005/
https://pubmed.ncbi.nlm.nih.gov/22010998/