The application uses filter settings that determine FDRs to distribute the confidence indicators for peptide matches. The filters label the peptide matches as follows:
- Green indicates matches that pass the filter associated with the strict FDR.
- Yellow indicates matches that pass the filter associated with the relaxed FDR but do not pass the filter associated with the strict FDR.
- Red indicates all other peptide matches.
Whenever you perform a decoy database search during a database search and apply filter settings to achieve the specified target FDRs, the same filters are used to distribute the confidence indicators.
The following figure gives an example of passing confidence indicators.