The decoy matches are certain to be spurious identifications, but we can't discriminate between true and false positives identified in the target database. FDR estimation was added in response to journals' guidelines on protein identification reports like the ones from Molecular and Cellular Proteomics. Mascot's FDR calculation incorporates ideas from different publications.
The fake matches are undoubtedly incorrect identifications, but we cannot distinguish between genuine and false alarms in the target database. FDR estimation was introduced as a response to journal guidelines on protein identification reports similar to those published in Molecular and Cellular Proteomics. Mascot's FDR calculation draws upon concepts from various publications.