Targetdecoy
Targetdecoy, more commonly known as the target-decoy strategy, is a method used in mass spectrometry–based proteomics to estimate the false discovery rate (FDR) of peptide-spectrum matches. It uses a decoy database of artificial sequences in addition to the real target sequences, providing a null model for random matches. By searching spectra against a concatenated target-decoy database, identifications that map to decoy sequences help gauge how many incorrect identifications are expected, enabling calibration of confidence scores and FDR control.
In practice, decoy sequences are generated by reversing, shuffling, or otherwise permuting real protein sequences. The
Targetdecoy is widely integrated into proteomics workflows and software tools (for example, in popular database search