False Discovery Rate (FDR) Curve

The figure below is the FDR curve for the identified peptide-spectrum matches (PSM). PEAKS keeps at most one peptide for each spectrum (peptides with only I/L isoform difference are counted as one). Thus, the number of PSMs is the same as the number of spectra with assigned peptides. The PSMs are sorted according to their -10lgP scores. The curve shows the FDR with respect to the number of PSMs to be kept in the final result. If a score threshold has been provided in the result filtering, a vertical dashed line indicates the score threshold.


Normally a <1% FDR is recommended for score filtering. But if you notice a rapid growth of FDR around the the 1% FDR threshold, you may decide to sacrifice several PSMs to significantly reduce the FDR.

The FDR curve is estimated with the decoy fusion method (an enhanced target-decoy method that is more conservative in keeping results) performed together with the PEAKS DB search. The “Estimate FDR” checkbox must be checked in the search parameters to enable this function.

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