The Target Decoy PSM Validator node specifies the PSM confidences on the basis of dynamic score-based thresholds. It calculates the node-dependent score thresholds needed to determine the FDRs, which are given as input parameters of the node. The Target Decoy PSM Validator node needs results from a target and a decoy search.

The following table describes the parameters for the Target Decoy PSM Validator node.

Target Decoy PSM Validator node parameters

Parameters

Description

Target/Decoy Selection

Is used to toggle the FDR calculation separate or concatenated (default):

  • Concatenated: For each spectrum the best PSM (target or decoy) is used to determine the score values at a given FDR.
  • Separate: For each spectrum the best target PSM and the best decoy PSM is used to determine the score values at a given FDR.

Target FDR (Strict)

Sets target false discovery rates for peptide matches of high confidence.

Range: 0.0–1.0; default: 0.01

Target FDR (Relaxed)

Sets target false discovery rates for peptide matches of medium confidence.

Range: 0.0–1.0; default: 0.05