For smaller data sets, use the Target Decoy PSM Validator node, which triggers a target and decoy search and calculates score thresholds to achieve the specified target FDR. The derived score thresholds for the strict and relaxed FDR separate the identified PSMs into high-, medium-, and low-confidence identifications.
Special Processing Workflow Nodes and Node Settings
The following figure illustrates the basic processing workflow to use for a decoy database search.
Special Consensus Workflow Nodes and Node Settings
The following figure illustrates the basic consensus workflow to use for a decoy database search.
Further Information
For information on the Target Decoy PSM Validator node, see the Target Decoy PSM Validator node in the Proteome Discoverer Help.