If you have a large dataset with thousands of target or decoy PSMs, use the Percolator node.
The Percolator node is a superior validation algorithm that uses a machine learning approach. However, Percolator needs a sufficient number of PSMs from the target and the decoy search.
Special Processing Workflow Nodes and Node Settings
The following figure shows the parameters available for the Percolator node. (For information about these parameters, see the Percolator node in the Proteome Discoverer Help.)
Special Consensus Workflow Nodes and Node Settings
The Peptide Validator node calculates false discovery rates for peptide groups based on the qvality algorithm when the Percolator node is in the processing workflow.
Further Information
For more information, see the Percolator node in the Proteome Discoverer Help.