See description of validation algorithm here.

To validate an Identification :

- Select one or multiple identifications to valid

- Right Click to display the popup

- Click on “Validate…” menu

In the Validation Dialog, fill the different Parameters :

- you can add multiple Peptides Prefilter Parameters ( Rank, Length, Score, e-Value, Identity p-Value, Homology p-Value) by selecting them in the combobox and clicking on Add Button '+'

- you can ensure a FDR on peptides which will reached according to the variable selected ( Score, e-Value, Identity p-Value, Homology p-Value )

- you can select the FDR estimator

- you can ensure a FDR on proteins

FDR can be used only for Identification with Decoy Data.