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.

Validating an identification can take some time. While it is not finished, the validated identifications are shown greyed with an hour glass over them.