To launch a validation on a dataset:

• right-click on its node in the project tree then select Validate tree or
• double-click to open identification table, then click Validate tree in the toolbar.

The following form appears :

The validation form handles several settings, especially :

• PSM Filters : use the selection box and the green button to add more filters on Peptide Spectrum Matches to be applied during the validation process : Score, Rank, Sequence Length, E-Value and P-Value.

• PSM Validation Parameters : choose on which param the Peptide FDR should be applied : Score, E-Value or P-Value.

• Merging Mode : determines if the merging operation should be done before the validation (on result sets) or after the validation process (on identification summaries)

When ready, click on Validate to launch the validation task. You can see it in the tasks panel. When the validation finishes, a notification will be displayed and the node icon will be colored in green.