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To launch a validation on a dataset, click on its node in the Project Tree on the left side of the Dataset Explorer.
Click on “Launch Validation” in the toolbar of the Infos tab. You can also right click on the dataset node and click on use the “Launch Validation” button.
The following form appears :
The Validation form handles several settings :
- Merge Result Sets : choosing “YES” will merge the Result Sets (corresponding to your result files) before launching the validation of the merged dataset. “NO” will validate the result sets separately and merge their result after the validation process.
- Force Target Decoy competition : 
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- Filters : let you filter the data that will be included in the validation results. For example, you might want to keep only the peptide of rank 1. To add a filter parameter, choose a setting in the selection box, click on the “+” button, then edit the threshold value of the parameter on its line.
- Validation Thresholds let you define the False Discovery Rate of your peptides and proteins. You must define on which parameter the Peptide FDR should be applied : (MORE DETAILS)
When ready, click on “Validate” to launch the validation task. You can see it in the tasks panel :
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