Hi Anette,

Unfortunately, while the protein search feature lets you search based on peptide scoring results, it does not let you set separate criteria based on the charge state as you can when you're looking at a single MS2 run.

To add a filter based on XCorr or DCn, click on the Edit View link on the peptide filter row. It should open the customizer with the Filter tab selected. Find XCorr in the list of fields and click on the Add button. Choose your criteria. Do the same for DeltaCn. Give the view a name and save it. Back on the protein search page, choose your saved view from the list and choose the "Custom View" radio button.

Thanks,
Josh