You can filter proteins with the Peptide and Protein Filter node. For information on this node, see the Peptide and Protein Filter node in the Proteome Discoverer Help.
When you place the Display Settings node in the consensus workflow, by default, the Proteins page displays only master proteins. If you want to filter the proteins on the Proteins page with a filter set other than the default, follow the procedure in Apply stored filters to a result File.