How do I save the list of proteins/entities that are the results of my database search?

You can save a group of entities identified from a database query by the following steps: open a New Group window by selecting “New Group” in the database pane, select the desired entities in the list pane below and drag them to the New Group window.  Once in the New Group window select “Save” to save your group.  A group can be mixture of different entity types.