With the newest ProteinPilot software 5.0, we can annotate the database search results with ontology information about each protein using the information available from the UniProt website. After the final list of proteins is assembled during the search, the software will ping the UniProt website and pull back the information to populate the group file. An internet connection must be active during the DB search for this to work. Note: this can only be done at the point of search, you cannot take a group file and get it annotated.
Depending on the species being searched, the proteins may not be as well annotated so sometimes you might see limited annotations because it is just not available.