Statistical inference (grouping and scoring) of proteins based on identified peptides is currently not supported in OpenMS. (There is a "ProteinInference" TOPP tool, but it doesn't solve the problem.)
To rectify this, the decision was made to add support for the existing protein inference engine Fido (http://noble.gs.washington.edu/proj/fido/) - which is free software and written in C++ - to OpenMS.

This ticket summarizes the discussion on the mailing list and tracks the progress on this issue.