Disclaimer this tool needs the results from ProteinInference and PSMBasedQuantification.
Results from PSMBasedQuantification contain detailed information about the quantification of every peptide, but only basic informations about the protein they originated from. This information is obtained during the ProteinInference. This tool takes the results from both tools and combines the qauntification information of each peptide with the more accurate information about the corresponding protein including its q-value.
Additional information about the tool can be found in the documentation.