Last year, we presented methodology to perform knowledge-based medical imaging informatics research on specific clinical scenarios where brain tumor patients are treated with Proton Beam Therapy (PT). In this presentation, we demonstrate the design and implementation of quantification and visualization tools to develop the knowledge base for therapy treatment planning based on DICOM-RT-ION objects. Proton Beam Therapy (PT) is a particular treatment that utilizes energized charged particles, protons, to deliver dose to the target region. Similar to traditional Radiation Therapy (RT), complex clinical imaging and informatics data are generated during the treatment process that guide the planning and the success of the treatment. Therefore, an Electronic Patient Record (ePR) System has been developed to standardize and centralize clinical imaging and informatics data and properly distribute data throughout the treatment duration. To further improve treatment planning process, we developed a set of decision support tools to improve the QA process in treatment planning process. One such example is a tool to assist in the planning of stereotactic PT cases where CT and MR images need to be analyzed simultaneously during treatment plan assessment. These tools are add-on features for DICOM standard ePR system of brain cancer patients and improve the clinical efficiency of PT treatment planning. Additional outcome data collected for PT cases are included in the overall DICOM-RT-ION database design as knowledge to enhance outcomes analysis for future PT adopters.