Proton Therapy is a type of radiotherapy to treat cancerous and benign tumours. A treatment planning system is used to find optimal treatment machine parameters that can deliver the prescribed radiation dose to the tumour while minimizing radiation dose to surrounding tissues as prescribed by the radiation oncologist. To ensure that the dose distribution predicted by the treatment planning system can be precisely delivered on the treatment machine, quality assurance (QA) is performed for each treatment plan before it is delivered to the patient. An important part of this QA consists of comparing the dose distribution predicted by the treatment planning system with the dose distribution obtained from measurements with an ion chamber array in water. To compare the measured against the predicted dose distribution, a commercial software tool is employed at the Center for Proton Therapy of the Paul Scherrer Institute. This tool currently cannot be operated autonomously but requires the intervention of a specialist, which is very time consuming. In this thesis, an automated tool for comparing dose distributions based on the gamma metric was developed and validated against the commercial software tool using dose distributions from the treatment planning system and verification measurements in water with an ion chamber array.