Custom scripts written in the Python programming language were used to determine the number of tissue-specific peaks using the pymsfilereader, NumPy and pandas libraries. First, the averaged mass spectrum from each tissue section and a region only containing matrix were generated and peaks with signal-to-noise values above 5 (for tissue spectrum) and above 3 (for matrix only spectrum) picked. Peaks present in both datasets within a tolerance of 3 ppm were then assumed to arise from the matrix and not the tissue.