Functional protein microarrays serve as an efficient platform for screening protein biochemical functions. Here we present ProCAT as a systematic approach to process and analyze data specific to functional protein microarrays. Calibrated by explicit test experiments, ProCAT has proven to be able to handle many types of functional protein microarray studies with three unique features. ProCAT includes novel scaling methods that provide robust and reproducible measurement for quantitative signals. This is crucial for protein microarrays as chip signal intensities often indicate strength of interactions. In addition, by calling positive candidates locally, ProCAT demonstrated excellent performance in identifying positives in comparison to global thresholds. Finally, each step has been integrated into a modular design to fit various experimental designs and stringency requirements.