ProCAT can be applied to many experiments using protein microarrays, such as kinase assays, protein-protein interactions and protein-DNA interactions. Thus far, the twoparameter scaling approach has only been used in single chip normalization; however, a similar strategy can be extended to rescale multiple slides by assuming signals in neighborhood windows on different slides are similarly distributed. Overall, ProCAT provides a powerful and flexible new approach for optimal processing and analysis of functional protein microarrays.