Two layers of filters are implemented in ProCAT. First, all positive spots from negative control experiments are removed. For example, in on-chip kinase assays, kinase dead alleles were probed on separate arrays using the same experimental conditions as used with wild-type kinases. Spots that produce signals in the absence of active kinase were identified by ProCAT and removed from the target lists of kinase probings. When probing tagged protein to detect protein-protein interaction, testing the epitope tag in the absence of the protein of interest is also an essential control. If proper negative control experiments are available, ProCAT will analyze them in the same way as regular experiments to construct experimental positive spot lists void of proteins producing positive signals under control conditions.