We have developed a new protein chip analysis tool (ProCAT) to deal with various artifacts specific to functional protein microarrays. The work started from a careful survey and characterization of all potential sources of systematic errors in protein microarrays. Specific approaches were then designed to deal with each type of noise. A correction approach is applied to reduce measurement errors in the background signals. In addition, spatial variations can be reduced efficiently through a novel two-parameter signal normalization approach and calling positive spots locally. After generating a list of positives, negative control slides are analyzed in the same approach and spots are subtracted from the list if they appear in the control slide. Slide features with poor signal qualities are also removed. Finally, signal intensities of the positives are normalized according to their protein amounts. All modules that account for the challenges in data processing specific to protein microarrays are built into ProCAT and tested.