ProCAT contains a flexible modular design whose individual components can be adjusted according to the experimental designs and stringency level selected by the users. Six sequential modules are currently implemented in ProCAT before a final annotation report is assembled ( Figure 1 ). These modules carry out: background correction; signal normalization; positive spot identification; spot cross-reactivity filter; signal qualities inspection; and protein amount normalization. The performance of many of the steps was tested using several types of experiments as described below.