A similar high-density peptide microarray driven approach was next used to address the specificity of the protease chymotrypsin, which is known to preferentially cleave at the C-terminal of tyrosine, phenylalanine and tryptophan (albeit not if followed by a proline). A high-density peptide microarray containing about 50,000 peptides (16,526 unique peptides) was generated according to the theme Ac-GAGAXXXXGAGA, treated with chymotrypsin, labeled with TAMRA and quantitated by fluorescence microscopy. The resulting data was used to train an NNAlign method (using the settings described in Figure 5 ). The correlation scatterplot of the measured versus predicted values exhibits a very strong linear correlation with a Pearson of r = 0.943 demonstrating that the peptide microarray data contains a consistent signal that reliably has been captured by the NNAlign method.