A total of 294 edible protein sequences and 5 commercial proteases listed in the BIOPEP database were analyzed in silico. The frequency (A), a parameter in silico described previously, was examined further to calculating the ratio of truncated peptides with Xaa-proline and/or Xaa-alanine to all peptide fragments in a protein hydrolyzed with a protease, using the BIOPEP database. Then the in vitro DPP-IV inhibitory activity was determined using the same 15 protein and protease combinations to evaluate their relationship. The result shows that A values considering the number of Xaa-proline + Xaa-alanine exhibited a strong correlation with in vitro DPP-IV inhibition rates by Pearson’s correlation analysis (r = 0.6993; P < 0.05). Therefore, the in silico approach is effective to predict DPP-IV inhibitory activities in vitro of protein hydrolysates.