CleaveScope─An Easy Tool for Protease Specificity Analysis from LC-MS/MS Data

Here we present CleaveScope, a lightweight standalone software tool for rapid and flexible analysis of protease specificity using LC-MS/MS data. The program accepts XML output files from the Mascot search engine, performs automated extraction and alignment of cleavage sites, and builds frequency matrices of amino acid residues surrounding scissile bonds. CleaveScope supports various normalization strategies, including direct normalization, percentage difference, and Z-score, enabling robust detection of amino acid preferences. The results are visualized as customizable heatmaps and sequence logos, which reflect statistically significant residue patterns around cleavage sites. The software is freely available at https://github.com/MiKonstantinov/CleaveScope.