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CleaveScope─Una herramienta fácil para el análisis de especificidad de proteasas a partir de datos LC-MS/MS

Mihail Konstantinov¹, Ilya Toropygin¹

¹Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia.

Analytical chemistry

|February 18, 2026

Abstract:

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.

Palabras clave:

especificidad de proteasas LC-MS/MS análisis de sitios de escisión bioinformática proteómica

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