Updated project metadata. Within the cell, chemical reactions are often confined and organized through a modular architecture. In this project, a cell-free nanoscale model was analyzed that exploits this compartmentalization principle to perform regulated protein unfolding and degradation. To this end, protein degradation products resulting from degradation by the protease chymotrypsin, which was encapsulated in a DNA nanocompartment, were identified and quantified using an LFQ algorithm.