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Cathepsin E (CatE) and D (CatD) are the major aspartic proteinases in the endolysosomal pathway. They have similar specificity and therefore it is difficult to distinguish between them, as known substrates are not exclusively specific for one or the other. In this paper we present a substrate-based assay, which is highly relevant for immunological investigations because it detects both CatE and CatD in antigen-processing organelles. Therefore it could be used to study the involvement of these proteinases in protein degradation and the processing of invariant chain. An assay combining a new monospecific CatE antibody and the substrate, MOCAc-Gly-Lys-Pro-Ile-Leu-Phe-Phe-Arg-Leu-Lys(Dnp)-D-Arg-NH2[where MOCAc is (7-methoxycoumarin-4-yl)acetyl and Dnp is dinitrophenyl], is presented. This substrate is digested by both proteinases and therefore can be used to detect total aspartic proteinase activity in biological samples. After depletion of CatE by immunoprecipitation, the remaining activity is due to CatD, and the decrease in activity can be assigned to CatE. The activity of CatE and CatD in cytosolic, endosomal and lysosomal fractions of B cells, dendritic cells and human keratinocytes was determined. The data clearly indicate that CatE activity is mainly located in endosomal compartments, and that of CatD in lysosomal compartments. Hence this assay can also be used to characterize subcellular fractions using CatE as an endosomal marker, whereas CatD is a well-known lysosomal marker. The highest total aspartic proteinase activity was detected in dendritic cells, and the lowest in B cells. The assay presented exhibits a lower detection limit than common antibody-based methods without lacking the specificity.