Cathepsin S (CTSS) is a lysosomal cysteine protease of the papain family. It plays a major role in the processing of the MHC class IIassociated invariant chain. It has been implicated in the pathogenesis of several diseases such as Alzheimer’s disease and degenerative disorders associated with the cells of the mononuclear phagocytic system. Mouse Cathepsin S is synthesized as a preproenzyme of 340 amino acid residues consisting a signal peptide (residues 117), a pro region (residues 18122), and the mature enzyme (residues 123340). Cathepsin S is less abundant in tissues than Cathepsins B, L and H. The activity of recombinant mouse CTSS is measured by its ability to cleave a fluorogenic peptide substrate Mca-Arg-Pro-Lys-Pro-Val-Glu-Nval-Trp-Arg-Lys(Dnp)-NH2 in the assay buffer 50 mM NaOAc, 5 mM DTT, 250 mM NaCl, pH 4.5. The rmCTSS is diluted to 50 ug/ml in assay buffer, then incubated at room temperature for 2h. The incubated rmCTSS is diluted to 5 ug/mL in assay buffer. Loading into a black well plate 50 µL of 5 ug/mL rmCTSS and start the reaction by adding 50 µL of 20 µM substrate, with a substrate blank containing 50 µL assay buffer, 50 µL substrate, and no rmCTSS. Then read at excitiation and emission wavelengths of 320 nm and 405 nm, respectively, in kinetic mode for 5 minutes. The specific activity of recombinant mouse CTSS is > 10 pmol/min/µg.