before I will answer your question I would like to ask you one question. What is the fate of cells exposed to BafA for 30 min? Are they collected or cultured in fresh growth medium? If the later is the case how many hours after washing off the drug is the experiment conducted? Typically, protein abundance does not change in response to drug exposure for short period of time, however acidification of lysosomes may affect protein transport from and to the cytosol in the long term. Do you know if BAfA accumulates into the lysosomes? I know that this is the case with NH4Cl. In any case the safest way is to perform western blot analysis to show the levels of expression of cathepsin D

Thank you Paschalis, I'm just curiously about a report that this treatment lead to majority of matured cathepsin loss. I doubt how can cathepsin can be eliminated so fast when lysosome is deactivated by BafA.