Gamma-secretase modulators (GSMs) include selected non-steroidal anti-inflammatory drugs such as flurbiprofen that selectively lowers the neurotoxic amyloid-beta peptide Abeta(1-42). GSMs are attractive targets for Alzheimer's disease, in contrast to 'inverse GSMs,' such as fenofibrate, which selectively increase the level of Abeta(1-42). A methodology for screening of Abeta modulating drugs was developed utilizing an Abeta-producing neuroblastoma cell line stably transfected with mutant human amyloid precursor protein, immunoprecipitation of Abeta peptides, and mass spectroscopic quantitation of Abeta(1-37)/Abeta(1-38)/Abeta(1-40)/Abeta(1-42) using an Abeta internal standard. The unexpected conclusion of this work was that in this system, drug effects are independent of gamma-secretase. The methodology recapitulated reported results for modulation of Abeta by GSMs. However, control experiments in which exogenous Abeta(1-40)/Abeta(1-42) was added (i) to drug-treated wild-type cells or (ii) to conditioned media from these wild-type cells, gave comparable patterns of Abeta modulation. These results, suggesting that drugs modulate the ability of cell-derived factors to degrade Abeta, was interrogated by adding protease inhibitors and performing molecular weight cut-off fractionation. The results confirmed that modulation of Abeta(1-40)/Abeta(1-42) was mediated by selective proteolysis. Treatment of N2a cells with flurbiprofen or fenofibric acid selectively enhanced Abeta(1-42) clearance by extracellular proteolysis; treatment with HCT-1026 or fenofibrate (esters of flurbiprofen and fenobric acid) inhibited clearance of Abeta(1-40) and Abeta(1-42).