γ-Secretase complexes are involved in the generation of amyloid-β (Aβ) in the 
brain. Therefore, γ-secretase has been proposed as a potential therapeutic 
target in Alzheimer disease (AD). Targeting γ-secretase activity in AD requires 
the pharmacological dissociation of the processing of physiological relevant 
substrates and the generation of "toxic" Aβ. Previous reports suggest the 
differential targeting of γ-secretase complexes, based on their subunit 
composition, as a valid strategy. However, little is known about the biochemical 
properties of the different complexes, and key questions regarding their Aβ 
product profiles should be first addressed. Here, we expressed, purified, and 
analyzed, under the same conditions, the endopeptidase and carboxypeptidase-like 
activities of the four γ-secretase complexes present in humans. We find that the 
nature of the catalytic subunit in the complex affects both activities. 
Interestingly, PSEN2 complexes discriminate between the Aβ40 and Aβ38 production 
lines, indicating that Aβ generation in one or the other pathway can be 
dissociated. In contrast, the APH1 subunit mainly affects the 
carboxypeptidase-like activity, with APH1B complexes favoring the generation of 
longer Aβ peptides. In addition, we determined that expression of a single human 
γ-secretase complex in cell lines retains the intrinsic attributes of the 
protease while present in the membrane, providing validation for the in vitro 
studies. In conclusion, our data show that each γ-secretase complex produces a 
characteristic Aβ signature. The qualitative and quantitative differences 
between different γ-secretase complexes could be used to advance drug 
development in AD and other disorders.