Alzheimer disease (AD) is characterized by progressive memory loss, reduction in cognitive functions, and damage to the brain. The beta-amyloid precursor protein can be sequentially cleaved by beta-secretase and gamma-secretase. Mutations in the presenilin1(PS1) are the most common cause of Familial Alzheimer's disease (FAD). PS1 mutations can alter the activity of gamma-secretase on the cleavage of the beta-amyloid precursor protein, causing increased A beta production. Previous studies show that the beta APP-C-terminal fragment is first cleaved by beta-scretase, primarily generating long fragments of A beta 48 and A beta 49, followed by the stepwise cleavage of every three amino acid residues at the C terminus, resulting in A beta 48-, 45-, 42 line and A beta 49-, 46-, 43-, 40 line. Here, we used LC-MS/MS to analyze unique peptides IAT, WA, ITL, TVI, IVI through sequential cleavage, combined with ELISA to test the level of A beta 42 and A beta 40 for validation. The results show that most FAD mutant PS1 can alter the level of A beta 42 and A beta 40 monitored by the A beta 42/A beta 40 ratio. Among them, six mutants (1143T, H163P, S170F, Q223R, M233V, and G384A) affect the A beta 42/40 ratio through both A beta 49-40 and A beta 48-38 lines; L166P through decreasing the A beta 49-40 line, six mutants (I143V, M146V, G217A, F280A, L381V, and L392V) through increasing the A beta 48-42 line. More importantly, we found some mutations can affect the gamma-secretase cleavage preference of alpha-CTF and beta-CTF. In conclusion, we found that the FAD PS1 mutations mainly increase the generation of A beta 42 by decreasing the cleavage of A beta 42-A beta 38 and A beta 43-A beta 40.