AbstractObjective:The most common pathogenesis for familial Alzheimer's disease (FAD) involves misprocessing (or alternative processing) of the amyloid precursor protein (APP) by γ‐secretase due to mutations of the presenilin 1 (PS1) gene. This misprocessing/alternative processing leads to an increase in the ratio of the level of a minor γ‐secretase reaction product (Aβ42) to that of the major reaction product (Aβ40). Although no PS1 mutations are present, altered Aβ42/40 ratios are also observed in sporadic Alzheimer's disease (SAD), and these altered ratios apparently reflect deposition of Aβ42 as amyloid.Methods:Using immunoprecipitation‐mass spectrometry with quantitative accuracy, we analyzed in the cerebrospinal fluid (CSF) of various clinical populations the peptide products generated by processing of not only APP but also an unrelated protein, alcadein (Alc). Alc undergoes metabolism by the identical APP α‐secretases and γ‐secretases, yielding a fragment that we have named p3‐Alcα because of the parallel genesis of p3‐Alcα peptides and the p3 fragment of APP. As with Aβ, both major and minor p3‐Alcαs are generated. We studied the alternative processing of p3‐Alcα in various clinical populations.Results:We previously reported that changes in the Aβ42/40 ratio showed covariance in a linear relationship with the levels of p3‐Alcα [minor/major] ratio in media conditioned by cells expressing FAD‐linked PS1 mutants. Here we studied the speciation of p3‐Alcα in the CSF from 3 groups of human subjects (n = 158): elderly nondemented control subjects; mild cognitive impairment (MCI) subjects with a clinical dementia rating (CDR) of 0.5; SAD subjects with CDR of 1.0; and other neurological disease (OND) control subjects. The CSF minor p3‐Alcα variant, p3‐Alcα38, was elevated (p < 0.05) in MCI subjects or SAD subjects, depending upon whether the data were pooled and analyzed as a single cohort or analyzed individually as 3 separate cohorts.Interpretation:These results suggest that some SAD may involve alternative processing of multiple γ‐secretase substrates, raising the possibility that the molecular pathogenesis of SAD might involve γ‐secretase dysfunction. Ann Neurol 2011;69:1026–1031