In this study, we report a detailed analysis of the different variants of amyloid- (A) peptides in the brains and the cerebrospinal fluid from APP23 transgenic mice, expressing amyloid precursor protein with the Swedish familial Alzheimer disease mutation, at different ages. Using one-and two-dimensional gel electrophoresis, immunoblotting, and mass spectrometry, we identified the A peptides A(1-40), -(1-42), -(1-39), -(1-38), -(1-37), -(2-40), and -(3-40) as well as minor amounts of pyroglutamate-modified A (A(N3pE)) and endogenous murine A in brains from 24-month-old mice. Chemical modifications of the N-terminal amino group of A were identified that had clearly been introduced during standard experimental procedures. To address this issue, we additionally applied amyloid extraction in ultrapure water. Clear differences between APP23 mice and Alzheimer disease (AD) brain samples were observed in terms of the relative abundance of specific variants of A peptides, such as A(N3pE), A(1-42), and N-terminally truncated A(2/3-42). These differences to human AD amyloid were also noticed in a related mouse line transgenic for human wild type amyloid precursor protein. Taken together, our findings suggest different underlying molecular mechanisms driving the amyloid deposition in transgenic mice and AD patients.The major histopathological hallmarks of Alzheimer disease (AD) 2 are neuritic plaques and neurofibrillary tangles that are composed of aggregates of the amyloid- (A) peptide and hyperphosphorylated Tau protein, respectively (1-5). A peptides are generated from the amyloid precursor protein (APP) by two proteolytic enzymes called -and ␥-secretases (for reviews see Refs. 6 -8). The resulting A peptides represent a heterogeneous group of peptides with different lengths. A(1-40) is the predominant form released from cultured cells (9) and in biological fluids, such as blood (10) and cerebrospinal fluid (CSF) (11). Longer forms ending at amino acid 42 are believed to be particularly important in the pathogenesis of AD due to a higher propensity to aggregate (12). A accumulation in the AD brain likely starts many years before cognitive deficits become evident (13,14). The reported inverse association of in vivo cortical binding of Pittsburgh Compound-B and CSF A42 suggests that brain amyloid deposition and low CSF A42 are mechanistically related (13,15). Based on the amyloid cascade hypothesis stating a central role of A in AD, several therapeutic strategies targeting A and aiming for inhibition of disease progression are pursued. The more advanced of these potential therapeutic approaches include inhibition or modulation of cellular A production and A-targeted immunotherapy (16,17).Animal models of the human disease are important research tools to facilitate the study of the pathophysiology, and they have been widely used for testing potential therapeutic approaches. The APP23 mouse line (18) represents one out of several well established transgenic mouse models that display key features of ...