Alzheimer's disease (AD) is marked by the presence of neurofibrillary tangles and amyloid plaques in the brain of patients. To study plaque formation, we report on further quantitative and qualitative analysis of human and mouse amyloid β peptides (Aβ) from brain extracts of transgenic mice overexpressing the London mutant of human amyloid precursor protein (APP). Using enzyme-linked immunosorbant assays (ELISAs) specific for either human or rodent Aβ, we found that the peptides from both species aggregated to form plaques. The ratios of deposited Aβ1–42/1–40 were in the order of 2–3 for human and 8–9 for mouse peptides, indicating preferential deposition of Aβ42. We also determined the identity and relative levels of other Aβ variants present in protein extracts from soluble and insoluble brain fractions. This was done by combined immunoprecipitation and mass spectrometry (IP/MS). The most prominent peptides truncated either at the carboxyl- or the amino-terminus were Aβ1–38 and Aβ11–42, respectively, and the latter was strongly enriched in the extracts of deposited peptides. Taken together, our data indicate that plaques of APP-London transgenic mice consist of aggregates of multiple human and mouse Aβ variants, and the human variants that we identified were previously detected in brain extracts of AD patients.