MALDI mass spectrometry imaging (MSI) reveals molecular and structural heterogeneity of amyloid-β in sporadic Alzheimer's disease and Down syndrome.

UNLABELLED: Alzheimer’s disease (AD) and Down syndrome (DS) are both characterized by early accumulation of amyloid-β (Aβ), but the underlying mechanisms differ. In DS, lifelong overproduction of Aβ due to triplication of the APP gene drives pathology, whereas in sporadic AD (sAD) impaired clearance and altered processing are considered to be major contributors to Aβ pathology. Despite these shared hallmarks, it remains unclear whether the molecular composition of plaques, such as Aβ isoform distribution and post-translational modifications, is truly comparable between the two conditions. Most published studies rely on bulk tissue or antibody-based methods, which average across plaques and overlook truncated or modified Aβ isoforms, such as N-terminally or C-terminally truncated forms or pyroglutamate-modified species. Here, we applied a reflector-mode matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) approach, integrated with histology and immunoassay, to characterize Aβ pathology in postmortem brain tissue from DS, sAD, and non-demented control patients at single-plaque resolution. We demonstrate that Aβ plaques and neurofibrillary tangles are significantly larger in DS than in sAD, consistent with more aggressive disease progression. Molecular profiling revealed distinct peptide repertoires between the diseases. DS plaques contained nearly twice as many N-terminally truncated Aβ peptides as sAD, with proportionally similar contributions from Aβx-40 and Aβx-42, and uniquely harbored Aβ2-42, AβpE3-42, Aβ3-40, Aβ4-42, Aβ8-42, and AβpE11-40/42. In contrast, sAD plaques were dominated by truncated Aβ40 while Aβ42 remained largely full-length, and only sAD contained bi-terminally truncated isoforms such as Aβ2-37, Aβ2-39, and Aβ9-38. Overall, inter-peptide correlations between the relative abundances of all Aβ peptides as performed across individual plaques were significantly stronger in sAD than in DS, indicating that peptide levels co-vary more consistently within sAD plaques. Collectively, these findings indicate that Aβ plaques in DS and sAD differ in their molecular composition and peptide profiles. Beyond providing mechanistic insight, these findings highlight the need to tailor Aβ-targeting therapies to disease-specific peptide signatures, particularly for individuals with DS, who are at exceptionally high risk of dementia and have been underrepresented in clinical research. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40478-026-02280-4.