AbstractBackgroundProteomic profile changes have been reported in the brains from individuals having Alzheimer’s disease. However, it is not yet clear whether they represent a continuous process from mild to severe changes, or whether the proteins become involved step‐by‐step in a hierarchal manner. Additionally, in previous studies, cases with initial Aβ plaque and NFT pathology were considered as controls, and brain homogenates were not separated into distinct fractions. Therefore, there is a gap of knowledge regarding the initial steps of AD pathogenesis and the spatial resolution of the respective protein changes in terms of subcellular distribution.MethodWe analyzed soluble, dispersible (insoluble proteins and vesicles in mixtures with the intra‐/extracellular fluid), membrane‐associated (SDS‐soluble), and plaque‐associated (formic‐acid‐soluble) fractions of brain homogenates from 19 control cases without AD pathology, 17 pathologically preclinical AD (p‐preAD), and 17 symptomatic AD (symAD) cases by label‐free liquid chromatography coupled to tandem mass spectrometry. Proteomic changes and related pathways involved in p‐preAD and symAD were determined by integrated analyses combining quantitative proteomics, neuropathological measurements, regression analysis, and gene ontology overrepresentation tests.ResultThree hierarchical classes of proteins, namely early‐ and late‐responding proteins and gradually changing proteins were identified across control, p‐preAD and symAD samples. Additionally, five proteins exhibited reduced abundance in the soluble fraction accompanied by increase in the membrane‐associated fraction between symAD and the group of p‐preAD + control cases, suggesting pathological alterations in their functions. Gene ontology analysis showed that the synaptic vesicle cycle and other endocytosis‐related pathways were overrepresented by early‐responding and gradually changing proteins, whereas caspase‐mediated cleavage of cytoskeletal proteins were enriched in the late‐responding protein class.ConclusionWe identified an apparent hierarchy of key proteins in the human brain during AD pathogenesis, from which the early responding proteins point to pathways that are not yet a main focus in AD research. This hierarchy of proteome change in the neocortex clearly distinguished the preclinical phase from the symptomatic phase and identified the synaptic vesicle cycle as a likely primary affected function in AD initiation. Our results may open new roads for therapies by intervening on those key proteins and their respective pathways.