Membrane Proteome Remodeling in Female APP/PS1 Mice Following M1 Muscarinic Receptor Modulation Revealed by Peptidisc-Enabled DIA-MS.

Alzheimer's disease (AD) is associated with dysregulation of membrane proteins controlling amyloid processing, synaptic signaling, and neuronal communication, yet most proteomic studies focus on soluble fractions, limiting insight into membrane-centered pathology. Here, we apply a membrane-mimetic, data-independent acquisition workflow to define disease- and drug-induced remodeling of the cortical membrane proteome in an APP mouse model of AD. Female wildtype B6C3F1/J and APP/PS1 mice were aged to 9 months, treated ± the M1 positive allosteric modulator VU0486846, and validated by enrichment of APP in cortical membranes of APP/PS1 mice. This confirmed pathological context enabled direct interrogation of membrane remodeling, revealing pronounced, genotype-specific changes characterized by selective enrichment of AD-linked membrane proteins including RyR2, PLD3, ITM2C, and CNTNAP2, alongside broader shifts in pathways related to calcium signaling, synaptic organization, and membrane trafficking. In contrast, wildtype membranes were enriched in proteins associated with axon guidance and synaptic structure, such as EPHA5 and ROBO2. M1 activation produced minimal changes in wildtype mice but selectively enhanced proteins linked to neuronal trafficking and synaptic plasticity in APP/PS1 mice, including SORCS2, PLXND1, and CADM1, indicating preferential engagement of disease-altered pathways. These findings demonstrate that AD-associated remodeling is concentrated at the membrane level and highlight Peptidisc-enabled membrane proteomics as a powerful approach to resolve disease mechanisms and therapeutic target engagement.