Extracellular amyloid plaques and intracellular neurofibrillary tangles are the pathological hallmarks of Alzheimer’s Disease (AD). It takes on average 19 years for amyloidβ (Aβ) peptides to deposit as insoluble plaques from onset to clinical dementia symptoms in AD. Such long-lived proteins and peptides without degradation and clearance can undergo further post-translational modifications (PTM). Several biochemical and analytical approaches have estimated very high degree of isomerization and racemization of Asp and Ser residues in Aβ purified from the insoluble plaques, along with sequential loss of the N-terminal amino acids. In this study we have characterized the most common isomerization and racemization of the Asp-1 and Asp-7 residues of the Aβ peptides present in AD brain based on both their chromatographic resolution as well as their collisional cross section (CCS) using high resolution ion mobility (IM) Q-TOF mass spectrometer (Agilent 6560). Using stable isotope labeled peptides we have also quantified the amount of these isomers/racemers in the different fractionated biochemical pools of the frontal cortex grey matter of human AD and control brains. Distribution of these isomerized and racemized peptides change from lower levels in the soluble/cytosol to higher levels in the insoluble/aggregated debris in AD brain, also indicating loss in the biochemical exchange of the pool of Aβ with the progression of the disease. These findings have implications in Aβ neurotoxicity, oligomerization, structures of amyloid fibrils present in the AD brain as well establishing CSF/blood-based biomarkers.