Several neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), and enigmatic disease on Guam that shares features of both called Parkinson‐Dementia Complex (PDC) are proposed to derive from pathological protein that share a number of potentially inter‐related biochemical features including misfolding, decreased surfactant solubility, aggregation into amyloid or inclusions, and extensive post‐translational modifications. We have employed stable isotope dilution techniques coupled with liquid chromatography followed by tandem mass spectrometry as a means of discovering those proteins that adopt a pathological phenotype in these diseases. Our first set of experiments used laser capture microdissected (LCM) to obtain neurofibrillary tangles (NFTs) from brain sections of patients with AD, or neocortical Lewy Bodies from individuals Dementia with Lewy bodies. Our work has confirmed the presence of many proteins previously associated with these structures, and identified new protein constituents subsequently confirmed by immunohistochemistry. Our second set of experiments used reduced surfactant solubility to enrich for those proteins that may adopt pathological configurations in diseased tissue. We discovered approximately 100 proteins with reduced surfactant solubility that were not identified previously in any of these diseases, and discovered some surfactant insoluble proteins already known in one disease in another. For example, we discovered surfactant‐insoluble alpha‐synuclein in PDC frontal cortex despite the lack of Lewy bodies. Finally, we have used these datasets to screen for post‐translational modifications on these pathologic proteins. These results demonstrate the power of proteomic‐based discovery tools in the comprehensive assessment of pathological protein in neurodegenerative diseases.