Lysosomal dysfunction is linked to several neurodegenerative diseases. Recent GWAS studies have implicated genes in endo-lysosomal pathways as risk factors for developing frontotemporal dementia (FTD) and Alzheimer’s disease (AD). However current tools to study protein interactions of these pathways in situ are limited. In this thesis, I enhanced a proximity-based proteomics tool to capture an unbiased interactome of a protein of interest in mouse brains. The tool, called Biotinylation by Antibody Recognition (BAR), utilizes existing immunohistochemistry protocols on fixed tissue in addition to activating HRP-conjugated secondaries bound to primary of interest. Activation of HRP generates biotin radicals that bind to proteins in the vicinity that can be collected for proteomics. I investigated the robustness of this method targeting lysosomes in GRN-/- mice. GRN codes for progranulin, a lysosomal glycoprotein, and is implicated as an FTD and AD GWAS hit. I used human inducible pluripotent stem cell (iPSC) derived neurons and microglia for follow up studies. Additionally, I tested a cell type-specific marker for microglia using BAR to assess its applicability to generate whole cell interactomes in situ for FTD and AD using GRN-/- and APPNLF mice respectively. Here, I showed that lysosomes have an increased abundance of proteolytic enzymes with progranulin loss. Subsequently, I showed that despite this increase, there is a decrease in the enzymatic activity. Additionally, there was an upregulation of microglial proteins in this dataset consistent with literature. Proximity labeled proteomics of GRN-/- microglia showed increased lysosomal enzymes and components of the complement pathway as seen before. Lastly, I demonstrated that endo-lysosomal pathways are affected early in microglia from APPNLF brains, consistent with lysosomal dysfunction seen in AD. Collectively, these findings confirm the validity of using BAR-based proteomics in fixed brain slices. And lastly, this dataset implicates endo-lysosomal dysfunction as the converging pathway in neurodegenerative diseases.