Chronic neurodegenerative diseases, such as Alzheimer’s, Parkinson’s and Prion diseases are all characterized by the protein conformational changes that result in misfolding and aggregation of one of the host proteins. Among these, Prion diseases are distinct from other neurodegenerative diseases, in that the misfolded protein (PrPSc) is infectious. The PrPSc is a misfolded and aggregated beta-sheet-rich isoform of the normal cellular prion protein (PrP). PrP is a glycoprotein with two N-linked glycans and this post-translational modification has critical roles in prion protein expression, distribution on neuronal cells and disease pathogenesis. Recent evidence in prion pathogenesis suggests that apart from the glycosylation of prion protein, the entire cellular glycosylation machinery is modified during pathogenesis. Herein I report the comparative analysis of prion-infected and un-infected mouse brain using integrated global proteomics and glycoproteomics approaches. Enrichment of glycoproteins using hydrazide beads, both at the protein level and tryptic peptide levels was performed to maximize glycoprotein/peptide coverage. N-glycopeptides were released from hydrazide support by PNGase-F removal of glycans and the resulting peptides were then labeled with stable isotopic dimethyl labeling and are analyzed by quantitative LC-MS analysis. In order to improve glycoprotein coverage, I have also applied alternate methods, such as HILIC and ZIC-HILIC for enrichment. Changes at global proteome and N-glycosite levels will be studied in prion-infected and normal brains, so that the prion disease associated alterations in glycosylation site occupancy can be measured.