Summary Within a cell, a number of pathways contribute to the repair and clearance of proteins and are required for maintaining protein homeostasis (proteostasis). A common feature of proteostatic pathways is their ability to act on a range of client proteins that vary based on cellular and environmental conditions. The molecular mechanisms of the selectivity of many proteostatic pathways remain incompletely understood. The overall goal of our research program is to investigate the mechanisms that determine the selectivity of proteostatic pathways by conducting functional analyses on proteome-wide scales. As a first step towards this long-term objective, we have focused on investigating the global selectivities of the macroautophagy pathway and methionine sulfoxide reductases. Macroautophagy can selectively target specific proteins and organelles for lysosomic degradation. Using novel proteomic approaches, we have identified subsets of proteins that rely on macroautophagy for their constitutive turnover. We have also shown that selective autophagic degradation plays a major role in maintaining protein homeostasis in quiescent cells and that alterations in autophagic flux is a pathologic feature of prion infected cells. Our future research will focus on understanding the molecular mechanisms of the differential selectivity of basal macroautophagy and investigating the prevalence and regulation of selective macroautophagy in quiescent and prion infected cells. The methionine sulfoxide reductase (Msr) system is an important repair pathway for oxidized methionine residues in proteins. To facilitate global analyses of the selectivity of Msrs, we have developed novel proteomic approaches for accurate quantitation of methionine oxidation on proteome-wide scales. Using these approaches, we plan to investigate the extent of methionine oxidation in proteomes of cells and tissues that are deficient in specific Msrs under normal and oxidative stress conditions. Together, the proposed experiments will provide insights into the mechanisms of client selection by macroautophagy and Msr pathways. Our studies will also examine the role of these two pathways in mitigating protein damage that occurs under specific proteotoxic stress conditions.