Stress-induced autophagy leads to major cellular remodeling. During autophagy, a new organelle, the autophagosome, is formed that shuttles cellular material to lysosomes for degradation. Quantitative mass spectrometry-based proteomics is a powerful research strategy for the description of spatio-temporal protein dynamics during autophagy. This technique allows the identification of protein-protein interactions and of specific post-translational modifications. In addition, current methods enable the in-depth characterization of cellular as well as organellar composition changes and the global analysis of signaling networks. Thus, a plastic picture of the cell can be drawn. In this review we describe recent advances in MS-based proteomics approaches and their implications for autophagy-related research questions.