Macrophages clear exhausted, damaged, and sick cells in our bodies, as well as exogenous pathogens, cellular debris, and atherosclerotic plaques. When macrophages recognize and engulf their targets through ligand-receptor interactions prior to destruction in the lysosome, this process is referred to as phagocytosis. Phagocytosis is a vital process in our innate immune system and is altered in diseases, including cancer and infection. In our lab we are interested in understanding how macrophage phagocytosis decisions are made and the implications of phagocytosis on macrophage function. To study these processes, we leverage chemical biology tools, in particular mass spectrometry-based proteomics. In this seminar I will present two stories: In the first story, we discover a novel ‘don’t eat me’ ligand expressed by the pathogen Borrelia burgdorferi, which signals through the established mammalian anti-phagocytic receptor SIRPa as a means by which to evade immune clearance. In the second story, we develop a novel chemical proteomics technique to understand how the macrophage cell surface protein repertoire changes during the process of cancer cell phagocytosis. This proteomic alteration negatively impacts macrophage phagocytosis and explains changes to macrophage function and metabolism in the tumor microenvironment. Taken together these projects highlight the power of chemical biology and mass spectrometry in the study of macrophage function and mechanism.