Mass spectrometry has made it possible to quantify proteomes at remarkable depth, but understanding infection requires moving beyond protein abundance to the interactions and molecular assemblies that define cellular function. In this talk, I will discuss how we use size-exclusion chromatography coupled to mass spectrometry (SEC-MS) to map protein complexes and interaction networks across infection-relevant systems. By combining co-fractionation profiles with computational analysis and targeted validation, we can reconstruct proteome-scale interaction maps and identify changes in protein organization that would remain hidden in conventional expression-based measurements. I will highlight how these approaches can be used to study bacterial and phage biology, uncover previously uncharacterized protein functions and generate mechanistic hypotheses directly from complex proteomic data. Together, these studies show how proteome-scale interaction maps can reveal protein function and generate mechanistic hypotheses during infection.