  Proteins congregate into complexes to perform fundamental cellular functions.
Phenotypic outcomes, in health and disease, are often mechanistically driven by
the remodeling of protein complexes by protein coding mutations or cellular
signaling changes in response to molecular cues. Here, we present an affinity
purification mass spectrometry (APMS) proteomics protocol to quantify and
visualize global changes in protein protein interaction (PPI) networks between
pairwise conditions. We describe steps for expressing affinity tagged bait
proteins in mammalian cells, identifying purified protein complexes,
quantifying differential PPIs, and visualizing differential PPI networks.
Specifically, this protocol details steps for designing affinity tagged bait
gene constructs, transfection, affinity purification, mass spectrometry sample
preparation, data acquisition, database search, data quality control, PPI
confidence scoring, cross run normalization, statistical data analysis, and
differential PPI visualization. Our protocol discusses caveats and limitations
with applicability across cell types and biological areas.
