Spatiotemporal Profiling of Cytosolic Signaling Complexes in Living Cells by Highly Selective Proximity Proteomics

APEX2-mediated proximity labeling pioneers in situ capture of spatiotemporal protein complexes in living cells but is limited by its high background. Here, we developed an optimized probe BP5 with much lower labeling noise. Combining the new proximity labeling with label-free quantitative proteomics, we made pair-wise comparison with current version of biotin phenol probe and show the high selectivity of our newly developed probe. Moreover, wesystematically characterized spatiotemporal interactome of a previously less appreciated EGFR signaling core component STS1 at five time points. The side-by-side comparison with affinity purification-mass spectrometry confirmed the comparable performance for exploring EGFR core complexes. This study provided a proof of concept that our new system can be an effective system broadly applied to investigate transient protein-protein interactions.