Protein interaction networks are dynamically remodeled during signaling and proteostasis, but many transient, low-stoichiometry, or degradation-coupled contacts are lost during affinity purification and difficult to distinguish from proximity-labeling backgrounds. Here, we introduce photocatalytic zero-length proximity crosslinking (PZPC), a genetically encoded, blue-light-controlled strategy that covalently captures protein-of-interest-containing covalent complexes in living cells. We further develop LinkMasser, a blind-search crosslinking mass spectrometry algorithm that identifies unknown crosslink-associated mass offsets, revealing an oxidative Lys–His zero-length coupling signature underlying PZPC-mediated crosslinking. Using the ubiquitin-independent degradation factor midnolin as a benchmark system, PZPC recovered inducible transcription factors and short-lived regulatory proteins largely missed by conventional AP–MS, leading to the identification of five novel midnolin substrates. We next applied PZPC to 63 human F-box proteins, generating a family-wide proximity atlas of 554 candidate interactors and functionally validating 81 candidate substrates from 257 tested proteins. By coupling this atlas to an antiviral signaling screen, we identified FBXO44 as a positive regulator of the RIG-I–MAVS–IFN pathway and degraded ADAR1, EIF3B, and TUFM as FBXO44-regulated negative modulators of antiviral signaling. These results establish PZPC as a scalable framework for resolving dynamic protein networks and uncovering E3-regulated signaling circuits in living cells.