Recent advances in spatial proteomics by super-resolution proximity labeling

Super-resolution proximity labeling (SR-PL) advances spatial proteomics beyond conventional protein-level enrichment, enabling residue-resolved analysis of subcellular organization in living cells. Conventional proximity labeling relies on streptavidin-based capture and on-bead digestion, producing protein-centric readouts with limited structural insight. In contrast, SR-PL directly recovers biotinylated peptides and identifies labeled amino acid residues by LC-MS/MS. These site-specific labels serve as direct evidence of proximity, allowing for the precise mapping of protein surfaces, solvent accessibility and interaction interfaces. By linking spatial proximity to specific structural features, SR-PL enables mechanistic interpretation of spatial proteomic data and reframes proximity labeling as a structure-informed analytical framework. Recent advances in affinity capture strategies-including engineered probes, reversible affinity matrices, and optimized antibody reagents-have improved selective enrichment and gentle peptide release while reducing background contamination. Together, these developments position SR-PL for broad applications such as membrane topology mapping, organelle contact site analysis, and ligand-dependent interactions.