Recent advances in spatial proteomics by super-resolution proximity labeling.

Area of Science:

• Cellular and Molecular Biology
• Proteomics
• Biochemistry

Background:

• Conventional proximity labeling methods provide protein-level data with limited structural resolution.
• Current techniques often involve streptavidin capture and on-bead digestion, restricting detailed analysis.
• Understanding subcellular organization requires residue-specific information.

Purpose of the Study:

• To introduce and detail Super-resolution proximity labeling (SR-PL) as an advancement in spatial proteomics.
• To enable residue-resolved analysis of subcellular organization in living cells.
• To reframe proximity labeling as a structure-informed analytical framework.

Main Methods:

• SR-PL directly recovers biotinylated peptides.
• Liquid chromatography-tandem mass spectrometry (LC-MS/MS) identifies labeled amino acid residues.
• Advances in affinity capture strategies improve enrichment and reduce background.

Main Results:

• SR-PL provides site-specific labels as direct evidence of proximity.
• Enables precise mapping of protein surfaces, solvent accessibility, and interaction interfaces.
• Facilitates mechanistic interpretation of spatial proteomic data.

Conclusions:

• SR-PL advances spatial proteomics beyond conventional enrichment methods.
• The technique allows for residue-resolved analysis of subcellular organization.
• SR-PL has broad applications including membrane topology and organelle contact site analysis.