Combining Proximity Labeling and Cross-Linking Mass Spectrometry for Proteomic Dissection of Nuclear Envelope Interactome

Proximity labeling (PL) and chemical cross-linking (XL) mass spectrometry are two powerful methods to dissect protein–protein interactions (PPIs) in cells. Although PL typically captures neighboring proteins within a range of 10–20 nm of a single bait protein, chemical XL defines direct protein–protein contacts within 1 nm in a systemic manner. Here, we develop a new method, named PL/XL-MS, to harness the advantages of both PL and XL. PL/XL-MS can enrich a subcellular compartment by PL and simultaneously identify PPIs of multiple proteins from XL data. We applied PL/XL-MS to dissect the human nuclear envelope interactome. PL/XL-MS successfully enriched the nuclear envelope proteins and identified most known inner nuclear membrane proteins. By searching the cross-linked peptides, we successfully observed 109 literature-curated PPIs of 14 nuclear envelope proteins. Based on the homoprotein XL data, we experimentally characterized a nuclear matrix protein, Matrin-3, and observed its preferential localization near the nuclear envelope. PL/XL-MS is a simple and general method for studying protein networks in a subproteome of interest.