Publication date: Jul 15, 2025

It is crucial to investigate protein functions in specific subcellular environments. Cross-linking mass spectrometry is a powerful tool to map the direct interactome of proteins by identifying inter-protein cross-links. However, it is challenging to identify inter-protein cross-linked peptides due to their low abundance. We chemically synthesize the cross-linkers ePDES1 and ePDES2 with an alkyne group and a compound with azide linked to a phosphate group to enrich for cross-linked peptides. Based on the high-quality cross-linking spectra of ePDES1 and ePDES2, our methods achieve the identification of hundreds of directly interacting proteins or substrates of thioredoxins in the nucleus and mitochondria.

Semantics

Original Article