Is it possible to use cross-linking mass spectrometry to identify protein-protein interactions in living cells?
Cross-linking mass spectrometry is a powerful tool to elucidate protein-protein interactions and macromolecular structure based on cross-linker distances between specific amino acid residues. In a recent study led by Zheng Ser, we illustrate how the well-established target-decoy strategy employed in modern mass spectrometry proteomics can be extended for accurate identification of protein-protein interactions. As a result, we provide optimized methods for detecting protein complex cross-links in live human cells. This should be widely useful for defining the organization of proteins in cellular complexes that have been difficult to purify or reconstitute, such as those that involve chromatin and many other membraneless organelles and phase separated assemblies.