A scalable multiplexed platform to accelerate protein interactome discovery

Chromatographic fractionation-mass spectrometry (CF-MS) allows for mapping native protein-protein interactions and macromolecular complexes on a proteome-scale but is tedious and resource intensive for comparative analysis. Here, we present a more parsimonious and reproducible multiplexing CF-MS platform for measuring multi-protein assemblies across different experimental samples simultaneously with an order-of-magnitude faster than previous approaches. We used this innovative strategy to elucidate protein networks in control and breast cancer cells models in parallel within two weeks of total MS instrument time.