Multiplexed affinity-based protein complex purification

Here we proved the principle of a multiplexed affinity-based protein complex purification (MAPcP) technique that targets simultaneous extraction of multiple protein complexes with superior purity. Microspheres of various sizes and coupled with different affinity probes extract several protein complexes concurrently and specifically. After the coextraction, flow-field flow fractionation (Fl-FFF) rapidly washes the microspheres as well as separates them based on their sizes to recover the clean individual complex for downstream analysis. Demonstration of the parallel extraction of two immuno-complexes from the yeast whole cell lysate showed that MAPcP can enhance the sample purity significantly compared to the traditional centrifugation and magnetic pull-down methods used for small scale protein purification. Simultaneous isolation of multiple protein complexes can facilitate the elucidation of the functional relationship among protein complexes and improve our understanding of the biological network.