In silico classification and identification co-purified protein complexes yield new structures and multiple MSP assembly states

Native protein complexes have garnered interest as targets for structural dissemination. Cryogenic electron microscopy (cryoEM) with its ability to image protein mixtures is the most promising tool to enable structural proteomics. Additionally, image processing has evolved to deal with conformational and compositional heterogeneity. Integrative approaches, namely mass spectrometry in conjunction with cryoEM have made it possible to characterize and identify complex mixtures. However, this comes at a cost of generating models and interpreting mass spectra. Here we present a modified approach that only requires electron micrographs and a computer for unsupervised model building and protein identification. We were able to identify co-purified membrane proteins, resulting in a novel structure and unexpected nanodisc assemblies, which imply direct interaction between membrane proteins and membrane scaffolding proteins.