Politis, A.; Stengel, F.; Hall, Z.; Hernández, H.; Leitner, A.; Walzthoeni, T.; Robinson, C. V. & Aebersold, R. A mass spectrometry-based hybrid method for structural modeling of protein complexes. Nat Methods, 2014, 11, 403-406
We describe a method that integrates data derived from different mass spectrometry (MS)-based techniques with a modeling strategy for structural characterization of protein assemblies. We encoded structural data derived from native MS, bottom-up proteomics, ion mobility-MS and chemical cross-linking MS into modeling restraints to compute the most likely structure of a protein assembly. We used the method to generate near-native models for three known structures and characterized an assembly intermediate of the proteasomal base.