Combining Surface-Induced Dissociation and Charge Detection Mass Spectrometry to Reveal the Native Topology of Heterogeneous Protein Complexes

Charge detection mass spectrometry (CDMS) enables the direct mass measurement of heterogenous samples on the megadalton scale, as the charge state for a single ion is determined simultaneously with mass to charge ratio (m/z). Surface-induced dissociation (SID) is an effective activation method to dissociate the noncovalent protein complexes without extensive gas-phase restructuring, producing various subcomplexes reflective of the native protein topology. Here, we demonstrate that using CDMS after SID on the Orbitrap platform offers subunit connectivity, topology, proteoform information, and relative interfacial strengths of the intact macromolecular assemblies. SID dissects the capsids (~3.7 MDa) of adeno-associated viruses (AAVs) into trimer-containing fragments (3mer, 6mer, 9mer, 15mer, etc) that can be detected by the individual ion mass spectrometry (I2MS) approach on Orbitrap instruments. SID coupled to CDMS provides unique structural insights into heterogenous assembles that are not obtained by traditional MS measurements.