Surface-Induced Dissociation of Anionic vs Cationic Native-like Protein Complexes

Characterizing protein-protein interactions, stoichiometries, and subunit connectivity is key to understanding how subunits assemble in biologically relevant multi-subunit protein complexes. Native mass spectrometry (nMS) has emerged as a powerful tool to study protein complexes due to its low sample requirements and tolerance for heterogeneity. For such nMS studies, positive mode ionization is routinely used and charge reduction, through the addition of solution additives, is often used, as the resulting lower charge states are often more compact and considered more native like. When studied with surface-induced dissociation, charge reduced complexes often give increased structural information over their “normal-charged” counter parts. A disadvantage of charge-reduction is that increased adduction, and hence peak broadening, is often observed when charge-reducing solution additives are present. Recent studies have shown that protein complexes ionized using negative mode generally form in lower charge states relative to positive mode. Here we demonstrate that the lower charged protein complex anions, activated by SID in an ultrahigh mass range Orbitrap mass spectrometer, fragment in a manner consistent with their solved structure, hence providing substructural information. Negative mode ionization in ammonium acetate offers the advantage of charge reduction without the peak broadening associated with solution phase charge reduction additives and provides direct structural information, when coupled with SID.