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

<p>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. </p>

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

<p>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. </p>

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

<p>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. </p>

Surface-induced dissociation of protein complexes on a cyclic ion mobility spectrometer

Characterization of protein assemblies and amyloid aggregates by CIU, CID, SIU, and SID on a cyclic ion mobility spectrometer.

Surface-Induced Dissociation of Protein Complexes Selected by Trapped Ion Mobility Spectrometry

<p><a>Native mass spectrometry, particularly in conjunction with gas-phase ion mobility spectrometry measurements, has proven useful as a structural biology tool for evaluating the stoichiometry, conformation, and topology of protein complexes. Here, we demonstrate the combination of trapped ion mobility spectrometry (TIMS) and surface-induced dissociation (SID) on a Bruker SolariX XR 15 T FT-ICR mass spectrometer for structural analysis of protein complexes. We successfully performed SID on mobility-selected protein complexes, including streptavidin tetramer and cholera toxin B with bound ligand. Additionally, TIMS-SID was employed on a mixture of peptides bradykinin desR1 and desR9 to mobility separate and identify the individual peptides. Importantly, results show that native-like conformations can be maintained throughout the TIMS analysis. The TIMS-SID spectra are analogous to SID spectra acquired using quadrupole mass selection, indicating little measurable, if any, structural rearrangement during mobility selection. Mobility parking was used on the ion or mobility of interest and 50 to 200 SID mass spectra were averaged. High quality TIMS-SID spectra were acquired over a period of 2-10 minutes, comparable to or slightly longer than SID coupled with ion mobility on various instrument platforms in our laboratory. The ultrahigh resolving power of the 15 T FT-ICR allowed for the identification and relative quantification of overlapping SID fragments with the same nominal <i>m/z</i> based on isotope patterns and shows promise as a platform to probe small mass differences, such as protein-ligand binding or post-translational modifications. These results represent the potential of TIMS-SID-MS for the analysis of both protein complexes and peptides.</a></p>