Top-down protein characterization facilitated by ion/ion reactions on a quadrupole/time of flight platform

In comparison to bottom-up proteomics approaches, whereby peptides derived from proteolytic digestion are analyzed, top-down approaches, involving direct analysis of intact proteins, provide higher specificity for protein identification and are better-suited for the characterization of sequence variants. However, top-down protein characterization usually requires more sophisticated instrumentation and methodologies to deal with the more complex tandem mass spectra derived from dissociation of high mass multiply charged intact proteins. Gas-phase ion/ion reactions are universally applicable and have proved to be useful in mixture analysis and top-down biomolecule characterization. The coupling of the ion/ion proton transfer reaction in the context of MS/MS has been demonstrated to expand informing power in top-down protein characterization, particularly with platforms that employ electrodynamic ion trap and TOF mass analysis. In addition, probing protein primary structure using ion/ion electron transfer dissociation usually provides extensive structurally informative fragmentation and also allows for the localization of labile PTMs. Here, the performance of the widely used quadrupole/TOF platform, equipped with ion/ion reaction functionality, for top-down protein characterization is summarized, and various methodologies employing ion/ion reactions are reviewed.