Charge site manipulation to enhance top-down fragmentation efficiency

In recent years, top-down mass spectrometry has become a widely used approach to study proteoforms; however, improving sequence coverage remains an important goal. Here, two different proteins, alpha-synuclein and bovine carbonic anhydrase, were subjected to top-down collision-induced dissociation (CID) after electrospray ionisation. Two high-boiling solvents, DMSO and propylene carbonate, were added to the protein solution in low concentration (2%) and the effects on the top-down fragmentation patterns of the proteins were systematically investigated. Each sample was measured in triplicate, which revealed highly reproducible differences in the top-down CID fragmentation patterns in the presence of a solution additive, even if the same precursor charge state was isolated in the quadrupole of the instrument. Further investigation supports the solution condition-dependent selective formation of different protonation site isomers as the underlying cause of these differences. Higher sequence coverage was often observed in the presence of additives, and the benefits of this approach became even more evident when datasets from different solution conditions were combined, as increases up to 35% in cleavage coverage were obtained. Overall, this approach therefore represents a promising opportunity to increase top-down fragmentation efficiency.

Automated summary

In recent years, top-down mass spectrometry has been widely used to study proteoforms, with the goal of improving sequence coverage. This study investigated the effects of two high-boiling solvents, DMSO and propylene carbonate, on the top-down fragmentation patterns of two different proteins. The results revealed reproducible differences in the fragmentation patterns in the presence of these additives, potentially due to the selective formation of different protonation site isomers. The presence of additives often led to higher sequence coverage, and combining datasets from different solution conditions further increased cleavage coverage.