Inert Gas Modulation of Electron-Based Fragmentation for Proteomics

E-Msion, Inc., Corvallis OR

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Abstract

The identification and quantification of biological macromolecules remain challenging despite major advances in the speed, resolution and mass accuracy of modern mass spectrometers. A key weakness with current instrumentation lies in the methods used to induce fragmentation. The reliance in particular on collision-induced dissociation (CID) has limited such analyses to bottom-up workflows of trypsin-digested peptides of 10-30 residues. When subjected to CID, many fragile PTMs on these short peptides are lost in complex fragmentation channels. An alternative fragmentation methodology called electron capture dissociation (ECD) is well known for producing exceptionally clean spectra of entire proteins while also preserving PTMs. The difficulty arises from confining enough low-energy electrons to efficiently fragment peptide bonds, which has prevented its adoption in most mass spectrometers. At e-MSion, we have developed an efficient electron-fragmentation technology called ExD to confine electrons using only DC static fields and a carefully sculpted magnetic field. Two major advantages of our technology over competing fragmentation techniques such as ETD are speed and simplicity and we are achieving remarkable results with large native proteins. However, the remaining challenge for the widespread adoption of our technology is the relatively lower efficiency with doubly and triply charged peptides, which remain the core activity for most proteomic facilities. While testing our ExD cell attached directly to the high gas pressure ion mobility cell in the Waters Synapt G2, we have discovered that that having nitrogen gas flow through our cell can increase fragmentation efficiency for doubly charged peptides from 3-5% to over 50%. The feasibility question we pose for this phase I application is how to best use gas flow to maximize the fragmentation of peptides and other low-charged molecules in our ExD cell. To accomplish this objective, our primary aim is to optimize the ExD cell design for introduce gas near the filament chamber to better thermalize (cool) electrons to improve electron capture. We hypothesize inert gas near the filament can better distribute electrons within the cell to improve electron capture. Results from these aims will establish how to dramatically improve electron-based fragmentation for bottom up proteomics in mass spectrometry. The adoption of our technology is an extremely cost-effective solution that will accelerate the ability of many NIH investigators to probe disease mechanisms, to characterize complex macromolecules in biological samples with increased accuracy and speed, reduce the rate of false discoveries and misidentifications, and reveal new details not possible by current approaches.