Modulating pressure in the Orbitrap improves sensitivity and mass resolution in charge detection mass spectrometry.

Native mass spectrometry has become a key method for studying macromolecular assemblies, providing insights into structures, stoichiometries, and binding interactions. A key aspect for the transmission of electrospray-generated bioparticles into the mass analyzer is the use of gas for collisional cooling and ion desolvation. However, in Orbitrap-based mass spectrometry, the elevated pressure may negatively affect ions, as collisions with background gas can destabilize ion trajectories, potentially leading to incorrect mass determination. These effects are amplified when the pressure in the collision cell is high, as required for large biological assemblies, and when ions are measured for (ultra)long acquisition times in the Orbitrap, as required for high-resolution mass spectrometry. To address these issues, we modified a standard Q Exactive™ UHMR by installing a pulsed valve to control gas flow and limit gas leakage into the Orbitrap. This way, ion transmission and desolvation are maintained while the ultrahigh vacuum in the mass analyzer is enhanced during acquisition. We show that this improves ion detection of various assemblies, including adeno-associated viruses, IgM, and plasmid DNA, with superior mass accuracy and resolving power. The pulsed valve implementation will benefit nearly all mass measurements, setting the stage for next-generation Orbitrap-based, single-ion mass spectrometry.