The Omnitrap Platform: A Versatile Segmented Linear Ion Trap for Multidimensional Multiple-Stage Tandem Mass Spectrometry

Abstract

Multidimensional multiple-stage tandem processing of ions is demonstrated successfully in a novel segmented linear ion trap. The enhanced performance is enabled by incorporating the entire range of ion activation methods into a single platform in a highly dynamic fashion. The ion activation network comprises external injection of reagent ions, radical neutral species, photons, electrons, and collisions with neutrals. Axial segmentation of the two-dimensional trapping field provides access to a unique functionality landscape through a system of purpose-designed regions for processing ions with maximum flexibility. Design aspects of the segmented linear ion trap, termed the Omnitrap platform, are highlighted, and motion of ions trapped by rectangular waveforms is investigated experimentally by mapping the stability diagram, tracing secular frequencies, and exploring different isolation techniques. All fragmentation methods incorporated in the Omnitrap platform involving radical chemistry are shown to provide complete sequence coverage for partially unfolded ubiquitin. Three-stage (MS3) tandem mass spectrometry experiments combining collision-induced dissociation of radical ions produced by electron meta-ionization and further involving two intermediate steps of ion isolation and accumulation are performed with high efficiency, producing information rich spectra with signal-to-noise levels comparable to those obtained in a two-stage (MS2) experiment. The advanced capabilities of the Omnitrap platform to provide in-depth top-down MSn characterization of proteins are portrayed. Performance is further enhanced by connecting the Omnitrap platform to an Orbitrap mass analyzer, while successful integration with time-of-flight analyzers has already been demonstrated.

The TopSpec system: new levels in antibody characterisation by top-down mass spectrometry

“…At the core of the TopSpec project is the Omnitrap platform, developed and built by Fasmatech and available for Thermo Scientific™, Q-Exactive™ and Exploris™ 480 instruments (Papanastasiou et al, 2022). The Omnitrap device adds a plethora of ion activation and fragmentation techniques to the system, vastly expanding its capabilities in probing intact antibody ions for enhanced amino acid sequence and modification information.…”

Next-generation precision antibody profiling; from science fiction to reality

“…The biggest problem in top-down MS/MS: sequencing of large proteins is addressed by implementing novel gas-phase radical reactions in the ground-breaking MS/MS device, the Omnitrap™ (Papanastasiou et al, 2022). An ion mobility (IM) device is attached to it, providing hardware deconvolution of overlapping isotopic clusters that present a daunting problem for deconvolution algorithms.…”

De novo glycan sequencing by electronic excitation dissociation MS2-guided MS3 analysis on an Omnitrap-Orbitrap hybrid instrument

“…49 In this study, we took advantage of a new ExD cell design on a prototype Omnitrap instrument. 50 Fig. 1a shows the schematic of an Omnitrap platform, consisting of a system of linear ion trap segments, connected to the rear of the HCD cell of a QE-HF Orbitrap instrument via a transfer hexapole.…”