Simulation of Ion Motion in FAIMS through Combined Use of SIMION and Modified SDS

A key application of field asymmetric waveform ion mobility spectrometry (FAIMS) has been in selectively transmitting trace analyte ions that are present in a complex ion mixture to a mass spectrometer (MS) for identification and quantification. The overall sensitivity of FAIMS-MS, however, still needs to be significantly improved through the optimization of ion transmission into FAIMS and at the FAIMS-MS interface. Processes that cause ion losses include diffusion, space charge, separation field in the FAIMS and fringe fields around the edges of the FAIMS electrodes. These were studied here by first developing an algorithm using SIMION as its core structure to compute ion trajectory at different ratios of electric field to buffer gas number density (E/N). The E/N was varied from a few Td to ∼80 Td by using an asymmetric square waveform. The algorithm was then combined with statistical diffusion simulation (SDS) model, columbic repulsion, and a parabolic gas flow profile to realistically simulate current transmission and peak shape. The algorithm was validated using a FAIMS model identical to the Sionex Corporation SVAC model. Ions modeled included low mass ions with Ko in the range of 2.17 (m = 55) to 1.39 cm2·V−1·s−1 (m = 368). Good agreement was achieved between simulated and experimental CV (peak maxima) values, peak width (fwhm), and transmitted ion current Ioutput. The model was then used to study fringe fields in a simple arrangement where a 0.5 mm (w) gap was created between the FAIMS exit and a capillary inlet (i.d. = 0.5 mm). At an optimum CV (11.8 V), only ∼17% (1.3 pA) of the total ion current that correlate to CV = 11.8 V, entered the capillary; bulk of the ion loss was caused by the fringe fields. Current transmission into the capillary was improved, however, by applying a 500 V DC bias across w (0.5 mm)

Simulation of Ion Motion in FAIMS through Combined Use of SIMION and Modified SDS

A key application of field asymmetric waveform ion mobility spectrometry (FAIMS) has been in selectively transmitting trace analyte ions that are present in a complex ion mixture to a mass spectrometer (MS) for identification and quantification. The overall sensitivity of FAIMS-MS, however, still needs to be significantly improved through the optimization of ion transmission into FAIMS and at the FAIMS-MS interface. Processes that cause ion losses include diffusion, space charge, separation field in the FAIMS and fringe fields around the edges of the FAIMS electrodes. These were studied here by first developing an algorithm using SIMION as its core structure to compute ion trajectory at different ratios of electric field to buffer gas number density (E/N). The E/N was varied from a few Td to ∼80 Td by using an asymmetric square waveform. The algorithm was then combined with statistical diffusion simulation (SDS) model, columbic repulsion, and a parabolic gas flow profile to realistically simulate current transmission and peak shape. The algorithm was validated using a FAIMS model identical to the Sionex Corporation SVAC model. Ions modeled included low mass ions with Ko in the range of 2.17 (m = 55) to 1.39 cm2·V−1·s−1 (m = 368). Good agreement was achieved between simulated and experimental CV (peak maxima) values, peak width (fwhm), and transmitted ion current Ioutput. The model was then used to study fringe fields in a simple arrangement where a 0.5 mm (w) gap was created between the FAIMS exit and a capillary inlet (i.d. = 0.5 mm). At an optimum CV (11.8 V), only ∼17% (1.3 pA) of the total ion current that correlate to CV = 11.8 V, entered the capillary; bulk of the ion loss was caused by the fringe fields. Current transmission into the capillary was improved, however, by applying a 500 V DC bias across w (0.5 mm)

Characterization of an Omnitrap-Orbitrap Platform Equipped with Infrared Multiphoton Dissociation, Ultraviolet Photodissociation, and Electron Capture Dissociation for the Analysis of Peptides and Proteins

We describe an instrument configuration based on the Orbitrap Exploris 480 mass spectrometer that has been coupled to an Omnitrap platform. The Omnitrap possesses three distinct ion-activation regions that can be used to perform resonant-based collision-induced dissociation, several forms of electron-associated fragmentation, and ultraviolet photodissociation. Each section can also be combined with infrared multiphoton dissociation. In this work, we demonstrate all these modes of operation in a range of peptides and proteins. The results show that this instrument configuration produces similar data to previous implementations of each activation technique and at similar efficiency levels. We demonstrate that this unique instrument configuration is extremely versatile for the investigation of polypeptides

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

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

An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies

We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry (MS)-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio (m/z)-resolved imaging for the comprehensive study of the higher-order molecular structure of macromolecular assemblies (MMAs). A bespoke TOF analyzer has been coupled to the higher-energy collisional dissociation cell of an ultrahigh mass range hybrid quadrupole-Orbitrap MS. A 193 nm excimer laser was employed to photofragment MMA ions. A combination of microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphor screen-TPX3CAM assemblies have been used as axial and orthogonal imaging detectors, respectively. The instrument can operate in four different modes, where the UVPD-generated fragment ions from the native MMA ions can be measured with high-mass resolution or imaged in a mass-resolved manner to reveal the relative positions of the UVPD fragments postdissociation. This information is intended to be utilized for retrieving higher-order molecular structural details that include the conformation, subunit stoichiometry, and molecular interactions as well as to understand the dissociation dynamics of the MMAs in the gas phase

An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies

We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry (MS)-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio (m/z)-resolved imaging for the comprehensive study of the higher-order molecular structure of macromolecular assemblies (MMAs). A bespoke TOF analyzer has been coupled to the higher-energy collisional dissociation cell of an ultrahigh mass range hybrid quadrupole-Orbitrap MS. A 193 nm excimer laser was employed to photofragment MMA ions. A combination of microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphor screen-TPX3CAM assemblies have been used as axial and orthogonal imaging detectors, respectively. The instrument can operate in four different modes, where the UVPD-generated fragment ions from the native MMA ions can be measured with high-mass resolution or imaged in a mass-resolved manner to reveal the relative positions of the UVPD fragments postdissociation. This information is intended to be utilized for retrieving higher-order molecular structural details that include the conformation, subunit stoichiometry, and molecular interactions as well as to understand the dissociation dynamics of the MMAs in the gas phase