Increased ion throughput using tristate ion-gate multiplexing

Nonlinear Frequency Modulation for Fourier Transform Ion Mobility Mass Spectrometry Improves Experimental Efficiency

Through optimization of terminal frequencies and effective sampling rates, we have developed nonlinear sawtooth-shaped frequency sweeps for efficient Fourier transform ion mobility mass spectrometry (FT-IM-MS) experiments. This is in contrast to conventional FT-IM-MS experiments where ion gates are modulated according to a linear frequency sweep. Linear frequency sweeps are effective but can be hindered by the amount of useful signal obtained using a single sweep over a large frequency range imposed by ion gating inefficiencies, particularly small ion packets, and gate depletion. These negative factors are direct consequences of the inherently low gate pulse widths of high-frequency ion gating events, placing an upper bound on FT-IM-MS performance. Here, we report alternative ion modulation strategies. Sawtooth frequency sweeps may be constructed for the purpose of either extending high-SNR transients or conducting efficient signal-averaging experiments for low-SNR transients. The data obtained using this approach show high-SNR signals for a set of low-mass tetraalkylammonium salts (<1000 m/z) where resolving powers in excess of 500 are achieved. Data for low-SNR obtained for multimeric protein complexes streptavidin (53 kDa) and GroEL (800 kDa) also reveal large increases in the signal-to-noise ratio for reconstructed arrival time distributions.

Ultra-Fast Ion Mobility Spectrometer for High-Throughput Chromatography

Fast chromatography systems especially developed for high sample throughput applications require sensitive detectors with a high repetition rate. These high throughput techniques, including various chip-based microfluidic designs, often benefit from detectors providing subsequent separation in another dimension, such as mass spectrometry or ion mobility spectrometry (IMS), giving additional information about the analytes or monitoring reaction kinetics. However, subsequent separation is required at a high repetition rate. Here, we therefore present an ultra-fast drift tube IMS operating at ambient pressure. Short drift times while maintaining high resolving power are reached by several key instrumental design features: short length of the drift tube, resistor network of the drift tube, tristate ion shutter, and improved data acquisition electronics. With these design improvements, even slow ions with a reduced mobility of just 0.94 cm2/(V s) have a drift time below 1.6 ms. Such short drift times allow for a significantly increased repetition rate of 600 Hz compared with previously reported values. To further reduce drift times and thus increase the repetition rate, helium can be used as the drift gas, which allows repetition rates of up to 2 kHz. Finally, these significant improvements enable IMS to be used as a detector following ultra-fast separation including chip-based chromatographic systems or droplet microfluidic applications requiring high repetition rates.

An economical setup for atmospheric pressure chemical ionization drift tube ion-mobility mass spectrometry

Ion-mobility (IM) separations-performed in conjunction with mass spectrometry (MS)-increase selectivity of MS analyses. However, IM-MS instruments are costly, and many laboratories are only equipped with standard MS instruments without an IM separation stage. Therefore, it is appealing to upgrade the existing mass spectrometers with low-cost IM separation devices. Such devices can be constructed using widely available materials such as printed-circuit boards (PCBs). We demonstrate coupling of an economical PCB-based IM spectrometer (disclosed previously) with a commercial triple quadrupole (QQQ) mass spectrometer. The presented PCB-IM-QQQ-MS system incorporates an atmospheric pressure chemical ionization (APCI) source, drift tube comprising desolvation and drift regions, ion gates, and transfer line to the mass spectrometer. The ion gating is accomplished with the aid of two floated pulsers. The separated ions are divided into packets, which are sequentially introduced to the mass spectrometer. Volatile organic compounds (VOCs) are transferred with the aid of nitrogen gas flow from the sample chamber to the APCI source. The operation of the system has been demonstrated using standard compounds. The limits of detection for 2,4-lutidine, (-)-nicotine, and pyridine are 2.02 × 10^-7 M, 1.54 × 10^-9 mol, and 4.79 × 10^-10 mol, respectively. The system was also used to monitor VOCs emitted from the porcine skin after exposure to nicotine patches, and VOCs released from meat undergoing the spoilage process. We believe this simple APCI-PCB-IM-QQQ-MS platform can be reproduced by others to augment the capabilities of the existing MS instrumentation.

Regarding the Influence of Additives and Additional Plasma-Induced Chemical Ionization on Adduct Formation in ESI/IMS/MS

Ion mobility spectrometers (IMS) separate ions based on their ion mobility, which depends mainly on collision cross-section, mass, and charge of the ions. However, the performance is often hampered in electrospray ionization (ESI) by the appearance of multiple ion mobility peaks in the spectrum for the same analyte due to clustering and additional sodium adducts. In this work, we investigate the influence of solvents and buffer additives on the detected ion mobility peaks using ESI. Additionally, we investigate the effects of an additional chemical ionization (CI) induced by plasma ionization on the ions formed by electrospray. For this purpose, we coupled our high-resolution IMS with a resolving power of R_p = 100 to a time-of-flight mass spectrometer. Depending on the analyte and the chosen additives, the ionization process can be influenced during the electrospray process. For the herbicide isoproturon, the addition of 5 mM sodium acetate results in the formation of the sodium adduct [M + Na]⁺, which is reflected in the ion mobility K₀ of 1.22 cm²/(V·s). In contrast, the addition of 5 mM ammonium acetate yields the protonated species [M + H]⁺ and a correspondingly higher K₀ of 1.29 cm²/(V·s). In some cases, as with the herbicide pyrimethanil, the addition of sodium acetate can completely suppress ionizations. By carefully choosing the solvent additive for ESI-IMS or additional CI, the formation of different ion mobility peaks can be observed. This can facilitate the assignment of ions to ion mobility peaks using IMS as a compact, stand-alone instrument, e.g., for on-site analysis.

A Comparison of the Performance of Modular Standalone Do-It-Yourself Ion Mobility Spectrometry Systems

As the spectrum of ion mobility spectrometry (IMS) applications expands and more experimental configurations are developed, identifying the correct platform for an experimental campaign becomes more challenging for researchers. Additionally, metrics that compare performance (Rp, for example) often have nuanced differences in definition between platforms that render direct comparisons difficult. Here we present a comparison of three do-it-yourself (DIY) drift tubes that are relatively low cost and easy to construct, where the performance of each is evaluated based on three different metrics: resolving power, the ideality of resolving powers, and accuracy/precision of K0 values. The standard PCBIMS design developed by Reinecke and Clowers (Reinecke, T.; Clowers, B. H. HardwareX 2018, 4, e00030) provided the highest resolving power (>90) and the highest ideality of resolving power ratios (>90% at best) of the three systems. However, the flexible tube (FlexIMS) construction as described by Smith et al. (Smith, B. L. Anal. Chem. 2020, 92 (13), 9104-9112) exhibited the highest degree of precision of K0 values (relative standard deviation of <0.42%). Depending on the application, the drift tube variants presented and evaluated here offer a low-cost alternative to commercial drift-tube systems with levels of performance that approach theoretical maxima.

Ion-neutral clustering alters gas-phase hydrogen-deuterium exchange rates

The rates and mechanisms of chemical reactions that occur at a phase boundary often differ considerably from chemical behavior in bulk solution, but remain difficult to quantify. Ion-neutral interactions are one such class of chemical reactions whose behavior during the nascent stages of solvation differs from bulk solution while occupying critical roles in aerosol formation, atmospheric chemistry, and gas-phase ion separations. Through a gas-phase ion separation technique utilizing a counter-current flow of deuterated vapor, we quantify the degree of hydrogen-deuterium exchange (HDX) and ion-neutral clustering on a series of model chemical systems (i.e. amino acids). By simultaneously quantifying the degree of vapor association and HDX, the effects of cluster formation on reaction kinetics are realized. These results imply that cluster formation cannot be ignored when modeling complex nucleation processes and biopolymer structural dynamics.

Improving Ion Mobility Mass Spectrometry of Proteins through Tristate Gating and Optimization of Multiplexing Parameters

Coupling drift tube ion mobility (IM) to Fourier transform mass spectrometry (FT-MS) affords the opportunity for gas-phase separation of ions based on size and conformation with high-resolution mass analysis. However, combining IM and FT-MS is challenging because ions exit the drift tube on a much faster time scale than the rate of mass analysis. Fourier transform (FT) and Hadamard transform multiplexing methods have been implemented to overcome the duty-cycle mismatch, offering new avenues for obtaining high-resolution, high-mass-accuracy analysis of mobility-selected ions. The gating methods used to integrate the drift tube with the FT mass analyzer discriminate against the transmission of large, low-mobility ions owing to the well-known gate depletion effect. Tristate gating strategies have been shown to increase ion transmission for drift tube IM-FT-MS systems through implementation of dual ion gating, controlling the quantity and timing of ions through the drift tube to reduce losses of slow-moving ions. Here we present an optimized set of multiplexing parameters for tristate gating ion mobility of several proteins on an Orbitrap mass spectrometer and further report parameters for increased ion transmission and mobility resolution as well as decreased experimental times from 15 min down to 30 s. On average, peak intensities in the arrival time distributions (ATDs) for ubiquitin increased 2.1× on average, while those of myoglobin increased by 1.5× with a resolving power increase on average of 11%.

Considerations for Generating Frequency Modulation Waveforms for Fourier Transform-Ion Mobility Experiments

By casting the information regarding an ion population's mobility in the frequency domain, the coupling of time-dispersive ion mobility techniques is now imminently compatible with slower mass analyzers such as ion traps. Recent reports have detailed the continued progress toward maximizing the efficiency of the Fourier transform ion mobility-mass spectrometry (FT-IM-MS) experiments, but few reports have outlined the intersection between the practical considerations of implementation against the theoretical limits imposed by traditional signal processing techniques. One of the important concerns for Fourier-based multiplexing experiments is avoiding signal aliasing as a product of undersampled signals that may occur during data acquisition. In addition to traditional considerations such as detector sampling frequency, the limitations (i.e., maximum measurable drift time) imposed by experimental mass scan duration and the frequency sweep used for ion gate modulation must also be assessed. This work aims to connect the fundamental underpinnings of FT-IM-MS experiments and the associated experimental parameters that are encountered when coupling the comparatively fast separations in the mobility domain with the slower m/z scanning common for ion-trap mass analyzers. In addition to stating the relevant theory that applies to the FT-IM-MS experiment, this report highlights how aliased signals will manifest post Fourier transform in reconstructed arrival time distributions and calculated mobilities.

Characterization of a Modulated X-ray Source for Ion Mobility Spectrometry

As a highly deployed field instrument for the detection of narcotics, explosives, and chemical warfare agents, drift tube ion mobility spectrometry relies heavily upon the performance of the ionization source and mechanism of ion beam modulation. For this instrumental platform, ion chemistry plays a critical role in the performance of the instrument from a sensitivity and selectivity perspective; however, a range of instrumental components also occupy pivotal roles. Most notably, the mechanism of ion modulation or ion gating is a primary contributor to peak width in a drift tube ion mobility experiment. Unfortunately, physical ion gates rarely perform perfectly, and in addition to serving as physical impediments to ion transmission, their modulation also has undesirable field effects. Using a recently developed modulated, non-radioactive X-ray source, we detail the performance of an ion mobility spectrometry (IMS) system that is free of a gating structure and utilizes the pulsed nature of the modulated X-ray source (MXS) for both ion generation and initiation of the IMS experiment. After investigating the influence of pulse duration and spatial X-ray beam width on the analytical performance of the instrument, the possibility of using multiplexing with a shutterless system is explored. By increasing ion throughput, the observed multiplexing gain compared to a signal-averaged spectrum approaches the theoretical maximum and illustrates the capability of the MXS-IMS system to realize significant signal to noise improvements.

Modeling the modulation characteristics of the Bradbury-Nielsen gate in ion mobility spectrometers

The Bradbury-Nelson gate (BNG) is a common device used for ion control in time-of-flight mass spectrometry and ion mobility spectrometry (IMS). A dual-location control model was employed in order to better understand the behavior of ions around a modulated BNG. This model illustrated that the ions are released from the starting location and truncated at the cutoff location. The shapes of the starting and cutoff locations are both curved with similar curvature, and the cutoff location is situated further back. Therefore, the distance between the two locations is a key parameter leading to the ion loss during modulation and is influenced by the gating voltage difference. Through simulations and experiments, the ion loss is verified to increase with the increase in the gating voltage difference. Taking a Fourier transform IMS as an example, by reducing the gating voltage difference from 150 to 50 V, the signal-to-noise ratio of the time domain result was improved from 91.7 to 386.5 and the resolving power was improved from 40.9 to 63.6. In addition, the superposition effect of multicycle modulation is shown and explained by the model. When the modulated frequency is too rapid and the closing time is insufficient for all the ions to be consumed, some ions continue to exist between the two locations, and the residual ions then enter the drift region during the next few cycles. This phenomenon needs to be avoided because the total number of ions entering the drift region will then increase uncontrollably.

Miniaturized Photo-Ionization Fourier Deconvolution Ion Mobility Spectrometer for the Detection of Volatile Organic Compounds

Because of its simplicity, reliability, and sensitivity, the drift tube ion mobility spectrometer (IMS) has been recognized as the equipment of choice for the on-site monitoring and identification of volatile organic compounds (VOCs). However, the performance of handheld IMS is often limited by the size, weight, and drift voltage, which heavily determine the sensitivity and resolving power that is crucial for the detection and identification of VOCs. In this work, we present a low-cost, miniaturized drift tube ion mobility spectrometer incorporated with a miniaturized UV ionization lamp and a relatively low drift voltage. The sensitivity and resolving power are boosted with the implementation of Fourier deconvolution multiplexing compared to the conventional signal averaging data acquisition method. The drift tube provides a high resolving power of up to 52 at a drift length of 41 mm, 10 mm ID dimensions, and a drift voltage of 1.57 kV. Acetone, benzene, dimethyl methyl phosphonate, methyl salicylate, and acetic acid were evaluated in the developed spectrometer and showed satisfactory performance.

Exploring the Conformations and Binding Location of HMGA2·DNA Complexes Using Ion Mobility Spectrometry and 193 nm Ultraviolet Photodissociation Mass Spectrometry

Although it is widely accepted that protein function is largely dependent on its structure, intrinsically disordered proteins (IDPs) lack defined structure but are essential in proper cellular processes. Mammalian high mobility group proteins (HMGA) are one such example of IDPs that perform a number of crucial nuclear activities and have been highly studied due to their involvement in the proliferation of a variety of disease and cancers. Traditional structural characterization methods have had limited success in understanding HMGA proteins and their ability to coordinate to DNA. Ion mobility spectrometry and mass spectrometry provide insights into the diversity and heterogeneity of structures adopted by IDPs and are employed here to interrogate HMGA2 in its unbound states and bound to two DNA hairpins. The broad distribution of collision cross sections observed for the apo-protein are restricted when HMGA2 is bound to DNA, suggesting that increased protein organization is promoted in the holo-form. Ultraviolet photodissociation was utilized to probe the changes in structures for the compact and elongated structures of HMGA2 by analyzing backbone cleavage propensities and solvent accessibility based on charge-site analysis, which revealed a spectrum of conformational possibilities. Namely, preferential binding of the DNA hairpins with the second of three AT-hooks of HMGA2 is suggested based on the suppression of backbone fragmentation and distribution of DNA-containing protein fragments.

Separation and Collision Cross Section Measurements of Protein Complexes Afforded by a Modular Drift Tube Coupled to an Orbitrap Mass Spectrometer

New developments in analytical technologies and biophysical methods have advanced the characterization of increasingly complex biomolecular assemblies using native mass spectrometry (MS). Ion mobility methods, in particular, have enabled a new dimension of structural information and analysis of proteins, allowing separation of conformations and providing size and shape insights based on collision cross sections (CCSs). Based on the concepts of absorption-mode Fourier transform (aFT) multiplexing ion mobility spectrometry (IMS), here, a modular drift tube design proves capable of separating native-like proteins up to 148 kDa with resolution up to 45. Coupled with high-resolution Orbitrap MS, binding of small ligands and cofactors can be resolved in the mass domain and correlated to changes in structural heterogeneity observed in the ion-neutral CCS distributions. We also demonstrate the ability to rapidly determine accurate CCSs for proteins with 1-min aFT-IMS-MS sweeps without the need for calibrants or correction factors.

Effect of Traveling Waveform Profiles on Collision Cross Section Measurements in Structures for Lossless Ion Manipulations

We evaluated the effect of four different waveform profiles (Square, Sine, Triangle, and asymmetric Sawtooth) on the accuracy of collision cross section (CCS) measurements using traveling wave ion mobility spectrometry (TWIMS) separations in structures for lossless ion manipulations (SLIM). The effects of the waveform profiles on the accuracy of the CCS measurements were evaluated for four classes of compounds (lipids, peptides, steroids, and nucleosides) at different TW speeds (126-206 m/s) and amplitudes (15-89 V). For the lipids and peptides, the TWIMS-based CCS (TWCCS) deviations from the corresponding drift-tube-based CCS (DTCCS) measurements were significantly lower in experiments conducted using the Sawtooth waveform compared to the square waveform. This observation can be rationalized by the lower maximum electric field experienced by ions with a Sawtooth waveform, as compared to the other waveforms, resulting in a lower probability for significant ion heating. We also observed that given approximately comparable resolution for all four waveforms, the Sawtooth waveform resulted in lower TWCCS error and a better agreement with DTCCS values than the Square waveform. In addition, for the steroids and nucleosides, an opposite TWCCS trend was observed, with higher errors with the Sawtooth waveform and lower with the Square waveform, suggesting that these molecules tend to become slightly more compact under ion heating conditions. Under optimum conditions, all TWCCS measurements on the SLIM platform were within 0.5% of those measured in the drift tube ion mobility spectrometry.

Accelerating prototyping experiments for traveling wave structures for lossless ion manipulations

Traveling wave structures for lossless ion manipulation (TW-SLIM) has proven a valuable tool for the separation and study of gas-phase ions. Unfortunately, many of the traditional components of TW-SLIM experiments manifest practical and financial barriers to the technique's broad implementation. To this end, a series of technological innovations and methodologies are presented which enable for simplified SLIM experimentation and more rapid TW-SLIM prototyping. In addition to the use of multiple independent board sets that comprise the present SLIM system, we introduce a low-cost, multifunctional traveling wave generator to produce TW within the TW-SLIM. This square-wave producing unit proved effective in realizing TW-SLIM separations compared to traditional approaches. Maintaining a focus on lowering barriers to implementation, the present set of experiments explores the use of on-board injection (OBI) methods, which offer potential alternatives to ion funnel traps. These OBI techniques proved feasible and the ability of this simplified TW-SLIM platform to enhance ion accumulation was established. Further experimentation regarding ion accumulation revealed a complexity to ion accumulation within TW-SLIM that has yet to be expounded upon. Lastly, the ability of the presented TW-SLIM platform to store ions for extended periods (1 s) without significant loss (<10%) was demonstrated. The aforementioned experiments clearly establish the efficacy of a simplified TW-SLIM platform which promises to expand adoption and experimentation of the technique.

Synchronized Stepped Frequency Modulation for Multiplexed Ion Mobility Measurements

Implementation of frequency-encoded multiplexing for ion mobility spectrometry (e.g., Fourier transform ion mobility spectrometry (FT-IMS)) has facilitated the direct coupling of drift tube ion mobility instrumentation with ion-trap mass analyzers despite their duty cycle mismatch. Traditionally, FT-IMS experiments have been carried out to utilize continuous linear frequency sweeps that are independent of the scan rate of the ion-trap mass analyzer, thus creating a situation where multiple frequencies are swept over two sequential mass scans. This in turn creates a degree of ambiguity in which the ion current derived from a single modulation frequency cannot be assigned to a single data point in the frequency-modulated signal. In an effort to eliminate this ambiguity, this work describes a discrete stepwise function to modulate the ion gates of the IMS while synchronization between the generated frequencies and the scan rate of the linear ion trap is achieved. While the number of individual frequencies used in the stepped frequency sweeps is less than in continuous linear modulation experiments, there is no loss in performance and high levels of precision are maintained across differing combinations of terminal frequencies and scan lengths. Furthermore, the frequency-scan synchronization enables further data-processing techniques such as linear averaging of the frequency modulated signal to drastically improve signal-to-noise ratio for both high and low intensity analytes.

Implementing Digital-Waveform Technology for Extended m/z Range Operation on a Native Dual-Quadrupole FT-IM-Orbitrap Mass Spectrometer

Here, we describe a digital-waveform dual-quadrupole mass spectrometer that enhances the performance of our drift tube FT-IMS high-resolution Orbitrap mass spectrometer (MS). The dual-quadrupole analyzer enhances the instrument capabilities for studies of large protein and protein complexes. The first quadrupole (q) provides a means for performing low-energy collisional activation of ions to reduce or eliminate noncovalent adducts, viz., salts, buffers, detergents, and/or endogenous ligands. The second quadrupole (Q) is used to mass-select ions of interest for further interrogation by ion mobility spectrometry and/or collision-induced dissociation (CID). Q is operated using digital-waveform technology (DWT) to improve the mass selection compared to that achieved using traditional sinusoidal waveforms at floated DC potentials (>500 V DC). DWT allows for increased precision of the waveform for a fraction of the cost of conventional RF drivers and with readily programmable operation and precision (Hoffman, N. M. . A comparison-based digital-waveform generator for high-resolution duty cycle. Review of Scientific Instruments 2018, 89, 084101).

Masked Multiplexed Separations to Enhance Duty Cycle for Structures for Lossless Ion Manipulations

The experimental paradigm of one ion packet release per spectrum severely hinders throughput in broadband ion mobility spectrometry (IMS) systems (e.g., drift tube and traveling wave systems). Ion trapping marginally mitigates this problem, but the duty cycle deficit is amplified when moving to high resolution, long pathlength systems. As a consequence, new multiplexing strategies that maximize throughput while preserving peak fidelity are essential for high-resolution IMS separations [e.g., structures for lossless ion manipulations (SLIMs) and multi-pass technologies]. Currently, broadly applicable deconvolution strategies for Hadamard-based ion multiplexing are limited to a narrow range of modulation sequences and do not fully maximize the ion signal generated during separation across an extended path length. Compared to prior Hadamard deconvolution errors that rely upon peak picking or discrete error classification, the masked deconvolution matrix technique exploits the knowledge that Hadamard transform artifacts are reflected about the central, primary signal [i.e., the true arrival time distribution (ATD)]. By randomly inducing mathematical artifacts, it is possible to identify spectral artifacts simply by their high degree of variability relative to the core ATD. It is important to note that the deweighting approach using the masked deconvolution matrix does not make any assumptions about the underlying transform and is applicable to any multiplexing strategy employing binary sequences. In addition to demonstrating a 100-fold increase in the total number of ions detected, the effective deconvolution of data from 5, 6, 7, and 8-bit pseudo-random sequences expands the utility and efficiency of the SLIM platform.

Perturbation-induced high-frequency pulsing of nano-ESI with facile ion selection at atmospheric pressure

Nano-ESI is a commonly used ionization technique with continually expanding analytical advantages. Here, we report a facile way for high-frequency (500-3800 Hz) pulsing of nano-ESI, providing a high flux of mobility-selected ions. The pulsing is accomplished using a relatively low-voltage modulation (80 V peak-to-peak) of an electrode placed <1 cm downstream of a nano-ESI emitter biased to a constant potential. Configuring the electrode as an ion gate enables mobility-based ion selection by scanning the modulation frequency. Our investigations indicate that the electrode modulation perturbs continuous nano-ESI, resulting in solution accumulation at the emitter tip between spray pulses. Selective transmission of ions occurs at frequencies corresponding to harmonics of a fundamental frequency determined by the travel time of each ion from the emitter to the ion gate (pulsing electrode). Remarkably, the intensities of ions selected in this fashion are similar across the harmonics, suggesting that the ionization efficiencies of analytes have minimal dependence on the accumulated volume at the emitter tip. Moreover, intensities of ion-mobility-selected analytes using this technique reach >50% of those in continuous nano-ESI without ion selection, underscoring efficient ion generation via high-frequency pulsing. These findings indicate the potential of the pulsed nano-ESI for enhanced analytical utility, such as a high-flux selected-reagent-ion supplier at atmospheric pressure, and chart new avenues to further enhance the analytical performance of nano-ESI.