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

Phase Modulation to Increase Ion Throughput for Ion Mobility-Time-of-Flight Experiments

Implementing a phase-based gating scheme with structures for lossless ion manipulation and a time-of-flight mass analyzer significantly enhances analytical efficiency. Phased ion mobility spectrometry substantially reduces the experimental analysis duration compared to single injection, signal-averaged structures for lossless ion manipulation (SLIM), without compromising separative capabilities. Notably, the observed duty cycle in phased ion mobility spectrometry increases 10x compared to signal-averaged SLIM experiments. A 6-m SLIM system, integrated with a time-of-flight mass analyzer, demonstrates equivalent separative capabilities and resolving power in both signal-averaged and phased-ion mobility modes. However, substantial duty cycle and ion efficiency improvements are evident during phased ion mobility spectrometry. The determination of the numerical integer required for accurate arrival times can be achieved algebraically or directly derived from measured arrival times in signal-averaged experiments. This methodology seamlessly integrates into existing single-gated SLIM or drift tube ion mobility-mass spectrometry instrumentation with minimal experimental adjustments, directly enhancing the observed duty cycle and reducing experimental analysis times.

Efficient Coupling of Structures for Lossless Ion Manipulations with Ion Trap Mass Analyzers Using Phase Modulation

Phased structures for lossless ion manipulation offer significant improvements over the scanning second gate method for coupling with ion trap mass analyzers. With an experimental run time of under 1 min for select conditions and an average run time of less than 4 min, this approach significantly reduces experimental time while enhancing the temporal duty cycle. The outlined SLIM system connects to an ion trap mass analyzer via a PCB stacked ring ion guide, which replaces the commercial ion optics and capillary inlet. By applying a discrete and repeating injection pulse and solving a series of algebraic equations, the system reconstructs an arrival time distribution with a minimal degree of error with enhanced ion throughput. To demonstrate the feasibility of this approach, the 3.4-m SLIM system resolves gas-phase conformers for various small peptides and proteins. This system and methodology also enable direct implementation between SLIM and ion trap mass analyzers traditionally interfaced with front separation systems such as liquid chromatography.

Coupling Online Size Exclusion Chromatography with Charge Detection-Mass Spectrometry Using Hadamard Transform Multiplexing

Charge detection mass spectrometry (CD-MS) is a powerful technique for the analysis of large, heterogeneous biomolecules. By directly measuring the charge states of individual ions, CD-MS can measure the masses from spectra where conventional deconvolution approaches fail due to the lack of isotopic resolution or distinguishable charge states. However, CD-MS is inherently slow because hundreds or thousands of spectra need to be collected to produce adequate ion statistics. The slower speed of CD-MS complicates efforts to couple it with online separation techniques, which limit the number of spectra that can be acquired during a chromatographic peak. Here, we present the application of Hadamard transform multiplexing to online size exclusion chromatography (SEC) coupled with Orbitrap CD-MS, with a goal of using SEC for separating complex mixtures prior to CD-MS analysis. We developed a microcontroller to deliver pulsed injections from a large sample loop onto a SEC for online CD-MS analysis. Data showed a series of peaks spaced according to the pseudorandom injection sequence, which were demultiplexed with a Hadamard transform algorithm. The demultiplexed data revealed improved CD-MS signals while preserving retention time information. This multiplexing approach provides a general solution to the inherent incompatibilities of online separations and CD-MS detection that will enable a range of applications.

UniChromCD for Demultiplexing Time-Resolved Charge Detection-Mass Spectrometry Data

Charge detection mass spectrometry (CD-MS) enables characterization of large, heterogeneous analytes through the analysis of individual ion signals. Because hundreds to thousands of scans must be acquired to produce adequate ion statistics, CD-MS generally requires long analysis times. The slow acquisition speed of CD-MS complicates efforts to couple it with time-dispersive techniques, such as chromatography and ion mobility, because it is not always possible to acquire enough scans from a single sample injection to generate sufficient ion statistics. Multiplexing methods based on Hadamard and Fourier transforms offer an attractive solution to this problem by improving the duty cycle of the separation while preserving retention/drift time information. However, integrating multiplexing with CD-MS data processing is complex. Here, we present UniChromCD, a new module in the open-source UniDec package that incorporates CD-MS time-domain data processing with demultiplexing tools. Following a detailed description of the algorithm, we demonstrate its capabilities using two multiplexed CD-MS workflows: Hadamard-transform size-exclusion chromatography and Fourier-transform ion mobility. Overall, UniChromCD provides a user-friendly interface for analysis and visualization of time-resolved CD-MS data.

Recent advances in high-resolution traveling wave-based ion mobility separations coupled to mass spectrometry

Recently, ion mobility spectrometry-mass spectrometry (IMS-MS) has become more readily incorporated into various omics-based workflows. These growing applications are due to developments in instrumentation within the last decade that have enabled higher-resolution ion mobility separations. Two such platforms are the cyclic (cIMS) and structures for lossless ion manipulations (SLIM), both of which use traveling wave ion mobility spectrometry (TWIMS). High-resolution separations achieved with these techniques stem from the drastically increased pathlengths, on the order of 10 s of meters to >1 km, in both cIMS-MS and SLIM IMS-MS, respectively. Herein, we highlight recent developments and advances, for the period 2019-2023, in high-resolution traveling wave-based IMS-MS through instrumentation, calibration strategies, hyphenated techniques, and applications. Specifically, we will discuss applications including CCS calculations in multipass IMS-MS separations, coupling of IMS-MS with chromatography, imaging, and cryogenic infrared spectroscopy, and isomeric separations of glycans, lipids, and other small metabolites.

Evaluating Ion Accumulation and Storage in Traveling Wave Based Structures for Lossless Ion Manipulations

Structures for lossless ion manipulations (SLIM) technology has demonstrated high resolving power ion mobility separation and flexibility to integrate complex ion manipulations into a single experimental platform. To enable IMS separations, trapping/accumulating ions inside SLIM (or in-SLIM) prior to injection of a packet for separations provides ease of operation and reduces the need for dedicated ion traps external to SLIM. To fully characterize the ion accumulation process, we have evaluated the effect of TW amplitudes, ion collection times, and storage times on the "in-SLIM" accumulation process. The study utilized a SLIM module comprising 5 distinct tracks, each with a specific ion accumulation configuration. The effect of the TW conditions on the accumulation process was investigated for a 3-peptide mixture: kemptide, angiotensin II, and neurotensin at a TW speed of 106 m/s. The effect of ion accumulation time/collection time and storage time was investigated, in addition to TW amplitude. Overall, the signal of the analyte ions increased when the ion collection time increased from 49 to 163 ms but decreased when the ion collection time increased further to 652 ms due to the space charge effects. Ion losses were observed at high TW amplitudes (e.g., 15 Vp-p and 20 Vp-p). In addition, under space charge conditions (e.g., collection times of 163 and 652 ms), the signal of the analyte ions decreased with an increase in storage times for all TW amplitudes applied to the trapping region. For ion accumulation, the data indicate that gentler TW conditions must be utilized to minimize ion losses and fragments to benefit from the "in-SLIM" accumulation process. Wider SLIM tracks provided better performance than those with narrower tracks.

Implementation of an Open-Source Multiplexing Ion Gate Control for High Kinetic Energy Ion Mobility Spectrometry (HiKE-IMS)

With ion mobility spectrometry increasingly used in mass spectrometry to enhance separation by increasing orthogonality, low ion throughput is a challenge for the drift-tube ion mobility experiment. The High Kinetic Energy Ion Mobility Spectrometer (HiKE-IMS) is no exception and routinely uses duty cycles of less than 0.1%. Multiplexing techniques such as Fourier transform and Hadamard transform represent two of the most common approaches used in the literature to improve ion throughput for the IMS experiment; these techniques promise increased duty cycles of up to 50% and an increased signal-to-noise ratio (SNR). With no instrument modifications required, we present the implementation of Hadamard Transform on the HiKE-IMS using a low cost, high-speed (600 MHz), open source microcontroller, a Teensy 4.1. Compared to signal average mode, 7- to 10-bit pseudorandom binary sequences resulted in increased analyte signal by over a factor of 3. However, the maximum SNR gain of 10 did not approach the theoretical 2n-1 gain largely due to capacitive coupling of the ion gate modulation with the Faraday plate used as a detector. Even when utilizing an inverse Hadamard technique, capacitive coupling was not completely eliminated. Regardless, the benefits of multiplexing IMS coupled to mass spectrometers are well documented throughout literature, and this first effort serves as a proof of concept for multiplexing HiKE-IMS. Finally, the highly flexible Teensy used in this effort can be used to multiplex other devices or can be used for Fourier transform instead of Hadamard transform.

Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section

The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.

Almost perfect sequence modulated multiplexing ion mobility spectrometry

RATIONALE

Multiplexing ion mobility spectrometry with multiple ion injection pulses was used to achieve a high duty cycle and thus improve the signal-to-noise (S/N) ratio while maintaining high resolving power compared with the traditional single-pulse signal averaging method. Historically, an ion mobility spectrum was reconstructed by various multiplexing methods including Fourier transform ion mobility spectrometry (FT-IMS), Hadamard transform ion mobility spectrometry (HT-IMS), and linear frequency modulation correlation ion mobility spectrometry (LFM-CIMS) sequence or Barker code.

METHODS

To achieve an artifact-free multiplexing ion mobility spectrum, an almost perfect sequence (APS) with correlation technique was proposed to modulate the Bradbury-Nielson ion gate and was compared with FT-IMS, HT-IMS, LFM-IMS, and the traditional single-pulse signal averaging method.

RESULTS

Experimental results showed that there are no artifact peaks in the APS-IMS spectra except an inverted mirror peak, and the S/N ratio was improved 5-8 times with a repetition time of 40-60 ms, corresponding to the improvement in the duty cycle. With the same duty cycle and similar acquisition time, APS-IMS showed a higher S/N ratio than HT-IMS for its unique autocorrelation response.

CONCLUSIONS

The APS-IMS technique offered a higher duty cycle and relatively shorter modulation period compared with reported multiplexing methods and is suitable to track rapidly changing signals without losing information and adding extra transformation artifact peaks.

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.

High-Throughput Multiplexed Infrared Spectroscopy of Ion Mobility-Separated Species Using Hadamard Transform

Coupling vibrational ion spectroscopy with high-resolution ion mobility separation offers a promising approach for detailed analysis of biomolecules in the gas phase. Improvements in the ion mobility technology have made it possible to separate isomers with minor structural differences, and their interrogation with a tunable infrared laser provides vibrational fingerprints for unambiguous database-enabled identification. Nevertheless, wide analytical application of this technique requires high-throughput approaches for acquisition of vibrational spectra of all species present in complex mixtures. In this work, we present a novel multiplexed approach and demonstrate its utility for cryogenic ion spectroscopy of peptides and glycans in mixtures. Since the method is based on Hadamard transform multiplexing, it yields infrared spectra with an increased signal-to-noise ratio compared to a conventional signal averaging approach.

High-Resolution Ion-Mobility-Enabled Peptide Mapping for High-Throughput Critical Quality Attribute Monitoring

Characterization and monitoring of post-translational modifications (PTMs) by peptide mapping is a ubiquitous assay in biopharmaceutical characterization. Often, this assay is coupled to reversed-phase liquid chromatographic (LC) separations that require long gradients to identify all components of the protein digest and resolve critical modifications for relative quantitation. Incorporating ion mobility (IM) as an orthogonal separation that relies on peptide structure can supplement the LC separation by providing an additional differentiation filter to resolve isobaric peptides, potentially reducing ambiguity in identification through mobility-aligned fragmentation and helping to reduce the run time of peptide mapping assays. A next-generation high-resolution ion mobility (HRIM) technique, based on structures for lossless ion manipulations (SLIM) technology with a 13 m ion path, provides peak capacities and higher resolving power that rivals traditional chromatographic separations and, owing to its ability to resolve isobaric peptides that coelute in faster chromatographic methods, allows for up to 3× shorter run times than conventional peptide mapping methods. In this study, the NIST monoclonal antibody IgG1κ (NIST RM 8671, NISTmAb) was characterized by LC-HRIM-MS and LC-HRIM-MS with collision-induced dissociation (HRIM-CID-MS) using a 20 min analytical method. This approach delivered a sequence coverage of 96.5%. LC-HRIM-CID-MS experiments provided additional confidence in sequence determination. HRIM-MS resolved critical oxidations, deamidations, and isomerizations that coelute with their native counterparts in the chromatographic dimension. Finally, quantitative measurements of % modification were made using only the m/z-extracted HRIM arrival time distributions, showing good agreement with the reference liquid-phase separation. This study shows, for the first time, the analytical capability of HRIM using SLIM technology for enhancing peptide mapping workflows relevant to biopharmaceutical characterization.