Uncertainty Estimations for Collision Cross Section Determination via Uniform Field Drift Tube-Ion Mobility-Mass Spectrometry

CCSfind: A tool for chemically informed LC-IM-MS database building

In addition to providing critical knowledge of the accurate mass of ions, ion mobility-mass spectrometry (IM-MS) delivers complementary data relating to the conformation and size of ions in the form of an ion mobility spectrum and derived parameters, namely, the ion's mobility (K) and the IM-derived collision cross section (CCS). However, the maximum amount of information obtained in IM-MS measurements is not currently transferred into analytical databases including the full mobility spectra (CCS distributions) as well as capturing of additional ion species (e.g., adducts) into the same compound entry. We introduce CCSfind, a new tool for building comprehensive databases from experimental IM-MS measurements of small molecules. CCSfind allows predicted ion species to be chosen for input chemical formulae, which are then targeted by CCSfind after parsing open source mzML input files to provide a unified set of results within a single data processing step. CCSfind can handle both chromatographically separated isomers and IM separation of isomeric ions (e.g., "protomers" or conformers of the same ion species) with simple user control over the output for new database entries in SQL format. Files of up to 1 GB can be processed in less than 2 min on a desktop computer with 32 GB RAM with computational time scaling linearly with the size of the input mzML file or the number of input molecular formulae. Results are manually reviewed, annotated with experimental settings, before committing the database where the full dataset can be retrieved.

MobiLipid: A Tool for Enhancing CCS Quality Control of Ion Mobility-Mass Spectrometry Lipidomics by Internal Standardization

Ion mobility-mass spectrometry (IM-MS) offers benefits for lipidomics by obtaining IM-derived collision cross sections (CCS), a conditional property of an ion that can enhance lipid identification. While drift tube (DT) IM-MS retains a direct link to the primary experimental method to derive CCS values, other IM technologies rely solely on external CCS calibration, posing challenges due to dissimilar chemical properties between lipids and calibrants. To address this, we introduce MobiLipid, a novel tool facilitating the CCS quality control of IM-MS lipidomics workflows by internal standardization. MobiLipid utilizes a newly established DTCCSN2 library for uniformly (U)13C-labeled lipids, derived from a U13C-labeled yeast extract, containing 377 DTCCSN2 values. This automated open-source R Markdown tool enables internal monitoring and straightforward compensation for CCSN2 biases. It supports lipid class- and adduct-specific CCS corrections, requiring only three U13C-labeled lipids per lipid class-adduct combination across 10 lipid classes without requiring additional external measurements. The applicability of MobiLipid is demonstrated for trapped IM (TIM)-MS measurements of an unlabeled yeast extract spiked with U13C-labeled lipids. Monitoring the CCSN2 biases of TIMCCSN2 values compared to DTCCSN2 library entries utilizing MobiLipid resulted in mean absolute biases of 0.78% and 0.33% in positive and negative ionization mode, respectively. By applying the CCS correction integrated into the tool for the exemplary data set, the mean absolute CCSN2 biases of 10 lipid classes could be reduced to approximately 0%.

Development of a Modular, Open-Source, Reduced-Pressure, Drift Tube Ion Mobility Spectrometer

Toward the goal of minimizing construction costs while maintaining high performance, a new, reduced-pressure, drift tube ion mobility system is coupled with an ion trap mass analyzer through a custom ion shuttle. The availability of reduced-pressure ion mobility systems remains limited due to comparatively expensive commercial options and limited shared design features in the open literature. This report details the complete design and benchmarking characteristics of a reduced-pressure ion mobility system. The system is constructed from FR4 PCB electrodes and encased in a PTFE vacuum enclosure with custom torque-tightened couplers to utilize standard KF40 bulkheads. The PTFE enclosure directly minimizes the overall system expenses, and the implementation of threaded brass inserts allows for facile attachments to the vacuum enclosure without damaging the thermoplastic housing. Front and rear ion funnels maximize ion transmission and help mitigate the effects of radial ion diffusion. A custom planar ion shuttle transports ions from the exit of the rear ion funnel into the ion optics of an ion trap mass analyzer. The planar ion shuttle can couple the IM system to any contemporary Thermo Scientific ion trap mass analyzer. Signal stability and ion intensity remain unchanging following the implementation of the planar ion shuttle when compared to the original stacked ring ion guide. The constructed IM system showed resolving powers up to 85 for various small molecules and proteins using the Fourier transform from a ∼1 m drift tube. Recorded mobilities derived from first principles agree with published literature results with an average error of 1.1% and an average error toward literature values using single field calibration of <1.3%.

Solvent Composition Can Have a Measurable Influence on the Ion Mobility-Derived Collision Cross Section of Small Molecules

Ion mobility (IM) is an important analytical technique for increasing identification coverage of metabolites in untargeted studies, especially when integrated into traditional liquid chromatography-mass spectrometry workflows. While there has been extensive work surrounding best practices to obtain and standardize collision cross section (CCS) measurements necessary for comparing across different IM techniques and laboratories, there has been little investigation into experimental factors beyond the mobility separation region that could potentially influence CCS measurements. The first-principles derived CCS of 15 chemical standards were evaluated across 27 aqueous:organic solvent compositions using a high-precision drift tube instrument. A small but measurable dependency of the CCS on the solvent composition was observed, with the larger analytes from this study (m/z > 400) exhibiting a characteristic increase in CCS at the intermediate (40-60%) solvent compositions. Parallels to the behavior of solvent viscosity and protonation site tautomers (protomers) were noted, although the origin of these solvent-dependent CCS trends is as yet unclear. Taken together, these findings document a solvent dependency on CCS, which, while minor (<0.5%), identifies an important need for reporting the solvent system when utilizing CCS in comparative ion mobility studies.

Surveying the mugineic acid family: Ion mobility - quadrupole time-of-flight mass spectrometry (IM-QTOFMS) characterization and tandem mass spectrometry (LC-ESI-MS/MS) quantification of all eight naturally occurring phytosiderophores

Phytosiderophores (PS) are root exudates released by grass species (Poaceae) that play a pivotal role in iron (Fe) plant nutrition. A direct determination of PS in biological samples is of paramount importance in understanding micronutrient acquisition mediated by PS. To date, eight plant-born PS have been identified; however, no analytical procedure is currently available to quantify all eight PS simultaneously with high analytical confidence. With access to the full set of PS standards for the first time, we report comprehensive methods to both fully characterize (IM-QTOFMS) and quantify (LC-ESI-MS/MS) all eight naturally occurring PS belonging to the mugineic acid family. The quantitative method was fully validated, yielding linear results for all eight analytes, and no unwanted interferences with soil and plant matrices were observed. LOD and LOQ values determined for each PS were below 11 and 35 nmol L-1, respectively. The method's precision under reproducibility conditions (intra- and inter-day) of measurement was less than 2.5% RSD for all analytes. Additionally, all PS were annotated with high-resolution mass spectrometric fragment spectra and further characterized via drift tube ion mobility-mass spectrometry. The collision cross-sections obtained for primary ion species yielded a valuable database for future research focused on in-depth PS studies. The new quantitative method was applied to analyse root exudates from Fe-controlled and deficient barley, oat, rye, and sorghum plants. All eight PS, including mugineic acid (MA), 3"-hydroxymugineic acid (HMA), 3"-epi-hydroxymugineic acid (epi-HMA), hydroxyavenic acid (HAVA), deoxymugineic acid (DMA), 3"-hydroxydeoxymugineic acid (HDMA), 3"-epi-hydroxydeoxymugineic acid (epi-HDMA) and avenic acid (AVA) were for the first time successfully identified and quantified in root exudates of various graminaceous plants using a single analytical procedure. These newly developed methods can be applied to studies aimed at improving crop yield and micronutrient grain content for food consumption via plant-based biofortification.

New Approach for the Identification of Isobaric and Isomeric Metabolites

The structural elucidation of metabolite molecules is important in many branches of the life sciences. However, the isomeric and isobaric complexity of metabolites makes their identification extremely challenging, and analytical standards are often required to confirm the presence of a particular compound in a sample. We present here an approach to overcome these challenges using high-resolution ion mobility spectrometry in combination with cryogenic vibrational spectroscopy for the rapid separation and identification of metabolite isomers and isobars. Ion mobility can separate isomeric metabolites in tens of milliseconds, and cryogenic IR spectroscopy provides highly structured IR fingerprints for unambiguous molecular identification. Moreover, our approach allows one to identify metabolite isomers automatically by comparing their IR fingerprints with those previously recorded in a database, obviating the need for a recurrent introduction of analytical standards. We demonstrate the principle of this approach by constructing a database composed of IR fingerprints of eight isomeric/isobaric metabolites and use it for the identification of these isomers present in mixtures. Moreover, we show how our fast IR fingerprinting technology allows to probe the IR fingerprints of molecules within just a few seconds as they elute from an LC column. This approach has the potential to greatly improve metabolomics workflows in terms of accuracy, speed, and cost.

Integrating ion mobility into comprehensive multidimensional metabolomics workflows: critical considerations

BACKGROUND

Ion mobility (IM) separation capabilities are now widely available to researchers through several commercial vendors and are now being adopted into many metabolomics workflows. The added peak capacity that ion mobility offers with minimal compromise to other analytical figures-of-merit has provided real benefits to sensitivity and structural selectivity and have allowed more specific metabolite annotations to be assigned in untargeted workflows. One of the greatest promises of contemporary IM-enabled instrumentation is the capability of operating multiple analytical dimensions inline with minimal sample volumes, which has the potential to address many grand challenges currently faced in the omics fields. However, comprehensive operation of multidimensional mass spectrometry comes with its own inherent challenges that, beyond operational complexity, may not be immediately obvious to practitioners of these techniques.

AIM OF REVIEW

In this review, we outline the strengths and considerations for incorporating IM analysis in metabolomics workflows and provide a critical but forward-looking perspective on the contemporary challenges and prospects associated with interpreting IM data into chemical knowledge.

KEY SCIENTIFIC CONCEPTS OF REVIEW

We outline a strategy for unifying IM-derived collision cross section (CCS) measurements obtained from different IM techniques and discuss the emerging field of high resolution ion mobility (HRIM) that is poised to address many of the contemporary challenges associated with ion mobility metabolomics. Whereas the LC step limits the throughput of comprehensive LC-IM-MS, the higher peak capacity of HRIM can allow fast LC gradients or rapid sample cleanup via solid-phase extraction (SPE) to be utilized, significantly improving the sample throughput.

Revealing the differences in collision cross section values of small organic molecules acquired by different instrumental designs and prediction models

The number of open access databases containing experimental and predicted collision cross section (CCS) values is rising and leads to their increased use for compound identification. However, the reproducibility of reference values with different instrumental designs and the comparison between predicted and experimental CCS values is still under evaluation. This study compared experimental CCS values of 56 small molecules (Contaminants of Emerging Concern) acquired by both drift tube (DT) and travelling wave (TW) ion mobility mass spectrometry (IM-MS). The TWIM-MS included two instrumental designs (Synapt G2 and VION). The experimental ^TWCCS_N2 values obtained by the TWIM-MS systems showed absolute percent errors (APEs) < 2% in comparison to experimental DTIMS data, indicating a good correlation between the datasets. Furthermore, ^TWCCS_N2 values of [M - H]^- ions presented the lowest APEs. An influence of the compound class on APEs was observed. The applicability of prediction models based on artificial neural networks (ANN) and multivariate adaptive regression splines (MARS), both built using TWIM-MS data, was investigated for the first time for the prediction of ^DTCCS_N2 values. For [M+H]⁺ and [M - H]^- ions, the 95th percentile confidence intervals of observed APEs were comparable to values reported for both models indicating a good applicability for DTIMS predictions. For the prediction of ^DTCCS_N2 values of [M+Na]⁺ ions, the MARS based model provided the best results with 73.9% of the ions showing APEs below the threshold reported for [M+Na]⁺. Finally, recommendations for database transfer and applications of prediction models for future DTIMS studies are made.

Comparability of Steroid Collision Cross Sections Using Three Different IM-HRMS Technologies: An Interplatform Study

Steroids play key roles in various biological processes and are characterized by many isomeric variants, which makes their unambiguous identification challenging. Ion mobility-mass spectrometry (IM-MS) has been proposed as a suitable platform for this application, particularly using collision cross section (CCS) databases obtained from different commercial IM-MS instruments. CCS is seen as an ideal additional identification parameter for steroids as long-term repeatability and interlaboratory reproducibility of this measurand are excellent and matrix effects are negligible. While excellent results were demonstrated for individual IM-MS technologies, a systematic comparison of CCS derived from all major commercial IM-MS technologies has not been performed. To address this gap, a comprehensive interlaboratory comparison of 142 CCS values derived from drift tube (DTIM-MS), traveling wave (TWIM-MS), and trapped ion mobility (TIM-MS) platforms using a set of 87 steroids was undertaken. Besides delivering three instrument-specific CCS databases, systematic comparisons revealed excellent interlaboratory performance for 95% of the ions with CCS biases within ±1% for TIM-MS and within ±2% for TWIM-MS with respect to DTIM-MS values. However, a small fraction of ions (<1.5%) showed larger biases of up to 7% indicating that differences in the ion conformation sampled on different instrument types need to be further investigated. Systematic differences between CCS derived from different IM-MS analyzers and implications on the applicability for nontargeted analysis are critically discussed. To the best of our knowledge, this is the most comprehensive interlaboratory study comparing CCS from three different IM-MS technologies for analysis of steroids and small molecules in general.

Critical evaluation of the role of external calibration strategies for IM-MS

The major benefits of integrating ion mobility (IM) into LC-MS methods for small molecules are the additional separation dimension and especially the use of IM-derived collision cross sections (CCS) as an additional ion-specific identification parameter. Several large CCS databases are now available, but outliers in experimental interplatform IM-MS comparisons are identified as a critical issue for routine use of CCS databases for identity confirmation. We postulate that different routine external calibration strategies applied for traveling wave (TWIM-MS) in comparison to drift tube (DTIM-MS) and trapped ion mobility (TIM-MS) instruments is a critical factor affecting interplatform comparability. In this study, different external calibration approaches for IM-MS were experimentally evaluated for 87 steroids, for which ^TWCCS_N2, ^DTCCS_N2 and ^TIMCCS_N2 are available. New reference CCS_N2 values for commercially available and class-specific calibrant sets were established using DTIM-MS and the benefit of using consolidated reference values on comparability of CCS_N2 values assessed. Furthermore, use of a new internal correction strategy based on stable isotope labelled (SIL) internal standards was shown to have potential for reducing systematic error in routine methods. After reducing bias for CCS_N2 between different platforms using new reference values (95% of ^TWCCS_N2 values fell within 1.29% of ^DTCCS_N2 and 1.12% of ^TIMCCS_N2 values, respectively), remaining outliers could be confidently classified and further studied using DFT calculations and CCS_N2 predictions. Despite large uncertainties for in silico CCS_N2 predictions, discrepancies in observed CCS_N2 values across different IM-MS platforms as well as non-uniform arrival time distributions could be partly rationalized.

Identification of Mobility-Resolved N-Glycan Isomers

Glycan analysis has evolved considerably during the last decade. The advent of high-resolution ion-mobility spectrometry has enabled the separation of isomers with only the slightest of structural differences. However, the ability to separate such species raises the problem of identifying all the mobility-resolved peaks that are observed, especially when analytical standards are not available. In this work, we report an approach based on the combination of IMSⁿ with cryogenic vibrational spectroscopy to identify N-glycan reducing-end anomers. By identifying the reducing-end α and β anomers of diacetyl-chitobiose, which is a disaccharide that forms part of the common core of all N-glycans, we are able to assign mobility peaks to reducing anomers of a selection of N-glycans of different sizes, starting from trisaccharides such as Man-1 up to glycans containing nine monosaccharide units, such as G2. By building an infrared fingerprint database of the identified N-glycans, our approach allows unambiguous identification of mobility peaks corresponding to reducing-end anomers and distinguishes them from positional isomers that might be present in a complex mixture.

Collision Cross-Section Calibration Strategy for Lipid Measurements in SLIM-Based High-Resolution Ion Mobility

Structures for lossless ion manipulation-based high-resolution ion mobility (HRIM) interfaced with mass spectrometry has emerged as a powerful tool for the separation and analysis of many isomeric systems. IM-derived collision cross section (CCS) is increasingly used as a molecular descriptor for structural analysis and feature annotation, but there are few studies on the calibration of CCS from HRIM measurements. Here, we examine the accuracy, reproducibility, and practical applicability of CCS calibration strategies for a broad range of lipid subclasses and develop a straightforward and generalizable framework for obtaining high-resolution CCS values. We explore the utility of using structurally similar custom calibrant sets as well as lipid subclass-specific empirically derived correction factors. While the lipid calibrant sets lowered overall bias of reference CCS values from ∼2-3% to ∼0.5%, application of the subclass-specific correction to values calibrated with a broadly available general calibrant set resulted in biases <0.4%. Using this method, we generated a high-resolution CCS database containing over 90 lipid values with HRIM. To test the applicability of this method to a broader class range typical of lipidomics experiments, a standard lipid mix was analyzed. The results highlight the importance of both class and arrival time range when correcting or scaling CCS values and provide guidance for implementation of the method for more general applications.

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.

Toward High-Throughput Cryogenic IR Fingerprinting of Mobility-Separated Glycan Isomers

Infrared (IR) spectroscopy is a powerful tool used to infer detailed structural information on molecules, often in conjunction with quantum-chemical calculations. When applied to cryogenically cooled ions, IR spectra provide unique fingerprints that can be used for biomolecular identification. This is particularly important in the analysis of isomeric biopolymers, which are difficult to distinguish using mass spectrometry. However, IR spectroscopy typically requires laser systems that need substantial user attention and measurement times of tens of minutes, which limits its analytical utility. We report here the development of a new high-throughput instrument that combines ultrahigh-resolution ion-mobility spectrometry with cryogenic IR spectroscopy and mass spectrometry, and we apply it to the analysis of isomeric glycans. The ion mobility step, which is based on structures for lossless ion manipulations (SLIM), separates glycan isomers, and an IR fingerprint spectrum identifies them. An innovative cryogenic ion trap allows multiplexing the acquisition of analyte IR fingerprints following mobility separation, and using a turn-key IR laser, we can obtain spectra and identify isomeric species in less than a minute. This work demonstrates the potential of IR fingerprinting methods to impact the analysis of isomeric biomolecules and more specifically glycans.

Plate-height model of ion mobility-mass spectrometry: Part 2-Peak-to-peak resolution and peak capacity

In a previous work, we explored zone broadening and the achievable plate numbers in linear drift tube ion mobility-mass spectrometry through developing a plate-height model [1]. On the basis of these findings, the present theoretical study extends the model by exploring peak-to-peak resolution and peak capacity in ion mobility separations. The first part provides a critical overview of chromatography-influenced resolution equations, including refinement of existing formulae. Furthermore, we present exact resolution equations for drift tube ion mobility spectrometry based on first principles. Upon implementing simple modifications, these exact formulae could be readily extended to traveling wave ion mobility separations and to cases when ion mobility spectrometry is coupled to mass spectrometry. The second part focuses on peak capacity. The well-known assumptions of constant plate number and constant peak width form the basis of existing approximate solutions. To overcome their limitations, an exact peak capacity equation is derived for drift tube ion mobility spectrometry. This exact solution is rooted in a suitable physical model of peak broadening, accounting for the finite injection pulse and subsequent diffusional spreading. By borrowing concepts from the theoretical toolbox of chromatography, we believe that the present study will help in integrating ion mobility spectrometry into the unified language of separation science.

Resolving Power and Collision Cross Section Measurement Accuracy of a Prototype High-Resolution Ion Mobility Platform Incorporating Structures for Lossless Ion Manipulation

A production prototype structures for lossless ion manipulation ion mobility (SLIM IM) platform interfaced to a commercial high-resolution mass spectrometer (MS) is described. The SLIM IM implements the traveling wave ion mobility technique across a ∼13m path length for high-resolution IM (HRIM) separations. The resolving power (CCS/ΔCCS) of the SLIM IM stage was benchmarked across various parameters (traveling wave speeds, amplitudes, and waveforms), and results indicated that resolving powers in excess of 200 can be accessed for a broad range of masses. For several cases, resolving powers greater than 300 were achieved, notably under wave conditions where ions transition from a nonselective "surfing" motion to a mobility-selective ion drift, that corresponded to ion speeds approximately 30-70% of the traveling wave speed. The separation capabilities were evaluated on a series of isomeric and isobaric compounds that cannot be resolved by MS alone, including reversed-sequence peptides (SDGRG and GRGDS), triglyceride double-bond positional isomers (TG 3, 6, 9 and TG 6, 9, 12), trisaccharides (melezitose, raffinose, isomaltotriose, and maltotriose), and ganglioside lipids (GD1b and GD1a). The SLIM IM platform resolved the corresponding isomeric mixtures, which were unresolvable using the standard resolution of a drift-tube instrument (∼50). In general, the SLIM IM-MS platform is capable of resolving peaks separated by as little as ∼0.6% without the need to target a specific separation window or drift time. Low CCS measurement biases <0.5% were obtained under high resolving power conditions. Importantly, all the analytes surveyed are able to access high-resolution conditions (>200), demonstrating that this instrument is well-suited for broadband HRIM separations important in global untargeted applications.

Exploring the Impacts of Conformer Selection Methods on Ion Mobility Collision Cross Section Predictions

The prediction of structure dependent molecular properties, such as collision cross sections as measured using ion mobility spectrometry, are crucially dependent on the selection of the correct population of molecular conformers. Here, we report an in-depth evaluation of multiple conformation selection techniques, including simple averaging, Boltzmann weighting, lowest energy selection, low energy threshold reductions, and similarity reduction. Generating 50 000 conformers each for 18 molecules, we used the In Silico Chemical Library Engine (ISiCLE) to calculate the collision cross sections for the entire data set. First, we employed Monte Carlo simulations to understand the variability between conformer structures as generated using simulated annealing. Then we employed Monte Carlo simulations to the aforementioned conformer selection techniques applied on the simulated molecular property: the ion mobility collision cross section. Based on our analyses, we found Boltzmann weighting to be a good trade-off between precision and theoretical accuracy. Combining multiple techniques revealed that energy thresholds and root-mean-squared deviation-based similarity reductions can save considerable computational expense while maintaining property prediction accuracy. Molecular dynamic conformer generation tools like AMBER can continue to generate new lowest energy conformers even after tens of thousands of generations, decreasing precision between runs. This reduced precision can be ameliorated and theoretical accuracy increased by running density functional theory geometry optimization on carefully selected conformers.