Effective Temperature of Ions in Traveling Wave Ion Mobility Spectrometry

Exploring the Conformational Landscape of Poly(l-lysine) Dendrimers Using Ion Mobility Mass Spectrometry

Ion mobility mass spectrometry (IM-MS) measures the mass, size, and shape of ions in the same experiment, and structural information is provided via collision cross-section (CCS) values. The majority of commercially available IM-MS instrumentation relies on the use of CCS calibrants, and here, we present data from a family of poly(l-lysine) dendrimers and explore their suitability for this purpose. In order to test these compounds, we employed three different IM-MS platforms (Agilent 6560 IM-QToF, Waters Synapt G2, and a home-built variable temperature drift tube IM-MS) and used them to investigate six different generations of dendrimers in two buffer gases (helium and nitrogen). Each molecule gives a highly discrete CCS distribution suggestive of single conformers for each m/z value. The DTCCSN2 values of this series of molecules (molecular weight: 330-16,214 Da) range from 182 to 2941 Å2, which spans the CCS range that would be found by many synthetic molecules including supramolecular compounds and many biopolymers. The CCS values for each charge state were highly reproducible in day-to-day analysis on each instrument, although we found small variations in the absolute CCS values between instruments. The rigidity of each dendrimer was probed using collisionally activated and high-temperature IM-MS experiments, where no evidence for a significant CCS change ensued. Taken together, this data indicates that these polymers are candidates for CCS calibration and could also help to reconcile differences found in CCS measurements on different instrument geometries.

Manipulating Non-Dissociative Transformations of Gaseous Ion Ensembles Prior to Ion-Mobility Separation

Molecules with multiple sites capable of accepting protons form ensembles of protomers. The manifested protomer ratios in such ensembles are influenced by many experimental conditions. In a Synapt G2 ion mobility (IM)-enabled mass spectrometry system, there are several physical locations where ion population changes can be manifested. Using APCI-generated protomers of aminonaphthalenes, we investigated its intramolecular proton transfers from the N-protomer to the C-protomer. This lossless transformation of the N-protomer to the thermodynamically favored C-protomer can take place in the ion source itself. Initially, we learned that the cone gas slows down the transformation to the C-protomer. Gaseous ions are then accelerated in the first vacuum region, where ions undergo collisional activation (heating), which facilitates the transformation to the C-protomer. Afterward, the ions are mass selected and transferred to the pre-IM (Trap)-collision cell, where ions can also be transformed to the thermodynamically favored protomers. Trap accumulated ions are then released to the IM separator via a helium-filled entry cell. The role of helium is to minimize ion activation and scattering taking place upon entry to the high-pressure T-Wave IM separator (TWIMS). The helium cell is known to increase the IM peak resolution. However, we found that significant changes occur depending on the presence or absence of helium. Without helium, source-generated protomers rapidly changed to a predominantly thermodynamically favorable ensemble protomers. Apparently, the introduction of helium into the precell induced a dramatic decrease in collisional "heating" effect, which effectively slowed down the conversion rate of the amino-protomer into the more favorable ring-protomer. The final message is that mobilograms should not be considered as direct real-time, or intrinsic, representations of the protomer ratios in the ion source.

Structural studies of supramolecular complexes and assemblies by ion mobility mass spectrometry

Recent advances in instrumentation and development of computational strategies for ion mobility mass spectrometry (IM-MS) studies have contributed to an extensive growth in the application of this analytical technique to comprehensive structural description of supramolecular systems. Apart from the benefits of IM-MS for interrogation of intrinsic properties of noncovalent aggregates in the experimental gas-phase environment, its merits for the description of native structural aspects, under the premises of having maintained the noncovalent interactions innate upon the ionization process, have attracted even more attention and gained increasing interest in the scientific community. Thus, various types of supramolecular complexes and assemblies relevant for biological, medical, material, and environmental sciences have been characterized so far by IM-MS supported by computational chemistry. This review covers the state-of-the-art in this field and discusses experimental methods and accompanying computational approaches for assessing the reliable three-dimensional structural elucidation of supramolecular complexes and assemblies by IM-MS.

Measurement of very low-molecular weight metabolites by traveling wave ion mobility and its use in human urine samples

The collision cross-sections (CCS) measurement using ion mobility spectrometry (IMS) in combination with mass spectrometry (MS) offers a great opportunity to increase confidence in metabolite identification. However, owing to the lack of sensitivity and resolution, IMS has an analytical challenge in studying the CCS values of very low-molecular-weight metabolites (VLMs ≤ 250 Da). Here, we describe an analytical method using ultrahigh-performance liquid chromatography (UPLC) coupled to a traveling wave ion mobility-quadrupole-time-of-flight mass spectrometer optimized for the measurement of VLMs in human urine samples. The experimental CCS values, along with mass spectral properties, were reported for the 174 metabolites. The experimental data included the mass-to-charge ratio (m/z), retention time (RT), tandem MS (MS/MS) spectra, and CCS values. Among the studied metabolites, 263 traveling wave ion mobility spectrometry (TWIMS)-derived CCS values (TWCCSN2) were reported for the first time, and more than 70% of these were CCS values of VLMs. The TWCCSN2 values were highly repeatable, with inter-day variations of <1% relative standard deviation (RSD). The developed method revealed excellent TWCCSN2 accuracy with a CCS difference (ΔCCS) within ±2% of the reported drift tube IMS (DTIMS) and TWIMS CCS values. The complexity of the urine matrix did not affect the precision of the method, as evidenced by ΔCCS within ±1.92%. According to the Metabolomics Standards Initiative, 55 urinary metabolites were identified with a confidence level of 1. Among these 55 metabolites, 53 (96%) were VLMs. The larger number of confirmed compounds found in this study was a result of the addition of TWCCSN2 values, which clearly increased metabolite identification confidence.

Altering Conformational States of Dynamic Ion Populations using Traveling Wave Structures for Lossless Ion Manipulations

With its capacity to store and translate ions across considerable distances and times, traveling wave structures for lossless ion manipulations (TW-SLIM) provide the foundation to expand the scope of ion mobility spectrometry (IMS) experiments. While promising, the dynamic electric fields and consequential ion-neutral collisions used to realize extensive degrees of separation have a considerable impact on the empirical results and the fundamental interpretation of observed arrival time distributions. Using a custom-designed set of TW-SLIM boards (∼9 m) coupled with a time-of-flight mass spectrometer (SLIM-ToF), we detail the capacity to systematically alter the gas-phase distribution of select peptide conformers. In addition to discussing the role charge-transfer may play in TW-SLIM experiments that occur at extended time scales, the ability of the SLIM-ToF to perform tandem IMS was leveraged to confirm that both the compact and elongated conformers of bradykinin2+ undergo interconversion within the SLIM. Storage experiments in which ions are confined within SLIM using static potential wells suggest that factors aside from TW-induced ion motion contribute to interconversion. Further investigation into this matter suggests that the use of radio frequency (RF) fields to confine ions within SLIM may play a role in ion heating. Aside from interconversion, storage experiments also provide insight into charge transfer behavior over the course of extended periods. The results of the presented experiments suggest that considerations should be taken when analyzing labile species and inform strategies for the TW-SLIM design and method development.

Exploring the Aggregation Propensity of PHF6 Peptide Segments of the Tau Protein Using Ion Mobility Mass Spectrometry Techniques

Peptide and protein aggregation involves the formation of oligomeric species, but the complex interplay between oligomers of different conformations and sizes complicates their structural elucidation. Using ion mobility mass spectrometry (IM-MS), we aim to reveal these early steps of aggregation for the Ac-PHF6-NH2 peptide segment from tau protein, thereby distinguishing between different oligomeric species and gaining an understanding of the aggregation pathway. An important factor that is often neglected, but which can alter the aggregation propensity of peptides, is the terminal capping groups. Here, we demonstrate the use of IM-MS to probe the early stages of aggregate formation of Ac-PHF6-NH2, Ac-PHF6, PHF6-NH2, and uncapped PHF6 peptide segments. The aggregation propensity of the four PHF6 segments is confirmed using thioflavin T fluorescence assays and transmission electron microscopy. A novel approach based on post-IM fragmentation and quadrupole selection on the TIMS-Qq-ToF (trapped ion mobility) spectrometer was developed to enhance oligomer assignment, especially for the higher-order aggregates. This approach pushes the limits of IM identification of isobaric species, whose signatures appear closer to each other with increasing oligomer size, and provides new insights into the interpretation of IM-MS data. In addition, TIMS collision cross section values are compared with traveling wave ion mobility (TWIMS) data to evaluate potential instrumental bias in the trapped ion mobility results. The two IM-MS instrumental platforms are based on different ion mobility principles and have different configurations, thereby providing us with valuable insight into the preservation of weakly bound biomolecular complexes such as peptide aggregates.

Ion mobility calculations of flexible all-atom systems at arbitrary fields using two-temperature theory

Ion mobility spectrometry (IMS) separates and analyzes ions based on their mobility in a gas under an electric field. When the field is increased, the mobility varies in a complex way that depends on the relative velocity between gas and ion, their electrostatic potential interactions, and the effects from direct impingement. Recently, the two-temperature theory, primarily developed for monoatomic ions in monoatomic gases, has been extended to study mobilities at arbitrary fields using polyatomic ions in polyatomic gases, with some success. However, this extension poses challenges, such as inelastic collisions between gas and ion and structural modifications of ions as they heat up. These challenges become significant when working with diatomic gases and flexible molecules. In a previous study, experimental mobilities of tetraalkylammonium salts were obtained using a FAIMS instrument, showing satisfactory agreement with numerical two-temperature theory predictions. However, deviations occurred at fields greater than 100 Td. To address this issue, this paper introduces a modified high-field calculation method that accounts for the structural changes in ions due to field heating. The study focuses on tetraheptylammonium (THA+), tetradecylammonium (TDA+), and tetradodecylammonium (TDDA+) salts. Molecular structures were generated at various temperatures using MM2 forcefield. The mobility was calculated using IMoS 1.13 with two-temperature trajectory method calculations up to the fourth approximation. Multiple effective temperatures were considered, and a linear weighing system was used to create mobility vs. reduced field strength plots. The results suggest that the structural enlargement due to ion heating plays a significant role in mobility at high fields, aligning better with experimental data. FAIMS' dispersion plots also show improved agreement with experimental results. However, the contribution of inelastic collisions and energy transfer to rotational degrees of freedom in gas molecules remains a complex and challenging aspect.

Elucidating the Mechanism of Multispecific Antibody Aggregation through Subunit Analysis

Multispecific antibody constructs are quickly becoming more common constructs in biopharmaceuticals to improve specificity and efficacy. While the advent of this technology has led to improved therapeutics, its development has challenged the analytical tools through which these therapeutics are characterized. Moreover, new critical quality attributes, such as aggregation, have challenged the approaches to characterization even further. Herein, we describe a novel native subunit analysis using IdeS and IgdE analyzed by native size exclusion chromatography coupled with mass spectrometry to interrogate the mechanism of aggregation in a multispecific antibody. Digestion by IdeS and IdgE allows for the retention and detection of noncovalent interactions thereafter. Aggregation was localized to single-chain fragment variables (scFvs) wherein a domain swapping mechanism between VH1/VL2 and VH2/VL1 occurs.

Evaluation for Ion Heating of H2A-H2B Dimer in Ion Mobility Spectrometry-Mass Spectrometry

Ion mobility spectrometry-mass spectrometry (IMS-MS) provides m/z values and collision cross sections (CCSs) of gas-phase ions. In our previous study, an intrinsically disordered protein, the H2A-H2B dimer, was analyzed using IMS-MS, resulting in two conformational populations of CCS. Based on experimental and theoretical approaches, this resulted from a structural diversity of intrinsically disordered regions. We predicted that this phenomenon is related to ion heating in the IMS-MS instrument. In this study, to reveal the effect of ion heating from parameters in the IMS-MS instrument on the conformational population of the H2A-H2B dimer, we investigated the arrival time distributions of the H2A-H2B dimer by changing values of three instrumental parameters, namely, cone voltage located in the first vacuum chamber, trap collision energy (trap CE) for tandem mass spectrometry, and trap bias voltage for the entrance of IMS. These results revealed that the two populations observed for the H2A-H2B dimer were due to the trap bias voltage. Furthermore, to evaluate the internal energies of the analyte ions with respect to each parameter, benzylpyridinium derivatives were used as temperature-sensitive probes. The results showed that the trap CE voltage imparts greater internal energy to the ions than the trap bias voltage. In addition, this slight change in the internal energy caused by the trap bias voltage resulted in the structural diversity of the H2A-H2B dimer. Therefore, the trap bias voltage should be set with attention to the properties of the analytes, even if the effect of the trap bias voltage on the internal energy is negligible.

Optimum collision energies for proteomics: The impact of ion mobility separation

Ion mobility spectrometry (IMS) is a widespread separation technique used in various research fields. It can be coupled to liquid chromatography-mass spectrometry (LC-MS/MS) methods providing an additional separation dimension. During IMS, ions are subjected to multiple collisions with buffer gas, which may cause significant ion heating. The present project addresses this phenomenon from the bottom-up proteomics point of view. We performed LC-MS/MS measurements on a cyclic ion mobility mass spectrometer with varied collision energy (CE) settings both with and without IMS. We investigated the CE dependence of identification score, using Byonic search engine, for more than 1000 tryptic peptides from HeLa digest standard. We determined the optimal CE values-giving the highest identification score-for both setups (i.e., with and without IMS). Results show that lower CE is advantageous when IMS separation is applied, by 6.3 V on average. This value belongs to the one-cycle separation configuration, and multiple cycles may supposedly have even larger impact. The effect of IMS is also reflected in the trends of optimal CE values versus m/z functions. The parameters suggested by the manufacturer were found to be almost optimal for the setup without IMS; on the other hand, they are obviously too high with IMS. Practical consideration on setting up a mass spectrometric platform hyphenated to IMS is also presented. Furthermore, the two CID (collision induced dissociation) fragmentation cells of the instrument-located before and after the IMS cell-were also compared, and we found that CE adjustment is needed when the trap cell is used for activation instead of the transfer cell. Data have been deposited in the MassIVE repository (MSV000090944).

Right in two: capabilities of ion mobility spectrometry for untargeted metabolomics

This mini review focuses on the opportunities provided by current and emerging separation techniques for mass spectrometry metabolomics. The purpose of separation technologies in metabolomics is primarily to reduce complexity of the heterogeneous systems studied, and to provide concentration enrichment by increasing sensitivity towards the quantification of low abundance metabolites. For this reason, a wide variety of separation systems, from column chemistries to solvent compositions and multidimensional separations, have been applied in the field. Multidimensional separations are a common method in both proteomics applications and gas chromatography mass spectrometry, allowing orthogonal separations to further reduce analytical complexity and expand peak capacity. These applications contribute to exponential increases in run times concomitant with first dimension fractionation followed by second dimension separations. Multidimensional liquid chromatography to increase peak capacity in metabolomics, when compared to the potential of running additional samples or replicates and increasing statistical confidence, mean that uptake of these methods has been minimal. In contrast, in the last 15 years there have been significant advances in the resolution and sensitivity of ion mobility spectrometry, to the point where high-resolution separation of analytes based on their collision cross section approaches chromatographic separation, with minimal loss in sensitivity. Additionally, ion mobility separations can be performed on a chromatographic timescale with little reduction in instrument duty cycle. In this review, we compare ion mobility separation to liquid chromatographic separation, highlight the history of the use of ion mobility separations in metabolomics, outline the current state-of-the-art in the field, and discuss the future outlook of the technology. "Where there is one, you're bound to divide it. Right in two", James Maynard Keenan.

Gas-phase structure of polymer ions: Tying together theoretical approaches and ion mobility spectrometry

An increasing number of studies take advantage of ion mobility spectrometry (IMS) coupled to mass spectrometry (IMS-MS) to investigate the spatial structure of gaseous ions. Synthetic polymers occupy a unique place in the field of IMS-MS. Indeed, due to their intrinsic dispersity, they offer a broad range of homologous ions with different lengths. To help rationalize experimental data, various theoretical approaches have been described. First, the study of trend lines is proposed to derive physicochemical and structural parameters. However, the evaluation of data fitting reflects the overall behavior of the ions without reflecting specific information on their conformation. Atomistic simulations constitute another approach that provide accurate information about the ion shape. The overall scope of this review is dedicated to the synergy between IMS-MS and theoretical approaches, including computational chemistry, demonstrating the essential role they play to fully understand/interpret IMS-MS data.

MobCal-MPI 2.0: an accurate and parallelized package for calculating field-dependent collision cross sections and ion mobilities

Ion mobility spectrometry (IMS), which can be employed as either a stand-alone instrument or coupled to mass spectrometry, has become an important tool for analytical chemistry. Because of the direct relation between an ion's mobility and its structure, which is intrinsically related to its collision cross section (CCS), IMS techniques can be used in tandem with computational tools to elucidate ion geometric structure. Here, we present MobCal-MPI 2.0, a software package that demonstrates excellent accuracy (RMSE 2.16%) and efficiency in calculating low-field CCSs via the trajectory method (≤30 minutes on 8 cores for ions with ≤70 atoms). MobCal-MPI 2.0 expands on its predecessor by enabling the calculation of high-field mobilities through the implementation of the 2^nd order approximation to two-temperature theory (2TT). By further introducing an empirical correction to account for deviations between 2TT and experiment, MobCal-MPI 2.0 can compute accurate high-field mobilities that exhibit a mean deviation of <4% from experimentally measured values. Moreover, the velocities used to sample ion-neutral collisions were updated from a weighted to a linear grid, enabling the near-instantaneous evaluation of mobility/CCS at any effective temperature from a single set of N₂ scattering trajectories. Several enhancements made to the code are also discussed, including updates to the statistical analysis of collision event sampling and benchmarking of overall performance.

Are the Gas-Phase Structures of Molecular Elephants Enduring or Ephemeral? Results from Time-Dependent, Tandem Ion Mobility

The structural stability of biomolecules in the gas phase remains an important topic in mass spectrometry applications for structural biology. Here, we evaluate the kinetic stability of native-like protein ions using time-dependent, tandem ion mobility (IM). In these tandem IM experiments, ions of interest are mobility-selected after a first dimension of IM and trapped for up to ∼14 s. Time-dependent, collision cross section distributions are then determined from separations in a second dimension of IM. In these experiments, monomeric protein ions exhibited structural changes specific to both protein and charge state, whereas large protein complexes did not undergo resolvable structural changes on the timescales of these experiments. We also performed energy-dependent experiments, i.e., collision-induced unfolding, as a comparison for time-dependent experiments to understand the extent of unfolding. Collision cross section values observed in energy-dependent experiments using high collision energies were significantly larger than those observed in time-dependent experiments, indicating that the structures observed in time-dependent experiments remain kinetically trapped and retain some memory of their solution-phase structure. Although structural evolution should be considered for highly charged, monomeric protein ions, these experiments demonstrate that higher-mass protein ions can have remarkable kinetic stability in the gas phase.

Validation of Field-Dependent Ion-Solvent Cluster Modeling via Direct Measurement of Cluster Size Distributions

Ion mobility spectrometry is widely used in analytical chemistry, either as a stand-alone technique or coupled to mass spectrometry. Ions in the gas phase tend to form loosely bound clusters with surrounding solvent vapors, artificially increasing the collisional cross section and the mass of the ion. This, in turn, affects ion mobility and influences separation. Further, ion-solvent clusters play an important role in most ionization mechanisms occurring in the gas phase. Consequently, a deeper understanding of ion-solvent cluster association and dissociation processes is desirable to guide experimental design and interpretation. A few computational models exist, which aim to describe the amount of clustering as a function of the reduced electric field strength, bath gas pressure and temperature, and the chemical species probed. It is especially challenging to model ion mobility under high reduced electrical field strengths due to the nonthermal conditions created by the field. In this work, we aim to validate a recently proposed first-principles model by comparing its predictions with direct measurements of cluster size distributions over a range of 20-120 Td as observed using a High Kinetic Energy Ion Mobility Spectrometer coupled to a mass spectrometer (HiKE-IMS-MS). By studying H⁺(H₂O)_n, [MeOH + H + n(H₂O)]⁺, [ACE + H + n(H₂O)]⁺, and [PhNH₂ + H + n(H₂O)]⁺ as test systems, we find very good agreement between model and experiment, supporting the validity of the computational workflow. Further, the detailed information gained from the modeling yields important insights into the cluster dynamics within the HiKE-IMS, allowing for better interpretation of the measured ion mobility spectra.

Disassembly Mechanisms and Energetics of Polymetallic Rings and Rotaxanes

Understanding the fundamental reactivity of polymetallic complexes is challenging due to the complexity of their structures with many possible bond breaking and forming processes. Here, we apply ion mobility mass spectrometry coupled with density functional theory to investigate the disassembly mechanisms and energetics of a family of heterometallic rings and rotaxanes with the general formula [NH₂RR'][Cr₇MF₈(O₂C^tBu)₁₆] with M = Mn^II, Fe^II, Co^II, Ni^II, Cu^II, Zn^II, Cd^II. Our results show that their stability can be tuned both by altering the d-metal composition in the macrocycle and by the end groups of the secondary ammonium cation [NH₂RR']⁺. Ion mobility probes the conformational landscape of the disassembly process from intact complex to structurally distinct isobaric fragments, providing unique insights to how a given divalent metal tunes the structural dynamics.

Food metabolomics: Latest hardware-developments for nontargeted food authenticity and food safety testing

The analytical requirements for food testing have increased significantly in recent years. On the one hand, because food fraud is becoming an ever-greater challenge worldwide, and on the other hand because food safety is often difficult to monitor due to the far-reaching trade chains. In addition, the expectations of consumers on the quality of food have increased, and they are demanding extensive information. Cutting-edge analytical methods are required to meet these demands. In this context, non-targeted metabolomics strategies using mass and nuclear magnetic resonance spectrometers (mass spectrometry [MS]) have proven to be very suitable. MS-based approaches are of particular importance as they provide a comparatively high analytical coverage of the metabolome. Accordingly, the efficiency to address even challenging issues is high. A variety of hardware developments, which are explained in this review, have contributed to these advances. In addition, the potential of future developments is highlighted, some of which are currently not yet commercially available or only used to a comparatively small extent but are expected to gain in importance in the coming years.

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.

Ion mobility-high resolution mass spectrometry in doping control analysis. Part II: Comparison of acquisition modes with and without ion mobility

In the second part of this study, a systematic comparison was made between two ion fragmentation acquisition modes, namely data-independent acquisition (DIA) and DIA with ion mobility spectrometry (IMS) technology. These two approaches were applied to the analysis of 192 doping agents in urine. Group I included 102 compounds such as stimulants, diuretics, narcotics, and β2-agonists, while Group II contained 90 compounds included steroids, glucocorticoids, and hormone and metabolic modulators. Important method parameters were examined and compared, including the fragmentation, sensitivity, and assignment capability with the minimum occurrence of false positive hits. The results differed between Group I and II in number of detected fragments when exploring the MS/MS spectra. In Group I only 13%, while in the Group II 64% of the substances had a higher number of fragments in DIA-IMS mode vs. DIA. In terms of sensitivity, the performance of the two modes with and without activated IMS dimension was identical for about 50% of the doping agents. The sensitivity was higher without IMS, i.e. in simple DIA mode, for 20-40% of remaining doping agents. Despite this sensitivity reduction with IMS, 82% of compounds from both Groups met the minimum required performance level (MRPL) criteria of the World Anti-Doping Agency (WADA) when the DIA-IMS mode was applied. Automated data processing is important in routine doping analysis. Therefore, processing methods were optimized and evaluated for the prevalence of false peak assignments by analysing the target substances at different concentrations in urine samples. Overall, a significantly higher number of misidentified compounds was observed in Group II, with an almost 2-fold higher number of misidentifications in DIA compared to DIA-IMS. This result highlights the benefit of the IMS dimension to reduce the rate of false positive in screening analysis. The optimized UHPLC-IM-HRMS method was finally applied to the analysis of urine samples from administration studies including nine doping agents from both Groups. However, to limit the number of interferences from the biological matrix, an emphasis is needed on the adequate settings of the data processing method.

Ion Mobility Mass Spectrometry Uncovers Guest-Induced Distortions in a Supramolecular Organometallic Metallosquare

The encapsulation of the tetracationic palladium metallosquare with four pyrene-bis-imidazolylidene ligands [1]4+ with a series of organic molecules was studied by Electrospray ionization Travelling Wave Ion-Mobility Mass Spectrometry (ESI TWIM-MS). The method allowed to determine the Collision Cross Sections (CCSs), which were used to assess the size changes experienced by the host upon encapsulation of the guest molecules. When fullerenes were used as guests, the host is expanded ΔCCS 13 Å2 and 23 Å2 , for C60 or C70 , respectively. The metallorectangle [1]4+ was also used for the encapsulation of a series of polycyclic aromatic hydrocarbons (PAHs) and naphthalenetetracarboxylic diimide (NTCDI), to form complexes of formula [(NTCDI)2 (PAH)@1]4+ . For these host:guest adducts, the ESI IM-MS studies revealed that [1]4+ is expanded by 47-49 Å2 .. The energy-minimized structures of [1]4+ , [C60 @1]4+ , [C70 @1]4+ , [(NTCDI)2 (corannulene)@1]4+ in the gas phase were obtained by DFT calculations.Introduction.

"Thermometer" Ions Can Fragment Through an Unexpected Intramolecular Elimination: These Are Not the Fragments You Are Looking For

Benzylpyridinium analogs are effective thermometer ions since monitoring the formation of the benzylium fragment produced from heterolytic cleavage of the C-N bond can be linked to the ion's internal energy. In this study, three para-substituted benzylpyridinium ions containing ethoxy (OEt), isopropoxy (OiPr) and tert-butoxy (OtBu) substitutents were synthesized and evaluated as chemical thermometers. Intriguingly, the product ion spectra of the three benzylpyridinium ions were dominated by m/z 107 instead of the anticipated benzylium species. Deuterium labeling suggested that the m/z 107 fragment resulted from an intramolecular elimination (E_i), which formed via a four-membered transition state (TS). The fragmentation pathway appears to be an anomaly within the mass spectrometry literature, as four-membered pericyclic TSs are usually accompanied by the formation of an exceptionally stable neutral molecule (e.g., CO₂). Quantum-chemical calculations confirmed our hypothesis that stabilization of the strained TS is afforded by hyperconjugation (ΔG^‡ tert-butoxy < isopropyoxy < ethoxy).

The Charge-State and Structural Stability of Peptides Conferred by Microsolvating Environments in Differential Mobility Spectrometry

The presence of solvent vapor in a differential mobility spectrometry (DMS) cell creates a microsolvating environment that can mitigate complications associated with field-induced heating. In the case of peptides, the microsolvation of protonation sites results in a stabilization of charge density through localized solvent clustering, sheltering the ion from collisional activation. Seeding the DMS carrier gas (N₂) with a solvent vapor prevented nearly all field-induced fragmentation of the protonated peptides GGG, AAA, and the Lys-rich Polybia-MP1 (IDWKKLLDAAKQIL-NH₂). Modeling the microsolvation propensity of protonated n-propylamine [PrNH₃]⁺, a mimic of the Lys side chain and N-terminus, with common gas-phase modifiers (H₂O, MeOH, EtOH, iPrOH, acetone, and MeCN) confirms that all solvent molecules form stable clusters at the site of protonation. Moreover, modeling populations of microsolvated clusters indicates that species containing protonated amine moieties exist as microsolvated species with one to six solvent ligands at all effective ion temperatures (T_eff) accessible during a DMS experiment (ca. 375-600 K). Calculated T_eff of protonated GGG, AAA, and Polybia-MPI using a modified two-temperature theory approach were up to 86 K cooler in DMS environments seeded with solvent vapor compared to pure N₂ environments. Stabilizing effects were largely driven by an increase in the ion's apparent collision cross section and by evaporative cooling processes induced by the dynamic evaporation/condensation cycles incurred in the presence of an oscillating electric separation field. When the microsolvating partner was a protic solvent, abstraction of a proton from [MP1 + 3H]³⁺ to yield [MP1 + 2H]²⁺ was observed. This result was attributed to the proclivity of protic solvents to form hydrogen-bond networks with enhanced gas-phase basicity. Collectively, microsolvation provides analytes with a solvent "air bag," whereby charge reduction and microsolvation-induced stabilization were shown to shelter peptides from the fragmentation induced by field heating and may play a role in preserving native-like ion configurations.

Exploring Conformational Landscapes Using Trap and Release Tandem Ion Mobility Spectrometry

The dynamics and thermodynamics of structural changes in isolated glu-fibrinopeptide B (GluFib) were investigated by tandem ion mobility spectrometry (IMS). Doubly protonated GluFib²⁺ ions were first selected by IMS and then stored for a controlled duration in a thermalized ion trap. Temperature-induced conformational changes were finally monitored by IMS as a function of trapping time. Based on this procedure, isomerization rates and equilibrium populations of the different conformers were determined as a function of temperature. We demonstrate that the measured thermodynamic quantities can be directly compared to simulated observables from ensemble molecular modeling based on appropriate order parameters. We obtained good qualitative agreement with replica-exchange molecular dynamics simulations based on the AMOEBA force field and processed using the weighted histogram analysis method. This suggests that the balance between Coulomb repulsion and optimal charge solvation is the main source of the observed conformational bistability. Our results emphasize the differences between the kinetically driven quasi-equilibrium distributions obtained after collisional activation and the thermodynamically driven distributions from the present equilibrium experiments due to entropic effects. As a consequence, our measurements not only allow straightforward determination of Arrhenius activation energies but also yield the relative enthalpy and entropy changes associated to a structural transition.

An Improved Calibration Approach for Traveling Wave Ion Mobility Spectrometry: Robust, High-Precision Collision Cross Sections

The combination of ion-mobility (IM) separation with mass spectrometry (MS) has impacted global measurement efforts in areas ranging from food analysis to drug discovery. Reasons for the broad adoption of IM-MS include its significantly increased peak capacity, duty-cycle, and ability to reconstruct fragmentation data in parallel, all of which greatly enable the analyses of complex mixtures. More fundamentally, however, measurements of ion-gas molecule collision cross sections (CCSs) are used to support compound identification and quantitation efforts as well as study the structures of large biomolecules. As the first commercialized form of IM-MS, Traveling Wave Ion Mobility (TWIM) devices are operated at low pressures (∼3 mbar) and voltages, are relatively short (∼25 cm), and separate ions on a timescale of tens of milliseconds. These qualities make TWIM ideally suited for hybridization with MS. Owing to the complicated motion of ions in TWIM devices, however, IM transit times must be calibrated to enable CCS measurements. Applicability of these calibrations has hitherto been restricted to primarily singly charged small molecules and some classes of large, multiply charged ions under a significantly narrower range of instrument conditions. Here, we introduce and extensively characterize a dramatically improved TWIM calibration methodology. Using over 2500 experimental TWIM data sets, covering ions that span over 3.5 orders of magnitude of molecular mass, we demonstrate robust calibrations for a significantly expanded range of instrument conditions, thereby opening up new analytical application areas and enabling the expansion of high-precision CCS measurements for both existing and next-generation TWIM instrumentation.

Assessing Collision Cross Section Calibration Strategies for Traveling Wave-Based Ion Mobility Separations in Structures for Lossless Ion Manipulations

The collision cross section (CCS) is an important property that aids in the structural characterization of molecules. Here, we investigated the CCS calibration accuracy with traveling wave ion mobility spectrometry (TWIMS) separations in structures for lossless ion manipulations (SLIM) using three sets of calibrants. A series of singly negatively charged phospholipids and bile acids were calibrated in nitrogen buffer gas using two different TW waveform profiles (square and sine) and amplitudes (20, 25, and 30 V_0-p). The calibration errors for the three calibrant sets (Agilent tuning mixture, polyalanine, and one assembled in-house) showed negligible differences using a sine-shaped TW waveform. Calibration errors were all within 1-2% of the drift tube ion mobility spectrometry (DTIMS) measurements, with lower errors for sine waveforms, presumably due to the lower average and maximum fields experienced by ions. Finally, ultrahigh-resolution multipass (long path length) SLIM TWIMS separations demonstrated improved CCS calibration for phospholipid and bile acid isomers.

Evaluation of Trapped Ion Mobility Spectrometry Source Conditions Using Benzylammonium Thermometer Ions

A key aspect of reduced pressure ion mobility spectrometry (IMS) experiments is to identify experimental conditions that minimize the role of collisional energy transfer that allows for assessing effective ion-neutral collision cross sections of metabolites, peptides, and proteins in "native-like" or compact states. Across two separate experimental campaigns using a prototype trapped ion mobility spectrometer (TIMS) coupled to a time-of-flight mass spectrometer, we present independent findings that support the results recently published by Morsa et al. using a different set of thermometer ions (Morsa et al. Anal. Chem. 2020, 92 (6), 4573-4582). First, using five para-substituted benzylammonium ions, we conducted survival yield experiments to assess ion internal energy across different experimental settings. Results from the present set of experiments illustrate that greater ion heating occurs at lower pressures and higher voltage settings applied to the TIMS. At the "softest" settings where the benzylammonium thermometer ions have an effective average energy of 1.73 eV, we observe the majority of bradykinin in the compact state. Under more extreme operating conditions where the energy of the benzylammonium ions varies from 1.83 to 1.86 eV, the bradykinin transitions from the compact to the elongated state. In addition to independently confirming the findings of Morsa et al., we also report the mobilities for the benzylammonium parent and fragment ions using the tandem drift-tube-TIMS calibration procedure described by Naylor et al. ( J. Am. Soc. Mass Spectrom. 2019, 30 (10), 2152-2162).

High-Precision, Gas-Phase Hydrogen/Deuterium-Exchange Kinetics by Mass Spectrometry Enabled by Exchange Standards

Mass spectrometry (MS) has become a primary tool for identifying and quantifying biological molecules. In combination with other orthogonal techniques, such as gas-phase hydrogen/deuterium exchange (gHDX), MS is also capable of probing the structure of ions. However, gHDX kinetics can depend strongly on many factors, including laboratory temperature, instrumental conditions, and instrument platform selection. These effects can lead to high variability with gHDX measurements, which has hindered the broader adoption of gHDX for structural MS. Here we introduce an approach for standardizing gHDX measurements using cosampled standards. Quantifying the exchange kinetics for analytes relative to the exchange kinetics of the standards results in greater accuracy and precision than the underlying absolute measurements. The standardization was found to be effective for several types of analytes including small molecules and intact proteins. A subset of analytes showed deviations in their standardized exchange profiles that are attributed to field heating and the concomitant conformational isomerization. Inclusion of helium during the gHDX process for collisional cooling helps mitigate such variations in exchange kinetics related to ion heating. We anticipate that the outcomes of this research will enable the broader use of gHDX in MS-based workflows for molecular identification and isomer differentiation.

A new azobenzene-based design strategy for detergents in membrane protein research

Mass spectrometry enables the in-depth structural elucidation of membrane protein complexes, which is of great interest in structural biology and drug discovery. Recent breakthroughs in this field revealed the need for design rules that allow fine-tuning the properties of detergents in solution and gas phase. Desirable features include protein charge reduction, because it helps to preserve native features of protein complexes during transfer from solution into the vacuum of a mass spectrometer. Addressing this challenge, we here present the first systematic gas-phase study of azobenzene detergents. The utility of gas-phase techniques for monitoring light-driven changes of isomer ratios and molecular properties are investigated in detail. This leads to the first azobenzene detergent that enables the native mass spectrometry analysis of membrane proteins and whose charge-reducing properties can be tuned by irradiation with light. More broadly, the presented work outlines new avenues for the high-throughput characterization of supramolecular systems and opens a new design strategy for detergents in membrane protein research.

How Hot Are Your Ions in Differential Mobility Spectrometry?

Ions can experience significant field-induced heating in a differential mobility cell. To investigate this phenomenon, the fragmentation of several para-substituted benzylpyridinium "thermometer" ions (R = OMe, Me, F, Cl, H, CN) was monitored in a commercial differential mobility spectrometer (DMS). The internal energy of each benzylpyridinium derivative was characterized by monitoring the degree of fragmentation to obtain an effective temperature, T_eff, which corresponds to a temperature consistent with treating the observed fragmentation ratio using a unimolecular dissociation rate weighted by a Boltzmann distribution at a temperature T. It was found that ions are sufficiently thermalized after initial activation from the ESI process to the temperature of the bath gas, T_bath. Once a critical field strength was surpassed, significant fragmentation of the benzylpyridinium ions was detected. At the maximum bath gas temperature (450 K) and separation voltage (SV; 4400 V) for our instrument, T_eff for the benzylpyridinium derivatives ranged from 664 ± 9 K (p-OMe) to 759 ± 17 K (p-H). The extent of activation at a given SV depends on the ion's mass, degrees of freedom, (N_DoF), and collision frequency as represented by the ion's collision cross section. Plots of T_eff vs the product of ion mass and N_DoF and the inverse of collision cross section produce strong linear relationships. This provides an attractive avenue to estimate ion temperatures at a given SV using only intrinsic properties. Moreover, experimentally determined T_eff correlate with theoretically predicted T_eff using with a self-consistent method based on two-temperature theory. The various instrumental and external parameters that influence T_eff are additionally discussed.

Ion Mobility Spectrometry: Fundamental Concepts, Instrumentation, Applications, and the Road Ahead

Ion mobility spectrometry (IMS) is a rapid separation technique that has experienced exponential growth as a field of study. Interfacing IMS with mass spectrometry (IMS-MS) provides additional analytical power as complementary separations from each technique enable multidimensional characterization of detected analytes. IMS separations occur on a millisecond timescale, and therefore can be readily nested into traditional GC and LC/MS workflows. However, the continual development of novel IMS methods has generated some level of confusion regarding the advantages and disadvantages of each. In this critical insight, we aim to clarify some common misconceptions for new users in the community pertaining to the fundamental concepts of the various IMS instrumental platforms (i.e., DTIMS, TWIMS, TIMS, FAIMS, and DMA), while addressing the strengths and shortcomings associated with each. Common IMS-MS applications are also discussed in this review, such as separating isomeric species, performing signal filtering for MS, and incorporating collision cross-section (CCS) values into both targeted and untargeted omics-based workflows as additional ion descriptors for chemical annotation. Although many challenges must be addressed by the IMS community before mobility information is collected in a routine fashion, the future is bright with possibilities.

SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes

We report on separations of ion isotopologues and isotopomers using ultrahigh-resolution traveling wave-based Structures for Lossless Ion Manipulations with serpentine ultralong path and extended routing ion mobility spectrometry coupled to mass spectrometry (SLIM SUPER IMS-MS). Mobility separations of ions from the naturally occurring ion isotopic envelopes (e.g., [M], [M+1], [M+2], ... ions) showed the first and second isotopic peaks (i.e., [M+1] and [M+2]) for various tetraalkylammonium ions could be resolved from their respective monoisotopic ion peak ([M]) after SLIM SUPER IMS with resolving powers of ∼400-600. Similar separations were obtained for other compounds (e.g., tetrapeptide ions). Greater separation was obtained using argon versus helium drift gas, as expected from the greater reduced mass contribution to ion mobility described by the Mason-Schamp relationship. To more directly explore the role of isotopic substitutions, we studied a mixture of specific isotopically substituted (15N, 13C, and 2H) protonated arginine isotopologues. While the separations in nitrogen were primarily due to their reduced mass differences, similar to the naturally occurring isotopologues, their separations in helium, where higher resolving powers could also be achieved, revealed distinct additional relative mobility shifts. These shifts appeared correlated, after correction for the reduced mass contribution, with changes in the ion center of mass due to the different locations of heavy atom substitutions. The origin of these apparent mass distribution-induced mobility shifts was then further explored using a mixture of Iodoacetyl Tandem Mass Tag (iodoTMT) isotopomers (i.e., each having the same exact mass, but with different isotopic substitution sites). Again, the observed mobility shifts appeared correlated with changes in the ion center of mass leading to multiple monoisotopic mobilities being observed for some isotopomers (up to a ∼0.04% difference in mobility). These mobility shifts thus appear to reflect details of the ion structure, derived from the changes due to ion rotation impacting collision frequency or momentum transfer, and highlight the potential for new approaches for ion structural characterization.

Topological Characterization of Coordination-Driven Self-assembly Complexes: Applications of Ion Mobility-Mass Spectrometry

Coordination-driven self-assembly (CDSA) is increasingly used to synthesize coordination complexes containing metal-centered electron acceptors and typically nitrogen-containing electron donors. Characterization of the structures obtained from CDSA via crystallographic or spectroscopic means is limited due to difficulties in forming single crystals for X-ray studies and overlapping precursor and product signals in NMR. Here, we employ ion mobility-mass spectrometry (IM-MS), which provides a direct measure of size and shape of the CDSA complexes, to study the intact reaction products of a rhomboid-shaped complex. This approach negates the need for product isolation and crystallization and allows for tracking of the product distribution as a function of time. A potential challenge of IM-MS is that the size/shape of the observed CDSA complexes can vary with internal energy; however, we show that proper tuning of the instrument reduces the effects of collisional activation thereby allowing for retention of ion conformations that reflect solution-phase ion structures. Graphical Abstract.

Adduct ion formation as a tool for the molecular structure assessment of ten isomers in traveling wave and trapped ion mobility spectrometry

RATIONALE

The separation of isomeric compounds with major differences in their physiochemical and pharmacokinetic properties is of particular importance in pharmaceutical R&D. However, the structural assessment and separation of these compounds with current analytical techniques and methods are still a challenge. In this study, we describe strategies to separate the various structural and stereo-isomers.

METHODS

The separation of ten structural and stereo-isomers was investigated using Trapped and Travelling Wave ion mobility spectrometry (TIMS and TWIMS). Different strategies including adduct ion formation with Na, Li, Ag and Cs as well as fragmentation before and after the ion mobility cell were applied to separate the isomeric compounds.

RESULTS

All the counter ions (in particular Na) strongly coordinated with the test analytes in all the IMS systems. The highest resolving power was achieved for the sodium and lithium adducts using TIMS-time-of-flight (TOF). However, some separation was attained on a Synapt HDMS system with its unique potential to monitor the ion mobility of the product ions. The elution order of the adduct ions was the same in all instruments, in which, unexpectedly, the para-substituted isomer of the [M + Na]⁺ species had the lowest collision cross section followed by the meta- and ortho-isomers.

CONCLUSIONS

The formation of adduct ions could facilitate the separation of structural and even stereo-isomers by generating different molecular conformations. In addition, fragmenting isomers before or after the ion mobility cell is a valuable strategy to separate and also to assess the structures of adducts and different conformers.

Gas Phase Stability of Protein Ions in a Cyclic Ion Mobility Spectrometry Traveling Wave Device

Ion mobility mass spectrometry (IM-MS) allows separation of native protein ions into “conformational families”. Increasing the IM resolving power should allow finer structural information to be obtained and can be achieved by increasing the length of the IM separator. This, however, increases the time that protein ions spend in the gas phase and previous experiments have shown that the initial conformations of small proteins can be lost within tens of milliseconds. Here, we report on investigations of protein ion stability using a multipass traveling wave (TW) cyclic IM (cIM) device. Using this device, minimal structural changes were observed for Cytochrome C after hundreds of milliseconds, while no changes were observed for a larger multimeric complex (Concanavalin A). The geometry of the instrument (Q-cIM-ToF) also enables complex tandem IM experiments to be performed, which were used to obtain more detailed collision-induced unfolding pathways for Cytochrome C. The instrument geometry provides unique capabilities with the potential to expand the field of protein analysis via IM-MS.

A Semi-Empirical Framework for Interpreting Traveling Wave Ion Mobility Arrival Time Distributions

The inherent structural heterogeneity of biomolecules is an important biophysical property that is essential to their function, but is challenging to characterize experimentally. We present a workflow that rapidly and quantitatively assesses the conformational heterogeneity of peptides and proteins in the gas phase using traveling wave ion mobility (TWIM) arrival time distributions (ATDs). We have established a set of semi-empirical equations that model the TWIM ATD peak width and resolution across a wide range of wave amplitudes (V) and wave velocities (v). In addition, a conformational broadening parameter, δ, can be extracted from this analysis that reports on the contribution of conformational heterogeneity to the broadening of TWIM ATD peak width during ion mobility separation. We use this δ value to evaluate the conformational heterogeneity of a set of helical peptides, and our analysis correlates well with previous peak width observations reported for these ions. Furthermore, we use molecular dynamics simulations to independently investigate the general flexibility of these peptides in the gas phase, and generate similar trends found in experimental TWIM data. Finally, we extended our analysis to Avidin, a 64-kDa homotetramer, and quantify the structural heterogeneity of this intact complex using TWIM ATD data as a function of cross-linking. We observe an initial reduction in δ values as a function of cross-linker concentration, demonstrating the sensitivity of our δ value analysis to changes in flexibility of the assembly.

Recommendations for reporting ion mobility Mass Spectrometry measurements

Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0 ) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

Application of molecular dynamics simulation to improve the theoretical prediction for collisional cross section of aromatic compounds with long alkyl chains in crude oils

RATIONALE

Molecular dynamics (MD) simulations with finite temperature were performed to improve the theoretical prediction of collisional cross section (CCS) values, especially for aromatic compounds containing long alkyl chains.

METHODS

In this study, the CCS values of 11 aromatic compounds with long alkyl chains were calculated by MD simulations while considering internal energy at 300, 500, and 700 K, and the results were compared with experimentally determined values.

RESULTS

The CCS values calculated at higher energies showed better agreement with the experimental values. Polycyclic aromatic hydrocarbons (PAHs) such as pentacene and benz[b]anthracene were also investigated, and better agreement between the theoretical and experimental results was observed when higher temperature (or higher internal energy) was considered.

CONCLUSIONS

The data presented in this study show that the internal degrees of freedom of ions must be considered to accurately predict the CCS values of aromatic compounds with a flexible structure measured by ion mobility mass spectrometry.

Ultra-high-resolution ion mobility spectrometry-current instrumentation, limitations, and future developments

With recent advances in ionization sources and instrumentation, ion mobility spectrometers (IMS) have transformed from a detector for chemical warfare agents and explosives to a widely used tool in analytical and bioanalytical applications. This increasing measurement task complexity requires higher and higher analytical performance and especially ultra-high resolution. In this review, we will discuss the currently used ion mobility spectrometers able to reach such ultra-high resolution, defined here as a resolving power greater than 200. These instruments are drift tube IMS, traveling wave IMS, trapped IMS, and field asymmetric or differential IMS. The basic operating principles and the resulting effects of experimental parameters on resolving power are explained and compared between the different instruments. This allows understanding the current limitations of resolving power and how ion mobility spectrometers may progress in the future. Graphical abstract.

Intermediates of N-Heterocyclic Carbene (NHC) Dimerization Probed in the Gas Phase by Ion Mobility Mass Spectrometry: C-H⋅⋅⋅:C Hydrogen Bonding Versus Covalent Dimer Formation

N-Heterocyclic carbenes (NHCs, :C) can interact with azolium salts (C-H⁺ ) by either forming a hydrogen-bonded aggregate (CHC⁺ ) or a covalent C-C bond (CCH⁺ ). In this study, the intramolecular NHC-azolium salt interactions of aromatic imidazolin-2-ylidenes and saturated imidazolidin-2-ylidenes have been investigated in the gas phase by traveling wave ion mobility mass spectrometry (TW IMS) and DFT calculations. The TW IMS experiments provided evidence for the formation of these important intermediates in the gas phase, and they identified the predominant aggregation mode (hydrogen bond vs. covalent C-C) as a function of the nature of the interacting carbene-azolium pairs.

Ion-peptide interactions between alkali metal ions and a termini-protected dipeptide: modeling a portion of the selectivity filter in K+ channels

Potassium channels have the unique ability to allow the selective passage of potassium ions at near diffusion-free rates while inhibiting the passage of more abundant sodium ions. Local interactions between chemical functional groups and the ions are responsible for both selectivity and transport. As an initial step in characterizing these interactions, the structures of Na+ and K+ complexed to the Ac-Tyr-NHMe peptide have been determined from infrared laser spectroscopy and supporting ab initio calculations. Ac-Tyr-NHMe, a termini-protected peptide sequence, replicates the GYG portion of one of the four peptide chains comprising the selectivity filter of a K+ channel. This peptide contains two carbonyl groups, among the eight C[double bond, length as m-dash]O groups forming the S1 binding site of the selectivity filter. Three conformations have been identified for both ions by laser IR-IR double resonance methods. Two conformations have the ion bound to the two C[double bond, length as m-dash]O groups. The third conformation has, in addition, a cation-π interaction with the aromatic ring of tyrosine, i.e. tridentate binding. The relative contributions of the three conformers are approximately the same for K+Ac-Tyr-NHMe, while the tridentate conformer is preferred for Na+Ac-Tyr-NHMe. These differences will be discussed in the context of ion mobility and selectivity.

Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry

This study explored the use of modular nucleic acid (NA) standards to generate calibration curves capable of translating primary ion mobility readouts into corresponding collision cross section (CCS) data. Putative calibrants consisted of single- (ss) and double-stranded (ds) oligo-deoxynucleotides reaching up to ∼40 kDa in size (i.e., 64 bp) and ∼5700 Å(2) in CCS. To ensure self-consistency among reference CCS values, computational data obtained in house were preferred to any experimental or computational data from disparate sources. Such values were obtained by molecular dynamics (MD) simulations and either the exact hard sphere scattering (EHSS) or the projection superposition approximation (PSA) methods, and then plotted against the corresponding experimental values to generate separate calibration curves. Their performance was evaluated on the basis of their correlation coefficients and ability to provide values that matched the CCS of selected test samples mimicking typical unknowns. The results indicated that the predictive power benefited from the exclusion of higher charged species that were more susceptible to the destabilizing effects of Coulombic repulsion. The results revealed discrepancies between EHSS and PSA data that were ascribable to the different approximations used to describe the ion mobility process. Within the boundaries defined by these approximations and the challenges of modeling NA structure in a solvent-free environment, the calibrant sets enabled the experimental determination of CCS with excellent reproducibility (precision) and error (accuracy), which will support the analysis of progressively larger NA samples of biological significance.