Can ion mobility mass spectrometry and density functional theory help elucidate protonation sites in 'small' molecules?

Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling

The use of collision cross section (CCS) values derived from ion mobility studies is proving to be an increasingly important tool in the characterization and identification of molecules detected in complex mixtures. Here, a novel machine learning (ML) based method for predicting CCS integrating both molecular modeling (MM) and ML methodologies has been devised and shown to be able to accurately predict CCS values for singly charged small molecular weight molecules from a broad range of chemical classes. The model performed favorably compared to existing models, improving compound identifications for isobaric analytes in terms of ranking and assigning identification probability values to the annotation. Furthermore, charge localization was seen to be correlated with CCS prediction accuracy and with gas-phase proton affinity demonstrating the potential to provide a proxy for prediction error based on chemical structural properties. The presented approach and findings represent a further step towards accurate prediction and application of computationally generated CCS values.

Investigation of low-temperature partitioning with dispersive solid-phase extraction for quantification of pesticides in apples followed by electrospray-ionization mobility spectrometry: Comparison with conventional procedure

Ion mobility spectrometry (IMS) has a promising application prospect in food surveillance. However, due to the complexity of food matrix and trace levels of pesticide residues, the effective and rapid detection of pesticides by IMS has been a challenge, especially when using electrospray ionization (ESI) as an ion source. In this study, low-temperature partitioning with dispersive solid-phase extraction (LTP-dSPE) was explored and compared with conventional procedures. Both methods were validated for the quantification of eight pesticides in apples, obtaining a limit of detection (LOD) of 0.02-0.12 mg/kg for LTP-dSPE and 0.02-0.09 mg/kg for conventional solid-phase extraction (SPE), lower than those usually stipulated by government legislation in food matrices. For LTP-dSPE, the matrx effect (ME) ranged from -16.3 to -68.6 %, lower than that for the SPE method, ranging from -70.0 to -92.9 %. The results showed satisfactory efficiency and precision, with recovery values ranging from 67.9 to 115.4 % for LTP-dSPE and from 62.0 to 114.8 % for conventional SPE, with relative standard deviations below 13.0 %. Notably, the proposed LTP-dSPE/ESI-IMS has been shown to be more cost-effective, easier to use, more environment-friendly, more accessible, and, most importantly, less matrix effect than the conventional method, thereby being suitably applicable to a wide range of food safety applications.

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.

Understanding of protomers/deprotomers by combining mass spectrometry and computation

Multifunctional compounds may form different prototropic isomers under different conditions, which are known as protomers/deprotomers. In biological systems, these protomer/deprotomer isomers affect the interaction modes and conformational landscape between compounds and enzymes and thus present different biological activities. Study on protomers/deprotomers is essentially the study on the acidity/basicity of each intramolecular functional group and its effect on molecular structure. In recent years, the combination of mass spectrometry (MS) and computational chemistry has been proven to be a powerful and effective means to study prototropic isomers. MS-based technologies are developed to discriminate and characterize protomers/deprotomers to provide structural information and monitor transformations, showing great superiority than other experimental methods. Computational chemistry is used to predict the thermodynamic stability of protomers/deprotomers, provide the simulated MS/MS spectra, infrared spectra, and calculate collision cross-section values. By comparing the theoretical data with the corresponding experimental results, the researchers can not only determine the protomer/deprotomer structure, but also investigate the structure-activity relationship in a given system. This review covers various MS methods and theoretical calculations and their devotion to isomer discrimination, structure identification, conformational transformation, and phase transition investigation of protomers/deprotomers.

Analytical key issues and challenges in the LC-MS/MS determination of antibiotics in wastewater

The research on antibiotics occurrence in the aquatic environment has become a hot topic in the last years due to their potential negative effects, associated to possible bacterial antibiotic-resistance, after continuous exposure to these compounds. Most of antibiotic residues are not completely removed in the wastewater treatment plants (WWTPs) and end up in the aquatic environment through treated wastewater (WW). The development of reliable analytical methodologies for the determination of antibiotics in influent (IWW) and effluent wastewater (EWW) is needed with different purposes, among others: monitoring their occurrence in the aquatic environment, performing environmental risk assessment, estimating removal efficiencies of WWTPs, or estimating the consumption of these compounds. In this paper, we perform an in-depth investigation on analytical key issues that pose difficulties in the determination of antibiotics in complex matrices, such as WW, and we identify challenges to be properly addressed for successful analysis. The analytical technique selected was liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), as it is the most powerful and widely applied at present for antibiotic residues determination. The mass spectrometric behavior of 18 selected antibiotics, the chromatographic performance, ion ratio variations associated to the sample matrix when using different precursor ions or protomers, and the macrolides adsorption to glass vial, were some of the issues studied in this work. On the basis of the detailed study performed, an analytical LC-MS/MS method based on sample direct injection has been developed for quantification of 18 antibiotics in IWW and EWW, allowing their determination at low ng L^-1 levels.

Highly Sensitive Molecularly Imprinted Polymer-Based Electrochemical Sensors Enhanced by Gold Nanoparticles for Norfloxacin Detection in Aquaculture Water

The overuse of antibiotics in aquaculture and pharmaceuticals and their subsequent leaking into the environment have been demonstrated to be a potential route for creating antibiotic resistance in bacteria. In order to assess the impact of this problem and take regulatory measures, it is necessary to develop tools that allow for the detection of antibiotics in environmental samples in a routine, low-cost manner. In this study, we integrated gold nanoparticles (AuNPs) into a molecularly imprinted polymer (MIP) membrane to fabricate a new sensor for the detection of norfloxacin in pharmaceuticals and aquaculture samples. The receptor layers were characterized by scanning electron microscopy, electrochemical impedance spectroscopy, and Raman spectroscopy. The results of these studies demonstrate that the addition of AuNPs to the polymer network enhanced the sensor sensitivity by at least a factor of two. The MIP-AuNPs sensor has a low detection limit (0.15 ng/mL, S/N = 3) with a wide linear range and very high sensitivity. The selectivity of the fabricated sensor was measured in the sample containing other antibiotics (like chloramphenicol, ciprofloxacin, and levofloxacin). Rapid and precise norfloxacin detection in pharmaceutical compounds and fishpond water samples indicates that the fabricated sensor has the potential to be used for routine screening of aquacultures and pharmaceutical processes.

Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics

Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM-MS), for metabolomics and lipidomics applications in a variety of fields including life, biomedical, and food sciences. IM-MS provides three main technical advantages over traditional LC-MS workflows. Firstly, in addition to mass, IM-MS allows collision cross-section values to be measured for metabolites and lipids, a physicochemical identifier related to the chemical shape of an analyte that increases the confidence of identification. Second, IM-MS increases peak capacity and the signal-to-noise, improving fingerprinting as well as quantification, and better defining the spatial localization of metabolites and lipids in biological and food samples. Third, IM-MS can be coupled with various fragmentation modes, adding new tools to improve structural characterization and molecular annotation. Here, we review the state-of-the-art in IM-MS technologies and approaches utilized to support metabolomics and lipidomics applications and we assess the challenges and opportunities in this growing field.

Different ion mobility-mass spectrometry coupling techniques to promote metabolomics

Metabolomics has become increasingly popular in recent years for many applications ranging from clinical diagnosis, human health to biotechnological questioning. Despite technological advances, metabolomic studies are still currently limited by the difficulty of identifying all metabolites, a class of compounds with great chemical diversity. Although lengthy chromatographic analyses are often used to obtain comprehensive data, many isobar and isomer metabolites still remain unresolved, which is a critical point for the compound identification. Currently, ion mobility spectrometry is being explored in metabolomics as a way to improve metabolome coverage, analysis throughput and isomer separation. In this review, all the steps of a typical workflow for untargeted metabolomics are discussed considering the use of an ion mobility instrument. An overview of metabolomics is first presented followed by a brief description of ion mobility instrumentation. The ion mobility potential for complex mixture analysis is discussed regarding its coupling with a mass spectrometer alone, providing gas-phase separation before mass analysis as well as its combination with different separation platforms (conventional hyphenation but also multidimensional ion mobility couplings), offering multidimensional separation. Various instrumental and analytical conditions for improving the ion mobility separation are also described. Finally, data mining, including software packages and visualization approaches, as well as the construction of ion mobility databases for the metabolite identification are examined.

Protomer Formation Can Aid the Structural Identification of Caffeine Metabolites

The structural annotation of isomeric metabolites remains a key challenge in untargeted electrospray ionization/high-resolution mass spectrometry (ESI/HRMS) metabolomic analysis. Many metabolites are polyfunctional compounds that may form protomers in electrospray ionization sources and therefore yield multiple peaks in ion mobility spectra. Protomer formation is strongly structure-specific. Here, we explore the possibility of using protomer formation for structural elucidation in metabolomics on the example of caffeine, its eight metabolites, and structurally related compounds. It is observed that two-thirds of the studied compounds formed high- and low-mobility species in high-resolution ion mobility. Structures in which proton hopping was hindered by a methyl group at the purine ring nitrogen (position 3) yielded structure-indicative fragments with collision-induced dissociation (CID) for high- and low-mobility ions. For compounds where such a methyl group was not present, a gas-phase equilibrium could be observed for tautomeric species with two-dimensional ion mobility. We show that the protomer formation and the gas-phase properties of the protomers can be related to the structure of caffeine metabolites and facilitate the identification of the structural isomers.

Cyclic Peptide Protomer Detection in the Gas Phase: Impact on CCS Measurement and Fragmentation Patterns

With the recent improvements in ion mobility resolution, it is now possible to separate small protomeric tautomers, called protomers. In larger molecules above 1000 Da such as peptides, a few studies suggest that protomers do exist as well and may contribute to their gas-phase conformational heterogeneity. In this work, we observed a CCS distribution that can be explained by the presence of protomers of surfactin, a small lipopeptide with no basic site. Following preliminary density functional theoretical calculations, several protonation sites in the gas phase were energetically favorable in positive ionization mode. Experimentally, at least three near-resolved IM peaks were observed in positive ionization mode, while only one was detected in negative ionization mode. These results were in good agreement with the DFT predictions. CID breakdown curve analysis after IM separation showed different inflection points (CE₅₀) suggesting that different intramolecular interactions were implied in the stabilization of the structures of surfactin. The fragment ratio observed after collision-induced fragmentation was also different, suggesting different ring-opening localizations. All these observations support the presence of protomers on the cyclic peptide moieties of the surfactin. These data strongly suggest that protomeric tautomerism can still be observed on molecules above 1000 Da if the IM resolving power is sufficient. It also supports that the proton localization involves a change in the 3D structure that can affect the experimental CCS and the fragmentation channels of such peptides.

Influence Exerted by the Solvent Effect on the Mobility Peak of 1,8-Naphthalic Anhydride in Ion Mobility Spectrometry

The collision cross-section (CCS) values of ions determined by ion mobility-mass spectrometry (IM-MS) can be used to deduce the shape and size of the ions. For each compound, as well as its isomer or tautomer, a unique arrival time peak was obtained in extracted ion mobility (EIM) spectra, which corresponded to a specific CCS value. However, the generation of solvated ions by electrospray ionization (ESI) increases the number of mobility peaks, which makes the EIM spectra difficult to interpret. In this study, solvent clusters formed by acetonitrile and methanol around 1,8-naphthalic anhydride (1,8-NA) cations ([C₁₂H₆O₃ + H]⁺_1,8-NA) were investigated using trapped ion mobility spectrometry-time-of-flight mass spectrometry (TIMS-TOF MS). The effects of infusion flow rate, nebulizer gas pressure, drying gas rate, and drying gas temperature on the formation of solvent clusters from acetonitrile and methanolic solution were systematically studied. The formation of solvent clusters was observed with infusion flow rates increased, which was manifested by the larger experimental CCS values of [C₁₂H₆O₃ + H]⁺_1,8-NA. Acetonitrile tended to form solvent clusters around ions more readily than methanol. These solvent clusters were stable enough to be detected by TIMS, but they cannot survive under ion activation conditions of mass spectrometry (MS). Increasing the nebulizer gas pressure seems to be a better way to eliminate the formation of solvent clusters in TIMS-TOF MS and give a "cleaner" EIM spectra. The current research demonstrates that more attention should be paid to the solvent effect on CCS values and their interpretation.

Solvent-Mediated Proton-Transfer Catalysis of the Gas-Phase Isomerization of Ciprofloxacin Protomers

Understanding how neutral molecules become protonated during positive-ion electrospray ionization (ESI) mass spectrometry is critically important to ensure analytes can be efficiently ionized, detected, and unambiguously identified. The ESI solvent is one of several parameters that can alter the dominant site of protonation in polyfunctional molecules and thus, in turn, can significantly change the collision-induced dissociation (CID) mass spectra relied upon for compound identification. Ciprofloxacin─a common fluoroquinolone antibiotic─is one such example whereby positive-ion ESI can result in gas-phase [M + H]⁺ ions protonated at either the keto-oxygen or the piperazine-nitrogen. Here, we demonstrate that these protonation isomers (or protomers) of ciprofloxacin can be resolved by differential ion mobility spectrometry and give rise to distinctive CID mass spectra following both charge-directed and charge-remote mechanisms. Interaction of mobility-selected protomers with methanol vapor (added via the throttle gas supply) was found to irreversibly convert the piperazine N-protomer to the keto-O-protomer. This methanol-mediated proton-transport catalysis is driven by the overall exothermicity of the reaction, which is computed to favor the O-protomer by 93 kJ mol^-1 (in the gas phase). Conversely, gas phase interactions of mobility-selected ions with acetonitrile vapor selectively depletes the N-protomer ion signal as formation of stable [M + H + CH₃CN]⁺ cluster ions skews the apparent protomer population ratio, as the O-protomer is unaffected. These findings provide a mechanistic basis for tuning protomer populations to ensure faithful characterization of multifunctional molecules by tandem mass spectrometry.

Predicting ion mobility as a function of the electric field for small ions in light gases

High resolution mobility devices such as Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) and Differential Mobility spectrometers (DMS) use strong electric fields to gas concentration ratios, E/N, to separate ions in the gas phase. While extremely successful, their empirical results show a non-linear, ion-dependent relation between mobility K and E/N that is difficult to characterize. The one-temperature theory Mason-Schamp equation, which is the most widely used ion mobility equation, unfortunately, cannot capture this behavior. When the two-temperature theory is used, it can be shown that the K-E/N behavior can be followed quite closely numerically by equating the effect of increasing the field to an increase in the ion temperature. This is attempted here for small ions in a Helium gas environment showing good agreement over the whole field range. To improve the numerical characterization, the Lennard-Jones (L-J) potentials may be optimized. This is attempted for Carbon, Hydrogen, Oxygen and Nitrogen at different degrees of theory up to the fourth approximation, which is assumed to be exact. The optimization of L-J improves the accuracy yielding errors of about 3% on average. The fact that a constant set of L-J potentials work for the whole range of E/N and for several molecules, also suggests that inelastic collisions can be circumvented in calculations for He. The peculiar K-E/N hump behaviors are studied, and whether mobility increases or decreases with E/N is shown to derive from a competition between relative kinetic energy and the interaction potentials.

Electronic spectroscopy of differential mobility-selected prototropic isomers of protonated para-aminobenzoic acid

para-Aminobenzoic acid (PABA) was electrosprayed from mixtures of protic and aprotic solvents, leading to formation of two prototropic isomers in the gas phase whose relative populations depended on the composition of the electrospray solvent. The two ion populations were separated in the gas phase using differential mobility spectrometry (DMS) within a nitrogen-only environment at atmospheric pressure. Under high-field conditions, the two prototropic isomers eluted with baseline signal separation with the N-protonated isomer having a more negative CV shift than the O-protonated isomer, in accord with previous DMS studies. The conditions most favorable for formation and separation of each tautomer were used to trap each prototropic isomer in a quadrupole ion trap for photodissociation action spectroscopy experiments. Spectral interrogation of each prototropic isomer in the UV region (3-6 eV) showed good agreement with previously recorded spectra, although a previously reported band (4.8-5.4 eV) was less intense for the O-protonated isomer in our measured spectrum. Without DMS selection, the measured spectra contained features corresponding to both protonated isomers even when solvent conditions were optimised for formation of a single isomer. Interconversion between protonated isomers within the ion trap was observed when protic ESI solvents were employed, leading to spectral cross contamination even with mobility selection. CCSD vertical excitation energies and vertical gradient (VG) Franck-Condon simulations are presented and reproduce the measured spectral features with near-quantitative agreement, providing supporting evidence for spectral assignments.

Atmospheric Pressure Drift Tube Ion Mobility Spectrometry Coupled with Two-Dimensional Tandem Mass Spectrometry

Atmospheric pressure drift tube ion mobility was coupled with two-dimensional tandem mass spectrometry (2D MS/MS) in a linear ion trap to simultaneously collect ion mobility and the entire MS/MS data domain. Utilizing ion intensities from precursor ion and neutral loss scan lines, ion mobility spectra of multiple compounds with particular functional groups were acquired in a single experiment. Functional group-specific ion mobility spectra were demonstrated for a standard mixture of lipids. Additionally, ion mobility was used to separate isobaric ions prior to 2D MS/MS. The combination of these two methods offers improvements for the analysis of complex mixtures.

Investigations into pesticide charge site isomers using conventional IM and cIM systems

A growing number of pesticides are being used around the world necessitating strict regulatory policies to guarantee consumer safety. Liquid Chromatography - Mass Spectrometry (LC-MS) is a highly sensitive method for pesticide screening, which provides retention time, mass/charge ratios and the relative abundances of characteristic product ions. Variability in the latter necessitates relatively large tolerances (±30%, SANCO/12682/2019, current EU regulation). One cause of this variability may stem from the presence of different charge-site isomers (charge carrier being a proton, sodium cation, potassium cation and alike); each yielding a set of different product ions, of which the relative ratios are influenced by solution and ion source conditions. Consequently, varying relative abundances may be observed for analyte ions produced from calibration standards, chemical residues in food matrices and across different instruments. Ion Mobility Spectrometry (IMS) is a fast, gas phase separation technique which can resolve charge-site isomers based on differences in their collisional cross sections (CCSs). We previously used the IM device embedded in LC-IM-MS geometry to generate a pesticide CCS database and subsequently focussed upon identification of pesticides which form charge-site isomers. Latterly, we applied this approach to screen food commodities for pesticide residues. In some instances, isomer separation was clear, however sometimes broad, unresolved distributions were observed. Using a high-resolution cyclic IM device (cIM) we resolved and determined CCS values of species of indoxacarb, spinosad, fenpyroximate, epoxiconazole, metaflumizone and avermectin. Furthermore, utilising novel cIM functionalities (tandem-IM) we discovered that two spinosyn sodimers can interconvert in the gas phase.

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

Determination of drugs and drug metabolites by ion mobility-mass spectrometry: A review

Ion mobility-mass spectrometry (IM-MS) has gained increased applications in the characterization and identification of drugs and drug metabolites, largely owning to the complementary separation of analyte ions based on their gas-phase size and shape in the IM dimension in addition to their mass-to-charge ratios. In this review, we discuss recent advances in such applications. We first introduce various types of IM techniques, focusing on those that allow the measurement of collision cross section (CCS), the physical property of an ion that reflects its gas-phase size and shape. Next, we discuss the IM-MS landscape of the large chemical space of drugs and multimodal distributions of certain drugs in IM separation due to the presence of protomers. We then review drug metabolism reactions and discuss the application of IM-MS in separation and identification of isomeric drug metabolites. Subsequently, we discuss various approaches to generate theoretical and predicted CCS data, including theory-based calculation methods and data-driven prediction models, and currently available resources on these approaches. Finally, current limitations and future directions of application of IM-MS are discussed.

Characterization of the Impact of Drug Metabolism on the Gas-Phase Structures of Drugs Using Ion Mobility-Mass Spectrometry

Conventional strategies for drug metabolite identification employ a combination of liquid chromatography-mass spectrometry (LC-MS), which offers higher throughput but provides limited structural information, and nuclear magnetic resonance spectroscopy, which can achieves the most definitive identification but lacks throughput. Ion mobility-mass spectrometry (IM-MS) is a rapid, two-dimensional analysis that separates ions on the basis of their gas-phase size and shape (reflected by collision cross section, CCS) and their mass-to-charge (m/z) ratios. The rapid nature of IM separation combined with the structural information provided by CCS make IM-MS a promising technique for obtaining more structural information on drug metabolites without sacrificing analytical throughput. Here, we present an in vitro biosynthesis coupled with IM-MS strategy for rapid generation and analysis of drug metabolites. Drug metabolites were generated in vitro using pooled subcellular fractions derived from human liver and analyzed using a rapid flow injection-IM-MS method. We measured CCS values for 19 parent drugs and their 37 metabolites generated in vitro (78 values in total), representing a wide variety of metabolic modifications. Post-IM fragmentation and computational modeling were used to support metabolite identifications and explore the structural characteristics driving behaviors observed in IM separation. Overall, we found the effects of metabolic modifications on the gas-phase structures of the metabolites to be highly dependent upon the structural characteristics of the parent compounds and the specific position of the modification. This in vitro biosynthesis coupled with rapid IM-MS analysis workflow represents a promising platform for rapid and high-confidence identification of drug metabolites, applicable at a large scale.

Investigations into the performance of travelling wave enabled conventional and cyclic ion mobility systems to characterise protomers of fluoroquinolone antibiotic residues

RATIONALE

Fluoroquinolones (FLQs) have been shown to form protomers with distinctive fragment profiles. Experimental parameters affect protomer formation, impacting observed conventional tandem mass spectrometric (MS/MS) dissociation and multiple reaction monitoring (MRM) transition reproducibility. Collision cross section (CCS) measurement can provide an additional identification metric and improved ion mobility (IM) separation strategies could provide further understanding of fluctuations in fragmentation when using electrospray ionisation (ESI).

METHODS

Porcine muscle tissue was fortified with nine fluoroquinolone antibiotics. Extracts were cleaned using QuEChERS dispersive extraction. Separation was achieved via ultra-high-performance liquid chromatography (UHPLC) and analysis performed using positive ion ESI coupled with linear T-wave IM (N₂ and CO₂ drift gas) and cyclic IM-MS (calibrated to perform accurate mass and CCS measurement).

RESULTS

IM-resolved protomeric species have been observed for nine FLQs (uniquely three for danofloxacin). Long-term reproducibility and cross-platform T-wave/cIM studies have demonstrated CCS metric errors <1.5% when compared with a FLQ protomer reference CCS library. When comparing FLQ protomer separation using a standard, linear T-wave IM separator (N₂ /CO₂ ) and using a high-resolution cyclic T-wave device (N₂ ), protomer peak-to-peak resolution ranged between Rs = 1 to Rs = 6 for the IM strategies utilised.

CONCLUSIONS

CCS is a reliable cross platform metric; specific FLQ CCS identification fingerprints have been produced, illustrating the potential to compliment MS/MS specificity or provide an alternative identification metric. Using cIM there is opportunity to correlate the erratic nature of protomer formation with the analytical conditions used and to gain further understanding of ionisation/dissociation mechanisms taking place during routine analyses.

Using differential ion mobility spectrometry to perform class-specific ion-molecule reactions of 4-quinolones with selected chemical reagents

Gas phase ion/molecule reactions are often used in analytical applications to support the analysis of isomers or to identify specific functional groups of organic molecules. Until now, deliberate chemical reactions have not been performed in differential ion mobility spectrometry (DMS) devices except for hydrogen exchange and cluster formation. The present work extends that of Colorado and Brodbelt (Anal Chem 66:2330-5, 1994) on ion/molecule reactions in an ion trap mass spectrometer. In this study, class-specific chemical reactions of 4-quinolone antibiotics with various chemical reagents were used to demonstrate the analytical utility of ion/molecule reactions in a DMS drift cell. For these reactions, dehydrated reactive precursor ions were initially formed and made to undergo annulation reactions with selected reagents within the timescale of the DMS separation. Careful study of the energies required for dissociation of the adducts confirmed the covalent nature of the newly formed bond; thus demonstrating the analytical utility of this approach. Graphical abstract.

Selecting and identifying gas-phase protonation isomers of nicotineH+ using combined laser, ion mobility and mass spectrometry techniques

Protonation isomers of gas-phase nicotineH⁺ are separated and assigned using a combination of FAIMS and UV photodissociation action spectroscopy.

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.

Predicting ion mobility collision cross sections directly from standard quantum chemistry software

A method is proposed to predict ions' collision cross-sectional area from properties that are already evaluated in standard quantum chemistry software. Computed molecular isodensity surface areas recover the predictions of existing projection approximations. Computed solvent cavity areas give comparable accuracy. This provides a simplified workflow for assigning ion-mobility mass spectra.

Transformation of the gas-phase favored O-protomer of p-aminobenzoic acid to its unfavored N-protomer by ion activation in the presence of water vapor: An ion-mobility mass spectrometry study

An ion-mobility mass spectrometry study showed that the preferred O-protonated form of p-aminobenzoic in the gas phase can be converted to the thermodynamically less favored N-protomer by in-source collision-induced ion activation during the ion transfer process from the atmospheric region to the first vacuum region if the humidity is high in the ion source. Upon the addition of water vapor to the nitrogen gas used to promote the solid analyte to the gas phase under helium-plasma ionization conditions, the intensity of the ion-mobility arrival-time peak for the N-protomer increased dramatically. Evidently, the ion-activation process in the first vacuum region is able to provide the energy required to surmount the barrier to isomerize the O-protomer to the more energetic N-protomer. The transfer of the proton attached to the carbonyl oxygen atom of the O-protomer to the amino group takes place by a water-bridge mechanism. Apparently, the postionization transformations that take place during the transmission of ions from the atmospheric-pressure ion source to the detector, via different physical compartments of low to high vacuum, play an eminent role in determining the population ratios eventually manifested at the detector.

High performance collision cross section calculation-HPCCS

Since the commercial introduction of Ion Mobility coupled with Mass Spectrometry (IM-MS) devices in 2003, a large number of research laboratories have embraced the technique. IM-MS is a fairly rapid experiment used as a molecular separation tool and to obtain structural information. The interpretation of IM-MS data is still challenging and relies heavily on theoretical calculations of the molecule's collision cross section (CCS) against a buffer gas. Here, a new software (HPCCS) is presented, which performs CCS calculations using high perfomance computing techniques. Based on the trajectory method, HPCCS can accurately calculate CCS for a great variety of molecules, ranging from small organic molecules to large protein complexes, using helium or nitrogen as buffer gas with considerable gains in computer time compared to publicly available codes under the same level of theory. HPCCS is available as free software under the Academic Use License at https://github.com/cepid-cces/hpccs. © 2018 Wiley Periodicals, Inc.

The impact of environment and resonance effects on the site of protonation of aminobenzoic acid derivatives

The charge distribution in a molecule is crucial in determining its physical and chemical properties. Aminobenzoic acid derivatives are biologically active small molecules, which have two possible protonation sites: the amine (N-protonation) and the carbonyl oxygen (O-protonation). Here, we employ gas-phase infrared spectroscopy in combination with ion mobility-mass spectrometry and density functional theory calculations to unambiguously determine the preferred protonation sites of p-, m-, and o-isomers of aminobenzoic acids as well as their ethyl esters. The results show that the site of protonation does not only depend on the intrinsic molecular properties such as resonance effects, but also critically on the environment of the molecules. In an aqueous environment, N-protonation is expected to be lowest in energy for all species investigated here. In the gas phase, O-protonation can be preferred, and in those cases, both N- and O-protonated species are observed. To shed light on a possible proton migration pathway, the protonated molecule-solvent complex as well as proton-bound dimers are investigated.

Untrapping Kinetically Trapped Ions: The Role of Water Vapor and Ion-Source Activation Conditions on the Gas-Phase Protomer Ratio of Benzocaine Revealed by Ion-Mobility Mass Spectrometry

The role of water vapor in transforming the thermodynamically preferred species of protonated benzocaine to the less favored protomer was investigated using helium-plasma ionization (HePI) in conjunction with ion-mobility mass spectrometry (IM-MS). The IM arrival-time distribution (ATD) recorded from a neat benzocaine sample desorbed to the gas phase by a stream of dry nitrogen and ionized by HePI showed essentially one peak for the O-protonated species. However, when water vapor was introduced to the enclosed ion source, within a span of about 150 ms the ATD profile changed completely to one dominated by the N-protonated species. Under spray-based ionization conditions, the nature and composition of the solvents have been postulated to play a decisive role in defining the manifested protomer ratios. In reality, the solvent vapors present in the ion source (particularly the ambient humidity) indirectly dictate the gas-phase ratio of the protomers. Evidently, the gas-phase protomer ratio established at the confinement of the ions is readjusted by the ion-activation that takes place during the transmission of ions to the vacuum. Although it has been repeatedly stated that ions can retain a "memory" of their solution structures because they can be kinetically trapped, and thereby represent their solution-based stabilities, we show that the initial airborne ions can undergo significant transformations in the transit through the intermediate vacuum zones between the ion source and the mass detector. In this context, we demonstrate that the kinetically trapped N-protomer of benzocaine can be untrapped by reducing the humidity of the enclosed ion source. Graphical Abstract ᅟ.

Large-Scale Structural Characterization of Drug and Drug-Like Compounds by High-Throughput Ion Mobility-Mass Spectrometry

Ion mobility-mass spectrometry (IM-MS) can provide orthogonal information, i.e., m/z and collision cross section (CCS), for the identification of drugs and drug metabolites. However, only a small number of CCS values are available for drugs, which limits the use of CCS as an identification parameter and the assessment of structure–function relationships of drugs using IM-MS. Here, we report the development of a rapid workflow for the measurement of CCS values of a large number of drug or drug-like molecules in nitrogen on the widely available traveling wave IM-MS (TWIM-MS) platform. Using a combination of small molecule and polypeptide CCS calibrants, we successfully determined the nitrogen CCS values of 1425 drug or drug-like molecules in the MicroSource Discovery Systems’ Spectrum Collection using flow injection analysis of 384-well plates. Software was developed to streamline data extraction, processing, and calibration. We found that the overall drug collection covers a wide CCS range for the same mass, suggesting a large structural diversity of these drugs. However, individual drug classes appear to occupy a narrow and unique space in the CCS–mass 2D spectrum, suggesting a tight structure–function relationship for each class of drugs with a specific target. We observed bimodal distributions for several antibiotic species due to multiple protomers, including the known fluoroquinolone protomers and the new finding of cephalosporin protomers. Lastly, we demonstrated the utility of the high-throughput method and drug CCS database by quickly and confidently confirming the active component in a pharmaceutical product.

Influence of Ionization Source Conditions on the Gas-Phase Protomer Distribution of Anilinium and Related Cations

The gas-phase-ion generation technique and specific ion-source settings of a mass spectrometer influence heavily the protonation processes of molecules and the abundance ratio of the generated protomers. Hitherto that has been attributed primarily to the nature of the solvent and the pH. By utilizing electrospray ionization and ion-mobility mass spectrometry (IM-MS), we demonstrate, even in the seemingly trivial case of protonated aniline, that the protomer ratio strongly depends on the source conditions. Under low in-source ion activation, nearly 100% of the N-protomer of aniline is produced, and it can be subsequently converted to the C-protomer by collisional activation effected by increasing the electrical potential difference between the entrance and exit orifices of the first vacuum region. This activation and transformation process takes place even before the ion is mass-selected and subjected to IM separation. Despite the apparent simplicity of the problem, the preferred protonation site of aniline in the gas phase-the amino group or the aromatic ring-has been a topic of controversy. Our results not only provide unambiguous evidence that ring- and nitrogen-protonated aniline can coexist and be interconverted in the gas phase, but also that the ratio of the protomers depends on the internal energy of the original ion. There are many dynamic ion-transformation and fragmentation processes that take place in the different physical compartments of a Synapt G2 HDMS instrument. Such processes can dramatically change the very identity even of small ions, and therefore should be taken into account when interpreting product-ion mass spectra. Graphical Abstract ᅟ.

Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers

Computational methods are employed to study the protomers in ESI-IM-MS.

Structural Characterization of Methylenedianiline Regioisomers by Ion Mobility-Mass Spectrometry, Tandem Mass Spectrometry, and Computational Strategies. 2. Electrospray Spectra of 3-Ring and 4-Ring Isomers

Building on results from our previous study of 2-ring methylenedianiline (MDA), a combined mass spectrometry approach utilizing ion mobility-mass spectrometry (IM-MS) and tandem mass spectrometry (MS/MS) coupled with computational methods enables the structural characterization of purified 3-ring and 4-ring MDA regioisomers in this current study. The preferred site of protonation for the 3-ring and 4-ring MDA was determined to be on the amino groups. Additionally, the location of the protonated amine along the MDA multimer was found to influence the gas phase stability of these molecules. Fragmentation mechanisms similar to the 2-ring MDA species were observed for both the 3-ring and 4-ring MDA. The structural characterization of 3-ring and 4-ring MDA isomers using modern MS techniques may aid polyurethane synthesis by the characterization of industrial grade MDA, multimeric MDA species, and methylene diphenyl diisocyanate (MDI) mixtures.

Decay mechanisms of protonated 4-quinolone antibiotics after electrospray ionization and ion activation

This study presents a detailed experimental investigation of charge isomers of protonated 4-quinolone antibiotics molecules formed during electrospray ionization (ESI) with proposed dissociation mechanisms after collisional activation. Piperazinyl quinolones have been previously shown to exhibit erratic behavior during tandem MS analyses of biological samples, which originated from varying ratios of two isomeric variants formed during ESI. Here, a combination of ESI-collision-induced dissociation (CID), differential ion mobility spectrometry (DMS), high resolution MS, and density functional theory (DFT) was used to investigate the underlying mechanisms of isomer formation and their individual dissociation behaviors. The study focused on ciprofloxacin; major findings were confirmed using structurally related 4-quinolones. DFT calculations showed a reversal of basicity for piperazinyl quinolones between liquid and gas phase. We provide an experimental comparison and theoretical treatment of factors influencing the formation ratio of the charge isomers during ESI, including solvent pH, protic/aprotic nature of solvent, and structural effects such as pK a and proton affinity. The actual dissociation mechanisms of the isomers of the protonated molecules were studied by separating the individual isomers via DMS-MS, which allowed type-specific CID spectra to be recorded. Both primary CID reactions of the two charge isomers originated from the same carboxyl group by charge-remote (CO(2) loss) and charge-mediated (H(2)O loss) fragmentation of the piperazinyl quinolones, depending on whether the proton resides on the more basic keto or the piperazinyl group, followed by a number of secondary dissociation reactions. The proposed mechanisms were supported by calculated energies of precursors, transition states, and products for competing pathways.