Studying Gas-Phase Interconversion of Tautomers Using Differential Mobility Spectrometry

Divergent Metabolic Fates of Aromatic Amino Acid-Derived Isomers: Insights from Ex Vivo Metabolomics and HDX-HRMS/MS-Based Resolution of Tautomers

Tautomers are one of the many types of isomers, and differences in tautomeric structures confer altered chemical and biological properties. Using ultrahigh-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) ex vivo metabolomics, we investigate, in whole blood, the divergent metabolism of enol and keto forms of indole-3-pyruvate (IPyA), a tautomeric product of aromatic amino acid metabolism. Two new compounds resulting from IPyA metabolism were discovered, 3-(1H-indol-3-yl)-2,3-dioxopropanoic acid or "indole-3-oxopyruvic acid" and glutathionyl-indole pyruvate (GSHIPyA), which were characterized via ultraviolet photodissociation (UVPD) and higher-energy collisional dissociation (HCD). Computational calculations support the hypothesis that GSHIPyA forms specifically through the enol form of IPyA. GSHIPyA is also hypothesized to be tautomeric, and a hydrogen-deuterium exchange-high-resolution tandem mass spectrometry (HDX-HRMS/MS) approach is developed to prove the presence of an enol and keto tautomer. HDX of GSHIPyA labels the keto form with an additional deuterium, relative to the enol form. HRMS/MS of the labeled isomers is employed to leverage the relationship of resolving power scaling inversely with the square root of m/z, for Orbitrap mass analyzers. HRMS/MS yields a smaller-molecular-weight deuterated tautomeric product ion, reducing the analyte ion m/z and thus lowering the resolving power necessary to separate the deuterated keto tautomer product ion from the [13]C product ion.

Impact of Protonation Sites on Collision-Induced Dissociation-MS/MS Using CIDMD Quantum Chemistry Modeling

Protonation is the most frequent adduct found in positive electrospray ionization collision-induced mass spectra (CID-MS/MS). In a parallel report Lee, J. J. Chem. Inf. Model. 2024, 10.1021/acs.jcim.4c00760, we developed a quantum chemistry framework to predict mass spectra by collision-induced dissociation molecular dynamics (CIDMD). As different protonation sites affect fragmentation pathways of a given molecule, the accuracy of predicting tandem mass spectra by CIDMD ultimately depends on the choice of its protomers. To investigate the impact of molecular protonation sites on MS/MS spectra, we compared CIDMD-predicted spectra to all available experimental MS/MS spectra by similarity matching. We probed 10 molecules with a total of 43 protomers, the largest study to date, including organic acids (sorbic acid, citramalic acid, itaconic acid, mesaconic acid, citraconic acid, and taurine) as well as aromatic amines including uracil, aniline, bufotenine, and psilocin. We demonstrated how different protomers can converge different fragmentation pathways to the same fragment ions but also may explain the presence of different fragment ions in experimental MS/MS spectra. For the first time, we used in silico MS/MS predictions to test the impact of solvents on proton affinities, comparing the gas phase and a mixture of acetonitrile/water (1:1). We also extended applications of in silico MS/MS predictions to investigate the impact of protonation sites on the energy barriers of isomerization between protomers via proton transfer. Despite our initial hypothesis that the thermodynamically most stable protomer should give the best match to the experiment, we found only weak inverse relationships between the calculated proton affinities and corresponding entropy similarities of experimental and CIDMD-predicted MS/MS spectra. CIDMD-predicted mechanistic details of fragmentation reaction pathways revealed a clear preference for specific protomer forms for several molecules. Overall, however, proton affinity was not a good predictor corresponding to the predicted CIDMD spectra. For example, for uracil, only one protomer predicted all experimental MS/MS fragment ions, but this protomer had neither the highest proton affinity nor the best MS/MS match score. Instead of proton affinity, the transfer of protons during the electrospray process from the initial protonation site (i.e., mobile proton model) better explains the differences between the thermodynamic rationale and experimental data. Protomers that undergo fragmentation with lower energy barriers have greater contributions to experimental MS/MS spectra than their thermodynamic Boltzmann populations would suggest. Hence, in silico predictions still need to calculate MS/MS spectra for multiple protomers, as the extent of distributions cannot be readily predicted.

Characterization of Anticancer Drug Protomers Using Electrospray Ionization and Ion Mobility Spectrometry-Mass Spectrometry

We used electrospray ionization and ion mobility spectrometry-mass spectrometry to detect and characterize the three anticancer drugs palbociclib, copanlisib, and olaparib. Ion mobility-mass spectrometry and density functional theory revealed that these compounds generate isomers during ionization (protomers) due to the presence of multiple protonation sites within their chemical structures. Our work has implications for understanding the solution- and gas-phase chemistry of these molecules during spray-based ionization processes.

Transition from vehicle to Grotthuss proton transfer in a nanosized flask: cryogenic ion spectroscopy of protonated p-aminobenzoic acid solvated with D2O

Proton transfer (PT) is one of the most ubiquitous reactions in chemistry and life science. The unique nature of PT has been rationalized not by the transport of a solvated proton (vehicle mechanism) but by the Grotthuss mechanism in which a proton is transported to the nearest proton acceptor along a hydrogen-bonded network. However, clear experimental evidence of the Grotthuss mechanism has not been reported yet. Herein we show by infrared spectroscopy that a vehicle-type PT occurs in the penta- and hexahydrated clusters of protonated p-aminobenzoic acid, while Grotthuss-type PT is observed in heptahydrated clusters, indicating a change in the PT mechanism depending on the degree of hydration. These findings emphasize the importance of the usually ignored vehicle mechanism as well as the degree of hydration. It highlights the possibility of controlling the PT mechanism by the number of water molecules in chemical and biological environments.

Highly Efficient Intramolecular Proton Transfer in p-Aminobenzoic Acid by a Single Ammonia Molecule as a Vehicle

Proton transfer is classified into two mechanisms: the Grotthuss (proton-relay) and vehicle mechanisms. It has been well studied on gas-phase proton transfer by a proton relay involving multiple molecules. However, a vehicle mechanism in which a single molecule transports a proton has rarely been reported. Here, we have obtained clear evidence that the proton transfers efficiently between the two protonation sites in protonated p-aminobenzoic acid (PABA·H+) by a single ammonia molecule as a vehicle. The gaseous PABA·H+ ions were reacted with NH3 or ND3 under single-collision conditions in a cold ion trap, and the proton-transferred ions were identified by cryogenic ion mobility-mass spectrometry. A reaction intermediate PABA·H+·NH3 was also detected for the first time. The reaction pathway search calculations and ab initio molecular dynamics simulations supported the present experimental finding that intramolecular proton transfer occurs very efficiently by the vehicle mechanism.

Dependence of Collision-Induced Mass Spectra of Protonated Michler's Ketone on the Nature of LC-MS Mobile Phase

Michler's ketone (MK) is a dimethylamino ketone that undergoes facile protonation under electrospray-ionization conditions to produce an ion of m/z 269. Initial LC-MS results showed that the collision-induced dissociation (CID) spectra of the m/z 269 ion depend heavily on the composition of the chromatographic mobile phase. Subsequent ion-mobility separation of the mass-selected m/z 269 ion revealed that protonated MK exists as two tautomeric forms. Moreover, the relative population of the two protomeric forms in the ion ensemble depends on the nature of the ambient molecules present in the atmospheric pressure ion source. For example, the ion-mobility arrival-time profile acquired from the mass-selected m/z 269 ion generated from an acetonitrile solution showed two peaks of near equal intensity. The peak with the shorter arrival time represented the O-protomer and that with the longer arrival time represented the N-protomer. However, when methanol or ammonia vapors were introduced to the ambient-pressure ion source, the intensity of the N-protomer peak decreased rapidly and that of the O-protomer signal soared until it became the dominant peak. When the introduction of methanol (or ammonia) vapors was stopped, the mobilogram signals gradually reverted back to their initial intensities. To rationalize this observation, we propose that the N-protomer of MK in the presence of methanol vapor undergoes transformation to the O-protomer by a Grotthuss-type mechanism via a methanol-based solvent bridge.

Mechanism of formation and ion mobility separation of protomers and deprotomers of diaminobenzoic acids and aminophthalic acids

Aminobenzoic acids are well-established candidates for understanding the formation of isomeric ions in positive mode electrospray ionization as they yield both N- and O-protomers (prototropic isomers) at the amine and carbonyl sites, respectively. In the present work, a combination of ion mobility-mass spectrometry and density functional theory calculations to determine the protonation and deprotonation behaviour of four diamino benzoic acid and four aminophthalic acid isomers is presented. The additional COOH group on the ring of aminophthalic acids provides experimental evidence regarding the mechanism of intramolecular NH₃⁺ → O proton transfer, which has been the subject of debate in recent years. To determine the proton acceptor O atom, ion mobility spectra of the fragments of protomers were used as a new method for the confidential assignment of the O-protomer structure, confirming only short-distance intramolecular NH₃⁺ → O proton transfer. Additionally, the substitution pattern both influences the basicity of the protonation sites and enables these molecules to form internal hydrogen bonds with the protonated or deprotonated sites. The formation of the hydrogen bonds in the deprotonated aminophthalic acids changed the charge distribution and subsequently their ion mobility-derived collision cross sections in nitrogen (CCS_N2) leading to separation of the four isomers studied. Finally, an interesting effect of the substitution pattern was observed as a synergistic electron-donating effect of the amine groups of 3,5-diaminobenzoic acid on enhancing the basicity of the carbon atom C2 of the ring and previously unreported formation of a C-protomer within aminobenzoic acid systems.

Chemical Transformations Can Occur during DMS Separations: Lessons Learned from Beer's Bittering Compounds

While developing a DMS-based separation method for beer's bittering compounds, we observed that the argentinated forms of humulone tautomers (i.e., [Hum + Ag]⁺) were partially resolvable in a N₂ environment seeded with 1.5 mol % of isopropyl alcohol (IPA). Attempting to improve the separation by introducing resolving gas unexpectedly caused the peaks for the cis-keto and trans-keto tautomers of [Hum + Ag]⁺ to coalesce. To understand why resolution loss occurred, we first confirmed that each of the tautomeric forms (i.e., dienol, cis-keto, and trans-keto) responsible for the three peaks in the [Hum + Ag]⁺ ionogram were assigned to the correct species by employing collision-induced dissociation, UV photodissociation spectroscopy, and hydrogen-deuterium exchange (HDX). The observation of HDX indicated that proton transfer was stimulated by dynamic clustering processes between IPA and [Hum + Ag]⁺ during DMS transit. Because IPA accretion preferentially occurs at Ag⁺, which can form pseudocovalent bonds with a suitable electron donor, solvent clustering also facilitated the formation of exceptionally stable microsolvated ions. The exceptional stability of these microsolvated configurations disproportionately impacted the compensation voltage (CV) required to elute each tautomer when the temperature within the DMS cell was varied. The disparity in CV response caused the peaks for the cis- and trans-keto species to merge when a temperature gradient was induced by the resolving gas. Moreover, simulations showed that microsolvation with IPA mediates dienol to trans-keto tautomerization during DMS transit, which, to the best of our knowledge, is the first observation of keto/enol tautomerization occurring within an ion-mobility device.

Modification of a Quadrupole/Orbitrap/Linear Quadrupole Ion Trap Tribrid Mass Spectrometer for Diagnostic Gas-Phase Ion-Molecule Reactions

Tandem mass spectrometry based on diagnostic gas-phase ion-molecule reactions represents a robust method for functional group identification in unknown compounds. To date, most of these reactions have been studied using unit-resolution instruments, such as linear quadrupole ion traps and triple quadrupoles, which cannot be used to obtain elemental composition information for the species of interest. In this study, a high-resolution mass spectrometer, a quadrupole/orbitrap/linear quadrupole ion trap tribrid, was modified by installing a portable reagent inlet system to obtain high-resolution data for ion-molecule reactions. Examination of a previously published test system, the reaction between protonated 1,1'-sulfonyldiimizadole with 2-methoxypropene, demonstrated the ability to perform ion-molecule reactions on the modified tribrid mass spectrometer. High-resolution data were obtained for ion-molecule reactions of three isobaric ions (protonated glycylalanine, protonated glutamine, and protonated lysine) with diethylmethoxyborane. On the basis of these data, the isobaric ions can be differentiated based on both their measured accurate mass as well as the different product ions they generated upon the ion-molecule reactions. In a different experiment, analyte ions were subjected to collision-induced dissociation (CID), and the structures of the resulting fragment ions were examined via diagnostic ion-molecule reactions. This experiment allows for the functional group interrogation of fragment ions and can be used to improve the understanding of the structures of fragment ions generated in the gas phase.

Hydration-induced protomer switching in p-aminobenzoic acid studied by cold double ion trap infrared spectroscopy

Para-Aminobenzoic acid (PABA) is a benchmark molecule to study solvent-induced proton site switching. Protonation of the carboxy and amino groups of PABA generates O- and N-protomers of PABAH⁺, respectively. Ion mobility mass spectrometry (IMS) and infrared photodissociation (IRPD) studies have claimed that the O-protomer most stable in the gas phase is converted to the N-protomer most stable in solution upon hydration with six water molecules in the gas-phase cluster. However, the threshold size has remained ambiguous because the arrival time distributions in the IMS experiments exhibit multiple peaks. On the other hand, IRPD spectroscopy could not detect the N-protomer for smaller hydrated clusters because of broad background due to annealing required to reduce kinetic trapping. Herein, we report the threshold size for O → N protomer switching without ambiguity using IR spectroscopy in a double ion trap spectrometer from 1300 to 1800 cm^-1. The pure O-protomer is prepared by electrospray, and size-specific hydrated clusters are formed in a reaction ion trap. The resulting clusters are transferred into a second cryogenic ion trap and the distribution of O- and N-protomers is determined by mid-IR spectroscopy without broadening. The threshold to promote O → N protomer switching is indeed five water molecules. It is smaller than the value reported previously, and as a result, its pentahydrated structure does not support the Grotthuss mechanism proposed previously. The extent of O → N proton transfer is evaluated by collision-assisted stripping IR spectroscopy, and the N-protomer population increases with the number of water molecules. This result is consistent with the dominant population of the N-protomer in aqueous solution.

Impact of Ambient Vapors on Spectra of 4-Nitroaniline Recorded under Atmospheric Solids Analysis Probe (ASAP) Mass Spectrometric Conditions

Thermally desorbed 4-nitroaniline (4-NA), upon atmospheric pressure chemical ionization (APCI), generates gaseous ions for its protonated species. The APCI mass spectrum recorded under mild in-source ion-activating conditions from 4-NA showed a peak at m/z 139, whereas that acquired under high ion-activating conditions showed two additional peaks at m/z 122 (^•OH loss) and 92 (^•NO loss). The spectrum changed instantaneously when acetonitrile vapor was introduced to the source. In the new spectrum, both m/z 122 and 92 peaks were absent, while a new peak appeared at m/z 93. Ion-mobility separation carried out with the m/z 139 ion revealed that the initial ion represented the thermodynamically favored nitro-protonated tautomer. The ion population changed to an ensemble dominated by the less-favored amino-protomer when acetonitrile vapor was introduced to the ion source. The amino-protomer, upon collisional activation, loses ^•NO₂ to generate an m/z 93 ion, which was confirmed to be the 4-dehydroanilinium ion. Ion mobility provided a practical way to monitor the changes secured by acetonitrile vapor because the two protomers showed different arrival times. Under spray-ionization conditions, the formation of the thermodynamically less favored protomer has been attributed to kinetic trapping. Our study demonstrated that the less favored amino-protomer could be generated by introducing acetonitrile vapor under nonspray conditions. Apparently, under APCI conditions, protonated water vapor attaches to the nitro group to generate a proton-bound heterodimer, which upon activation dissociates to yield the nitro-protomer. In contrast, protonated acetonitrile makes a tighter complex preferentially with the amino group, which upon activation breaks to the amino-protomer.

The origin of isomerization of aniline revealed by high kinetic energy ion mobility spectrometry (HiKE-IMS)

Although aniline is a relatively simple small molecule, the origin of its two peaks observed in ion mobility spectrometry (IMS) has remained under debate for at least 30 years. First hypothesized as a difference in protonation site (amine vs. benzene ring), each ion mobility peak differs by one Dalton when coupled with mass spectrometry where the faster mobility peak is the molecular ion peak, and the slower mobility peak is protonated. To complicate the deconvolution of structures, some previous literature shows the peaks as unresolved and thus proposes these species exist in equilibrium. In this work, we show that when measured with high kinetic energy ion mobility spectrometry (HiKE-IMS), the two peaks observed in spectra of both aniline and all n-fluoroanilines are fully separated (chromatographic resolution from 2-7, R_p > 110) and therefore not in equilibrium. The HiKE-IMS is capable of changing ionization conditions independently of drift region conditions, and our results agree with previous literature showing that ionization source settings (including possible fragmentation at this stage) are the only influence determining the speciation of the two aniline peaks. Finally, when the drift and reactant gas are changed to nitrogen, a third peak appears at high E/N for 2-fluoroaniline and 4-fluoroaniline for the first time in reported literature. As observed by HiKE-IMS-MS, the new third peak is also protonated showing that the para-protonated aniline and resulting fragment ion, molecular ion aniline, can be fully separated in the mobility domain for the first time. The appearance of the third peak is only possible due to the increased separation of the other two peaks within the HiKE-IMS.

A Portable Reagent Inlet System Designed to Diminish the Impact of Air and Water to Ion-Molecule Reactions Studied in a Linear Quadrupole Ion Trap

A portable reagent inlet system for a linear quadrupole ion trap (LQIT) mass spectrometer was designed to diminish the impact of air and water on gas-phase ion-molecule reactions. Compared to the traditional reagent mixing manifolds that has been extensively used for decades, the portable system is much simpler and has fewer junctions and a smaller inner space. These changes reduce the amount of air and water introduced into the mass spectrometer with the reagent. Furthermore, unlike the traditional manifolds, the portable system can be easily attached to or detached from the LQIT mass spectrometer. Finally, the price of the portable system is only 1/10 of that of a traditional manifold as estimated in 2022. Therefore, the portable system has several advantages over the traditional reagent mixing manifolds.

The hitchhiker's guide to dynamic ion-solvent clustering: applications in differential ion mobility spectrometry

This article highlights the fundamentals of ion-solvent clustering processes that are pertinent to understanding an ion's behaviour during differential mobility spectrometry (DMS) experiments. We contrast DMS with static-field ion mobility, where separation is affected by mobility differences under the high-field and low-field conditions of an asymmetric oscillating electric field. Although commonly used in mass spectrometric (MS) workflows to enhance signal-to-noise ratios and remove isobaric contaminants, the chemistry and physics that underpins the phenomenon of differential mobility has yet to be fully fleshed out. Moreover, we are just now making progress towards understanding how the DMS separation waveform creates a dynamic clustering environment when the carrier gas is seeded with the vapour of a volatile solvent molecule (e.g., methanol). Interestingly, one can correlate the dynamic clustering behaviour observed in DMS experiments with gas-phase and solution-phase molecular properties such as hydrophobicity, acidity, and solubility. However, to create a generalized, global model for property determination using DMS data one must employ machine learning. In this article, we provide a first-principles description of differential ion mobility in a dynamic clustering environment. We then discuss the correlation between dynamic clustering propensity and analyte physicochemical properties and demonstrate that analytes exhibiting similar ion-solvent interactions (e.g., charge-dipole) follow well-defined trends with respect to DMS clustering behaviour. Finally, we describe how supervised machine learning can be used to create predictive models of molecular properties using DMS data. We additionally highlight open questions in the field and provide our perspective on future directions that can be explored.

Conformational Changes Induced by Methyl Side-Chains in Protonated Tripeptides Containing Glycine and Alanine Residues

We present a systematic study of the conformational and isomeric populations in gas-phase protonated tripeptides containing glycine and alanine residues using infrared predissociation spectroscopy of cryogenically cooled ions. Specifically, the protonated forms of Gly-Gly-Gly, Ala-Gly-Gly, Gly-Ala-Gly, Gly-Gly-Ala, Ala-Ala-Gly, Ala-Gly-Ala, Gly-Ala-Ala, and Ala-Ala-Ala allow us to sample all permutations of the methyl side-chain position, providing a comprehensive view of the effects of this simple side-chain on the 3-D structure of the peptide. The individual structural populations for all but one of these peptide species are determined via conformer-specific IR-IR double-resonance spectroscopy and comparison with electronic structure predictions. The observed structures can be classified into three main families defined by the protonation site and the number of internal hydrogen bonds. The relative contribution of each structural family is highly dependent on the exact amino acid sequence of the tripeptide. These observed changes in structural population can be rationalized in terms of the electron-donating effect of the methyl side-chain modulating the local proton affinities of the amine and various carbonyl groups in the tripeptide.

Evaluating the Effects of Metal Adduction and Charge Isomerism on Ion-Mobility Measurements using m-Xylene Macrocycles as Models

Gas-phase ion-mobility spectrometry provides a unique platform to study the effect of mobile charge(s) or charge location on collisional cross section and ion separation. Here, we evaluate the effects of cation/anion adduction in a series of xylene and pyridyl macrocycles that contain ureas and thioureas. We explore how zinc binding led to unexpected deprotonation of the thiourea macrocyclic host in positive polarity ionization and subsequently how charge isomerism due to cation (zinc metal) and anion (chloride counterion) adduction or proton competition among acceptors can affect the measured collisional cross sections in helium and nitrogen buffer gases. Our approach uses synthetic chemistry to design macrocycle targets and a combination of ion-mobility spectrometry mass spectrometry experiments and quantum mechanics calculations to characterize their structural properties. We demonstrate that charge isomerism significantly improves ion-mobility resolution and allows for determination of the metal binding mechanism in metal-inclusion macrocyclic complexes. Additionally, charge isomers can be populated in molecules where individual protons are shared between acceptors. In these cases, interactions via drift gas collisions magnify the conformational differences. Finally, for the macrocyclic systems we report here, charge isomers are observed in both helium and nitrogen drift gases with similar resolution. The separation factor does not simply increase with increasing drift gas polarizability. Our study sheds light on important properties of charge isomerism and offers strategies to take advantage of this phenomenon in analytical separations.

Gas-Phase Reactivity of Phenylcarbyne Anions

Gas-phase reactivities of the phenylcarbyne anion and its four derivatives were studied using a linear quadrupole ion trap mass spectrometer. The phenylcarbyne anions were calculated to have a triplet ground state (singlet-triplet splittings of 4-9 kcal mol^-1), with the exception of the 4-cyanophenylcarbyne anion that has a singlet ground state (singlet-triplet splitting of -1.9 kcal mol^-1). Only the phenylcarbyne anions with a triplet ground state react with acetone and dimethyl disulfide via radical mechanisms. On the other hand, only the phenylcarbyne anion with a singlet ground state abstracts H₂O and H₂C═C═O from acetic acid via electrophilic addition of the reagents to the anion. Finally, two hydroxy-substituted phenylcarbyne anions (with triplet ground states) partially tautomerize with the assistance of reagent molecules to the more stable distonic phenylcarbene anions. This occurs via abstraction of a proton from the reagent by the phenylcarbyne anion to generate a neutral (triplet) phenylcarbene and a reagent anion, which is followed by proton abstraction from the hydroxyl group of the neutral phenylcarbene by the reagent anion to generate the distonic phenylcarbene anion in an excited triplet state. Experiments performed on deuterated hydroxy-substituted phenylcarbyne anions verified the mechanism. The reactivities of the distonic phenylcarbene anions were found to be quite different from those of the phenylcarbyne anions. For example, they were found to abstract CH₂ from acetonitrile, which is initiated by C-H insertion─typical singlet carbene reactivity.

Collision-assisted stripping for determination of microsolvation-dependent protonation sites in hydrated clusters by cryogenic ion trap infrared spectroscopy: the case of benzocaineH+(H2O)n

The protonation site of molecules can be varied by their surrounding environment. Gas-phase studies, including the popular techniques of infrared spectroscopy and ion mobility spectrometry, are a powerful tool for the determination of protonation sites in solvated clusters but often suffer from inherent limits for larger hydrated clusters. Here, we present collision-assisted stripping infrared (CAS-IR) spectroscopy as a new technique to overcome these problems and apply it in a proof-of-principle experiment to hydrated clusters of protonated benzocaine (H⁺BC), which shows protonation-site switching depending on the degree of hydration. The most stable protomer of H⁺BC in the gas phase (O-protonated) is interconverted into its most stable protomer in aqueous solution (N-protonated) upon hydration with three water molecules. CAS-IR spectroscopy enables us to unambiguously assign protonation sites and quantitatively determine the relative abundance of various protomers.

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.

Laser Photodissocation, Action Spectroscopy and Mass Spectrometry Unite to Detect and Separate Isomers

The separation and detection of isomers remains a challenge for many areas of mass spectrometry. This article highlights laser photodissociation and ion mobility strategies that have been deployed to tackle...

Protonation of Serine in Gas and Condensed and Microsolvated States in Aqueous Solution

Identification of molecules and elucidation of their chemical structure are ubiquitous problems in chemistry. Mass spectrometry (MS) can be used due to its sensitivity and versatility. For detection to occur, analytes must be ionized and transferred to the gas phase. Soft ionization processes such as electrospray ionization are popular; however, resulting microsolvated phases can alter the chemistry of analytes and therefore detection and identification. To understand these processes, we use computational methods to probe the ionization propensity of serine in the gas phase, aqueous microsolvated clusters, and aqueous solution. We show that the tautomeric form of serine is altered by the presence of water, as five water molecules can stabilize the zwitterionic tautomer. Inclusion of cosolutes such as ions can stabilize the zwitterion with as few as one or two water molecules present. We demonstrate that ionization propensity, as measured by gas phase bacisity, can increase by over 100 kJ/mol when placed in a small water-serine cluster, showing the sensitivity of the chemistry of microsolvated analytes. Finally, detailed analysis reveals that small droplets (less than seven water molecules) are extremely sensitive to addition of further water molecules. Beyond this limit, structural and electronic properties change little with droplet size.

IRMPD Spectroscopy of [PC (4:0/4:0) + M]+ (M = H, Na, K) and Corresponding CID Fragment Ions

Glycerophospholipids (GPs) are highly abundant in eukaryotic cells and take part in numerous fundamental physiological processes such as molecular signaling. The GP composition of samples is often analyzed using mass spectrometry (MS), but identification of some structural features, for example, differentiation of stereospecific numbering (sn) isomers by well-established tandem MS (MS²) methods, is challenging. In particular, the formation of 1,3-dioxolane over 1,3-dioxane intermediates proposed to be responsible for the sn-selectivity of these tandem MS strategies has not been validated by spectroscopic methods. In this work, we present infrared multiple photon dissociation (IRMPD) spectra of phosphatidylcholine (PC) ions [PC 4:0/4:0 + H/Na/K]⁺ and [PC 4:0/4:0 + Na/K - 183]⁺ fragments generated by electrospray ionization (ESI)-MS and collision-induced dissociation (CID), respectively. IRMPD spectra of protonated, sodiated, and potassiated PC 4:0/4:0 differ in the phosphate- and ester-related bands, which are increasingly shifted to lower wavenumbers with higher adduct masses. Comparison of calculated and experimental IR spectra indicates the presence of multiple, two and one isomer(s) for [PC 4:0/4:0 + H]⁺, [PC 4:0/4:0 + Na]⁺, and [PC 4:0/4:0 + K]⁺, respectively. Isomers exhibiting pronounced sn-1 ester-ion interactions are computationally predicted to be energetically preferred for all species and are in line with experimental results. IRMPD spectra of [PC 4:0/4:0 + Na/K - 183]⁺ are presented and shed the first light on the fragment ion structures, rationalizing MS-based lipidomics strategies that aim to characterize the sn-isomerism of GPs.

Action spectroscopy of the isolated red Kaede fluorescent protein chromophore

Incorporation of fluorescent proteins into biochemical systems has revolutionized the field of bioimaging. In a bottom-up approach, understanding the photophysics of fluorescent proteins requires detailed investigations of the light-absorbing chromophore, which can be achieved by studying the chromophore in isolation. This paper reports a photodissociation action spectroscopy study on the deprotonated anion of the red Kaede fluorescent protein chromophore, demonstrating that at least three isomers-assigned to deprotomers-are generated in the gas phase. Deprotomer-selected action spectra are recorded over the S1 ← S0 band using an instrument with differential mobility spectrometry coupled with photodissociation spectroscopy. The spectrum for the principal phenoxide deprotomer spans the 480-660 nm range with a maximum response at ≈610 nm. The imidazolate deprotomer has a blue-shifted action spectrum with a maximum response at ≈545 nm. The action spectra are consistent with excited state coupled-cluster calculations of excitation wavelengths for the deprotomers. A third gas-phase species with a distinct action spectrum is tentatively assigned to an imidazole tautomer of the principal phenoxide deprotomer. This study highlights the need for isomer-selective methods when studying the photophysics of biochromophores possessing several deprotonation sites.

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.

p-Aminobenzoic acid protonation dynamics in an evaporating droplet by ab initio molecular dynamics

Protonation equilibria are known to vary from the bulk to microdroplet conditions, which could induce many chemical and physical phenomena. Protonated p-aminobenzoic acid (PABA + H⁺) can be considered a model for probing the protonation dynamics in an evaporating droplet, as its protonation equilibrium is highly dependent on the formation conditions from solution via atmospheric pressure ionization sources. Experiments using diverse experimental techniques have shown that protic solvents allow formation of the O-protomer (PABA protonated in the carboxylic acid group) stable in the gas phase, while aprotic solvents yield the N-protomer (protonated in the amino group) that is the most stable protomer in solution. In this work, we explore the protonation equilibrium of PABA solvated by different numbers of water molecules (n = 0 to 32) using ab initio molecular dynamics. For n = 8-32, the protonation is either at the NH₂ group or in the solvent network. The solvent network interacts with the carboxylic acid group, but there is no complete proton transfer to form the O-protomer. For smaller clusters, however, solvent-mediated proton transfers to the carboxylic acid were observed, both via the Grotthuss mechanism and the vehicle or shuttle mechanism (for n = 1 and 2). Thermodynamic considerations allowed a description of the origins of the kinetic trapping effect, which explains the observation of the solution structure in the gas phase. This effect likely occurs in the final evaporation steps, which are outside the droplet size range covered by previous classical molecular dynamics simulations of charged droplets. These results may be considered relevant in determining the nature of the species observed in the ubiquitous ESI based mass spectrometry analysis, and in general for droplet chemistry, explaining how protonation equilibria are drastically changed from bulk to microdroplet conditions.

Electrostatically Tuning the Photodissociation of the Irgacure 2959 Photoinitiator in the Gas Phase by Cation Binding

The low-lying electronic states of Irgacure 2959, a Norrish-type I photoinitiator, complexed with a single metal cation are investigated in the gas phase by photodissociation action spectroscopy. Analysis of the band shifts using quantum chemical calculations (TD-DFT and SCS-CC2) reveals the underlying influence of the charge on the key electronic energy levels. Since the cations (H⁺, Li⁺, Na⁺, K⁺, Zn²⁺, Ca²⁺, and Mg²⁺) bind at varying distances, the magnitude of the electric field at the center of the chromophore due to the cation is altered, and this shifts the electronic states by different amounts. Photodissociation action spectra of cation-Irg complexes show that absorption transitions to the first ¹ππ* state are red-shifted with a magnitude proportional to the electric field strength (with red shifts >1 eV), and in most cases, the cation is essentially acting as a point charge. Calculations show that a neighboring ³nπ* state, a key state for the α-cleavage pathway, is destabilized (blue-shifted) by the orientated electric field. As such, if the ¹ππ*-³nπ* energy gap is reduced, increased intersystem crossing rates are expected, resulting in higher yields of the desired radical photoproducts, and this is controlled by the orientated electric field arising from the cation.

Effects of Analyte Concentration on the Protonation Sites of 4-Aminobenzoic Acid upon Atmospheric Pressure Chemical Ionization As Revealed by Gas-Phase Ion-Molecule Reactions

The most basic site of 4-aminobenzoic acid in aqueous solution is the amino nitrogen, while the carbonyl oxygen is calculated to be the most basic site in the gas phase. However, the preferred protonation site of 4-aminobenzoic acid upon electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) depends upon the ionization solvent and ion source parameters. The influence of the concentration of the analyte on the manifested protonation sites upon APCI has not been investigated and is reported here. Gas-phase ion-molecule reactions of trimethoxymethylsilane were used to identify the protonation sites of 4-aminobenzoic acid ionized using APCI with methanol or acetonitrile-water as the solvent. The nitrogen-protomer was found to be about twice as abundant as the oxygen-protomer at low analyte concentrations (10^-9-10^-6 M) in methanol solvent. This finding was rationalized on the basis of a previous finding that when the O-protomer is surrounded by more than eight methanol molecules in the gas phase it starts behaving as if it were in an aqueous solution and converts to the N-protomer. At greater analyte concentrations (≥10^-4 M), the amino group was predominantly protonated, which was rationalized based on the formation of a particularly stable proton-bound dimer of 4-aminobenzoic acid that preferentially dissociates to form the N-protomer. The above findings suggest that solution processes are much more important in APCI than commonly assumed, in agreement with recent literature. Indeed, when 1:1 (v/v) acetonitrile-water was used as the solvent system for 4-aminobenzoic acid, the N-protomer was predominantly generated at all analyte concentrations.

Discrimination between Protonation Isomers of Quinazoline by Ion Mobility and UV-Photodissociation Action Spectroscopy

The influence of oriented electric fields on chemical reactivity and photochemistry is an area of increasing interest. Within a molecule, different protonation sites offer the opportunity to control the location of charge and thus orientation of electric fields. New techniques are thus needed to discriminate between protonation isomers in order to understand this effect. This investigation reports the UV-photodissociation action spectroscopy of two protonation isomers (protomers) of 1,3-diazanaphthalene (quinazoline) arising from protonation of a nitrogen at either the 1- or 3-position. It is shown that these protomers are separable by field-asymmetric ion mobility spectrometry (FAIMS) with confirmation provided by UV-photodissociation (PD) action spectroscopy. Vibronic features in the UVPD action spectra and computational input allow assignment of the origin transitions to the S₁ and S₅ states of both protomers. These experiments also provide vital benchmarks for protomer-specific calculations and examination of isomer-resolved reaction kinetics and thermodynamics.

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.

Understanding Nontraditional Differential Mobility Behavior: A Case Study of the Tricarbastannatrane Cation, N(CH2CH2CH2)3Sn. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020;31:796-802. [PMID: 32129991 DOI: 10.1021/jasms.9b00042]

The effect of strong ion-solvent interactions on the differential mobility behavior of the tricarbastannatrane cation, N(CH₂CH₂CH₂)₃Sn⁺, has been investigated. Exotic "type D" dispersion behavior, which is intermediate to the more common types C and A behavior, is observed for gaseous N₂ environments that are seeded with acetone and acetonitrile vapor. Quantum chemical calculations and first-principles modeling show that under low-field conditions [N(CH₂CH₂CH₂)₃Sn + solvent]⁺ complexes containing a single solvent molecule survive the entire separation waveform duty cycle and interact weakly with the chemically modified environment. However, at high separation voltages, the ion-solvent bond dissociates and dynamic clustering ensues.

Measuring Electronic Spectra of Differential Mobility-Selected Ions in the Gas Phase

We describe the modification of a commercially available tandem differential mobility mass spectrometer (DMS) that has been retrofitted to facilitate photodissociation (PD) of differential mobility-separated, mass-selected molecular ions. We first show that a mixture of protonated quinoline/isoquinoline (QH⁺/iQH⁺) can be separated using differential mobility spectrometry. Efficient separation is facilitated by addition of methanol to the DMS environment and increased residence time within the DMS. In action spectroscopy experiments, we gate each isomer using appropriate DMS settings, trap the ions in the third quadrupole of a triple quadrupole mass spectrometer, and irradiate them with tunable light from an optical parametric oscillator (OPO). The resulting mass spectra are recorded as the OPO wavelength is scanned, giving PD action spectra. We compare our PD spectra with previously recorded spectra for the same species and show that our instrument reproduces previous works faithfully.

Effects of Residual Water in a Linear Quadrupole Ion Trap on the Protonation Sites of 4-Aminobenzoic Acid

In solution, the most basic site in 4-aminobenzoic acid is the amino nitrogen, while the carboxylic acid oxygen is the most basic site in the gas phase. However, the protonation site in the gas phase has been demonstrated to depend on the ionization solvents when ionized using positive ion mode electrospray ionization (ESI). In many of these studies, collision-activated dissociation (CAD) was used to differentiate the protomers. To explore the influence of different CAD conditions on the manifested protonation site, 4-aminobenzoic acid dissolved either in 1:1 acetonitrile-water or 3:1 methanol-water was ionized by  ESI and subjected to three different CAD experiments in a linear quadrupole ion trap/orbitrap mass spectrometer. Based on in-source CAD (ISCAD) and beam-type medium-energy CAD (MCAD), the proton resided on the nitrogen atom (N-protomer) when acetonitrile-water was used as the solvent system but on the oxygen atom (O-protomer) when methanol-water was used. Interestingly, a predominant N-protomer was observed when CAD was performed in the linear quadrupole ion trap (ITCAD), irrespective of the solvents used, in disagreement with literature. This unexpected result is rationalized based on the formation of long-lived water clusters of varying sizes for the protomers in the quadrupole ion trap due to residual water, low ion kinetic energies, long ion storage times, and relatively high pressure. Further, addition of extra water into the quadrupole ion trap resulted in nearly identical protomer distributions for both protomers. Therefore, this distribution must be near the equilibrium distribution caused by the presence of water clusters of varying sizes, some favoring the N-protomer and others the O-protomer.

Long-distance proton transfer induced by a single ammonia molecule: ion mobility mass spectrometry of protonated benzocaine reacted with NH3

A long-distance proton transfer via the vehicle mechanism in the absence of a hydrogen-bonded solvent-bridge in molecules.

LC-MS analysis of p-aminosalicylic acid under electrospray ionization conditions manifests a profound solvent effect

Under identical mass spectrometric conditions, chromatographic peak intensities of p-aminosalicylic acid recorded by LC-MS, using methanol as the mobile phase are drastically different from those acquired using is it acetonitrile as the eluent.

Quantitation of Cyclosporin A in Cell Culture Media by Differential Mobility Mass Spectrometry (DMS-MS/MS)

Cell permeability is an important factor in determining the bioavailability of therapeutics that is usually measured by cell culture testing. The concentration of pharmaceutical in a medium such as Hank's Balanced Salt Solution with HEPES organic buffer (HBSS-HEPES) is measured at a series of time points, making simplicity and high throughput of the analytical method important characteristics. We report an electrospray differential mobility spectrometry mass spectrometry method (nanoESI-DMS-MS) for the rapid determination of cyclosporin A (CsA, cyclosporine) concentration in such a buffer. DMS technology provides gas phase atmospheric pressure ion filtration for small-molecule bioanalytical methods that suppresses interfering ions and reduces chemical noise, without the use of chromatography. This allows simplified sample preparation, fast calibration curve development, and shortened analysis times. It has also been noted that the DMS prefilter can reduce contamination of the mass spectrometer by salts, thereby extending mass spectrometer system uptime.In the application described here, DMS-MS/MS is applied to cyclosporine A (CsA) in cell medium. Sample preparation is limited to dilution with an ammonium acetate-methanol-water mobile phase and the addition of CsA-d4 internal standard. The isotope ratio data are obtained in DMS-MS MRM mode observing NH₃ loss from the ammonium adduct of the two species. A calibration curve with high linearity (R² = 0.998) is rapidly obtained with nearly zero intercept, while it was found that a liquid chromatography LC-MS method required a preliminary SPE step to obtain a linear calibration curve. The time for data acquisition in the DMS-MS MRM method with flow injection (FIA) or infusion introduction at ESI flow of 400 nL/min is typically 30 s leading to a cycle time of less than 1 min.

Rapid Differentiation of Asian and American Ginseng by Differential Ion Mobility Spectrometry-Tandem Mass Spectrometry Using Stepwise Modulation of Gas Modifier Concentration

This study reports a rapid and robust method for the differentiation of Asian and American ginseng samples based on differential ion mobility spectrometry-tandem mass spectrometry (DMS-MS/MS). Groups of bioactive ginsenoside/pseudo-ginsenoside isomers, including Rf/Rg₁/F₁₁, Rb₂/Rb₃/Rc, and Rd/Re, in the ginseng extracts were sequentially separated using DMS with stepwise changes in the gas modifier concentration prior to MS analysis. The identities of the spatially separated ginsenoside/pseudo-ginsenoside isomers were confirmed by their characteristic compensation voltages at specific modifier loading and MS/MS product ions. As expected, Asian ginseng samples contained some Rf and an insignificant amount of F₁₁, whereas American ginseng samples had a high level of F₁₁ but no Rf. The origin of the whole and sliced ginseng could further be confirmed using the quantitative ratios of three sets of ginsenoside markers, namely, Rg₁/Re, Rb₁/Rg₁, and Rb₂/Rc. Based on our results, new benchmark ratios of Rg₁/Re < 0.15, Rb₁/Rg₁ > 2.15, and Rb₂/Rc < 0.26 were proposed for American ginseng (as opposed to Asian ginseng).

A Mechanistic Study of Protonated Aniline to Protonated Phenol Substitution Considering Tautomerization by Ion Mobility Mass Spectrometry and Tandem Mass Spectrometry

We report the use of ion mobility mass spectrometry (IMMS) and energy-resolved collisional activation to investigate gas-phase reactions of protonated aniline and protonated phenol. Protonated aniline prototropic tautomerization and nucleophilic substitution (SN1) to produce phenol with traces of water in the IMMS cell are reported. Tautomerization of protonated phenol and its ability to form protonated aniline in presence of ammonia in the gas phase are also observed. These results are supported by energy landscapes obtained from computational chemistry. These structure modifications in the IMMS cell affected the measured collision cross section (CCS). A thorough understanding of the gas-phase reactions occurring in IMMS appears mandatory before using the experimental CCS as a robust descriptor which is stated by the recent literature.

Augmenting Basin-Hopping With Techniques From Unsupervised Machine Learning: Applications in Spectroscopy and Ion Mobility

Evolutionary algorithms such as the basin-hopping (BH) algorithm have proven to be useful for difficult non-linear optimization problems with multiple modalities and variables. Applications of these algorithms range from characterization of molecular states in statistical physics and molecular biology to geometric packing problems. A key feature of BH is the fact that one can generate a coarse-grained mapping of a potential energy surface (PES) in terms of local minima. These results can then be utilized to gain insights into molecular dynamics and thermodynamic properties. Here we describe how one can employ concepts from unsupervised machine learning to augment BH PES searches to more efficiently identify local minima and the transition states connecting them. Specifically, we introduce the concepts of similarity indices, hierarchical clustering, and multidimensional scaling to the BH methodology. These same machine learning techniques can be used as tools for interpreting and rationalizing experimental results from spectroscopic and ion mobility investigations (e.g., spectral assignment, dynamic collision cross sections). We exemplify this in two case studies: (1) assigning the infrared multiple photon dissociation spectrum of the protonated serine dimer and (2) determining the temperature-dependent collision cross-section of protonated alanine tripeptide.

Effects of Solvent Vapor Modifiers for the Separation of Opioid Isomers in Micromachined FAIMS-MS

Opioid addiction is an escalating problem that is compounded by the introduction of synthetic opiate analogues such as fentanyl. Screening methods for these compound classes are challenged by the availability of synthetically manufactured analogues, including isomers of existing substances. High-field asymmetric-waveform ion mobility spectrometry (FAIMS) utilizes an alternating asymmetric electric field to separate ions by their different mobilities at high and low fields as they travel through the separation space. When coupled to mass spectrometry (MS), FAIMS enhances the separation of analytes from other interfering compounds with little to no increase in analysis time. Addition of solvent vapor into the FAIMS carrier gas has been demonstrated to enable and improve the separation of isomers. Here we investigate the effects of several solvents for the separation of four opioids. FAIMS-MS spectra with added solvent vapors show dramatic compensation field (CF) shifts for opioid [M+H]⁺ ions when compared to spectra acquired using dry nitrogen. Addition of vapor from aprotic solvents, such as acetonitrile and acetone, produces significantly improved resolution between the tested opioids, with baseline resolution achieved between certain opioid isomers. For protic solvents, notable CF shift differences were observed in FAIMS separations between addition of water vapor and vapors from small alcohols. Graphical Abstract.

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.

Determining molecular properties with differential mobility spectrometry and machine learning

The fast and accurate determination of molecular properties is highly desirable for many facets of chemical research, particularly in drug discovery where pre-clinical assays play an important role in paring down large sets of drug candidates. Here, we present the use of supervised machine learning to treat differential mobility spectrometry - mass spectrometry data for ten topological classes of drug candidates. We demonstrate that the gas-phase clustering behavior probed in our experiments can be used to predict the candidates' condensed phase molecular properties, such as cell permeability, solubility, polar surface area, and water/octanol distribution coefficient. All of these measurements are performed in minutes and require mere nanograms of each drug examined. Moreover, by tuning gas temperature within the differential mobility spectrometer, one can fine tune the extent of ion-solvent clustering to separate subtly different molecular geometries and to discriminate molecules of very similar physicochemical properties.

Gas-phase protomers of p-(dimethylamino)chalcone investigated by travelling-wave ion mobility mass spectrometry (TWIMS)

Results from ion-mobility (IM) separation experiments demonstrate that O- and N-protomers of p-(dimethylamino)chalcone (p-DMAC) can coexist in the gas phase. The relative populations of the two protomers strongly depend on the ion-generating settings and the conditions the precursor ions experience from the point of their gas-phase inception to the time of their detection. Under relatively dry source conditions, the ratio of the gas-phase protomers generated under helium-plasma ionization (HePI) conditions is biased towards the thermodynamically favored O-protomer. However, when the humidity of the enclosed ion source was increased, the IM arrival-time distribution profile of the mass-selected protonated precursor of p-DMAC changed rapidly to one dominated by the N-protomer. Under spray-ionization conditions, the formation of the thermodynamically less favored protomer has been generally attributed to a phenomenon called kinetic trapping. Herein, we demonstrate that the population of thermodynamically less favored N-protomer can be dramatically increased simply by introducing water vapor to the HePI ion source.