Cryogenic Ion Mobility-Mass Spectrometry Captures Hydrated Ions Produced During Electrospray Ionization

Structure and Stabilities of Solution and Gas Phase Protein Complexes

Collision-induced unfolding (CIU) has provided new levels of understanding of the stabilities and structure(s) for gas phase protein and protein complex ions formed by electrospray ionization (ESI). Variable-temperature (vT-ESI) data provide complementary information about temperature-induced folding/unfolding (TIU) reactions of solution phase ions. Results obtained by using CIU and TIU provide complementary information about stabilities of gas phase versus solution phase ions. Such comparisons may provide the most direct experimental approach to answer a long-standing question from Fred McLafferty: "For how long, under what conditions, and to what extent, can solution structure be retained without solvent?" Answers to this question require greater understanding of the (i) structure(s), stabilities, and dynamics of proteins/protein complexes in solution prior to ESI; (ii) effects of water removal by droplet fission and "freeze-drying" by evaporation of water from the nanodroplet; and (iii) potential reactions and structural changes that may occur as the ions traverse the heated capillary, the final stage in the transition to solvent-free gas phase ions. Here, we employ vT-ESI coupled with ion mobility-mass spectrometry (IM-MS) as a means to provide more detailed answers to the above-mentioned questions. Apo- and metalated-metallothionein-2A (MT), a cysteine-rich metal binding protein, and various proteoforms of transthyretin (TTR), a homotetrameric (56 kDa) retinol and thyroxine transporter protein complex were studied to examine distinct features of CIU and TIU across two different types of protein complexes. The results in this work shed light on the capabilities of CIU, TIU, and average charge state (Zavg) for probing the rugged energy landscape of native proteins and highlights the effects of water and cofactors (metal ions) on the structure and stabilities of proteins and protein complexes.

D-Amino acid recognition of tripeptides studied by ultraviolet photodissociation spectroscopy of hydrogen-bonded clusters

To understand the roles of D-amino acids, evaluating their chemical properties in living organisms is essential. Herein, D-amino acid recognition of peptides was investigated using a tandem mass spectrometer equipped with an electrospray ionization source and a cold ion trap. Ultraviolet (UV) photodissociation spectroscopy and water adsorption of hydrogen-bonded protonated clusters of tryptophan (Trp) enantiomers and tripeptides (SAA, ASA, and AAS, where S and A denote L-serine and L-alanine, respectively) were carried out at 8 K in the gas phase. In the UV photodissociation spectrum of H⁺(D-Trp)ASA, the bandwidth of the S₁-S₀ transition, which corresponds to the ππ* state of the Trp indole ring, was narrower than those of the other five clusters, H⁺(D-Trp)SAA, H⁺(D-Trp)AAS, H⁺(L-Trp)SAA, H⁺(L-Trp)ASA, and H⁺(L-Trp)AAS. In the UV photoexcitation of H⁺(D-Trp)ASA(H₂O)_n, which were formed via water adsorption on gas-phase H⁺(D-Trp)ASA, the evaporation of water molecules was the main photodissociation pathway. An NH₂CHCOOH-eliminated ion and H⁺ASA were observed in the product ion spectrum. By contrast, water molecules adsorbed on the other five clusters remained on the product ions for NH₂CHCOOH elimination and Trp detachment after the UV photoexcitation. The results indicated that the indole ring of Trp was located on the surface of H⁺(D-Trp)ASA, and the amino and carboxyl groups of Trp formed hydrogen bonds in H⁺(D-Trp)ASA. For the other five clusters, the indole rings of Trp were hydrogen bonded in the clusters, and the amino and carboxyl groups of Trp were present on the cluster surfaces.

Recent advances in mass spectrometry analysis of neuropeptides

Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.

Gentle nano-electrospray ion source for reliable and efficient generation of microsolvated ions

We present herein the design of a nano-electrospray ion source capable of reliable generation of large quantities of microsolvated ions. The source is based on a triple molecular skimmer scheme and can be quickly tuned to generate bare ions or their ionic complexes with up to more than 100 solvent molecules retained from solution. The performance of this source is illustrated by recording the mass spectra of distributions of ionic complexes of protonated water, amino acids, and a small protein ubiquitin. Protonated water complexes with more than 110 molecules and amino acids with more than 45 water molecules could be generated. Although the commercial ion source based on the double ion funnel design with orthogonal injection, which we used in our laboratory, is more efficient in generating ions than our triple skimmer ion source, they both exhibit comparable short-term stability in generating bare ions. In return, only the new source is capable of generating microsolvated ions.

Electrospray Ionization Ion Mobility Mass Spectrometry

Electrospray ionization ion mobility mass spectrometry (ESI-IMS-MS) is a rapidly progressing analytical technique for the examination of complex compounds in the gas phase. ESI-IMS-MS separates isomers, provides structural information, and quantitatively identifies peptides, lipids, carbohydrates, polymers, and metabolites in biological samples. ESI-IMS-MS has pharmaceutical, environmental, and manufacturing applications quickly characterizing drugs, petroleum products, and metal macromolecules. This review provides the history of ESI-IMS-MS development and applications to date.

THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY

Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Ion Mobility Separation Using a Dual-LIT Miniature Mass Spectrometer

Ion mobility (IM) has been increasingly used in combination with mass spectrometry (MS) for chemical and biological analysis. While implementation of IM with MS usually requires complex instrumentation with delicate controls, in this study we explored the potential of performing IM separation using dual-linear ion traps (LITs) in a miniature mass spectrometer, which was originally developed for performing comprehensive MS/MS scan functions with a simple instrumentation configuration. The IM separation was achieved by ion transfer between the LITs with dynamic gas flow. Its performance was characterized for analysis of a broad range of chemical and biological compounds including small organic compounds such as trisaccharides, raffinose, cellotriose, and melezitose, as well as protein conformers. The demonstrated technique serves as another example of developing powerful hybrid instrument functions with simple configurations and miniaturized sizes.

Gas-phase conformations of intrinsically disordered proteins and their complexes with ligands: Kinetically trapped states during transfer from solution to the gas phase

Flexible structures of intrinsically disordered proteins (IDPs) are crucial for versatile functions in living organisms, which involve interaction with diverse partners. Electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) has been widely applied for structural characterization of apo-state and ligand-associated IDPs via two-dimensional separation in the gas phase. Gas-phase IDP structures have been regarded as kinetically trapped states originated from conformational features in solution. However, an implication of the states remains elusive in the structural characterization of IDPs, because it is unclear what structural property of IDPs is preserved. Recent studies have indicated that the conformational features of IDPs in solution are not fully reproduced in the gas phase. Nevertheless, the molecular interactions captured in the gas phase amplify the structural differences between IDP conformers. Therefore, an IDP conformational change that is not observed in solution is observable in the gas-phase structures obtained by ESI-IM-MS. Herein, we have presented up-to-date researches on the key implications of kinetically trapped states in the gas phase with a brief summary of the structural dynamics of IDPs in ESI-IM-MS.

Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples

Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), reducing the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.

Hydration of Guanidinium Ions: An Experimental Search for Like-Charged Ion Pairs

Guanidinium ions (GdmH⁺) are reported to form stable complexes (GdmH⁺/GdmH⁺) in aqueous solution despite strong repulsive interactions between the like-charged centers. These complexes are thought to play important roles in protein folding, membrane penetration, and formation of protein dimers. Although GdmH⁺ ions are weakly hydrated, semiempirical calculations provide evidence that these like-charged complexes are stabilized by water molecules, which serve important structural and energetic roles. Specifically, water molecules bridge between the GdmH⁺ ions of GdmH⁺/GdmH⁺ complexes as well as complexes involving the guanidinium side chains of arginine. Potential biological significances of like-charged complexes have been largely confirmed by ab initio molecular dynamics simulations and indirect experimental evidence. We report cryo-ion mobility-mass spectrometry results for the GdmH⁺/GdmH⁺ ion pair confined in a nanodroplet- the first direct experimental observation of this like-charged complex. A second like-charged complex, described as a water-mediated complex involving GdmH⁺ and H₃O⁺, was also observed.

The effects of solution additives and gas-phase modifiers on the molecular environment and conformational space of common heme proteins

RATIONALE

The molecular environment is known to impact the secondary and tertiary structures of biomolecules both in solution and in the gas phase, shifting the equilibrium between different conformational and oligomerization states. However, there is a lack of studies monitoring the impacts of solution additives and gas-phase modifiers on biomolecules characterized using ion mobility techniques.

METHODS

The effect of solution additives and gas-phase modifiers on the molecular environment of two common heme proteins, bovine cytochrome c and equine myoglobin, is investigated as a function of the time after desolvation (e.g., 100-500 ms) using nanoelectrospray ionization coupled to trapped ion mobility spectrometry with detection by time-of-flight mass spectrometry. Organic compounds used as additives/modifiers (methanol, acetonitrile, acetone) were either added to the aqueous protein solution before ionization or added to the ion mobility bath gas by nebulization.

RESULTS

Changes in the mobility profiles are observed depending on the starting solution composition (i.e., in aqueous solution at neutral pH or in the presence of organic content: methanol, acetone, or acetonitrile) and the protein. In the presence of gas-phase modifiers (i.e., N₂ doped with methanol, acetone, or acetonitrile), a shift in the mobility profiles driven by the gas-modifier mass and size and changes in the relative abundances and number of IMS bands are observed.

CONCLUSIONS

We attribute the observed changes in the mobility profiles in the presence of gas-phase modifiers to a clustering/declustering mechanism by which organic molecules adsorb to the protein ion surface and lower energetic barriers for interconversion between conformational states, thus redefining the free energy landscape and equilibria between conformers. These structural biology experiments open new avenues for manipulation and interrogation of biomolecules in the gas phase with the potential to emulate a large suite of solution conditions, ultimately including conditions that more accurately reflect a variety of intracellular environments.

Combining Ion Mobility and Cryogenic Spectroscopy for Structural and Analytical Studies of Biomolecular Ions

Ion mobility spectrometry (IMS) has become a valuable tool in biophysical and bioanalytical chemistry because of its ability to separate and characterize the structure of gas-phase biomolecular ions on the basis of their collisional cross section (CCS). Its importance has grown with the realization that in many cases, biomolecular ions retain important structural characteristics when produced in the gas phase by electrospray ionization (ESI). While a CCS can help distinguish between structures of radically different types, one cannot expect a single number to differentiate similar conformations of a complex molecule. Molecular spectroscopy has also played an increasingly important role for structural characterization of biomolecular ions. Spectroscopic measurements, particularly when performed at cryogenic temperatures, can be extremely sensitive to small changes in a molecule's conformation and provide tight constraints for calculations of biomolecular structures. However, spectra of complex molecules can be heavily congested due to the presence of multiple stable conformations, each of which can have a distinct spectrum. This congestion can inhibit spectral analysis and complicate the extraction of structural information. Even when a single conformation is present, the conformational search process needed to match a measured spectrum with a computed structure can be overwhelming for peptides of more than a few amino acids, for example. We have recently combined ion mobility spectrometry and cryogenic ion spectroscopy (CIS) to characterize the structures of gas-phase biomolecular ions. In this Account, we illustrate how the coupling of IMS and CIS is by nature synergistic. On the one hand, IMS can be used as a conformational filter to reduce spectral congestion that arises from heterogeneous samples, facilitating structural analysis. On the other hand, highly resolved, cryogenic spectra can serve as a selective detector for IMS that can increase the effective resolution and hence the maximum number of distinct species that can be detected. Taken together, spectra and CCS measurements on the same system facilitates structural analysis and strengthens the conclusions that can be drawn from each type of data. After describing different approaches to combining these two techniques in such a way as to simplify the data obtained from each one separately, we present two examples that illustrate the type of insight gained from using spectra and CCS data together for characterizing gas-phase biomolecular ions. In one example, the CCS is used as a constraint for quantum chemical structure calculations of kinetically trapped species, where a lowest-energy criterion is not applicable. In a second example, we use both the CCS and a cryogenic infrared spectrum as a means to distinguish isomeric glycans.

A Decapeptide Hydrated by Two Waters: Conformers Determined by Theory and Validated by Cold Ion Spectroscopy

The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic level. We employ density functional calculations to compute a large pool of structures and vibrational spectra for a gas-phase complex, in which a doubly protonated decapeptide, gramicidin S, is solvated by two water molecules. Though most vibrations of this large complex are treated in a harmonic approximation, the water molecules and the vibrations of the host ion coupled to them are locally described by a quantum mechanical vibrational self-consistent field theory with second-order perturbation correction (VSCF-PT2). Guided and validated by the available cold ion spectroscopy data, the computational analysis identifies structures of the three experimentally observed conformers of the complex. They, mainly, differ by the hydration sites, of which the one at the Orn side chain is the most important for reshaping the peptide toward its native structure. The study demonstrates the ability of a quantum chemistry approach that intelligently combines the semiempirical and ab initio computations to disentangle a complex interplay of intra- and intermolecular hydrogen bonds in large molecular systems.

Following a Folding Transition with Capillary Electrophoresis and Ion Mobility Spectrometry

Ion mobility spectrometry (IMS) is increasingly used to describe solution-phase phenomena and has recently been used to establish the presence of multiple intermediates during the folding of a model polypeptide, polyproline. These observations, however, are made on gas-phase structures. Capillary electrophoresis (CE) is a complementary solution-phase technique, also based on the separation of charged species as a function of size and charge. Here, both ion mobility and capillary electrophoresis are used to follow the folding transition of a 13-mer polyproline peptide from the all-cis polyproline I (PPI) conformation to the all-trans polyproline II (PPII) conformation upon immersion in aqueous solvent. Synchronous folding processes are observed using both techniques. Eight conformers are observed using ion mobility. Although only five peaks are observed using capillary electrophoresis, these peaks can be modeled as sums of the observed IMS conformers; this is strong evidence that ion mobility is sampling solution-phase structures. CE measurements provide the first direct evidence that multiple folding intermediates are present in solution.

Cryogenic Ion Mobility-Mass Spectrometry: Tracking Ion Structure from Solution to the Gas Phase

Electrospray ionization (ESI) combined with ion mobility-mass spectrometry (IM-MS) is adding new dimensions, that is, structure and dynamics, to the field of biological mass spectrometry. There is increasing evidence that gas-phase ions produced by ESI can closely resemble their solution-phase structures, but correlating these structures can be complicated owing to the number of competing effects contributing to structural preferences, including both inter- and intramolecular interactions. Ions encounter unique hydration environments during the transition from solution to the gas phase that will likely affect their structure(s), but many of these structural changes will go undetected because ESI-IM-MS analysis is typically performed on solvent-free ions. Cryogenic ion mobility-mass spectrometry (cryo-IM-MS) takes advantage of the freeze-drying capabilities of ESI and a cryogenically cooled IM drift cell (80 K) to preserve extensively solvated ions of the type [M + xH](x+)(H2O)n, where n can vary from zero to several hundred. This affords an experimental approach for tracking the structural evolution of hydrated biomolecules en route to forming solvent-free gas-phase ions. The studies highlighted in this Account illustrate the varying extent to which dehydration can alter ion structure and the overall impact of cryo-IM-MS on structural studies of hydrated biomolecules. Studies of small ions, including protonated water clusters and alkyl diammonium cations, reveal structural transitions associated with the development of the H-bond network of water molecules surrounding the charge carrier(s). For peptide ions, results show that water networks are highly dependent on the charge-carrying species within the cluster. Specifically, hydrated peptide ions containing lysine display specific hydration behavior around the ammonium ion, that is, magic number clusters with enhanced stability, whereas peptides containing arginine do not display specific hydration around the guanidinium ion. Studies on the neuropeptide substance P illustrate the ability of cryo-IM-MS to elucidate information about heterogeneous ion populations. Results show that a kinetically trapped conformer is stabilized by a combination of hydration and specific intramolecular interactions, but upon dehydration, this conformer rearranges to form a thermodynamically favored gas-phase ion conformation. Finally, recent studies on hydration of the protein ubiquitin reveal water-mediated dimerization, thereby illustrating the extension of this approach to studies of large biomolecules. Collectively, these studies illustrate a new dimension to studies of biomolecules, resulting from the ability to monitor snapshots of the structural evolution of ions during the transition from solution to gas phase and provide unparalleled insights into the intricate interplay between competing effects that dictate conformational preferences.

Increasing Ubiquitin Ion Resistance to Unfolding in the Gas Phase Using Chloride Adduction: Preserving More "Native-Like" Conformations Despite Collisional Activation

Electrospray ionization (ESI) of ubiquitin from acidified (0.1%) aqueous solution produces abundant ubiquitin-chloride adduct ions, [M + nH + xCl]((n - x)+), that upon mild heating react via elimination of neutral HCl. Ion mobility collision cross section (CCS) measurements show that ubiquitin ions retaining chloride adducts exhibit CCS values similar to those of the "native-state" of the protein. Coupled with results from recent molecular dynamics (MD) simulations for the evolution of a salt-containing electrospray droplet, this study provides a more complete picture for how the presence of salts affects the evolution of protein conformers in the final stages of dehydration of the ESI process and within the instrument.

Protein Structural Studies by Traveling Wave Ion Mobility Spectrometry: A Critical Look at Electrospray Sources and Calibration Issues

The question whether electrosprayed protein ions retain solution-like conformations continues to be a matter of debate. One way to address this issue involves comparisons of collision cross sections (Ω) measured by ion mobility spectrometry (IMS) with Ω values calculated for candidate structures. Many investigations in this area employ traveling wave IMS (TWIMS). It is often implied that nanoESI is more conducive for the retention of solution structure than regular ESI. Focusing on ubiquitin, cytochrome c, myoglobin, and hemoglobin, we demonstrate that Ω values and collisional unfolding profiles are virtually indistinguishable under both conditions. These findings suggest that gas-phase structures and ion internal energies are independent of the type of electrospray source. We also note that TWIMS calibration can be challenging because differences in the extent of collisional activation relative to drift tube reference data may lead to ambiguous peak assignments. It is demonstrated that this problem can be circumvented by employing collisionally heated calibrant ions. Overall, our data are consistent with the view that exposure of native proteins to electrospray conditions can generate kinetically trapped ions that retain solution-like structures on the millisecond time scale of TWIMS experiments. ᅟ

Water-Mediated Dimerization of Ubiquitin Ions Captured by Cryogenic Ion Mobility-Mass Spectrometry

The dynamics, structures, and functions of most biological molecules are strongly influenced by the nature of the peptide's or protein's interaction with water. Here, cryogenic ion mobility-mass spectrometry studies of ubiquitin have directly captured a water-mediated protein-protein binding event involving hydrated, noncovalently bound dimer ions in solution, and this interaction has potential relevance to one of the most important protein-protein interactions in nature. As solvent is removed, dimer ions, viz. [2 M + 14H](14+), can be stabilized by only a few attached water molecules prior to dissociation into individual monomeric ions. The hydrophobic patch of ubiquitin formed by the side chains of Leu-8, Ile-44, and Val-70 meet all the necessary conditions for a protein-protein binding "hot spot," including the requirement for occlusion of water to nearby hydrophilic sites, and it is suggested that this interaction is responsible for formation of the hydrated noncovalent ubiquitin dimer.

Tandem ion mobility spectrometry coupled to laser excitation

This manuscript describes a new experimental setup that allows to perform tandem ion mobility spectrometry (IMS) measurements and which is coupled to a high resolution time-of-flight mass spectrometer. It consists of two 79 cm long drift tubes connected by a dual ion funnel assembly. The setup was built to permit laser irradiation of the ions in the transfer region between the two drift tubes. This geometry allows selecting ions according to their ion mobility in the first drift tube, to irradiate selected ions, and examine the ion mobility of the product ions in the second drift tube. Activation by collision is possible in the same region (between the two tubes) and between the second tube and the time-of-flight. IMS-IMS experiments on Ubiquitin are reported. We selected a given isomer of charge state +7 and explored its structural rearrangement following collisional activation between the two drift tubes. An example of IMS-laser-IMS experiment is reported on eosin Y, where laser irradiation was used to produce radical ions by electron photodetachment starting from doubly deprotonated species. This allowed measuring the collision cross section of the radical photo-product, which cannot be directly produced with an electrospray source.

Microheterogeneity within conformational states of ubiquitin revealed by high resolution trapped ion mobility spectrometry

The present work employs trapped ion mobility spectrometry (TIMS) for the analysis of ubiquitin ions known to display a multitude of previously unresolved interchangeable conformations upon electrospray ionization.

Advances in ion mobility-mass spectrometry instrumentation and techniques for characterizing structural heterogeneity

Enabling IM-MS instrumentation and techniques for characterizing sample structural heterogeneity have developed rapidly over the last five years.

Spectroscopic studies of kinetically trapped conformations in the gas phase: the case of triply protonated bradykinin

We explore conformational space of triply protonated bradykinin. Three conformational families are mobility-separated and spectroscopically characterized. Kinetically trapped structures are identified via annealing.

Fundamentals of trapped ion mobility spectrometry

Trapped ion mobility spectrometry (TIMS) is a relatively new gas-phase separation method that has been coupled to quadrupole orthogonal acceleration time-of-flight mass spectrometry. The TIMS analyzer is a segmented rf ion guide wherein ions are mobility-analyzed using an electric field that holds ions stationary against a moving gas, unlike conventional drift tube ion mobility spectrometry where the gas is stationary. Ions are initially trapped, and subsequently eluted from the TIMS analyzer over time according to their mobility (K). Though TIMS has achieved a high level of performance (R > 250) in a small device (<5 cm) using modest operating potentials (<300 V), a proper theory has yet to be produced. Here, we develop a quantitative theory for TIMS via mathematical derivation and simulations. A one-dimensional analytical model, used to predict the transit time and theoretical resolving power, is described. Theoretical trends are in agreement with experimental measurements performed as a function of K, pressure, and the axial electric field scan rate. The linear dependence of the transit time with 1/K provides a fundamental basis for determination of reduced mobility or collision cross section values by calibration. The quantitative description of TIMS provides an operational understanding of the analyzer, outlines the current performance capabilities, and provides insight into future avenues for improvement.

Evolution of Hydrogen-Bond Networks in Protonated Water Clusters H(+)(H2O)n (n = 1 to 120) Studied by Cryogenic Ion Mobility-Mass Spectrometry

Cryogenic (80 K) ion mobility-mass spectrometry (cryo-IM-MS) is employed to study structural transitions of protonated water clusters in both the small, H(+)(H2O)n (n = 1 to 30), and large, (n = 31 to ∼120), size regions. In agreement with previous studies, we find compelling evidence of regions of uniform cluster decay in the small size region, accompanied by sharp transition points whereby the loss of a single water monomer induces a different H-bonding motif. The investigation of the isomeric distribution of each species at 80 K reveals experimental evidence supporting the notion that H(+)(H2O)n (n = 6) is the smallest system to possess both Eigen- (H3O(+)) and Zundel- (H5O2(+)) centered structures. Cryo-IM-MS is particularly well-suited for studying clusters in the large size region, for which previous spectroscopic experimental studies are scarce.

Solvent-mediated folding of dicarboxylate dianions: aliphatic chain length dependence and origin of the IR intensity quenching

We combine infrared photodissociation spectroscopy with quantum chemical calculations to characterize the hydration behavior of microsolvated dicarboxylate dianions, (CH2)m(COO(-))2·(H2O)n, as a function of the aliphatic chain length m. We find evidence for solvent-mediated folding transitions, signaled by the intensity quenching of the symmetric carboxylate stretching modes, for all three species studied (m = 2, 4, 8). The number of water molecules required to induce folding increases monotonically with the chain length and is n = 9-12, n = 13, and n = 18-19 for succinate (m = 2), adipate (m = 4), and sebacate (m = 8), respectively. In the special case of succinate, the structural transition is complicated by the possibility of bridging water molecules that bind to both carboxylates with merely minimal chain deformation. On the basis of vibrational calculations on a set of model systems, we identify the factors responsible for intensity quenching. In particular, we find that the effect of hydrogen bonds on the carboxylate stretching mode intensities is strongly orientation dependent.

The periodic focusing ion funnel: theory, design, and experimental characterization by high-resolution ion mobility-mass spectrometry

Simulation-based development and experimental characterization of a DC-only ion funnel is described herein. Radial ion confinement is achieved via periodic focusing whereby a collisionally dampened effective potential is generated in the inertial frame of an ion traversing the device with appreciable velocity. The new device, termed a periodic focusing ion funnel (PF IF), provides an efficient alternative to the rf ion funnel providing high ion transmission with fewer electrodes, simplified electrical circuitry, and reduced power supply requirements. The utility of the PF IF for structural ion mobility-mass spectrometry (IM-MS) studies is demonstrated using model peptide ions (bradykinin, gramicidin S, and trpzip 1).

Locating protonated amines in clathrates

The structures and inherent stabilities of hydrated, protonated ammonia, select protonated primary, secondary, and tertiary amines as well as tetramethylammonium with 19-21 water molecules were investigated using infrared photodissociation (IRPD) spectroscopy and blackbody infrared radiative dissociation (BIRD) at 133 K. Magic number clusters (MNCs) with 20 water molecules were observed for all ions except tetramethylammonium, and the BIRD results indicate that these clusters have stable structures, which are relatively unaffected by addition of one water molecule but are disrupted in clusters with one less water molecule. IRPD spectra in the water free O-H stretch region are consistent with clathrate structures for the MNCs with 20 water molecules, whereas nonclathrate structures are indicated for tetramethylammonium as well as ions at the other cluster sizes. The locations of protonated ammonia and the protonated primary amines either in the interior or at the surface of a clathrate were determined by comparing IRPD spectra of these ions to those of reference ions; Rb(+) and protonated tert-butylammonia with 20 water molecules were used as references for an ion in the interior and at the surface of a clathrate, respectively. These results indicate that protonated ammonia is in the interior of the clathrate, whereas protonated methyl- and n-heptylamine are at the surface. Calculations suggest that the number of hydrogen bonds in these clusters does not directly correlate with structural stability, indicating that both the number and orientation of the hydrogen bonds are important. These experimental results should serve as benchmarks for computational studies aimed at elucidating ion effects on the hydrogen-bonding network of water molecules and the surface activity of ions.