Structural Elucidation of Fullerene Dimers by High-Resolution Ion Mobility Measurements and Trajectory Calculation Simulations

Non-targeted and targeted analysis of oxylipins in combination with charge-switch derivatization by ion mobility high-resolution mass spectrometry

Eicosanoids and other oxylipins play an important role in mediating inflammation as well as other biological processes. For the investigation of their biological role(s), comprehensive analytical methods are necessary, which are able to provide reliable identification and quantification of these compounds in biological matrices. Using charge-switch derivatization with AMPP (N-(4-aminomethylphenyl)pyridinium chloride) in combination with liquid chromatography ion mobility quadrupole time-of-flight mass spectrometry (LC-IM-QTOF-MS), we developed a non-target approach to analyze oxylipins in plasma, serum, and cells. The developed workflow makes use of an ion mobility resolved fragmentation to pinpoint derivatized molecules based on the cleavage of AMPP, which yields two specific fragment ions. This allows a reliable identification of known and unknown eicosanoids and other oxylipins. We characterized the workflow using 52 different oxylipins and investigated their fragmentation patterns and ion mobilities. Limits of detection ranged between 0.2 and 10.0 nM (1.0-50 pg on column), which is comparable with other state-of-the-art methods using LC triple quadrupole (QqQ) MS. Moreover, we applied this strategy to analyze oxylipins in different biologically relevant matrices, as cultured cells, human plasma, and serum. Graphical abstract.

Probing the structure of giant fullerenes by high resolution trapped ion mobility spectrometry

We present high-resolution trapped ion mobility spectrometry (TIMS) measurements for fullerene ions in molecular nitrogen.

Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation

Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H]^- ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H]^- and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H₂O-CO₂]^- and [M-H-H₂O]^- displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H₂O]^- ion from LTB₄ was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H₂O]^- product ions from LTB₄ was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. Graphical Abstract ᅟ.

Quantitative Collision Cross-Sections from FTICR Linewidth Measurements: Improvements in Theory and Experiment

Two corrections to the equation used in the cross-sectional areas by Fourier transform ion cyclotron resonance ("CRAFTI") technique are identified. In CRAFTI, ion collision cross-sections are obtained from the pressure-dependent ion linewidths in Fourier transform mass spectra. The effects of these corrections on the accuracy of the cross-sections obtained using the CRAFTI technique are evaluated experimentally using the 20 biogenic amino acids and several crown ether complexes with protonated alkyl monoamines. Good absolute agreement is obtained between the CRAFTI cross-sections and the corresponding cross-sections obtained using both static drift ion mobility spectrometry and computational simulations. These results indicate that the CRAFTI cross-sections obtained using the updated equation presented here are quantitatively descriptive of the size and shape of the gas-phase ions. Cross-sections that differ by less than 3% are measured for the isobaric isomers n-butylamine and tert-butylamine complexed with the crown ethers. This level of precision is similar to what has been achieved previously using traveling wave ion mobility devices. These results indicate that CRAFTI can be used to probe subtle structural differences between ions with approximately the same precision as that achieved in traveling wave ion mobility devices. Graphical Abstract ᅟ.

Ion mobility separation of deprotonated oligosaccharide isomers - evidence for gas-phase charge migration

There has been increasing evidence that certain isomeric glycans can be separated efficiently by ion mobility-mass spectrometry when deprotonated ions are analyzed. To better understand the fundamentals behind these separations, we here investigate the impact of ionisation mode and adduct formation using IM-MS, density-functional theory and ab initio molecular dynamics.

Effects of Charge State, Charge Distribution, and Structure on the Ion Mobility of Protein Ions in Helium Gas: Results from Trajectory Method Calculations

Collision cross section (Ω) values of gas-phase ions of proteins and protein complexes are used to probe the structures of the corresponding species in solution. Ions of many proteins exhibit increasing Ω-values with increasing charge state but most Ω-values calculated for protein ions have used simple collision models that do not explicitly account for charge. Here we use a combination of ion mobility mass spectrometry experiments with helium gas and trajectory method calculations to characterize the extents to which increases in experimental Ω-values with increasing charge state may be attributed to increased momentum transfer concomitant with enhanced long-range interactions between the protein ion and helium atoms. Ubiquitin and C-to-N terminally linked diubiquitin ions generated from different solution conditions exhibit more than a 2-fold increase in Ω with increasing charge state. For native and energy-relaxed models of the proteins and most methods for distributing charge, Ω-values calculated using the trajectory method increase by less than 1% over the range of charge states observed from typical solution conditions used for native mass spectrometry. However, the calculated Ω-values increase by 10% to 15% over the full range of charge states observed from all solution conditions. Therefore, contributions from enhanced ion-induced dipole interactions with increasing charge state are significant but without additional structural changes can account for only a fraction of the increase in Ω observed experimentally. On the basis of these results, we suggest guidelines for calculating Ω-values in the context of applications in biophysics and structural biology.

Benchmark Comparison for a Multi-Processing Ion Mobility Calculator in the Free Molecular Regime

A benchmark comparison between two ion mobility and collision cross-section (CCS) calculators, MOBCAL and IMoS, is presented here as a standard to test the efficiency and performance of both programs. Utilizing 47 organic ions, results are in excellent agreement between IMoS and MOBCAL in He and N_2, when both programs use identical input parameters. Due to a more efficiently written algorithm and to its parallelization, IMoS is able to calculate the same CCS (within 1%) with a speed around two orders of magnitude faster than its MOBCAL counterpart when seven cores are used. Due to the high computational cost of MOBCAL in N₂, reaching tens of thousands of seconds even for small ions, the comparison between IMoS and MOBCAL is stopped at 70 atoms. Large biomolecules (>10000 atoms) remain computationally expensive when IMoS is used in N₂ (even when employing 16 cores). Approximations such as diffuse trajectory methods (DHSS, TDHSS) with and without partial charges and projected area approximation corrections can be used to reduce the total computational time by several folds without hurting the accuracy of the solution. These latter methods can in principle be used with coarse-grained model structures and should yield acceptable CCS results. Graphical Abstract ᅟ.

Correlation between the shape of the ion mobility signals and the stepwise folding process of polylactide ions

In the field of polymer characterization, the use of ion mobility mass spectrometry (IMMS) remains mainly devoted to the temporal separation of cationized oligomers according to their charge states, molecular masses and macromolecular architectures in order to probe the presence of different structures. When analyzing multiply charged polymer ions by IMMS, the most striking feature is the observation of breaking points in the evolution of the average collision cross sections with the number of monomer units. Those breaking points are associated to the folding of the polymer chain around the cationizing agents. Here, we scrutinize the shape of the arrival time distribution (ATD) of polylactide ions and associate the broadening as well as the loss of symmetry of the ATD signals to the coexistence of different populations of ions attributed to the transition from opened to folded stable structures. The observation of distinct distributions reveals the absence of folded/extended structure interconversion on the ion mobility time scale (1-10 ms) and then on the lifetime of ions within the mass spectrometer at room temperature. In order to obtain information on the possible interconversion between the different observed populations upon ion activation, we performed IM-IM-MS experiments (tandem ion mobility measurements). To do so, mobility-selected ions were activated by collisions before a second mobility measurement. Interestingly, the conversion by collisional activation from a globular structure into a (partially) extended structure, i.e. the gas phase unfolding of the ions, was not observed in the energetic regime available with the used experimental setup. The absence of folded/extended interconversion, even upon collisional activation, points to the fact that the polylactide ions are 'frozen' in their specific 3D structure during the desolvation/ionization electrospray processes. Copyright © 2017 John Wiley & Sons, Ltd.

Collision Cross Sections for 20 Protonated Amino Acids: Fourier Transform Ion Cyclotron Resonance and Ion Mobility Results

We report relative dephasing cross sections for the 20 biogenic protonated amino acids measured using the cross sectional areas by Fourier transform ion cyclotron resonance (CRAFTI) technique at 1.9 keV in the laboratory reference frame, as well as momentum transfer cross sections for the same ions computed from Boltzmann-weighted structures determined using molecular mechanics. Cross sections generally increase with increasing molecular weight. Cross sections for aliphatic and aromatic protonated amino acids are larger than the average trend, suggesting these side chains do not fold efficiently. Sulfur-containing protonated amino acids have smaller than average cross sections, reflecting the mass of the S atom. Protonated amino acids that can internally hydrogen-bond have smaller than average cross sections, reflecting more extensive folding. The CRAFTI measurements correlate well with results from drift ion mobility (IMS) and traveling wave ion mobility (TWIMS) spectrometric measurements; CRAFTI results correlate with IMS values approximately as well as IMS and TWIMS values from independent measurements correlate with each other. Both CRAFTI and IMS results correlate well with the computed momentum transfer cross sections, suggesting both techniques provide accurate molecular structural information. Absolute values obtained using the various methods differ significantly; in the case of CRAFTI, this may be due to errors in measurements of collision gas pressure, measurement of excitation voltage, and/or dependence of cross sections on kinetic energy. Graphical Abstract ᅟ.

Ion mobility coupled to native mass spectrometry as a relevant tool to investigate extremely small ligand-induced conformational changes

Native and ion-mobility mass spectrometry reveal the conformational evolution over time of a peptide deformylase binding different ligands, which is consistent with slow-tight inhibition of the enzyme.

Collision cross sectional areas from analysis of Fourier transform ion cyclotron resonance line width: a new method for characterizing molecular structure

We demonstrate a technique for determining molecular collision cross sections via measuring the variation of Fourier transform ion cyclotron resonance (FTICR) line width with background damping gas pressure, under conditions where the length of the FTICR transient is pressure limited. Key features of our method include monoisotopic isolation of ions, the pulsed introduction of damping gas to a constant pressure using a pulsed leak valve, short excitation events to minimize collisions during the excitation, and proper choice of damping gas (Xe is superior to He). The measurements are reproducible within a few percent, which is sufficient for distinguishing between many structural possibilities and is comparable to the uncertainty in cross sections calculated from computed molecular structures. These techniques complement drift ion mobility measurements obtained on dedicated instruments. They do not require a specialized instrument, but should be easily performed on any FTICR mass spectrometer equipped with a pulsed leak valve.

Optimization of Algorithms for Ion Mobility Calculations

Ion mobility spectrometry (IMS) is increasingly employed to probe the structures of gas-phase ions, particularly those of proteins and other biological macromolecules. This process involves comparing measured mobilities to those computed for potential geometries, which requires evaluation of orientationally averaged cross sections using some approximate treatment of ion-buffer gas collisions. Two common models are the projection approximation (PA) and exact hard-spheres scattering (EHSS) that represent ions as collections of hard spheres. Though calculations for large ions and/or conformer ensembles take significant time, no algorithmic optimization had been explored. Previous EHSS programs were dominated by ion rotation operations that allow orientational averaging. We have developed two new algorithms for PA and EHSS calculations: one simplifies those operations and greatly reduces their number, and the other disposes of them altogether by propagating trajectories from a random origin. The new algorithms were tested for a representative set of seven ion geometries including diverse sizes and shapes. While the best choice depends on the geometry in a nonobvious way, the difference between the two codes is generally modest. Both are much more efficient than the existing software, for example faster than the widely used Mobcal (implementing EHSS) approximately 10-30-fold.

Bulk Production of a Strong Covalently Linked (C60Hx)2 Dimer

The high-pressure treatment of C60 in an H2 atmosphere at high temperatures leads to the efficient formation of a covalently bound dimer and some oligomeric species. The resulting hydrogenated C120 is an example of the bulk production of covalently bound derivatized fullerene cores. Matrix-assisted laser desorption/ionization in conjunction with reflectron time-of-flight mass spectrometry has been applied to the product analysis. The dissociation pattern of selected C120H(2x)+ ions (x > 30) indicates the dimeric structure of (C60H(x))2, as opposed to a giant hydrofullerene species possessing a fused C120 core. However, the results also clearly indicate a much stronger bonding (multiple sigma bonding) between the C60H(x) units than present in cycloaddition products. Evidence of a covalently linked dimer was obtained in labeling experiments, on the basis of which any laser-induced gas-phase aggregation of the C60H(x) monomer during the analysis is discounted.

Modeling the resolution and sensitivity of FAIMS analyses

Field asymmetric waveform ion mobility spectrometry (FAIMS) is rapidly gaining acceptance as a robust, versatile tool for post-ionization separations prior to mass-spectrometric analyses. The separation is based on differences between ion mobilities at high and low electric fields, and proceeds at atmospheric pressure. Two major advantages of FAIMS over condensed-phase separations are its high speed and an ion focusing effect that often improves sensitivity. While selected aspects of FAIMS performance are understood empirically, no physical model rationalizing the resolving power and sensitivity of the method and revealing their dependence on instrumental variables has existed. Here we present a first-principles computational treatment capable of simulating the FAIMS analyzer for virtually any geometry (including the known cylindrical and planar designs) and arbitrary operational parameters. The approach involves propagating an ensemble of ion trajectories through the device in real time under the influence of applied asymmetric potential, diffusional motion incorporating the high-field and anisotropic phenomena, and mutual Coulomb repulsion of ionic charges. Calculations for both resolution and sensitivity are validated by excellent agreement with measurements in different FAIMS modes for ions representing diverse types and analyte classes.

Gas-Phase Ion Mobilities and Structures of Benzene Cluster Cations (C6H6)n+, n = 2−6

Benzene clusters are generated by pulsed supersonic beam expansion, ionized by electron impact, mass-selected and then injected into a drift cell for ion mobility measurements in a helium buffer gas. The measured collision cross sections and theoretical calculations are used to determine the structures of the cluster cations (C(6)H(6))(n)(+) with n = 2-6. Density functional theory calculation, at an all-electron level and without any symmetry constraint, predicts that the dimer cation has two nearly degenerate ground state structures with the sandwich configuration more stable than the T-configuration by only 0.07 eV. The ion mobility experiment indicates that only one structure is observed for the mass-selected dimer cation at room temperature. The calculated cross section for the sandwich structure agrees very well (within 2.4%) with the experimental value. For the n = 3-6 clusters, the experiments suggest the presence of at least two structural isomers for each cluster. A Monte Carlo minimum-energy search technique using the 12-site OPLS potential for benzene is used to determine the structures of the lowest-energy isomers. The calculated cross sections for the two lowest-energy isomers of the n = 3-6 clusters agree well with the experimental results. The clusters' structures reveal two different growth patterns involving a sandwich dimer core or a pancake trimer stack core. The lowest-energy isomers of the n = 3-6 clusters incorporate the pancake trimer stack as the cluster's core. The trimer stack allows the charge to hop between two dimers, thus maximizing charge resonance interaction in the clusters. For larger clusters, the appearance of magic numbers at n = 14, 20, 24, 27, and 30 is consistent with the incorporation of a sandwich dimer cation within icosahedral, double icosahedral, and interpenetrating icosahedral structures. On the basis of the ion mobility results and the structural calculations, the parallel-stacked motif among charged aromatic-aromatic interactions is expected to play a major role in determining the structures of multi aromatic components. This conclusion may provide new insights for experimental and theoretical studies of molecular design and recognition involving aromatic systems.

Observation of "Stick" and "Handle" intermediates along the fullerene road

The hypothesis that fullerenes grow in a carbon plasma by the addition of C2 units (the "fullerene road") has been widely acclaimed as the most plausible mechanism for formation of larger fullerenes including C60 and C70. Calculations suggest that the association of C2 with fullerenes proceeds through two classes of intermediates, "sticks" and "handles." Here we report the observation of these species using high-resolution ion-mobility measurements for C(n) cations generated by laser vaporization of graphite and laser desorption of C60. Sticks with up to eight-atom chains have also been found.