Experimental Collision Cross Sections Research Articles

Chain Ejection Model for Electrospray Ionization of Unfolded Proteins: Evidence from Atomistic Simulations and Ion Mobility Spectrometry.

The ion evaporation model (IEM) and the charged residue model (CRM) represent cornerstones of any discussion related to the mechanism of electrospray ionization (ESI). Molecular dynamics (MD) simulations have confirmed that small ions such as Na+ are ejected from the surface of aqueous ESI droplets (IEM), while folded proteins in native ESI are released by water evaporation to dryness (CRM). ESI of unfolded proteins yields [M + zH] z+ ions that are much more highly charged than their folded counterparts. A chain ejection model (CEM) has been proposed to account for the protein ESI behavior under such non-native conditions (Konermann, L., et al. Anal. Chem. 2013, 85, 2-9). The CEM envisions that unfolded proteins are driven to the droplet surface by hydrophobic and electrostatic factors, followed by gradual ejection via intermediates where droplets carry extended protein tails. Thus far, it has not been possible to support the CEM through MD simulations using realistic protein models and atomistic force fields. Such endeavors require much larger droplets than in previous MD studies. Also, the incorporation of CEM-related H+ migration is difficult. This work overcomes these challenges in MD simulations on unfolded apo-myoglobin (aMb) in droplets with a 5.5 nm radius (∼22500 water molecules). We focused on solutions at pH ∼4 where the aMb solution charge coincides with the charge on some of the electrosprayed ions (22+ to 27+), such that H+ migration could be neglected. Na+ ions were added to ensure a droplet charge close to the Rayleigh limit. We found that 16 of 17 MD runs on various protonation patterns produced [M + zH] z+ ions via chain ejection. The predicted stretched-out aMb conformations were consistent with experimental collision cross sections. These results support the view that unfolded proteins follow the CEM. Overall, the IEM/CRM/CEM triad can account for a wide range of ESI scenarios involving various types of analytes.

Bent Keto Form of Curcumin, Preferential Stabilization of Enol by Piperine, and Isomers of Curcumin∩Cyclodextrin Complexes: Insights from Ion Mobility Mass Spectrometry.

A detailed examination of collision cross sections (CCSs) coupled with computational methods has revealed new insights into some of the key questions centered around curcumin, one of the most intensively studied natural therapeutic agents. In this study, we have distinguished the structures and conformers of the well-known enol and the far more elusive keto form of curcumin by using ion mobility mass spectrometry (IM MS). The values of the theoretically predicted isomers were compared with the experimental CCS values to confirm their structures. We have identified a bent structure for the keto form and the degree of bending was estimated. Using IM MS, we have also shown that ESI MS reflects the solution phase structures and their relative populations, in this case. Piperine, a naturally occurring heterocyclic compound, is known to increase the bioavailability of curcumin. However, it is still not clearly understood which tautomeric form of curcumin is better stabilized by it. We have identified preferential stabilization of the enol form in the presence of piperine using IM MS. Cyclodextrins (CDs) are used as well-known carriers in the pharmaceutical industry for increasing the stability, solubility, bioavailability, and tolerability of curcumin. However, the crystal structures of supramolecular complexes of curcumin∩CD are unknown. We have determined the structures of different isomers of curcumin∩CD (α- and β-CD) complexes by comparing the CCSs of theoretically predicted structures with the experimentally obtained CCSs, which will further help in understanding the specific role of the structures involved in different biological activities.

Analysis of isomeric opioids in urine using LC-TIMS-TOF MS

In the present work, a fast separation, identification and quantification workflow based on liquid chromatography coupled to trapped ion mobility in tandem with mass spectrometry (LC-TIMS-MS) is described for the analysis of common isomeric drugs of abuse and their metabolites in human urine. In particular, the analytical performance of LC-TIMS-MS is shown for identification based on retention time, collision cross section and accurate mass for three sets of common isomeric opioids and their deuterated analogs in urine. The LC-TIMS-MS analysis provided limits of detection of 1.4–35.2 ng/mL with demonstrated linearity up to 500 ng/mL, enabling discovery and targeted monitoring (DTM) of opioids in urine, with high precision in retention times (RT) (< 0.3%), collision cross sections (CCS) (< 0.6%) and mass accuracy (< 1 ppm) across multiple measurements using external calibration. A good agreement was observed between theoretical and experimental CCS from candidate structures optimized at the DFT/B3LYP level. The need for complementary liquid and mobility separations prior to mass analysis is shown for the analysis of complex mixtures, with mobility resolving power of 80–130. The reproducibility and high speed of LC-TIMS-MS analysis provides a powerful platform for drug and metabolite screening in biological matrices with higher precision and confidence than traditional LC-multiple reaction monitoring (MRM) approaches.

Optimization of long range potential interaction parameters in ion mobility spectrometry.

The problem of optimizing Lennard-Jones (L-J) potential parameters to perform collision cross section (CCS) calculations in ion mobility spectrometry has been undertaken. The experimental CCS of 16 small organic molecules containing carbon, hydrogen, oxygen, nitrogen, and fluoride in N2 was compared to numerical calculations using Density Functional Theory (DFT). CCS calculations were performed using the momentum transfer algorithm IMoS and a 4-6-12 potential without incorporating the ion-quadrupole potential. A ceteris paribus optimization method was used to optimize the intercept σ and potential well-depth ϵ for the given atoms. This method yields important information that otherwise would remain concealed. Results show that the optimized L-J parameters are not necessarily unique with intercept and well-depth following an exponential relation at an existing line of minimums. Similarly, the method shows that some molecules containing atoms of interest may be ill-conditioned candidates to perform optimizations of the L-J parameters. The final calculated CCSs for the chosen parameters differ 1% on average from their experimental counterparts. This result conveys the notion that DFT calculations can indeed be used as potential candidates for CCS calculations and that effects, such as the ion-quadrupole potential or diffuse scattering, can be embedded into the L-J parameters without loss of accuracy but with a large increase in computational efficiency.

Fullerene-Functionalized Monolayer-Protected Silver Clusters: [Ag29(BDT)12(C60) n]3- ( n = 1-9).

We report the formation of supramolecular adducts between monolayer-protected noble metal nanoclusters and fullerenes, specifically focusing on a well-known silver cluster, [Ag29(BDT)12]3-, where BDT is 1,3-benzenedithiol. We demonstrate that C60 molecules link with the cluster at specific locations and protect the fragile cluster core, enhancing the stability of the cluster. A combination of studies including UV-vis, high-resolution electrospray ionization mass spectrometry, collision-induced dissociation, and nuclear magnetic resonance spectroscopy revealed structural details of the fullerene-functionalized clusters, [Ag29(BDT)12(C60) n]3- ( n = 1-9). Density functional theory (DFT) calculations and molecular docking simulations affirm compatibility between the cluster and C60, resulting in its attachment at specific positions on the surface of the cluster, stabilized mainly by π-π and van der Waals interactions. The structures have also been confirmed from ion mobility mass spectrometry by comparing the experimental collision cross sections (CCSs) with the theoretical CCSs of the DFT-optimized structures. The gradual evolution of the structures with an increase in the number of fullerene attachments to the cluster has been investigated. Whereas the structure for n = 4 is tetrahedral, that of n = 8 is a distorted cube with a cluster at the center and fullerenes at the vertices. Another fullerene, C70, also exhibited similar behavior. Modified clusters are expected to show interesting properties.

High resolution-ion mobility mass spectrometry as an additional powerful tool for structural characterization of mycotoxin metabolites

This work was designed as a proof of concept, to demonstrate the successful use of the comparison between theoretical and experimental collision cross section (CCS) values to support the identification of isomeric forms. To this purpose, thirteen mycotoxins were considered and analyzed using drift time ion mobility mass spectrometry. A good linear correlation (r2 = 0.962) between theoretical and experimental CCS was found. The average ΔCCS was 3.2%, fully consistent with the acceptability threshold value commonly set at 5%. The agreement between theoretical and experimental CCS obtained for mycotoxin glucuronides suggested the potential of the CCS matching in supporting the annotation procedure.

Geometrical Structures of Gas Phase Chromium Oxide Cluster Anions Studied by Ion Mobility Mass Spectrometry

Structural assignments of gas phase chromium oxide cluster anions, CrmOn- (m = 1-7), have been achieved by comparison between experimental collision cross sections measured by ion mobility mass spectrometry and theoretical collision cross sections of optimized structures by quantum chemical calculations. In the mass spectrum, significant magic behavior between the numbers m and n was not observed for CrmOn-, while wide ranges of compositions were observed around CrmO2m+2- to (CrO3)m- as reported previously. The (CrO3)m- (m = 3-7) ions were assigned to have monocyclic-ring structures for m = 3-5 and bicyclic rings for m = 6 and 7. In addition, gradual structural change from these cyclic structures of (CrO3)m- to three-dimensional structures of CrmO2m+2- was found for m = 4-7. The energy levels of molecular orbitals of a calculated monocyclic structure of Cr5O15- were also found to be consistent with previous results of photoelectron spectroscopy, although those of the bicyclic isomer exhibited a different behavior. Moreover, the observation of abundant ions generated by collision induced dissociations at the inlet of the ion drift cell indicates that the larger sized (CrO3)m- (m > 5) series were unstable and easily dissociated to smaller ions.

Prediction of Collision Cross-Section Values for Small Molecules: Application to Pesticide Residue Analysis.

The use of collision cross-section (CCS) values obtained by ion mobility high-resolution mass spectrometry has added a third dimension (alongside retention time and exact mass) to aid in the identification of compounds. However, its utility is limited by the number of experimental CCS values currently available. This work demonstrates the potential of artificial neural networks (ANNs) for the prediction of CCS values of pesticides. The predictor, based on eight software-chosen molecular descriptors, was optimized using CCS values of 205 small molecules and validated using a set of 131 pesticides. The relative error was within 6% for 95% of all CCS values for protonated molecules, resulting in a median relative error less than 2%. In order to demonstrate the potential of CCS prediction, the strategy was applied to spinach samples. It notably improved the confidence in the tentative identification of suspect and nontarget pesticides.

Hybrid Mass Spectrometry Approaches to Determine How L-Histidine Feedback Regulates the Enzyzme MtATP-Phosphoribosyltransferase

SummaryMtATP-phosphoribosyltransferase (MtATP-PRT) is an enzyme catalyzing the first step of the biosynthesis of L-histidine in Mycobacterium tuberculosis, and proposed to be regulated via an allosteric mechanism. Native mass spectrometry (MS) reveals MtATP-PRT to exist as a hexamer. Conformational changes induced by L-histidine binding and the influence of buffer pH are determined with ion mobility MS, hydrogen deuterium exchange (HDX) MS, and analytical ultracentrifugation. The experimental collision cross-section (DTCCSHe) decreases from 76.6 to 73.5 nm2 upon ligand binding at pH 6.8, which correlates to the decrease in CCS calculated from crystal structures. No such changes in conformation were found at pH 9.0. Further detail on the regions that exhibit conformational change on L-histidine binding is obtained with HDX-MS experiments. On incubation with L-histidine, rapid changes are observed within domain III, and around the active site at longer times, indicating an allosteric effect.

Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry.

Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/trans isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.

Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization.

Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions. Graphical Abstract ᅟ.

Compositions and Structures of Vanadium Oxide Cluster Ions VmOn(±) (m = 2-20) Investigated by Ion Mobility Mass Spectrometry.

Stable compositions and geometrical structures of vanadium oxide cluster ions, VmOn(±), were investigated by ion mobility mass spectrometry (IM-MS). The most stable compositions of vanadium oxide cluster cations were (V2O4)(V2O5)(m-2)/2(+) and (VO2)(V2O5)(m-1)/2(+), depending on the clusters with even and odd numbers of vanadium atoms. Compositions one-oxygen richer than the cations, such as (V2O5)m/2(-) and (VO3)(V2O5)(m-1)/2(-), were predominantly observed for cluster anions. Assignments of these stable cluster ion compositions, which were determined as a result of collision-induced dissociations in IM-MS, can partly be explained with consideration of spin density distribution. By comparing the experimental collision cross sections (CCSs) obtained from ion mobility measurement with CCSs of the theoretically calculated structures, we confirmed the patterned growth of geometrical structures partially discussed in previous theoretical and spectroscopic studies. We showed that even sized (V2O5)m/2(±) where m = 6-12 had right polygonal prism structures except for the anionic V12O30(-), and for the clusters of odd numbers of vanadium m, cations and anions can either have bridged or pyramid structures. Both of the odd sized structures proposed were derivatives from the even sized right polygonal prism structures. The exception, V12O30(-), which had a CCS almost equal to that of the neighboring smaller V11O28(-), should have a structure of higher density than the right hexagonal prism, in which it was proposed to be a captured pyramid structure, derived from V11O28(-).

Isomer Separation of Polybrominated Diphenyl Ether Metabolites using nanoESI-TIMS-MS.

In this paper, high-resolution nano-electrospray ionization-trapped ion mobility spectrometry coupled to mass spectrometry (nESI-TIMS-MS) is used for the study of hydroxylated polybrominated diphenyl ether (OH-PBDE) metabolites. In particular, experimental ion-neutral collision cross sections (CCS) were measured for five structural OH-PBDE isomers using TIMS-MS. Candidate structures were proposed for each IMS band observed in good agreement with the experimental CCS measurements (5% error). The analytical power of TIMS-MS to baseline and partially separate structural isomers of OH-BDE in binary and ternary mixtures is shown for single charge species with a mobility resolving power of RIMS ~ 400. This work provides the proof of concept for the analysis of low concentration OH-PBDE in environmental samples based on accurate collision cross section and mass measurements without the need for derivatization and pre-fractionation protocols, thus significantly reducing the cost and analysis time.

Structural Elucidation of β-Lactam Diastereoisomers through Ion Mobility Mass Spectrometry Studies and Theoretical Calculations.

The ion mobility combined with mass spectrometry and theoretical calculations were used to characterize and separate six diastereoisomeric β-lactams. The influence of traveling wave height and wave velocity, size of the alkali metal ion (Li(+), Na(+) and K(+)) and drift gases with varying masses and polarizabilities (N2 and CO2) on separation efficacy was additionally examined. The best separation of diastereoisomers of β-lactams was observed for adducts with Na(+) and Li(+) ions, whereas other parameters had little impact on separation process. The isomeric β-lactams were characterized by both experimental and theoretical collision cross sections. The theoretically calculated values of collision cross sections obtained from extensive molecular dynamics and density functional theory calculations for model structures agreed well with those established experimentally. The relationship between separation efficacy and the configuration at the carbon atoms C5 and C6 of β-lactam ring was defined.

Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.

Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers.

Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes.

One attractive feature of ion mobility mass spectrometry (IM-MS) lies in its ability to provide experimental collision cross section (CCS) measurements, which can be used to distinguish different conformations that a protein complex may adopt during its gas-phase unfolding. However, CCS values alone give no detailed information on subunit structure within the complex. Consequently, structural characterization typically requires molecular modeling, which can have uncertainties without experimental support. One method of obtaining direct experimental evidence on the structures of these intermediates is utilizing gas-phase activation techniques that can effectively dissociate the complexes into substructures while preserving the native topological information. The most commonly used activation method, collision-induced dissociation (CID) with low-mass target gases, typically leads to unfolding of monomers of a protein complex. Here, we describe a method that couples IM-MS and surface-induced dissociation (SID) to dissociate the source-activated precursors of three model protein complexes: C-reactive protein (CRP), transthyretin (TTR), and concanavalin A (Con A). The results of this study confirm that CID involves the unfolding of the protein complex via several intermediates. More importantly, our experiments also indicate that retention of similar CCS between different intermediates does not guarantee retention of structure. Although CID spectra (at a given collision energy) of source-activated, mass-selected precursors do not distinguish between native-like, collapsed, and expanded forms of a protein complex, dissociation patterns and/or average charge states of monomer products in SID of each of these forms are unique.

How Closely Related Are Conformations of Protein Ions Sampled by IM-MS to Native Solution Structures?

Here, we critically evaluate the effects of changes in the ion internal energy (E(int)) on ion-neutral collision cross sections (CCS) of ions of two structurally diverse proteins, specifically the [M + 6H](6+) ion of ubiquitin (ubq(6+)), the [M + 5H](5+) ion of the intrinsically disordered protein (IDP) apo-metallothionein-2A (MT), and its partially- and fully-metalated isoform, the [CdiMT](5+) ion. The ion-neutral CCS for ions formed by "native-state" ESI show a strong dependence on E(int). Collisional activation is used to increase E(int) prior to the ions entering and within the traveling wave (TW) ion mobility analyzer. Comparisons of experimental CCSs with those generated by molecular dynamics (MD) simulation for solution-phase ions and solvent-free ions as a function of temperature provide new insights about conformational preferences and retention of solution conformations. The E(int)-dependent CCSs, which reveal increased conformational diversity of the ion population, are discussed in terms of folding/unfolding of solvent-free ions. For example, ubiquitin ions that have low internal energies retain native-like conformations, whereas ions that are heated by collisional activation possess higher internal energies and yield a broader range of CCS owing to increased conformational diversity due to losses of secondary and tertiary structures. In contrast, the CCS profile for the IDP apoMT is consistent with kinetic trapping of an ion population composed of a wide range of conformers, and as the E(int) is increased, these structurally labile conformers unfold to an elongated conformation.

Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure

The preservation of molecular ion three dimensional conformations of electrospray formed ions is a question that many researchers have asked and that can now be answered using ion mobility coupled to mass spectrometry. Indeed, ion mobility has the ability to separate ions according to their size-to-charge ratios in the gas-phase. Size is related to the mass and to the three-dimensional shape of a molecule. Therefore, by hyphenating ion mobility to mass spectrometry (IM-MS), one can sort ions according to both mass and shape. The challenge is to decipher structural information from ion mobility experiments. In this tutorial special feature, Valerie Gabelica and co-workers clarify how to interpret experimental collision cross section measurements in terms of three-dimensional structure for ions larger than 100 atoms and how these can be compared to those calculated for modelling three-dimensional structures of the ion of interest. Dr. Gabelica is an Inserm Research Director at the Institut Européen de Chimie et Biologie (Université de Bordeaux, France). Her research interests are centered on the detection, quantification and characterization of all the assemblies and tridimensional structures formed by nucleic acids in solution, using tailor-made MS-based approaches.

Identification and separation of saxitoxins using hydrophilic interaction liquid chromatography coupled to traveling wave ion mobility-mass spectrometry.

The aim of this work was to develop a reliable and efficient analytical method to characterise and differentiate saxitoxin analogues (STX), including sulphated (gonyautoxins, GTX) and non-sulphated analogues. For this purpose, hydrophilic interaction liquid chromatography (HILIC) was used to separate sulphated analogues. We also resorted to ion mobility spectrometry to differentiate the STX analogues because this technique adds a new dimension of separation based on ion gas phase conformation. Positive and negative ionisation modes were used for gonyautoxins while positive ionisation mode was used for non-sulphated analogues. Subsequently, the coupling of these three complementary techniques, HILIC-IM-MS, permitted the separation and identification of STX analogues; isomer differentiation was achieved in HILIC dimension while non-sulphated analogues were separated in the IM-MS dimension. Additional structural characteristics concerning the conformation of STXs could be obtained using IM-MS measurements. Thus, the collision cross sections (CCS) of STXs are reported for the first time in the positive ionisation mode. These experimental CCSs correlated well with the calculated CCS values using the trajectory method.

Isomer separation of iron oxide cluster cations by ion mobility mass spectrometry.

Geometrical structures of iron oxide cluster cations have been analyzed by ion mobility mass spectrometry. The series of (FeO)n(+) and FenOn+1(+) cluster cations were predominantly observed in a mass spectrum at high ion-injection energy into a drift cell. Arrival time distributions in the ion mobility spectrometry indicate that two structural isomers coexist for the (FeO)n(+) clusters at n ≥ 5. By comparison of experimental collision cross sections determined from the arrival times with theoretical ones, two-dimensional ring and sheet structures were assignable for (FeO)n(+) (n = 3-8). In addition to these isomers, compact three-dimensional structures were also found to be stable at (FeO)n(+) (n ≥ 6). Thus, the two-dimensional and three-dimensional structural isomers coexist for (FeO)n(+) (n = 6-8).