Conformation of Polyalanine and Polyglycine Dications in the Gas Phase: Insight from Ion Mobility Spectrometry and Replica-Exchange Molecular Dynamics

On the Conformation of Anionic Peptoids in the Gas Phase

Although N-(S)-phenylethyl peptoids are known to adopt helical structures in solutions, the corresponding positively charged ions lose their helical structure during the transfer from the solution to the gas phase due to the so-called charge solvation effect. We, here, considered negatively charged peptoids to investigate by ion mobility spectrometry-mass spectrometry whether the structural changes described in the positive ionization mode can be circumvented in the negative mode by a fine-tuning of the peptoid sequence, that is, by positioning the negative charge at the positive side of the helical peptoid macrodipole. N-(S)-(1-carboxy-2-phenylethyl) (Nscp) and N-(S)-phenylethyl (Nspe) were selected as the negative charge carrier and as the helix inductor, respectively. We, here, report the results of a joint theoretical and experimental study demonstrating that the structures adopted by the Nspe_nNscp anions remain compactly folded in the gas phase for chains containing up to 10 residues, whereas no evidence of the presence of a helical structure was obtained, even if, for selected sequences and lengths, different gas phase conformations are detected.

Interrogating the Quaternary Structure of Noncanonical Hemoglobin Complexes by Electrospray Mass Spectrometry and Collision-Induced Dissociation

Various activation methods are available for the fragmentation of gaseous protein complexes produced by electrospray ionization (ESI). Such experiments can potentially yield insights into quaternary structure. Collision-induced dissociation (CID) is the most widely used fragmentation technique. Unfortunately, CID of protein complexes is dominated by the ejection of highly charged monomers, a process that does not yield any structural insights. Using hemoglobin (Hb) as a model system, this work examines under what conditions CID generates structurally informative subcomplexes. Native ESI mainly produced tetrameric Hb ions. In addition, "noncanonical" hexameric and octameric complexes were observed. CID of all these species [(αβ)₂, (αβ)₃, and (αβ)₄] predominantly generated highly charged monomers. In addition, we observed hexamer → tetramer + dimer dissociation, implying that hexamers have a tetramer··dimer architecture. Similarly, the observation of octamer → two tetramer dissociation revealed that octamers have a tetramer··tetramer composition. Gas-phase candidate structures of Hb assemblies were produced by molecular dynamics (MD) simulations. Ion mobility spectrometry was used to identify the most likely candidates. Our data reveal that the capability of CID to produce structurally informative subcomplexes depends on the fate of protein-protein interfaces after transfer into the gas phase. Collapse of low affinity interfaces conjoins the corresponding subunits and favors CID via monomer ejection. Structurally informative subcomplexes are formed only if low affinity interfaces do not undergo a major collapse. However, even in these favorable cases CID is still dominated by monomer ejection, requiring careful analysis of the experimental data for the identification of structurally informative subcomplexes.

Conformation and bonding of 2-methoxypyridine and its monohydrate from rotational spectra

Rotational spectra of 2-methoxypyridine and its monohydrate have been characterized by pulsed jet Fourier transform microwave spectroscopy and complementary ab initio calculations. Rotational spectra of the parent monomer and seven mono-substituted isotopologues (¹³C and ¹⁵N) were measured in natural abundance, which allow determining the accurate structure of the skeleton of 2-methyoxypyridine. The barrier to the methyl internal rotation was determined from the A/E torsional symmetry species of the rotational transitions. For the 2-methyoxypyridine⋯H₂O complex, rotational spectra of the parent dimer and isotopologues formed with isotopically enriched water (H₂¹⁸O, HOD, DOH and D₂O) indicate that the observed isomer is stabilized by a strong OH⋯N and a secondary bifurcated (CH)₂⋯O weak hydrogen bonds. Bader's quantum theory of atoms in molecules and Johnson's non-covalent interaction analyses were applied and visualized to have a better understanding of the non-covalent interactions in 2-methyoxypyridine⋯H₂O.

Ion mobility resolved photo-fragmentation to discriminate protomers

RATIONALE

Among the sources of structural diversity in biomolecular ions, the co-existence of protomers is particularly difficult to take into account, which in turn complicates structural interpretation of gas-phase data.

METHODS

We investigated the sensitivity of gas-phase photo-fragmentation measurements and ion mobility spectrometry (IMS) to the protonation state of a model peptide derivatized with chromophores. Accessible interconversion pathways between the different identified conformers were probed by tandem ion mobility measurement. Furthermore, the excitation coupling between the chromophores has been probed through photo-fragmentation measurements on mobility-selected ions. All results were interpreted based on molecular dynamics simulations.

RESULTS

We show that protonation can significantly affect the photo-fragmentation yields. Especially, conformers with very close collision cross sections (CCSs) may display dramatically different photo-fragmentation yields in relation with different protonation patterns.

CONCLUSIONS

We show that, even if precise structure assignment based on molecular modeling is in principle difficult for large biomolecular assemblies, the combination of photo-fragmentation and IMS can help to identify the signature of protomer co-existence for a population of biomolecular ions in the gas phase. Such spectroscopic data are particularly suitable to follow conformational changes.

Collision cross section (CCS) measurement by ion cyclotron resonance mass spectrometry with short-time Fourier transform

RATIONALE

The collision cross section (CCS) is an important shape parameter which is often used in molecular structure investigation. In Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), the CCS affects the ion signal damping shape due to the effect of ion-neutral collisions. It is potential to obtain ion CCS values from FTICR-MS with the help of a proper ion-collision model.

METHODS

We have developed a rapid method to obtain the ion damping profile and CCS for mixtures by only one FTICR-MS measurement. The method utilizes short-time Fourier transform (STFT) to process FTICR-MS time domain signals. The STFT-processed result is a three-dimensional (3D) spectrum which has an additional time axis in addition to the conventional mass-to-charge ratio and intensity domains. The damping profile of each ion can be recognized from the 3D spectrum.

RESULTS

After extracting the decay profile of a specified ion, all the three ion-neutral collision models were tested in curve fitting. The hard-sphere model was proven to be suitable for our experimental setup. A linear relationship was observed between the CCS value and hard-sphere model parameters. Therefore, the CCS values of all the peaks were obtained through the addition of internal model compounds and linear calibration.

CONCLUSIONS

The proposed method was successfully applied to determine the CCSs of fatty acids and polyalanines in a petroleum gas oil matrix. This technique can be used for simultaneous measurement of cross sections for many ions in congested spectra.

Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry?

Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).

Multiple gas-phase conformations of proline-containing peptides: is it always cis/trans isomerization?

Ion mobility-mass spectrometry (IM-MS) is often employed to look at the secondary, tertiary, and quaternary structures of naked peptides and proteins in the gas-phase. Recently, it has offered a unique glimpse into proline-containing peptides and their cis/trans Xxx-Pro isomers. An experimental "signature" has been identified wherein a proline-containing peptide has its Pro residues substituted with another amino acid and the presence or absence of conformations in the IM-MS spectra is observed. Despite the high probability that one could attribute these conformations to cis/trans isomers, it is also possible that cis/trans isomers are not the cause of the additional conformations in proline-containing peptides. However, the experimental evidence of such a system has not been demonstrated or reported. Herein, we present the IM-MS analysis of Neuropeptide Y's wild-type (WT) signal sequence and Leu7Pro (L7P) mutant. Although comparison of arrival times and collision cross-sections of [M + 4H](4+) ions yields the cis/trans "signature", molecular dynamics indicates that a cis-Pro7 is not very stable and that trans-Pro7 conformations of the same cross-section arise with equal frequency. We believe that this work further underscores the importance of theoretical calculations in IM-MS structural assignments.

The structure of chromophore-grafted amyloid-β12–28 dimers in the gas-phase: FRET-experiment guided modelling

Theoretical modelling, ion mobility spectrometry and action-FRET experiments are combined to an experiment guided approach and used to elucidate the structure of chromophore-grafted amyloid-β_12–28 dimers in the gas-phase.

Chirality-dependent structuration of protonated or sodiated polyphenylalanines: IRMPD and ion mobility studies

Ion mobility experiments are combined with Infra-Red Multiple Photon Dissociation (IRMPD) spectroscopy and quantum chemical calculations for assessing the role of chirality in the structure of protonated and sodiated di- or tetra-peptides. Sodiated systems show a strong chirality dependence of the competition between Na(+)O and Na(+)π interactions. Chirality effects are more subtle in protonated systems and manifest themselves by differences in the secondary interactions such hydrogen bonds between neutral groups or those involving the aromatic rings.

CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study

The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.

Gas-phase conformations of capistruin - comparison of lasso, branched-cyclic and linear topologies

RATIONALE

Capistruin is a peptide synthesized by Burkholderia thailandensis E264, which displays a lasso topology. This knot-like structure confers interesting properties to peptides (e.g. antibacterial). Therefore, it is important to evaluate the sensitivity of structural characterization methods to such topological constraints.

METHODS

Ion mobility mass spectrometry (IMS-MS) experiments, using both drift tube and travelling wave instruments, were performed on lasso capistruin and on peptides with the same sequence, but displaying a branched-cyclic (un-threaded) or linear topology. Molecular dynamics (MD) simulations were then performed to further interpret the IMS results in terms of conformation.

RESULTS

The collision cross sections (CCSs) measured via IMS for the different forms of capistruin were found to be similar, despite their different topologies for the doubly charged species, but significant differences arise as the charge state is increased. MD simulations for the doubly charged linear peptide were consistent with the hypothesis that salt bridges are present in the gas phase. Moreover, through CCS measurements for peptides with site-specific mutations, the arginine residue at position 11 was found to play a major role in the stabilization of compact structures for the linear peptide.

CONCLUSIONS

Differences in peptide topologies did not yield marked signatures in their respective IMS spectra. Such signatures were only visible for relatively high charge states, that allow Coulomb repulsion to force unfolding. At low charge states, the topologically unconstrained linear form of capistruin was found to adopt charge solvation-constrained structures, possibly including salt bridges, with CCSs comparable to those measured for the topologically constrained lasso form.

Conformational changes in amyloid-beta (12-28) alloforms studied using action-FRET, IMS and molecular dynamics simulations

Small oligomers of the amyloid beta protein (Aβ) have been implicated as the neurotoxic agent leading to Alzheimer's disease, and in particular mutations in the hydrophobic core region comprising amino acids L17 to A21 have a large influence on the propensity for aggregate formation. It has been shown that the F19P alloform of Aβ forms small aggregates, but does not proceed to form large fibrils and plaques. In order to understand the origin of this behavior, the gas phase conformations for the different charge states of the wild-type 12-28 fragment of the amyloid beta and its F19P alloform were studied by a combination of action-FRET, ion-mobility spectrometry (IMS) and molecular dynamics simulations. Comparison of the experimental and theoretical action-FRET efficiencies and collision cross sections allowed the determination of the lowest energy conformational family for each alloform and charge state. For both alloforms, it was found that there is a change from globular to helical structure between the 3+ and 4+ charge states. Additional protonation to give 5+ and 6+ charge states caused unfolding of this helical motif, with the wild alloform showing β-turn like motifs and the F19P alloform random coil motifs. The presence of the helical to β-turn structural transition in the wild, but not the F19P, alloform may help to elucidate the origin of the large difference in aggregation behavior of the two alloforms.

Photocross-Linked Peptide-Protein Complexes Analysis: A Comparative Study of CID and ETD Fragmentation Modes

Protein-protein interactions are among the keys to organizing cellular processes in space and time. One of the only direct ways to identify such interactions in their cellular environment is to covalently bond the interacting partners to fix the interaction. Photocross-linking in living cells is thus a very promising technique. The feasibility of in cellulo photocross-linking reactions has been shown and mass spectrometry is a tool of choice to analyze photocross-linked proteins. However, the interpretation of the MS and MS/MS spectra of photocross-linked peptides remains one of the most important bottlenecks of the method and still limits its potential for large-scale applications (interactomics). Fundamental studies are still necessary to understand and characterize the fragmentation behavior of photocross-linked peptides. Here, we report the successful identification of the interaction sites in a well-characterized model of in vitro interaction between a protein and a peptide. We describe in detail the fragmentation pattern of these photocross-linked species in order to identify trends that could be generalized. In particular, we compare CID and ETD fragmentation modes (and HCD in a lesser extent), demonstrating the complementarity of both methods and the advantage of ETD for the analysis of photocross-linked species. The information should help further development of dedicated software to properly score MS/MS spectra of photocross-linked species.

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

Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section Ω(EXP). Molecular modelling is used to visualize what ion three-dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting Ω(CALC) are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with Ω(EXP) determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G-quadruplex [dTGGGGT]4, and we will present these detailed investigation in this tutorial.

Distance geometry protocol to generate conformations of natural products to structurally interpret ion mobility-mass spectrometry collision cross sections

Ion mobility-mass spectrometry (IM-MS) allows the separation of ionized molecules based on their charge-to-surface area (IM) and mass-to-charge ratio (MS), respectively. The IM drift time data that is obtained is used to calculate the ion-neutral collision cross section (CCS) of the ionized molecule with the neutral drift gas, which is directly related to the ion conformation and hence molecular size and shape. Studying the conformational landscape of these ionized molecules computationally provides interpretation to delineate the potential structures that these CCS values could represent, or conversely, structural motifs not consistent with the IM data. A challenge in the IM-MS community is the ability to rapidly compute conformations to interpret natural product data, a class of molecules exhibiting a broad range of biological activity. The diversity of biological activity is, in part, related to the unique structural characteristics often observed for natural products. Contemporary approaches to structurally interpret IM-MS data for peptides and proteins typically utilize molecular dynamics (MD) simulations to sample conformational space. However, MD calculations are computationally expensive, they require a force field that accurately describes the molecule of interest, and there is no simple metric that indicates when sufficient conformational sampling has been achieved. Distance geometry is a computationally inexpensive approach that creates conformations based on sampling different pairwise distances between the atoms within the molecule and therefore does not require a force field. Progressively larger distance bounds can be used in distance geometry calculations, providing in principle a strategy to assess when all plausible conformations have been sampled. Our results suggest that distance geometry is a computationally efficient and potentially superior strategy for conformational analysis of natural products to interpret gas-phase CCS data.

Structure of the Pb²⁺-deprotonated dGMP complex in the gas phase: a combined MS-MS/IRMPD spectroscopy/ion mobility study

The structure of the Pb(2+)-deprotonated 2'-deoxyguanosine-5'-monophosphate (dGMP) complex, generated in the gas phase by electrospray ionization, was examined by combining tandem mass spectrometry, mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and ion mobility. In the gas phase, the main binding site of Pb(2+) onto deprotonated dGMP is the deprotonated phosphate group, but the question is whether an additional stabilization of the metallic complex can occur via participation of the carbonyl group of guanine. Such macrochelates indeed correspond to the most stable structures according to theoretical calculations. A multiplexed experimental approach was used to characterize the gas-phase conformation of the metallic complex and hence determine the binding mode of Pb(2+) with [dGMP](-). MS/MS analysis, observation of characteristic bands by IRMPD spectroscopy, and measurement of the ion mobility collision cross section suggest that gaseous [Pb(dGMP)-H](+) complexes adopt a macrochelate folded structure, which consequently differs strongly from the zwitterionic forms postulated in solution from potentiometric studies.

Gas-phase structure of amyloid-β (12-28) peptide investigated by infrared spectroscopy, electron capture dissociation and ion mobility mass spectrometry

The gas-phase structures of doubly and triply protonated Amyloid-β12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - Cα bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and α-helix motifs.

Accurate structure, thermodynamic and spectroscopic parameters from CC and CC/DFT schemes: the challenge of the conformational equilibrium in glycine

The structures, relative stabilities, and infrared spectra of the six low-energy conformers of glycine have been characterized using a state-of-the-art quantum-mechanical approach allowing the bond distances, conformational enthalpies and vibrational frequencies to be determined well within the chemical accuracy. Transition state structures governing interconversion among the different energy minima have also been characterized. In detail, the gas-phase thermodynamic properties (at 15 K and 410 K) of the glycine conformers considered have been obtained with a 1 kJ mol(-1) accuracy, and it has been shown that the employment of DFT geometries usually reduces such accuracy by at most 0.1 kJ mol(-1). Regarding molecular structures, the use of two different composite schemes allowed us to further confirm the suitability of a rather cost-effective approach and provide geometrical parameters with an overall accuracy better than 0.002 Å for distances and 1 degree for angles. Thanks to a hybrid CC/DFT approach, the infrared spectra of all conformers considered and of several deuterated isotopologues have been reproduced (when experimental data were available) or predicted with an accuracy of 10 cm(-1). Finally, the joint thermodynamic and spectroscopic investigation allowed us to shed some light on the possible observation of elusive conformers. On the whole, the high accuracy of the computational results allows us to draw a fully consistent interpretation of the available experimental data and to obtain a more complete characterization of the potential energy surface of glycine.

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.

Statistical analysis of ion mobility spectrometry. I. Unbiased and guided replica-exchange molecular dynamics

Achieving (bio)macromolecular structural assignment from the interpretation of ion mobility spectrometry (IMS) experiments requires successful comparison with computer modeling. Replica-exchange molecular dynamics simulations with suitable force fields not only offer a convenient framework to locate relevant conformations, especially in the case of multiple-funnel energy landscapes, but they are also well suited to statistical analyses. In the present paper, we discuss two extensions of the method used to improve its efficiency in the context of IMS. Two doubly-protonated polyalanines [RA(4)XA(4)K + 2H](2+) with X=V and D appear as favorable cases for which the calculated collision cross-section distributions naturally agree with the measurements, providing reliable candidate structures. For these compounds, a careful consideration of other order parameters based on the weighted histogram method resolves several otherwise hidden underlying conformational families. In the case of a much larger peptide exhibiting bistability, assignment is more difficult but could be achieved by guiding the sampling with an umbrella potential using the square gyration radius as the biasing coordinate. Applied to triply protonated bradykinine, the two presented methods indicate that different conformations compatible with the measurements are very close in energy.

A scanning frequency mode for ion cyclotron mobility spectrometry

A new operational mode for an ion cyclotron mobility spectrometry instrument is explored as a possible means of performing high-resolution separations. The approach is based on oscillating fields that are applied to segmented regions of a circular drift tube. Ions with mobilities that are resonant with the frequency of field application are transmitted while nonresonant species are eliminated. An ion mobility spectrum is obtained by scanning the drift field application frequency. The approach is demonstrated by examining mixtures of ions produced by electrospraying the substance P peptide, as well as a mixture of tryptic peptides obtained by enzymatic digestion of cytochrome c. Drift field application frequency scans of substance P peptide ions show that it is possible to separate [M+2H](2+) ions, and compact and elongated forms of [M+3H](3+) ions. The resolution of different ions is related to the number of cycles for the analysis. At high cycle numbers (>50 3/4 or a drift length of 9242.03 cm) values of the resolving power can exceed 300 with a maximum resolving power of ∼400. The ability to tune the resolving power of a mobility-based separation by varying the ion cycle number has substantial analytical utility.

Ion trajectory simulations in a high-pressure cylindrical ion trap

We present the simulation of a cylindrical ion trap (CIT) at high pressure (5-25 Torr range). SIMION 7.0 software was used for the simulations. The effect of pressure, RF frequency and trap dimensions has been investigated. The shape of stability diagrams at non-zero pressure is drastically different from the one observed in vacuum. Preliminary experimental results are shown, using a r = z = 3 mm-long CIT at 12 Torr for trapping peptide and protein ions.