A versatile method of simulation of the operation of ion trap mass spectrometers

The Resonant Excitation Process in Commercial Quadrupole Ion Traps Revisited

The collision-induced resonant excitation process in real quadrupole ion traps is revisited theoretically and experimentally by explicitly including in the discussion the influence of higher order potential impurities. This includes mainly the dependence of the secular oscillation frequency f_ion on the ion's oscillation amplitude z_max. Due to frequency calibration, commercial ion traps use excitation frequencies f_exc that are higher than the theoretical secular oscillation frequency f_ion. This may lead to switching in frequency order between f_exc and f_ion that can allow ions to stay longer in on-resonance. It is also found that there is a most efficient but also a harshest excitation frequency, which are not identical. These phenomena are explained and described with a simple harmonic oscillator model and precise numerical calculations, using the trajectory simulation program ITSIM 5.0. Experimental MS² have been performed with the thermometer ion leucine-enkephalin, which are then in line with expectations from the trajectory calculations. The important difference to the existing literature is that, here, overexcitation is characterized by the observed a₄/b₄ fragment-ion ratio, while the fragmentation efficiency was kept constant. By slightly increasing the excitation frequency one can obtain drastically different effective collisional temperatures. This knowledge gives even commercial ion traps, without instrument adjustments, the possibility of producing energetically versatile fragment ion spectra. It is also shown that the damped driven harmonic oscillator cannot be used as a simplified model of the motion during the resonant excitation process in real ion traps.

Pulsed ion extraction diagnostics in a quadrupole ion trap linear time-of-flight mass spectrometer

Pulsed extraction techniques are investigated for a quadrupole ion trap (QIT) interfaced to a linear time-of-flight (TOF) mass analyzer. A nonfocusing short-pulse mode of operation is developed and characterized. The short-pulse mode creates a near-monoenergetic ion packet, which is useful for reaction kinetics experiments and for making diagnostic measurements of the ion cloud size in the trap. Monopolar and bipolar pulsing modes, with the voltage pulses applied to one or both QIT endcaps to extract the ions into the TOF region, are compared. Ion TOF peak distributions are characterized experimentally and by ion trajectory simulations. Also, first-order spatial (Wiley-McLaren) focusing of ions is characterized for the conventional long-pulse extraction mode. The nonparallel fields in the QIT, which serves as the first acceleration region in the linear-TOF mass spectrometer, are shown to degrade spatial focusing and mass resolution.

Quadrupole ion traps

The extraordinary story of the three-dimensional radiofrequency quadrupole ion trap, accompanied by a seemingly unintelligible theoretical treatment, is told in some detail because of the quite considerable degree of commercial success that quadrupole technology has achieved. The quadrupole ion trap, often used in conjunction with a quadrupole mass filter, remained a laboratory curiosity until 1979 when, at the American Society for Mass Spectrometry Conference in Seattle, George Stafford, Jr., of Finnigan Corp., learned of the Masters' study of Allison Armitage of a combined quadrupole ion trap/quadrupole mass filter instrument for the observation of electron impact and chemical ionization mass spectra of simple compounds eluting from a gas chromatograph. Stafford developed subsequently the mass-selective axial instability method for obtaining mass spectra from the quadrupole ion trap alone and, in 1983, Finnigan Corp. announced the first commercial quadrupole ion trap instrument as a detector for a gas chromatograph. In 1987, confinement of ions generated externally to the ion trap was demonstrated and, soon after, the new technique of electrospray ionization was shown to be compatible with the ion trap.

Ion trajectory simulation for electrode configurations with arbitrary geometries

A multi-particle ion trajectory simulation program ITSIM 6.0 is described, which is capable of ion trajectory simulations for electrode configurations with arbitrary geometries. The electrode structures are input from a 3D drawing program AutoCAD and the electric field is calculated using a 3D field solver COMSOL. The program CreatePot acts as interface between the field solver and ITSIM 6.0. It converts the calculated electric field into a field array file readable by ITSIM 6.0 and ion trajectories are calculated by solving Newton's equation using Runge-Kutta integration methods. The accuracy of the field calculation is discussed for the ideal quadrupole ion trap in terms of applied mesh density. Electric fields of several different types of devices with 3D geometry are simulated, including ion transport through an ion optical system as a function of pressure. Ion spatial distributions, including the storage of positively charged ions only and simultaneous storage of positively/negatively charged ions in commercial linear ion traps with various geometries, are investigated using different trapping modes. Inelastic collisions and collision induced dissociation modeled using RRKM theory are studied, with emphasis on the fragmentation of n-butylbenzene inside an ideal quadrupole ion trap. The mass spectrum of 1,3-dichlorobenzene is simulated for the rectilinear ion trap device and good agreement is observed between the simulated and the experimental mass spectra. Collisional cooling using helium at different pressures is found to affect mass resolution in the rectilinear ion trap.

Prediction of collective characteristics for ion ensembles in quadrupole ion traps without trajectory simulations

Fundamental aspects are presented of a two-temperature moment theory for quadrupole ion traps developed via transformation of the Boltzmann equation. Solutions of the moment equations correspond to changes in the ensemble average for any function of ion velocity, because the Boltzmann equation reflects changes to an ion distribution as a whole. The function of primary interest in this paper is the ion effective temperature and its behavior during ion storage and resonance excitation. Calculations suggest that increases in ion effective temperature during resonance excitation are due primarily to power absorption from the main RF trapping field rather than from the dipolar excitation signal. The dipolar excitation signal apparently serves mainly to move ions into regions of the ion trap where the RF electric field, and thus ion RF heating, is greater than near the trap center. Both ideal and non-ideal ion trap configurations are accounted for in the moment equations by incorporating parameterized variables a and q , which are modified versions of the commonly used forms for the DC and AC ring voltages, and b and d , which are new forms that account for the voltages applied to the endcaps. Besides extending the applicability of the moment equations to non-ideal quadrupole ion traps, the modified versions of the parameterized variables can have additional utility. Calculation of the spatial dependence of ion secular oscillation frequencies is demonstrated as an example.

Simulations of ion trapping in a micrometer-sized cylindrical ion trap

We have performed detailed SIMION simulations of ion behavior in micrometer-sized cylindrical ion traps (r0 = 1 microm). Simulations examined the effects of ion and neutral temperature, the pressure and nature of cooling gas, ion mass, trap voltage and frequency, space-charge, fabrication defects, and other parameters on the ability of micrometer-sized traps to store ions. At this size scale voltage and power limitations constrain trap operation to frequencies about 1 GHz and rf amplitudes of tens of volts. Correspondingly, the pseudopotential well depth of traps is shallow, and thermal energies contribute significantly to ion losses. Trapping efficiency falls off gradually as qz approaches 0.908, possibly complicating mass-selective trapping, ejection, or quantitation. Coulombic repulsion caused by multiple ions in a small-volume results in a trapping limit of a single ion per trap. If multiple ions are produced in a trap, all but one ion are ejected within a few microseconds. The remaining ion tends to have favorable trapping parameters and a lifetime about hundreds of microseconds; however, this lifetime is significantly shorter than it would have been in the absence of space-charge. Typical microfabrication defects affect ion trapping only minimally. We recently reported (IJMS 2004, 236, 91-104) on the construction of a massively parallel array of ion traps with dimensions of r0 = 1 microm. The relationship of the simulations to the expected performance of the microfabricated array is discussed.

Investigation into factors affecting precision in ion trap mass spectrometry using different scan directions and axial modulation potential amplitudes

Electrospray ionization mass spectra obtained from different scan directions are observed to be dependent on the axial modulation potential amplitudes used for resonant ejection and on the positive deviation caused by higher even-multipole fields present in most commercial ion traps. The axial modulation voltage influences the dissociation of ions during resonant ejection and the observed mass shifts. The higher even-multipole fields in commercial ion traps are known to influence resonant ejection from the ion trap and can cause a loss in mass resolution for peaks in reverse scan mass spectra compared with that obtained by the forward scan. However, along with the dissociation of ions during resonant ejection causing a loss in resolution, the possibility of resolving an isotopic distribution is also shown to be influenced by the mass shifts caused by the space charge. These mass shifts differ depending on the scan direction employed. A significant loss in resolution can also result from resonant ejection using non-optimal axial modulation voltages. We also present results showing the ejection of ions at betaz = 1/2 using the reverse scan mode without the axial modulation voltage. Ion ejection at betaz = 1/2 is uncommon in commercial (stretched ion traps) with the conventional analytical scan without the use of a frequency of the axial modulation voltage corresponding to this non-linear resonance.

Kinetic theory of radio frequency quadrupole ion traps. I. Trapping of atomic ions in a pure atomic gas

A kinetic theory based on the Boltzmann equation is developed for the trapping of atomic ions in a radio-frequency quadrupole ion trap containing enough neutral atoms that ion-neutral collisions cannot be ignored. The collisions are treated at the same level of sophistication and detail as is used to deal with the time- and space-dependent electric fields in the trap. As a result, microscopic definitions are obtained for the damping and stochastic forces that originate from such collisions. These definitions contrast with corresponding phenomenological terms added ad hoc in previous treatments to create damped Mathieu and Langevin equations, respectively. Furthermore, the theory indicates that either collisional cooling or heating of the ions is possible, depending upon details of the ion-neutral mass ratios and interaction potential. The kinetic theory is not dependent on any special assumptions about the electric field strengths, the ion-neutral interaction potentials, or the ion-neutral mass ratio. It also provides an ab initio way to describe the ion kinetic energies, temperatures, and other properties by a series of successive approximations.

"Fast excitation" CID in a quadrupole ion trap mass spectrometer

Collision-induced dissociation (CID) in a quadrupole ion trap mass spectrometer is usually performed by applying a small amplitude excitation voltage at the same secular frequency as the ion of interest. Here we disclose studies examining the use of large amplitude voltage excitations (applied for short periods of time) to cause fragmentation of the ions of interest. This process has been examined using leucine enkephalin as the model compound and the motion of the ions within the ion trap simulated using ITSIM. The resulting fragmentation information obtained is identical with that observed by conventional resonance excitation CID. "Fast excitation" CID deposits (as determined by the intensity ratio of the a(4)/b(4) ion of leucine enkephalin) approximately the same amount of internal energy into an ion as conventional resonance excitation CID where the excitation signal is applied for much longer periods of time. The major difference between the two excitation techniques is the higher rate of excitation (gain in kinetic energy) between successive collisions with helium atoms with "fast excitation" CID as opposed to the conventional resonance excitation CID. With conventional resonance excitation CID ions fragment while the excitation voltage is still being applied whereas for "fast excitation" CID a higher proportion of the ions fragment in the ion cooling time following the excitation pulse. The fragmentation of the (M + 17H)(17+) of horse heart myoglobin is also shown to illustrate the application of "fast excitation" CID to proteins.

Analytical performance of a miniature cylindrical ion trap mass spectrometer

The analytical performance of a fieldable cylindrical ion trap (CIT)-based miniature mass spectrometer is described. A detailed description of the instrument itself is to be found in the immediately preceding paper (Patterson, G. E.; Guymon, A. J.; Riter, L S.; Everly, M.; Griep-Raming, J.; Laughlin, B. C.; Ouyang, Z.; Cooks, R. G., Miniature Cylindrical Ion Trap Mass Spectrometer, Anal. Chem. 2002, 24, 6145-6153). Applications employing the MS/MS and MSn capabilities of the miniature instrument and analytical performance criteria are given here. The limit of detection for methyl salicylate, introduced as the pure vapor, is estimated as 1 pg. The resolution, R = m/delta m, where delta m, measured as full width at half-maximum, is estimated as 100. Monitoring of organic compounds in air is performed using a permeation membrane introduction device coupled to the mass spectrometer. Water monitoring is performed using an external membrane introduction mass spectrometry (MIMS) system, with acetophenone and toluene serving as model compounds. Data are given for chemical warfare agent simulants, methyl salicylate, and dimethyl methyl phosphonate (DMMP) in air. On-line detection of menthol vapor emitted from a cough drop is reported. Methyl salicylate in air gives a recognizable mass spectrum at 400 ppb in the ambient system, while use of a heated membrane brings the detection limit down to 10 ppb.

Correlations of chemical mass shifts of para-substituted acetophenones and benzophenones with Brown's sigma constants

Relationships between chemical mass shifts and physiochemical properties of ions are sought by examining substituted acetophenones, benzophenones, and pyridines in a modified ion trap mass spectrometer. Systematic changes in chemical mass shift occur with changes in substituent in the acetophenones and the benzophenones. Brown's sigma+ constant, which is a measure of electronic effects of substituents in reactions that involve positive charge development, is shown to correlate linearly with chemical mass shifts in para-substituted acetophenones and benzophenones. Brown's sigma+ constant also correlates with the ease of dissociation of the ions via a correlation with ionization energy. It is suggested that ease of dissociation is the underlying factor in determining chemical mass shifts. The experimental results also suggest that dissociative collisions between ions and buffer gas make a much greater contribution to chemical mass shifts than do elastic collisions.

Determination of the dissociation kinetics of a transient intermediate

Tandem mass spectrometry provides information on the dissociation pathways of gas-phase ions by providing a link between product ions and parent ions. However, there exists a distinct possibility that a parent ion does not dissociate directly to the observed product ion, but that the reaction proceeds through unobserved reaction intermediates. This work describes the discovery and kinetic analysis of an unobserved reaction intermediate with a quadrupole ion trap. [a4 - NH3] ions formed from [YG beta FL + H] ions dissociate to [(F*YG - NH3) - CO] ions. It is expected, however, from previous results, that [F*YG - NH3] ions should form prior to [(F*YG - NH3) - CO] ions. Double-resonance experiments are used to demonstrate the existence of intermediate [F*YG - NH3] ions. Various kinetic analyses are then performed using traditional collision-induced dissociation kinetics and double-resonance experiments. The phenomenological rates of formation and decay of peptide rearrangement ion dissociation products are determined by curve fitting decay and formation data generated with the kinetics experiments. The data generated predict an observable level of the intermediate in a time frame accessible but previously not monitored. By examining early product-ion formation, the intermediate ions, [F*YG - NH3]+, are observed.

Article

The quadrupole ion trap mass spectrometer is of great interest for chemical analysis. Nevertheless, negative ion studies using in situ ionization (negative ions created inside the ion trap) are difficult and limited. This paper describes the difficulties that occurred during negative ion analysis when using a commercial gas chromatography quadrupole ion trap mass spectrometer (GC/MS) system. Detection problems, due to simultaneous trapping of both positive and negative ions, are explained by the large kinetic energies of the ejected ions. Negative ion formation, produced by electron capture, is limited by the fundamental RF field, which imparts high kinetic energy to the electrons, precluding the possibility that the electrons will reach the thermal energies needed for electron capture processes. In addition, simultaneous confinement of negative and positive ions affects the recorded mass spectra. Space charge potentials that exist inside the ion trap (due to the ionization conditions necessary to detect negative ions) induce the destabilization of positive ions at higher m/z ratios, while negative ions in the same m/z range are stabilized. Moreover, loss of resolution and decalibration could occur for negative ions when they are ejected in the presence of positive ions with higher m/z ratios. At the very least, ion-ion reactions could limit the observation of negative ions. The understanding of these phenomena, viz. detection, formation, and simultaneous confinement, will permit the proposal of solutions for negative ion analysis with quadrupole ion trap mass spectrometers using in situ ionization.Key words: mass spectrometry, quadrupole ion trap, negative ion, perfluorotributylamine, space charge.

Origin of product ions in the MS/MS spectra of peptides in a quadrupole ion trap

Stored waveform inverse Fourier transform and double resonance techniques have been used in conjunction with a quadrupole ion trap to study the dissociation patterns of peptide ions. These experiments provide insight into the origin of individual product ions in an MS/MS spectrum. Results show for a series of leucine enkephalin analogues with five amino acid residues that the b4 ion is the main product ion through which many other product ions arise. It was also observed that the percentage of the a4 product ions that are formed directly from the protonated molecule (M + H)+ depends on the nature of the fourth amino acid residue. In addition, it was determined that in the peptides studies here lower series b ions (e.g., b3) arise from direct dissociation of higher series b ions (e.g., b4) only about 50% of the time.

Effects of heavy gases on the tandem mass spectra of peptide ions in the quadrupole ion trap

Heavy gases (xenon, argon, krypton, methane) have been used to improve the performance of the quadrupole ion trap when performing collision-induced dissociation on peptides. MS/MS spectra reveal that increased amounts of internal energy can be deposited into peptide ions and more structural information can be obtained. Specifically, the pulsed introduction of the heavy gases (as reported previously by Doroshenko, V. M.; Cotter, R. J. Anal. Chem. 1996, 68, 463) provides greater energy deposition without the deleterious effects that static pressures of heavy gas have on spectra. Internal energy deposition as indicated by a qualitative evaluation of MS/MS spectra shows pulsed introduction of heavy gases enables ions to obtain more internal energy than possible by using static pressures of the same heavy gases. A linear correlation is observed between the percentage of heavy gas added and the ratio of product ions used to reflect internal energy deposition. Results here also show that upon pulsed introduction of heavy gases, empirical optimization of a single frequency resonant excitation signal is no longer needed to obtain good MS/MS spectrometry efficiency. The presence of many low mass-to-charge ratio ions and the absence of side chain cleavages in the MS/MS spectra of peptides suggests that the propensity for consecutive fragmentations is increased with the pulsed introduction of heavy gases. In addition, by varying the delay time between introduction of the gas and application of the resonant excitation signal, the amount of fragmentation observed in MS/MS spectra can be changed.

Multiparticle simulation of ion motion in the ion trap mass spectrometer: Resonant and direct current pulse excitation

A PC-based program that simulates the behavior of a collection of ions is extended to include the effects of collisions with the buffer gas and enhanced visualization methods. The simulations are based on the quadrupole field associated with the actual ion trap electrode structure. Ionization is simulated in such a way as to distribute ionization events randomly over rf phase angles and yield a realistic collection of stored ions. The effects of buffer gas collisions on ion motion during both mass-selective instability and resonance ejection scans are found to include the expected dampening of spatial excursions as well as limitation of the kinetic energy of trapped ions. In both experiments, ion ejection occurs over a number of secular cycles in the vicinity of the theoretical instability point. Activation via a resonant ac signal or a short dc pulse is shown to result in phase-locking of the ions as well as the expected increase in the size of the excursions in the z direction and in ion kinetic energy. Collisions cause dephasing and loss of kinetic energy. Radial dc activation is compared with activation in the axial direction. Experimental data for dc pulse activation of the n-butylbenzene molecular ion are analyzed in phase space and the onset of surface-induced dissociation is correlated with changes in the experimental m/z 91 to m/z 92 fragment ion ratio. Poincaré sections are shown for resonantly excited ions and their value in demonstrating improvement of the resolution of these experiments over conventional mass-selective instability scans is shown.

Determination of ion frequencies in a quadrupole ion trap by using a fast direct current pulse as pump and a laser probe

A new technique has been developed which allows the direct measurement of frequencies of ions trapped in a quadrupole ion trap mass spectrometer. This pump/probe method employs a fast direct current (DC) pulse (pump) to displace a kinetically cooled ion population from the center of the trap, and a laser (probe) which recognizes when ions reappear at the center of the trap by the formation of photodissociation fragments. The translationally excited ions undergo periodic motion within the confines of the ion trap, and this periodic motion can be followed by recording the intensity of the photodissociation fragment as a function of the delay time between the DC pump and the laser probe. The DC pulse has a rise time of 15 ns; data are taken 1 ms after its application to allow stable ion motion to be sampled. Sampling of the ion cloud is done at 50 ns intervals, and fast Fourier transformation of the time-based data yields the ion frequencies and their relative magnitudes. Data are reported for ions derived from acetophenone (m/z 105) and 1,4-cyclohexadiene (m/z 80) under various trapping conditions corresponding to different Mathieu qz values. The measured fundamental secular frequencies, fz and fr, are found to agree well with those predicted. The presence of higher order multipole contributions to the trapping field is evident from such ion frequencies as the drive frequency, fRF,. The ability to measure ion frequencies under operating conditions provides a new tool for comparing simulated and experimental data. Simulation data from the program ITSIM, modified to account for the effects of collisions, are shown to predict the major frequency components observed in the experimental data.

Nonlinear resonance effects during ion storage in a quadrupole ion trap

Contributions of higher-order fields to the quadrupolar storage field produce nonlinear resonances in the quadrupole ion trap. Storing ions with secular frequencies corresponding to these nonlinear resonances allows absorption of power from the higher-order fields. This results in increased axial and radial amplitudes which can cause ion ejection and collision-induced dissociation (CID). Experiments employing long storage times and/or high ion populations, such as chemical ionization, ion-molecule reaction studies, and resonance excitation CID, can be particularly susceptible to nonlinear resonance effects. The effects of higher-order fields on stored ions are presented and the influence of instrumental parameters such as radiofrequency and direct current voltage (qZ and az values), ion population, and storage time are discussed.

Determination of positions, velocities, and kinetic energies of resonantly excited ions in the quadrupole ion trap mass spectrometer by laser photodissociation

The effects on ion motion caused by the application of a resonance AC dipole voltage to the end-cap electrodes of the quadrupole ion trap are described. An excimer laser is used to photodissociate benzoyl ions, and its triggering is phase locked to the AC voltage to follow the motion of the ion cloud as a function of the phase angle of the AC signal. Resonantly excited ions maintain a coherent motion in the presence of He buffer gas, which dissipates energy from the ions via collisions. Maximum ion displacements, which depend upon the potential well depth (q z value), occur twice each AC cycle. Axial components of ion velocities are determined by differentiating the displacements of the distributions with respect to time. The experimental data show that these velocities are maximized when the ion cloud passes through zero axial displacement, and they compare favorably with results calculated using a simple harmonic oscillator model. Axial components of ion kinetic energies are low (<5 eV) under the chosen experimental conditions. At low values of q2 (≈ 0.2), the width of the ion distribution increases as the ion cloud approaches the center of the trap and decreases as it approaches the end-cap electrodes. This effect is created by compaction of the ion trajectories when ion velocities are decreased.

Computer simulation of single-ion trajectories in paul-type ion traps

The computer simulation of single-ion trajectories using a number of computer programs is described together with associated theory. The programs permit calculation of ion trajectories while the ion is subjected to collisions with buffer gas of variable pressure, resonance excitation in any of three modes, and static or ramped DC and radiofrequency levels. Initially, the programs were designed for the calculation of ion trajectories in a quadrupole ion trap. The programs now permit such calculations for ions confined in traps having electrodes shaped to include percentages of hexapole and octupole components in the electric field as well as electrode surface geometries for which there is no closed-form expression. The Langevin collision theory is reviewed and a theoretical treatment of the multipole trap is presented.