MS/MS of ions in a low pressure linear ion trap using a pulsed gas

A pulsed valve was used to increase the pressure within the trapping region of a low-pressure linear ion trap by situating the pulsed valve close to the ion trapping region. The pressure was estimated to increase from a background pressure of 3.5e–5 Torr of nitrogen to 0.49 mTorr at the center of the trap. The increased pressure allowed excitation periods to be reduced from 100 to 25 ms without suffering losses in MS/MS efficiency during dipolar excitation. The reduction in excitation period translates into an increase in the overall duty cycle of the scan.     

The effects of pulsed introduction of buffer gas on ion storage and detection efficiencies in a quadrupole ion trap

The quadrupole ion trap is commonly operated with a constant background pressure of an inert, low molecular weight buffer gas. This inclusion of a buffer gas has been shown to increase the sensitivity and mass resolution of the instrument. Research to gain an understanding of these effects, both experimental and through simulations, has typically assumed that it is optimal to maintain a constant buffer gas pressure throughout the entire experiment This article describes the effects of the pulsed introduction of buffer gas at strategic points within the analytical scan and evaluates those events during which the presence of buffer gas is critical. By incorporating a pulsed valve within the ion trap manifold, both the presence and pressure of the buffer gas can be controlled and varied during the individual steps of the scan. The presence of helium buffer gas just before the ion ejection and detection event showed a greater increase in intensity of the ion signal than at any other time in the analytical scan. In addition, this increase in intensity upon pulsed introduction of buffer gas prior to detection is constant over a wide range of pulsed valve open times (i.e., pressures), whereas the signal enhancement upon pulsed introduction of the buffer gas before ionization is observed only over a narrow range of pulsed valve open times.     

Coupling of ion-molecule reactions with liquid chromatography on a quadrupole ion trap mass spectrometer

We report for the first time a coupling of gas-phase ion-molecule reactions with chromatographic separations on a quadrupole ion trap mass spectrometer. The interface was accomplished by using a pulsed valve for the introduction of a volatile neutral into the ion trap. The pulsed valve controller is synchronized with the mass spectrometer software. The setup requires some minor modifications to the vacuum system of the commercial quadrupole ion trap but most of the modifications are external to the mass spectrometer. Two applications of this interface are described: differentiation between two phosphoglucose positional isomers and detection of a phosphopeptide in a peptide mixture. Both applications are using the reactivity of trimethoxyborate towards a phosphate moiety in the negative ion mode. The detection of phosphopeptides hinges on our findings that non-phosphorylated peptide anions do not react with trimethoxyborate. This LC/MS detection can be easily visualized in terms of selected reaction monitoring.     

Model for ion injection into a quadrupole ion trap to assess the distribution of initial conditions of confinement

A pulsed ion-injection mode for a quadrupole ion trap is described. Switched direct current (d.c.) potentials are applied to the source and trap electrodes to inject the ions into the trap and slow them down. The injection time is sufficient to ensure a steady distribution of the injected ions at the beginning of the confinement.An elementary uni-dimensional model is detailed giving the axial positions and velocities of the ions injected into the trap. The ion distribution in phase space, the number of injected ions and the number of injected ions that will be trapped are also given. These expressions depend on ion position and velocity at the creation, applied potentials and spatial location of the source and trap electrodes.This model is validated by comparing simulation and experimental results. For this purpose the number of confined ions is plotted versus the slowing-down potentials applied on the ring and the upper end-cap of the trap. The size of the area of removable ions in the source is deduced from these results.     

Adaptation of a 3-D Quadrupole Ion Trap for Dipolar DC Collisional Activation

Means to allow for the application of a dipolar DC pulse to the end-cap electrodes of a three-dimensional (3-D) quadrupole ion trap for as short as a millisecond to as long as hundreds of milliseconds are described. The implementation of dipolar DC does not compromise the ability to apply AC waveforms to the end-cap electrodes at other times in the experiment. Dipolar DC provides a nonresonant means for ion acceleration by displacing ions from the center of the ion trap where they experience stronger rf electric fields, which increases the extent of micro-motion. The evolution of the product ion spectrum to higher generation products with time, as shown using protonated leucine enkephalin as a model protonated peptide, illustrates the broad-band nature of the activation. Dipolar DC activation is also shown to be effective as an ion heating approach in mimicking high amplitude short time excitation (HASTE)/pulsed Q dissociation (PQD) resonance excitation experiments that are intended to enhance the likelihood for observing low m/z products in ion trap tandem mass spectrometry.     

A novel high-performance fourier transform ion cyclotron resonance cell for improved biopolymer characterization

A new trapped ion cell design for use with Fourier transform ion cyclotron resonance mass spectrometry is described. The design employs 15 cylindrical ring electrodes to generate trapping potential wells and 32 separately assignable rod electrodes for excitation and detection. The rod electrodes are positioned internal to the ring electrodes and provide excitation fields that are thereby linearized along the magnetic field over the entire trapped ion volume. The new design also affords flexibility in the shaping of the trapping field using the 15 ring electrodes. Many different trapping well shapes can be generated by applying different voltages to the individual ring electrodes, ranging from quadratic to linearly ramped along the magnetic field axis, to a shape that is nearly flat over the entire trap volume, but rises very steeply near the ends of the trap. This feature should be useful for trapping larger ion populations and extension of the useful range of ion manipulation and dissociation experiments since the number of stages of ion manipulation or dissociation is limited in practice by the initial trapped ion population size. Predicted trapping well shapes for two different ring electrode configurations are presented, and these and several other possible configurations are discussed, as are the predicted excitation fields based on the use of rod electrodes internal to the trapping ring electrodes. Initial results are presented from an implementation of the design using a 3.5 T superconducting magnet. It was found that ions can be successfully trapped and detected with this cell design and that selected ion accumulation can be performed with the utilization of four rods for quadrupolar excitation. The initial results presented here illustrate the feasibility of this cell design and demonstrate differences in observed performance based upon different trapping well shapes.     

新型三角形电极圆环离子阱的理论模拟研究

圆环离子阱由于其离子储存能力明显优于相同体积下的三维离子阱,近年来被认为是离子阱小型化发展的另一个重要方向。为进一步优化圆环形离子阱的质谱性能,特别是质量分辨能力,本研究提出了一种由三角形电极构建的新型圆环离子阱,它由两个完全等同的、截面为三角形的圆环电极及两个大小不等的圆筒型电极所组成,离子通过共振激发方式弹出。通过理论模拟和对电极结构的优化,获得了具有非对称性的三角形电极结构,通过改善圆环结构,优化电场分布,提高了离子引出效率和离子阱的质量分辨能力,其中一种最优化结构的圆环离子阱对m/z 609离子的质量分辨率达到1486。     

Infrared multiple photon dissociation in the quadrupole ion trap via a multipass optical arrangement

The design of a novel multipass optical arrangement for use with infrared multiple photon dissociation (IRMPD) in the quadrupole ion trap is presented. This design circumvents previous problems of limited IR laser power, small IR absorption cross sections for many molecules, and the limited ion statistics of trapping and detection of ions for IRMPD in the quadrupole ion trap. In contrast to previous designs that utilized the quadrupole ion store, the quadrupole ion trap was operated in the mass selective instability mode with concurrent resonance ejection. The instrumental design consisted of a modified ring electrode with three spherical concave mirrors mounted on the inner surface of the ring. This modified design allowed for eight laser passes across the radial plane of the ring electrode. IRMPD of protonated bis(2-methoxyethyl)ether (diglyme) was used to characterize the performance of the multipass ring electrode. Two consecutive reactions for the IRMPD of protonated diglyme were observed with a lower energy channel predominant at less than 0.6 J (irradiation times from 1 to 30 ms) and a second channel predominant at energies greater than 0.6 J (irradiation times > 30 ms). Other studies presented include a discussion of the dissociation kinetics of protonated diglyme, the use of a pulsed valve for increased trapping efficiency of parent ion populations, and the effects of laser wavelength and of ion residence time in the radial plane of the ring electrode on photodissociation efficiency.     

Ion mobility studies of electronically excited states of atomic transition metal cations: Development of an ion mobility source for guided ion beam experiments

The design of an ion mobility source developed to couple to a guided ion beam tandem mass spectrometer is presented. In these exploratory studies, metal ions are created continuously by electron ionization of the volatile hexacarbonyls of the three group 6 transition metals. These ions are focused into a linear hexapole ion trap, which collects the ions and then creates high intensity pulses of ions, avoiding excessive ion losses resulting from the low duty cycle of pulsed operation. The ion pulses are injected into a six-ring drift cell filled with helium where ions having different electronic configurations can separate because they have different ion mobilities. Such separation is observed for chromium ions and compares favorably with the pioneering work of Kemper and Bowers (J. Phys. Chem.1991, 95, 5134). The results are then extended to Mo(+) and W(+), which also show efficient configuration separation. The source conditions needed for high intensities and good configuration separation are discussed in detail and suggestions for further improvements are also provided.     

Computer simulation of the gap-tripole ion trap with linear injection, 3D ion accumulation,and versatile packet ejection

The behavior of a completely new ion trap is shown with SIMION 7.0 simulations. The simulated trap, which was a mix of a linear and a 3D trap, was made by axially setting two ion guides with a gap between them. Each guide consisted of three rods with three symmetrically delayed radio frequency (rf) voltages (tripole). The "injected" ions were linearly contained by pulsed potentials on the entrance and exit plates. Then the three-dimensional (3D) rf field in the gap, which was created by the tripole special rod arrangement, could trap the ions when the translational energy was dampened by collisions with low-pressure nitrogen. Because the injected ions were trapped in the small gap, the trapping cycle could be repeated many times before ion ejection, so a high concentrated ion cloud could be obtained. This trapping and accumulation methodology is not possible in most conventional multipole linear traps with even number of poles. Compared with quadrupole linear trap at the same rf amplitude, tripole lost more ions due to strong charge repulsion in the ion cloud. However, tripole could catch up the ions at higher voltage. Radial and axial mass-independent ejection of the ions localized in the tripole gap was very simple, compared with conventional linear ion traps that need extra and complicated electrodes for effective axial ejection.     

Application of external customized waveforms to a commercial quadrupole ion trap

The Finnigan LCQ quadrupole ion trap has recently become part of the repertoire of instruments for many analytical laboratories. The LCQ commercial design, while employing complex waveforms to manipulate ions, does not allow the application of many state-of-the-art user-defined waveforms that enable one to perform other complex ion manipulations. The work presented here describes the simple modifications made to the LCQ electronics to allow the application of external customized waveforms. Results show that externally generated waveforms can be applied to the endcap electrodes while still working within the context of the commercial software and hardware. Double resonance, multiple ion isolation, and multiple ion excitation experiments are demonstrated to reveal the effectiveness of these modifications.     

A novel electric ion resonance cell design with high signal-to-noise ratio and low distortion for Fourier transform mass spectrometry

Performing wideband ion image current detection mass spectrometry experiments with an electric ion trap—e. g., the Paul trap—is a difficult task, as there is a strong crosstalk current induced by the high voltages of the radio frequency (rf) storage field. In a classic Paul trap the metallic hyperbolic electrodes (a ring electrode and two end cap electrodes) are shaped following the isopotential lines of the quadrupole potential distribution. In our new design the ring electrode is replaced by a cylindrical series of ring electrodes with a parabolic potential distribution, whereas the end cap electrodes are used without modification. Thus the quadrupole field within the trap remains unchanged but the capacitances between the electrodes and therefore the crosstalk currents are significantly reduced. The remaining crosstalk is balanced out by an electronic compensation technique. As a consequence the weak signals of the ion-induced charge can be detected with a wideband low-noise amplifier to perform Fourier transform mass spectrometry experiments with improved signal-to-noise ratio.     

Dual buffer gases for ion manipulation in a miniature ion trap mass spectrometer with a discontinuous atmospheric pressure interface

The discontinuous atmospheric pressure interface (DAPI) has been developed to allow a direct transfer of ions from atmosphere into an ion trap mass spectrometer with minimum pumping capability. Air is introduced into the trap with ions and used as a buffer gas for the ion trap operation. In this study, a method of introducing helium as a second buffer gas was developed for a miniature mass spectrometer using a dual DAPI configuration. The buffer gas effects on the performance of a linear ion trap (LIT) with hyperbolic electrodes were characterized for ion isolation, fragmentation and a mass-selective instability scan. Significant improvement was obtained with helium for resolutions of mass analysis and ion isolation, while moderate advantage was gained with air for collision-induced dissociation. The buffer gas can be switched between air and helium for different steps within a single scan, which allows further optimization of the instrument performance for tandem mass spectrometry.     

An Ion Mobility/Ion Trap/Photodissociation Instrument for Characterization of Ion Structure

A new instrument that combines ion mobility spectrometry (IMS) separations with tandem mass spectrometry (MS(n)) is described. Ion fragmentation is achieved with vacuum ultraviolet photodissociation (VUV PD) and/or collision-induced dissociation (CID). The instrument is comprised of an approximately 1 m long drift tube connected to a linear trap that has been interfaced to a pulsed F(2) laser (157 nm). Ion gates positioned in the front and the back of the primary drift region allow for mobility selection of specific ions prior to their storage in the ion trap, mass analysis, and fragmentation. The ion characterization advantages of the new instrument are demonstrated with the analysis of the isomeric trisaccharides, melezitose and raffinose. Mobility separation of precursor ions provides a means of separating the isomers and subsequent VUV PD generates unique fragments allowing them to be distinguished.     

Stability conditions for multiply reflecting electrostatic ion traps

Recently, Benner described an electrostatic ion trap based on the repetitive reflection of ions between two electrostatic mirrors. This paper presents stability conditions for spatial and temporal focusing that the trap must satisfy in order to achieve optimum resolution when operated as a mass spectrometer. Also presented is an example of a theoretical design satisfying both the spatial and temporal focusing conditions.     

Some properties of ion trajectories in the radial plane of an axially symmetric ion trap

In this article we analyse the trajectories of externally generated ions injected in the radial plane into the ion trap. The shape of the envelope curves for two-dimensional (2D) ion trajectories is determined. Conditions under which these envelope curves can be transformed into circles are found. We show that the amplitude of ion oscillations is a minimum in this case and that this mode corresponds to optimised ion trapping conditions. Also we discuss a ring-shaped ion trap mass spectrometer electrode system which consists of two ring electrodes, and which utilises ion trajectories with circular envelope curves.     

Off-axis field approximations for ion traps with apertures

In recent work (Int. J. Mass Spec., vol. 282, pp. 112–122) we have considered the effect of apertures on the fields inside rf traps at points on the trap axis. We now complement and complete that work by considering off-axis fields in axially symmetric (referred to as “3D”) and in two dimensional (“2D”) ion traps whose electrodes have apertures, i.e., holes in 3D and slits in 2D. Our approximation has two parts. The first, E_noAperture, is the field obtained numerically for the trap under study with apertures artificially closed. We have used the boundary element method (BEM) for obtaining this field. The second part, E_{dueToAperture}, is an analytical expression for the field contribution of the aperture.In E_{dueToAperture}, aperture size is a free parameter. A key element in our approximation is the electrostatic field near an infinite thin plate with an aperture, and with different constant-valued far field intensities on either side. Compact expressions for this field can be found using separation of variables, wherein the choice of coordinate system is crucial. This field is, in turn, used four times within our trap-specific approximation.The off-axis field expressions for the 3D geometries were tested on the quadrupole ion trap (QIT) and the cylindrical ion trap (CIT), and the corresponding expressions for the 2D geometries were tested on the linear ion trap (LIT) and the rectilinear ion trap (RIT). For each geometry, we have considered apertures which are 10%, 30%, and 50% of the trap dimension. We have found that our analytical correction term E_{dueToAperture}, though based on a classical small-aperture approximation, gives good results even for relatively large apertures.     

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.     

On-line capillary liquid chromatography tandem mass spectrometry on an ion trap/ reflectron time-of-flight mass spectrometer using the sequence tag database search approach for peptide sequencing and protein identification

Capillary high-performance liquid chromatography has been coupled on-line with an ion trap storage/reflectron time-of-flight mass spectrometer to perform tandem mass spectrometry for tryptic peptides. Selection and fragmentation of the precursor ions were performed in a three-dimensional ion trap, and the resulting fragment ions were pulsed out of the trap into a reflectron time-of-flight mass spectrometer for mass analysis. The stored waveform inverse Fourier transform waveform was applied to perform ion selection and an improved tickle voltage optimization scheme was used to generate collision-induced dissociation. Tandem mass spectra of various doubly charged tryptic peptides were investigated where a conspicuous y ion series over a certain mass range defined a partial amino acid sequence. The partial sequence was used to determine the identity of the peptide or even the protein by database search using the sequence tag approach. Several peptides from tryptic digests of horse heart myoglobin and bovine cytochrome c were selected for tandem mass spectrometry (MS/MS) where it was demonstrated that the proteins could be identified based on sequence tags derived from MS/MS spectra. This approach was also utilized to identify protein spots from a two-dimensional gel separation of a human esophageal adenocarcinoma cell line.     

Aspects of recent developments in ion-trap mass spectrometry

Methods which can be used to obtain mass spectra and tandem mass spectra by means of quadrupole ion traps are reviewed and illustrated. High-order (MSⁿ) experiments are described, as is energy-resolved mass spectrometry in which the internal energy deposited upon collision is systematically varied. Ionization methods which can be used in conjunction with ion traps are discussed with special emphasis on experiments in which ions are generated in an external source and injected into the trap for separation and detection. Ion traps are well-suited to on-line monitoring; the performance of membrane probes in these applications is discussed, and detection limits, response times and quantitative accuracy are outlined. Initial attempts to extend the mass range of ion traps have yielded data to more than 45 000 daltons. In addition to being suited to the study of collision-activated dissociation, the experiment on which most applications of tandem mass spectrometry depend, ion traps also allow ion/molecule reactions to be used for these purposes. Use of a pulsed valve to introduce reagent gases in pulses as short as 50 ms facilitates these experiments. Equilibrium conditions are attainable for fast ion/molecule reactions and measurement of equilibrium and rate constants is discussed. Because they combine a range of capabilities, ion traps are well-suited to the study of gaseous ion chemistry, illustrated here by the halomethylation of aromatic compounds, and the competitive dehydration and deamination of α,ω-amino alcohols.