A secondary ion microprobe ion trap mass spectrometer

An ion trap mass analyzer has been attached to an organic secondary ion microprobe. A pressure differential >100 can be maintained between the ion trap and microprobe. The well-focused secondary ion beam can transit a small (2 mm) diameter tube, but gas flow from ion trap to microprobe is impeded. This pressure differential allows the microprobe to retain imaging capability. Ion trap and microprobe data systems are integrated by taking advantage of the highly reproducible periodicity of the ion trap operating in resonant ejection mode and asynchronous signal and data acquisition afforded by commercially available interface cards. Secondary ion mass spectra and images obtained indicate an approximately 10-fold improvement in sensitivity, although preliminary evidence indicates low (<1%) trapping efficiency. Image data acquisition using the ion trap for mass analysis requires at least 10 times as much time compared to using a quadrupole mass filter because the mass-selected instability mode is used for mass analysis, i.e., mass resolution in the ion trap is not continuous as it is in the quadrupole.     

An ion trap-ion mobility-time of flight mass spectrometer with three ion sources for ion/ion reactions

This instrument combines the capabilities of ion/ion reactions with ion mobility (IM) and time-of-flight (TOF) measurements for conformation studies and top-down analysis of large biomolecules. Ubiquitin ions from either of two electrospray ionization (ESI) sources are stored in a three dimensional (3D) ion trap (IT) and reacted with negative ions from atmospheric sampling glow discharge ionization (ASGDI). The proton transfer reaction products are then separated by IM and analyzed via a TOF mass analyzer. In this way, ubiquitin +7 ions are converted to lower charge states down to +1; the ions in lower charge states tend to be in compact conformations with cross sections down to ～880 Ų. The duration and magnitude of the ion ejection pulse on the IT exit and the entrance voltage on the IM drift tube can affect the measured distribution of conformers for ubiquitin +7 and +6. Alternatively, protein ions are fragmented by collision-induced dissociation (CID) in the IT, followed by ion/ion reactions to reduce the charge states of the CID product ions, thus simplifying assignment of charge states and fragments using the mobility-resolved tandem mass spectrum. Instrument characteristics and the use of a new ion trap controller and software modifications to control the entire instrument are described.     

Transmission mode ion/ion proton transfer reactions in a linear ion trap

A new method is described for effecting ion/ion proton transfer reactions that involves storage of analyte ions while oppositely charged ions are transmitted through the stored ion population. In this approach, the products are captured and stored in the linear ion trap for subsequent mass analysis. Charge reduction of multiply charged protein ions is used as an example to illustrate the analytical usefulness of this method. In another variation of the transmission mode ion/ion reaction approach, two charge inversion experiments, implemented by passing analyte ions through a population of multiply charged reagent ions in a LIT, are also demonstrated. A pulsed dual ion source approach coupled with a hybrid triple quadrupole/linear ion trap instrument was used to demonstrate these two methods. The results for ion/ion reactions implemented using these so-called "transmission mode" experiments were comparable to those acquired using the more conventional mutual storage mode, both in terms of efficiency and information content of the spectra. An advantage of transmission mode experiments compared with mutual storage mode experiments is that they do not require any specialized measures to be taken to enable the simultaneous storage of oppositely charged ions.     

A pulsed triple ionization source for sequential ion/ion reactions in an electrodynamic ion trap

A pulsed triple ionization source, using a common atmosphere/vacuum interface and ion path, has been developed to generate different types of ions for sequential ion/ion reaction experiments in a linear ion trap-based tandem mass spectrometer. The triple ionization source typically consists of a nano-electrospray emitter for analyte formation and two other emitters, an electrospray emitter and an atmospheric pressure chemical ionization emitter or a second nano-electrospray emitter for formation of the two different reagent ions. The three emitters are positioned in a parallel fashion close to the sampling orifice of the tandem mass spectrometer. The potentials applied to each emitter are sequentially pulsed so that desired ions are generated separately in time and space. Sequential ion/ion reactions take place after analyte ions of interest and different set of reagent ions are sequentially injected into a linear ion trap, where axial trapping is effected by applying an auxiliary radio frequency voltage to the end lenses. The pulsed triple ionization source allows independent optimization of each emitter and can be readily coupled to any atmospheric pressure ionization interface with no need for instrument modifications, provided the potentials required to transmit the ion polarity of interest can be synchronized with the emitter potentials. Several sequential ion/ion reactions examples are demonstrated to illustrate the analytical usefulness of the triple ionization source in the study of gas-phase ion/ion chemistry.     

A wide-angle secondary ion probe for organic ion imaging

A secondary ion source has been developed for an organic ion microprobe capable of imaging samples up to 2 em in diameter. The source uses a focused 5 keY Cs⁺ ion beam which is rastered across the sample surface, and secondary ions from each point on the sample are collected and formed into a low energy beam to be analyzed by a quadrupole mass filter. Dynamic emittance matching is employed to deflect ions from off-axis points on the sample back onto the mass analyzer axis. Rastering and dynamic emittance matching are rapidly controlled by assembly language programs using an IBM/AT (80286) type computer. A low energy ion monitor was used to tune and evaluate the secondary ion source by providing a magnified cross-sectional image of the ion beam at the source exit aperture. A well-focused and centered secondary ion beam was obtained from each point on the sample, indicating that large-scale dynamic emittance matching with high collection efficiency is possible. Mass resolved images of grids and glycerol samples are shown to demonstrate the performance of the integrated secondary ion source mass analyzer and control system.     

Collisional activation of ions in RF ion traps and ion guides: The effective ion temperature treatment

Ion transfer and storage using inhomogeneous radio frequency (RF) electric fields in combination with gas-assisted ion cooling and focusing constitutes one of the basic techniques in mass spectrometry today. The RF motion of ions in the bath gas environment involves a large number of ion-neutral collisions that leads to the internal activation of ions and their effective "heating" (when a thermal distribution of internal energies results). The degree of ion activation required in various applications may range from a minimum level (e.g., slightly raising the average internal energy) to an intense level resulting in ion fragmentation. Several research groups proposed using the effective temperature as a measure of ion activation under conditions of multiple ion-neutral collisions. Here we present approximate relationships for the effective ion temperature relevant to typical operation modes of RF multipole devices. We show that RF ion activation results in near-thermal energies for ions occupying an equilibrium position at the center of an RF trap, whereas increased ion activation can be produced by shifting ions off-center, e.g., by means of an external DC electric field. The ion dissociation in the linear quadrupole ion trap using the dipolar DC ion activation has been observed experimentally and interpreted in terms of the effective ion temperature.     

Atom-probe field ion microscopy

The atom probe field ion microscope (AP-FIM) is a combination of a field ion microscope and a time-of-flight mass spectrometer with a single ion detection sensivity. With the field ion microscope topology of a surface, surface reactions and surface modifications can be studied in atomic detail. By time-of-flight measurements surface layers and interface layers can be chemically analyzed atom by atom and atomic layer by atomic layer. Compositional variations according to surface or interface segregation, precipitations, or surface changes in corrosion or in electrochemical layer formation etc. can be studied quantitatively on a subnanometer scale. Some of our studies on related problems will be decribed briefly.     

Simulated ion trajectory and induced signal in ion cyclotron resonance ion traps

We present a numerical method for computation of electrostatic (trapping) and time-varying (excitation) electric fields and the resulting ion trajectory and detected time-domain-induced voltage signal in a rectangular (or cubic) ion cyclotron resonance (ICR) ion trap. The electric potential is calculated by use of the superposition principle and relaxation method with a large number of grid points (e.g., 100 × 100 × 100 for a cubic trap). Complex ICR experiments and spectra may now be simulated with high accuracy. Ion trajectories may be obtained for any combination of trapping and excitation modes, including quadrupolar or cubic trapping in static or dynamic mode; and dipolar, quadrupolar, or parametric excitation with single-frequency, frequency-sweep (chirp), or stored waveform inverse Fourier transform waveforms. The resulting ion trajectory may be represented either as its three dimensional spatial path or as two-dimensional plots of x-, y-, or z-position, velocity, or kinetic energy versus time in the absence or presence of excitation. Induced current is calculated by use of the reciprocity principle, and simulated ICR mass spectra are generated by Fourier transform of the corresponding time-domain voltage signal.     

Mutual storage mode ion/ion reactions in a hybrid linear ion trap

Ion/ion proton transfer reactions involving mutual storage of both ion polarities in a linear ion trap (LIT) that comprises part of a hybrid triple quadrupole/linear ion trap mass spectrometer have been effected. Mutual ion storage in the x- and y-dimensions arises from the normal operation of the oscillating quadrupole field of the quadrupole array, while storage in the z-dimension is enabled by applying unbalanced radio-frequency amplitudes to opposing sets of rods of the array. Efficient trapping (>90%) is achieved for thermalized ions over periods of several seconds. Reactions were demonstrated for multiply charged protein/peptide cations formed by electrospray with anions derived from glow discharge ionization of perfluoro(methyldecalin) (PMD) introduced from the side of the LIT rod array. Doubly and singly charged protein ions are readily formed via ion/ion reactions. The parameters that affect ion/ion reactions are discussed, including the degree of RF unbalance on the LIT rods, vacuum pressure, nature of the buffer gas, reaction time, anion abundance, and the low mass cutoff for ion/ion reaction. The present system has a demonstrated upper mass-to-charge ratio limit of at least 33,000. The system also has high flexibility with respect to defining MS(n) experiments involving both collision-induced dissociation (CID) and ion/ion reactions. Experiments are demonstrated involving beam-type CID in the pressurized collision quadrupole (Q2) followed by ion/ion reactions involving the product ions in the LIT. Ion parking experiments are also demonstrated using the mutual storage ion/ion reaction mode in the LIT, with a parking efficiency over 60%.     

Characteristics of electrical field and ion motion in surface‐electrode ion traps

In this article, we calculated the potential function of the surface‐electrode ion trap (SEIT) by using Green's function method, optimized trap size, obtained the coefficients of the multipoles and analyzed ion trajectories in the RF potential. The optimized SEIT not only increases its trapping well depth by a factor of about 15, but also has relatively good linearity of the field (or large quadrupole component). The current design of SEIT can work well either as the ion guide for ion transmission or as the ion trap for ion confinement. Our research can be used to calculate the potential function in the SEIT with different device parameters, understand ion motions in the traps and optimize instrument performance. The method for calculating potential function can be expanded to planar and halo ion traps. Copyright © 2012 John Wiley & Sons, Ltd.     

Surfaces affect ion pairing

In water, positive ions attract negative ions. That attraction can be modulated if a hydrophobic surface is present near the two ions in water. Using computer simulations with explicit and implicit water, we study how an ion embedded on a hydrophobic surface interacts with another nearby ion in water. Using hydrophobic surfaces with different curvatures, we find that the contact interaction between a positive and negative ion is strongly affected by the curvature of an adjacent surface, either stabilizing or destabilizing the ion pair. We also find that the solvent-separated ion pair (SSIP) can be made more stable than the contacting ion pair by the presence of a surface. This may account for why bridging waters are often found in protein crystal structures. We also note that implicit solvent models do not account for SSIPs. Finally, we find that there are charge asymmetries: an embedded positive charge attracting a negative ion is different than an embedded negative charge attracting a positive ion. Such asymmetries are also not predicted by implicit solvent models. These results may be useful for improving computational models of solvation in biology and chemistry.     

Sodium ion attachment reactions in an ion trap mass spectrometer

The capabilities of ion traps to perform attachment reactions with alkali cations using classical scanning sequences have been exploited here with an ion trap mass spectrometer equipped with an external ion source to generate the reagent Na(+) ions. Kinetic studies have shown that, as expected, the attachment efficiency is very high, near-collision efficiency, and illustrate how the present method is particularly well suited for ion trap mass spectrometers. The large adaptability of the experimental conditions suggests that a wide range of organic molecules, characterized by a large alkali ion affinity, could be readily detected even at low levels. Applications of sodium ion attachment reactions are illustrated by the detection and characterization of explosives and some of their correlated pyrolytic degradation products. Detection -limits for phthalate compounds are shown to reach the low ng range of injected samples, without any noticeable difficulties in the full scan mode of acquiring mass spectra. Copyright 2000 John Wiley & Sons, Ltd.     

Secondary ion emission from glycerol under continuous and pulsed primary ion current

Secondary ion intensity from glycerol is measured as a function of 5 keV primary ion current density and is found to be linear over the range 0.1–1 μA cm^?2. The possibility that protonated glycerol, or some other condensed-phase precursor to secondary protonated glycerol, exists in solution and enhances secondary ion emission from glycerol is investigated. Kinetics for formation of such precursors by the primary ion beam are described and evaluated by pulsed primary ion beam experiments. Depletion rates are calculated assuming diffusion from the surface as the major loss mechanism Results of this analysis indicate that the mechanism for secondary emission of protonated glycerol does not involve formation of precursors, e.g. solution-phase protonated glycerol, directly or indirectly by the primary ion beam.     

Beam-type collisional activation of polypeptide cations that survive ion/ion electron transfer

Doubly protonated peptides that undergo an electron transfer reaction without dissociation in a linear ion trap can be subjected to beam-type collisional activation upon transfer from the linear ion trap into an adjacent mass analyzer, as demonstrated here with a hybrid triple quadrupole/linear ion trap system. The activation can be promoted by use of a DC offset difference between the ion trap used for reaction and the ion trap into which the products are injected of 12-16 V, which gives rise to energetic collisions between the transferred ions and the collision/bath gas employed in the linear ion trap used for ion/ion reactions. Such a process can be executed routinely on hybrid linear ion trap/triple quadrupole tandem mass spectrometers and is demonstrated here with several model peptides as well as a few dozen tryptic peptides. Collisional activation of the peptide precursor ions that survive electron transfer frequently provides structural information that is absent from the precursor ions that fragment spontaneously upon electron transfer. The degree to which additional structural information is obtained by collisional activation of the surviving singly charged peptide ions depends upon peptide size. Little or no additional structural information is obtained from small peptides (<8 residues) due to the high electron transfer dissociation (ETD) efficiencies noted for these peptides as well as the extensive sequence information that tends to be forthcoming from ETD of such species. Collisional activation of the surviving electron transfer products provided greatest benefit for peptides of 8-15 residues.     

Organic ion imaging beyond the limit of static secondary ion mass spectrometry

Secondary ion mass spectra and images were obtained from spikes of choline chloride, acetylcholine chloride, and methylphenylpyridinium iodide deposited onto specimens of porcine brain tissue. Samples were subsequently subjected to a dose of 10-keV Cs⁺ sufficient to suppress secondary ion emission characteristic of the targeted analytes. Following ablation of the samples by massive glycerol clusters generated by electrohydrodynamic emission, secondary ion mass spectra and images could be obtained that reflected the identity and location of the spiked analytes. The absolute intensity of secondary ion emission that followed ablation was found to be between 30 and 100% of the intensity obtained prior to exposure to the high dose of Cs’. Not all chemical noise is removed by ablation, however, so that the signal-to-noise ratios after ablation correspond to between 10 and 85% of their values observed under conditions of low primary ion dose.     

In-beam ionization by alkali ion attachment applying a two-filament ion source

A simple ion source was constructed for in-beam ionization by alkali ion attachment. A wire probe covered with sample was placed near an alkali ion emitter prepared from a mixture of silica gel and alkali halides. The ionization of various thermally labile compounds and of mixtures was investigated. Na⁺ proved to be the most suitable alkali ion for cationization. For monosaccharides experiments revealed the elimination of water upon ionization by Li⁺ attachment. The experimental set-up was also examined for measuring the heat of sublimation of organic solids.     

Ion trajectories in an electrostatic ion guide for external ion source fourier transform ion cyclotron resonance mass spectrometry

An electrostatic ion guide (EIG) that consists of concentric cylinder and central wire electrodes can transport ions efficiently from an external ion source to an ion cyclotron resonance (ICR) ion trap for mass analysis, with several advantages over current injection methods. Because the electrostatic force of the EIG captures ions in a stable orbit about the wire electrode, ions with initially divergent trajectories may be redirected toward the ICR ion trap for improved ion transmission efficiency. SIMION trajectory calculations (ion kinetic energy, 1–200 eV; elevation angle, 0.30 °; azimuthal angle, 0.360°) predict that ions of m/z 1000 may be transmitted through a strong (0.01 → 3.0-T) magnetic field gradient. Judicious choice of ion source position and EIG potential minimizes the spread in ion axial kinetic energy at the ICR ion trap. Advantages of the EIG include large acceptance angle, even for ions that have large initial kinetic energy and large radial displacement with respect to the central z-axis, low ion extraction voltage (5–20 V), and efficient trapping because ions need not be accelerated to high velocity to pass through the magnetic field gradient.     

Light-regulated ion transport through artificial ion channels based on TiO2 nanotubular arrays

Light-responsive artificial ion channels are created using self-organized TiO(2) nanotubular arrays, whose ion transport properties can be regulated by external ultraviolet light. The formation of electrostatic traps within TiO(2) nanotubes by UV light contributes to the light-regulated ion transport.     

Transmission mode ion/ion reactions in the radiofrequency‐only ion guide of hybrid tandem mass spectrometers

Transmission mode ion/ion reactions have been performed within the first quadrupole, the Q0 radiofrequency (RF)‐only quadrupole, of two types of hybrid tandem mass spectrometers (viz., triple quadrupole/linear ion trap and QqTOF instruments). These transmission mode reactions involved the storage of either the reagent species and the transmission of the analyte species through the Q0 quadrupole for charge inversion reactions or the storage of the analyte ions and transmission of the reagent ions as in charge reduction experiments. A key advantage to the use of transmission mode ion/ion reactions is that they do not require any instrument hardware modifications to provide interactions of oppositely charged ions and can be implemented in any instrument that contains a quadrupole or linear ion trap. The focus of this work was to investigate the potential of using the RF‐only quadrupole ion guide positioned prior to the first mass‐resolving element in a tandem mass spectrometer for ion/ion reactions. Two types of exemplary experiments have been demonstrated. One involved a charge inversion reaction and the other involved a charge reduction reaction in conjunction with ion parking. Ion/ion reactions proved to be readily implemented in Q0 thereby adding significantly greater experimental flexibility in the use of ion/ion reaction experiments with hybrid tandem mass spectrometers. Copyright © 2009 John Wiley & Sons, Ltd.     

Electrostriction, ion solvation, and solvent release on ion pairing

The theoretical mean molar electrostriction volume of electrolytic solvents, DeltaVel(solvent), was calculated from their properties: the relative pressure derivatives of the density (the compressibility) and permittivity and their second pressure derivatives. The molar electrostriction caused by ions at infinite dilution was taken as the differences of their standard partial molar volumes in the solution and their intrinsic volumes: DeltaVel(ion) = Vinfinity(ion) - Vin(ion). The ratio ninfinity = DeltaVel(ion)/DeltaVel(solvent) then represents the solvation number of the ion in the solvent at infinite dilution. Similarly, from the molar volume change on ion pair formation, DeltaVip, the ratio Deltanip = DeltaVip/DeltaVel(solvent) represents the number of solvent molecules released thereby. These values were tabulated for those solvents, ions, and ion pairs for which the relevant information could be found, the extension to nonaqueous solvents not having been attempted previously.