Trapped Ion Cell Research Articles

A conceptual approach for FT-ICR cell harmonization utilizing external shim electrodes

Recent advances in superconducting magnet technology make possible the construction of magnets with higher magnetic fields and regions of improved homogeneity, setting the stage for major advances in performance of Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS). In particular, combining these advances in superconducting magnets with the next generation of ICR ion detection cells, which incorporate harmonic trapping electric fields, will simultaneously improve resolving power, mass measurement accuracy, dynamic range and sensitivity of FT-ICR MS. Realizing these potential advances in FT-ICR performance depends critically on enhanced performance of the trapped ion cell, where analyte ions are confined for excitation and detection. To that end, we propose a focused conceptual approach for achieving cell harmonization that uses as a metric the spatial uniformity of the radial electric field divided by radius. This concept for cell harmonization is applied to two proof-of-principle examples for externally shimmed cell configurations developed using appropriate three-dimensional potential calculations. Both examples utilize external electrodes to generate the trapping potential that are electrically de-coupled from the detection and excitation electrodes. A nearly ideal 3D quadrupolar potential is achieved throughout the cell volume in these proof-of-principle designs that simultaneously simplify both mechanical construction and supply of electrical connections to FT-ICR cells.

Fourier Transform Mass Spectrometry

This article provides an introduction to Fourier transform-based mass spectrometry. The key performance characteristics of Fourier transform-based mass spectrometry, mass accuracy and resolution, are presented in the view of how they impact the interpretation of measurements in proteomic applications. The theory and principles of operation of two types of mass analyzer, Fourier transform ion cyclotron resonance and Orbitrap, are described. Major benefits as well as limitations of Fourier transform-based mass spectrometry technology are discussed in the context of practical sample analysis, and illustrated with examples included as figures in this text and in the accompanying slide set. Comparisons highlighting the performance differences between the two mass analyzers are made where deemed useful in assisting the user with choosing the most appropriate technology for an application. Recent developments of these high-performing mass spectrometers are mentioned to provide a future outlook.

Trapped-Ion Cell with Improved DC Potential Harmonicity for FT-ICR MS

The trapped-ion cell is a key component critical for optimal performance in Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS). To extend the performance of FT-ICR MS, we have developed a new cell design that is capable of generating a DC trapping potential which closely approaches that of an ideal Penning trap, i.e., a 3D axial quadrupolar potential distribution. The new cell design was built upon an open cylindrical geometry, supplemented with two pairs of cylindrical compensation segments. Electric potential calculations for trial cell geometries were aimed at minimizing spatial variations of the radial electric field divided by radius. The resulting cell proportions and compensation voltages delivered practically constant effective ion cyclotron frequency that was independent of ion radial and axial positions. Our customized 12 tesla FT-ICR instrument was upgraded with the new cell, and the performance was characterized for a range of ion excitation power and ion populations. Operating the compensated cell at increased postexcitation radii, approximately 0.7 of the cell inner radius, resulted in improved mass measurement accuracy together with increased signal intensity. Under these same operating conditions the noncompensated open cell configuration exhibited peak splitting and reduced signal life time. Mass accuracy tests using 11 calibrants covering a wide m/z range reproducibly produced under 0.05 ppm RMS precision of the internal calibration for reduced ion populations and the optimal excitation radius. Conditions of increased ion population resulted in a twofold improvement in mass accuracy compared with the noncompensated cell, due to the larger achievable excitation radii and correspondingly lower space charge related perturbations of the calibration law.

Collision induced ion ejection in an FTICR trapped-ion cell

A collision algorithm was used with SimIon to evaluate collision-mediated ion ejection mechanisms in the ICR MS experiment. These mechanisms were characterized based on kinetic energy, ion mass, applied trapping potential, and collision gas mass. It was found that there are three collision-based energy regimes for ion loss from a trapped-ion cell. The first region is characterized by low initial cyclotron kinetic energy, a radial ejection mode, and a very high collision ratio (>100 collisions per ejection). The second region is characterized by a medium to high initial cyclotron kinetic energy leading to axial ejection at low collision ratio (1 to 10 collisions per ejection). The third region is characterized by a high initial cyclotron kinetic energy, a radial ejection mode, and a collision ratio of unity. It was also determined that there is a radial cyclotron mode limit, approximately 40% of the cell radius, after which an ion is ejected after a single collision. This has important consequences on the damping of the FTICR signal, various cooling techniques, ion activation techniques, and the remeasurement experiment.

Alternative approaches to infrared multiphoton dissociation in an external ion reservoir

In this work we present variations on in-hexapole infrared multiphoton dissociation (IRMPD) for the characterization of modified oligonucleotides using an ESI-FTICR spectrometer. We demonstrate that IRMPD in the external ion reservoir provides a comprehensive series of fragments allowing thorough characterization of a wide range of oligonucleotides containing alternative backbones and 2′ substitutions. An alternative pulse sequence is presented that allows alternating MS and IRMPD MS/MS spectra to be acquired on a chromatographic timescale without loss in ionization duty cycle. Ions are excited to a larger cyclotron radius such that they “dodge” the IR laser beam that travels through the center of the trapped ion cell and impinges on the external ion reservoir creating IRMPD fragments that will be detected in the next scan. An alternative approach for directing IR radiation into the external ion reservoir using a hollow fiber waveguide as a photon conduit is presented. This approach offers a simple and robust alternative to the previously utilized on-axis scheme and may allow effective implementation with lower power lasers owing to the inherent increase in power density achieved by focusing the nascent laser beam into the hollow fiber waveguide.

Optimization of experimental parameters for electron capture dissociation of peptides in a Fourier transform mass spectrometer

This paper describes our effort in optimizing the experimental parameters for electron capture dissociation (ECD) of peptides in a commercially available Fourier-transform mass spectrometer. Using a built-in electrically heated filament electron gun, it was demonstrated that good quality ECD spectra of peptides (MW < 2500) could be obtained by irradiating the isolated peptide molecule-ions with a short pulse (50 ms) of low-energy (3–6 eV) electrons. In addition, we have also demonstrated that pulsing of inert cooling gas (argon) could further improve the intensity of the ECD-induced fragment ions. Due presumably to the influence of the strong magnetic field on the trajectories of electrons, the distance between the electron gun and the trapped-ion cell (i.e., 108 mm versus 20 mm) was found to have little influence on the efficiency of the ECD process(es). From a systematic study on the impact of the filament heating current, filament bias voltage, and electron irradiation time on the intensities of precursor ions and various fragment ions, it was postulated that subsequent capture of electrons by the fragment ions, i.e., neutralization of the fragment ions, might be a significant event for limiting the intensity of the fragment ions.

M/z‐Selective infrared multiphoton dissociation in a Penning trap using sidekick trapping and an rf‐tickle pulse

AbstractWe present a novel scheme for performing m/z‐selective infrared multiphoton dissociation (IRMPD) in a Penning trap. Ions are injected into the trapped ion cell of a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer and trapped using the ‘sidekick’ approach. Because this mode of ion trapping can result in an ion cloud precessing about the central axis of the cell with a significant magnetron radius, the effectiveness of conventional on‐axis IRMPD schemes can be adversely affected. Here we demonstrate that the non‐zero magnetron radius of the ion ensemble can be exploited with rf‐tickle pulses which excite, either in an m/z‐selective or broadband mode, the cyclotron frequency of the orbiting ions such that their flight path intercepts the on‐axis laser beam resulting in effective IRMPD. This approach has potential utility in the tandem mass spectrometric characterization of complex mixtures, suggests new approaches for two‐dimensional FTICR studies and, most importantly, represents a straightforward approach to improve the effectiveness of IRMPD for ions captured using sidekick trapping protocols. Copyright © 2001 John Wiley &amp; Sons, Ltd.

Gas-phase cleavage of PTC-derivatized electrosprayed tryptic peptides in an FT-ICR trapped-ion cell: mass-based protein identification without liquid chromatographic separation

Condensed phase protein sequencing typically relies on N-terminal labeling with phenylisothiocyanate (“Edman” reagent), followed by cleavage of the N-terminal amino acid. Similar Edman degradation has been observed in the gas phase by collision-activated dissociation of the N-terminal phenyl thiocarbamoyl protonated peptide [1] to yield complementary b 1 and y n-1 fragments, identifying the N-terminal amino acid. By use of infrared multiphoton (rather than collisional) activation, and Fourier transform ion cyclotron resonance (rather than quadrupole) mass analysis, we extend the method to direct analysis of a mixture of tryptic peptides. We validate the approach with bradykinin as a test peptide, and go on to analyze a mixture of 25 peptides produced by tryptic digestion of apomyoglobin. A b 1 + ion is observed for three of the Edman-derivatized peptides, thereby identifying their N-terminal amino-acids. Search of the SWISS-PROT database gave a single hit (myoglobin, from the correct biological species), based on accurate-mass FT-ICR MS for as few as one Edman-derivatized tryptic peptide. The method is robust—it succeeds even with partial tryptic digestion, partial Edman derivatization, and partial MS/MS IRMPD cleavage. Improved efficiency and automation should be straightforward.

Application of simultaneous excitation/detection to generate real-time excitation profiles in fourier transform ion cyclotron resonance mass spectrometry

Simultaneous excitation/detection (SED), which permits observation of ion motion during an excitation event, is used to generate real-time Fourier transform ion cyclotron resonance (FTICR) excitation profiles that track the radial extent of ion motion in a trapped-ion cell. The conventional FTICR excitation profile is collected in a series of individual experiments in which peak magnitude is monitored as excitation voltage is increased. In contrast, SED permits the single-scan detection of ion cyclotron motion within the trapped-ion cell and consequently yields the data that produces a real-time excitation profile. Data analysis techniques are presented that facilitate conversion of a time domain SED profile into an excitation profile. An order of magnitude decrease in the amount of time is required to acquire an excitation profile, while the precision of the measurement is improved. To demonstrate the utility of the technique, it is applied to the study of axial and radial ion loss mechanisms for argon, benzene, and acetophenone ions under different conditions. SED excitation profiles are also used to illustrate the facility of quadrupolar excitation for minimizing radial ion loss.

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.

A gated‐beam electrospray ionization source with an external ion reservoir. A new tool for the characterization of biomolecules using electrospray ionization mass spectrometry

In this work we describe a micro-electrospray ionization source equipped with an atmospheric pressure external ion shutter. The solenoid-activated shutter prevents the electrospray plume from entering the inlet capillary unless triggered to the ‘open’ position. When in the ‘closed’ position, a stable electrospray plume is maintained between the electrospray ionization (ESI) emitter and the electrically isolated face of the shutter. When the shutter is triggered, a ‘slice’ of ions is allowed to enter the inlet capillary and is subsequently accumulated in an external ion reservoir comprised of a radio frequency only (rf-only) hexapole and a pair of electrostatic elements. Following ion accumulation in the external ion reservoir, intact molecular ions of proteins, oligonucleotides, and noncovalent complexes can be stored for extended intervals (>30 minutes) prior to being transferred to the Fourier transform ion cyclotron resonance (FTICR) trapped ion cell for mass analysis. By introducing reactive gases directly into the external ion reservoir during the storage interval, ion-molecule reactions, such as H/D exchange, can be performed at high effective pressures. This scheme obviates the need for the long reaction times and delays associated with restoring base pressure in the trapped ion cell and allows H/D exchange reactions to be conducted in a fraction of the time required using conventional in-cell exchange approaches. The back face of the shutter arm contains an elastomeric material which can be positioned to seal the inlet to the mass spectrometer resulting in lower base pressure in the ion reservoir and the FTICR cell. Additionally, it is noted that blocking the ESI plume during non-accumulation events results in reduced fouling of the source electrodes and longer times between required source cleaning. Copyright © 1999 John Wiley & Sons, Ltd.

A gated-beam electrospray ionization source with an external ion reservoir. A new tool for the characterization of biomolecules using electrospray ionization mass spectrometry.

In this work we describe a micro-electrospray ionization source equipped with an atmospheric pressure external ion shutter. The solenoid-activated shutter prevents the electrospray plume from entering the inlet capillary unless triggered to the 'open' position. When in the 'closed' position, a stable electrospray plume is maintained between the electrospray ionization (ESI) emitter and the electrically isolated face of the shutter. When the shutter is triggered, a 'slice' of ions is allowed to enter the inlet capillary and is subsequently accumulated in an external ion reservoir comprised of a radio frequency only (rf-only) hexapole and a pair of electrostatic elements. Following ion accumulation in the external ion reservoir, intact molecular ions of proteins, oligonucleotides, and noncovalent complexes can be stored for extended intervals (>30 minutes) prior to being transferred to the Fourier transform ion cyclotron resonance (FTICR) trapped ion cell for mass analysis. By introducing reactive gases directly into the external ion reservoir during the storage interval, ion-molecule reactions, such as H/D exchange, can be performed at high effective pressures. This scheme obviates the need for the long reaction times and delays associated with restoring base pressure in the trapped ion cell and allows H/D exchange reactions to be conducted in a fraction of the time required using conventional in-cell exchange approaches. The back face of the shutter arm contains an elastomeric material which can be positioned to seal the inlet to the mass spectrometer resulting in lower base pressure in the ion reservoir and the FTICR cell. Additionally, it is noted that blocking the ESI plume during non-accumulation events results in reduced fouling of the source electrodes and longer times between required source cleaning.

High pressure chemistry in a Fourier transform ion cyclotron resonance mass spectrometer using a split-pair magnet

A new experimental method has been developed to probe ion/molecule reactions at gas pressures up to 0.1 torr. A Fourier transform ion cyclotron resonance (FTICR) mass spectrometer has been constructed to trap ions within the trapped ion cell at these pressures for time intervals up to several hundred milliseconds, allowing the ions to undergo several million collisions. Multiple pulsed valves inject the gaseous reagents in brief, high pressure bursts. A unique, high conductance vacuum chamber rapidly reduces the gas pressure from as high as 0.01 torr to near background pressures in 2–5 s for optimum operation of the FTICR for identifying the ionic products. A pressure of 0.1 torr is attainable but results in slower gas evacuation. High pressure operation of this instrument is demonstrated for ion chemistry in silane, argon, and silicon tetrafluoride. Pressures are sufficiently high to allow termolecular formation of adducts with the trapped ion cell. Negative ion formation in silane has greatly improved efficiency due to the high pressure ionization. Trace impurities at the ppm level in argon and silicon tetrafluoride are detected through chemical ionization afforded by the large number of ion/molecule collisions.

Multipole storage assisted dissociation, a novel in-source dissociation technique for electrospray ionization generated ions.

In this work we present a novel in-source dissociation scheme referred to as multipole storage assisted dissociation (MSAD) for electrospray ionization (ESI) generated ions in which dissociation is effected by employing extended ion accumulation intervals in a high pressure rf-only hexapole assembly prior to mass analysis. Following an extended ion accumulation interval in which ions are confined in the rf-only hexapole, ions are gated out of the hexapole, trapped, and mass analyzed in the trapped ion cell of a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. The accumulation region is comprised of an rf-only hexapole ion guide which separates two electrodes, a biased skimmer cone, and an auxiliary 'gate' electrode at the low pressure end of the hexapole. This technique should be applicable to other mass spectrometry platforms compatible with pulsed ionization sources including quadrupole ion traps, and time-of-flight mass analyzers. This concept is demonstrated with the dissociation of a small protein in which selective fragmentation is observed at labile amino acid linkages producing primarily y-type fragment ions.

Motional averaging of ions for control of magnetron motion in fourier transform ion cyclotron resonance open-geometry trapped-ion cells

Open trapped-ion cell geometries have been utilized extensively in external source Fourier transform ion cyclotron resonance (FTICR) applications. A fundamental difference between open and closed cells is that in open cells the radial electric field undergoes a shift in orientation as a function of z displacement. Ions confined near the cell radial centerline in the z center of the cell experience an outward-directed destabilizing field gradient force whereas ions at large axial amplitude encounter an inward-directed stabilizing force. Radial destabilization at the center of the cell is compensated by radial stabilization at increased z amplitude through motional averaging along the z axis. This suggests that conditions can be created in the open cell for which deleterious effects due to magnetron motion can be minimized. This contrasts with the closed cell, for which the radial electric field is outward directed at every point along the z axis. This unique aspect of the open geometry trapped-ion cell is demonstrated to reduce radial drift by control of the axial amplitude of the ion cloud. Suspended trapping and resonance excitation of the trapping motion are used to increase the ion z amplitude. For ions with increased z amplitude, the effective cyclotron frequency (ω +) approaches the unperturbed cyclotron frequency (ω c ) with virtual elimination of the magnetron frequency (ω −). This is observed in benzene for which ω + is observed only 16 Hz below ω c . Additionally, resonant excitation at the trapping frequency (2ω t ) was used to increase the axial extent of the ion cloud, raising cyclotron frequency up to 550 Hz. The cyclotron frequency shift also occurs without peak broadening. This radial trajectory stabilizing characteristic of the open cell was maximized using shallow trapping wells in nested traps that yielded cyclotron frequency shifts 300 Hz higher than the unperturbed cyclotron frequency. This is a result of longer ion residence time at the turnaround points in the trapping well (where the inward-directed radial electric field is greatest in magnitude), increased axial extent of the ion cloud due to ion Coulomb repulsion, and the shallower trapping well. The presence of large numbers of charges (electrons, negative ions) in the outer trapping wells of polarity opposite the positive ions in the central trapping well may compensate for the depression of cyclotron frequency due to space charge.

External source Fourier transform ion cyclotron resonance mass spectrometry by using a split-pair magnet

A new instrument has been designed, built, and tested for high performance Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) that allows operation at gas pressures of up to ∼20 Torr in the ion source and up to ∼0.01 Torr in the ion trap. FTICRMS performance is not compromised at these pressures due to an external, high throughput ion source and pulsed gas introduction/rapid gas evacuation of the vacuum chamber at the trapped ion cell. This system is the first to retain ions at 0.01-Torr gas pressure in the ion trap with high sensitivity. This performance is achieved while obtaining high mass resolution and ppm mass accuracies.

Gas-phase dimerization of dimethylaniline in an external electrospray Fourier transform mass spectrometer

N,N-Dimethylaniline (DMA) is a common starting material in graft copolymerization and photopolymerization processes when combined with an organic acid. Several anodic oxidation studies of DMA, in an acidic medium, have been performed. Numerous electrochemical studies imply that DMA has a tendency to dimerize, forming the tail-to-tail coupling product N,N,N',N'-tetramethylbenzydine (TMB). Here, external electrospray ionization Fourier transform mass spectrometry was used to investigate the dimerization and charging characteristics of DMA in an acidic medium in the absence of an applied electrochemical technique. DMA forms both tail-to-tail and head-to-tail dimer products, and the different linkage types were determined by employing tandem mass spectrometry for structure elucidation. In addition, it was found that desolvated protonated DMA ions accumulated and stored in the hexapole ion guide for 1-10 s before transport to the trapped ion cell can undergo gas-phase ion-molecule reactions to form dimeric products, including doubly charged species. Hence the hexapole storage region can be used to conduct ion-molecule reactions away from the low-pressure ion trap.

Correction of Time-of-Flight Shifted Polymeric Molecular Weight Distributions in Matrix-Assisted Laser Desorption/Ionization Fourier Transform Mass Spectrometry

Molecular weight distributions on an external injection matrix-assisted laser desorption/ionization Fourier transform mass spectrometer are subject to time-of-flight distortions as different ion velocities are probed with varied delay times between ionization and trapping (i.e., the trapping time). this phenomenon is used to advantage to reject low-mass matrix ions which would otherwise saturate the trapped ion cell; however, for accurate determination of molecular weight distributions of complex samples like polymeric systems, several mass spectra must be acquired at a series of different trapping times to compensate for this distortion. The spectra acquired should be superimposed (not summed) on the same m/z axis to yield the correct molecular weight distribution as summation of these spectra merely causes further distortions and can cause loss of signal/noise. Distortions due to TOF effects are probed with a calibration compound, poly(ethylene glycol) of peak mass (Mp) ∼ 1000 Da, as well as the more difficult to ionize polystyrene, which was obtained as a chromatographic molecular weight standard (MW 950). This polystyrene reference material was determined to have a ∼ 20% error in Mp.

Experimental methods to alleviate ion coupling effects in matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry

In Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry performed at high ion densities, coulombic interactions between ions of similar cyclotron frequencies may lead to coupled cyclotron motions. For ions residing in these modes, a coalescence of closely spaced ion frequencies will result, and the observed spectral line shape of otherwise distinct ion masses has the appearance of a single resonant cyclotron frequency. In this work, we use matrix-assisted laser desorption generated ions to provide examples of ion coupling and its effects on isotopic information. Two separate FT-ICR pulse sequences which alter the applied trap potentials are demonstrated to reverse the effects of ion coupling by reducing the ion density inside the trapped-ion cell. The result is a mass spectrum with a resolved isotopic envelope for previously coupled ion frequencies. Analytical benefits obtained with these pulse sequences when applied to a gramicidin-Dubos sample include a 300% increase in mass resolution and 100% improvement in mass measurement accuracy in the MALDI/FT-ICR spectrum.

"Colored" noise waveforms and quadrupole excitation for the dynamic range expansion of Fourier transform ion cyclotron resonance mass spectrometry.

Fourier transform ion cyclotron resonance (FTICR) mass spectrometry offers unparalleled analytical performance in most regards but has a dynamic range of typically no better than 10(2)-10(3). This limitation reportedly arises from two opposing constraints, involving the maximum number of ions that can be effectively trapped (10(6)-10(7)) and the minimum number of ions required to produce a detectable signal (10(2)-10(3)). A potential solution to this dynamic range limitation is presented, based on the application of selected-ion accumulation using quadrupole excitation. We show that lower concentration species can be effectively accumulated in the FTICR trapped ion cell, while the more abundant species are continually removed by the application of quadrupolar excitation in the form of band-limited or "colored" noise waveforms. The result is that "room" is made in the cell for lower abundance species, even during extended accumulation periods. This approach was demonstrated with mixtures of the bovine proteins, insulin, ubiquitin, and cytochrome c. For normal accumulation, the dynamic range was approximately 100. The application of selected-ion accumulation in the form of colored noise allowed the extension by 2 orders of magnitude and the detection of species of 1 x 10(-8) M concentration from a solution also containing another component at 9 x 10(-5) M. With this method, a putative new low abundance variant of bovine insulin was observed, and selected-ion accumulation and subsequent collisionally activated dissociation were used for its identification. Dipolar magnetron excitation was also explored to enhance selected-ion accumulation and was found to reduce the amount of buffer gas required for complete removal of the undesired species by a factor of 5. Further possible improvements are discussed, as are the complications due to the required balance between magnetron and cyclotron damping rates.