Laser-induced fluorescence for ion tomography in a Penning trap

Laser-induced ion fluorescence of laser-desorbed Ba⁺ ions provides a measure of the relative number of ions near the center of the Penning trap of a Fourier transform ion cyclotron resonance mass spectrometer. Here, we report the detection of Penning-trapped ions by ion fluorescence, subject to radially outward ion cloud expansion (because of ion-neutral collisions), radially inward ion cloud compression (because of quadrupolar axialization), and the effects of buffer gas pressure and electrostatic trapping potential on those processes. At high pressure and high trapping voltage, radial ejection is far more rapid than axial ejection; quadrupolar axialization increases the number of ions near the center of the trap as well as the length of time that ions may be trapped; higher pressure results in faster magnetron radial expansion; and the choice of azimuthal quadrupolar excitation waveform significantly affects the efficacy of axialization. Based on these results, we suggest that directly detected laser-induced ion fluorescence provides a general new tool for mapping the ion distribution and its time evolution in response to various excitatory and damping effects.     

Measurement of collision-induced dissociation rates for tantalum oxide ions in a quadrupole ion trap

A study of factors influencing the collision-induced dissociation (CID) rate of strongly bound diatomic ions effected via resonance excitation in a quadrupole ion trap is presented. From these studies, an approach to measuring the CID rates is described wherein product ion recovery is optimized and the effect of competitive processes (e.g., parent ion ejection and product ion reactions) on rate measurements are prevented from influencing rate measurements. Tantalum oxide ions (dissociation ENERGY = 8.2 eV), used as a model system, were formed via reactions of glow discharge generated Ta⁺ ions with residual gases in the ion trap. Neon (0.5 mtorr) was found to be a more favorable target gas for the dissociation of TaO⁺ than He and Ar, but collisional activation of TaO⁺ ions in neon during ion isolation by mass selective instability necessitated ion cooling prior to dissociation. A 25 ms delay time at q_z = 0.2 allowed for kinetic cooling of stored TaO⁺ ions and enabled precise dissociation rate measurements to be made. CID of TaO⁺ was determined to be most efficient at q_z = 0.67 (226 kHz for m/z 197). Suitable resonance excitation voltages and times ranged from 0.56 to 1.2 V_p-p and 1 to 68 ms, respectively. Under these conditions, measurement of rates approaching 80 s⁻¹ for the dissociation of TaO⁺ could be made without significant complications associated with competing processes, such as ion ejection.     

Determination of polychlorodibenzo-p-dioxins and polychlorodibenzofurans by gas chromatography/tandem mass spectrometry and gas chromatography/triple mass spectrometry in a quadrupole ion trap

The determination of tetra- to octachlorodibenzo-p-dioxins and tetra- to octachlorodibenzofurans (PCCD/Fs) by high-resolution gas chromatography/tandem mass spectrometry (HRGC/MS/MS) and high-resolution gas chromatography/triple mass spectrometry (HRGC/MS(3)) in a quadrupole ion trap, equipped with an external ion source, is presented. MS/MS involves a typical four-step process, namely ionization, parent ion isolation, collision-induced dissociation (CID) and mass analysis of the daughter ions. For the MS(3) experiment, the MS/MS scan function is used with the addition of selected daughter ion isolation, their CID and the mass analysis of second-generation product ions called 'grand-daughter ions.' For both methods, the energies necessary for the CID of the 17 PCDD/Fs were determined and optimized using multiple scan functions with different CID amplitudes. The CID efficiency, defined as the signal ratio of fragment ions detected from the major dissociation channels to molecular ions isolated, was 1.15-2.40 V for parent ion dissociation (MS/MS) and 1.05-1.50 V for daughter ion dissociation (MS(3)) and for all the chloro congeners. The same sensitivity (1 pg microl(-1)) can be reached with both the MS/MS and MS(3) methods and linear responses were obtained between 1 and 100 pg microl(-1) injected.     

Tailored noise waveform/collision-induced dissociation of ions stored in a linear ion trap combined with liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry

A new collision-induced dissociation (CID) technique based on broadband tailored noise waveform (TNW) excitation of ions stored in a linear ion trap has been developed. In comparison with the conventional sustained off-resonance irradiation (SORI) CID method commonly used in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), this MS/MS technique increases throughput by eliminating the long pump-down delay associated with gas introduction into the high vacuum ICR cell region. In addition, the TNW-CID method speeds spectrum acquisition since it does not require Fourier transformation, calculation of resonant frequencies and generation of the excitation waveforms. We demonstrate TNW-CID coupled with on-line capillary reverse-phase liquid chromatography separations for the identification of peptides. The experimental results are compared with data obtained using conventional quadrupole ion trap MS/MS and SORI-CID MS/MS in an ICR cell.     

Resonance excitation and dynamic collision-induced dissociation in quadrupole ion traps using higher-order excitation frequencies

Fragmentation of the pentapeptide leucine enkephalin (YGGFL) is accomplished via higher-order resonances combined with simultaneous analysis of low-mass product ions. Two methods of achieving excitation are explored: (1) 0.5 ms resonant excitation at the omega and at Omega-omega secular frequencies of ion motion (where Omega is the radio-frequency (rf) drive frequency) in a manner similar to both pulsed q collision-induced dissociation (PQD) and high amplitude short time excitation (HASTE), and (2) 0.5 ms pulse of the omega or at Omega-omega excitation frequencies when the secular frequency of the ions is quickly swept across resonance conditions (pulsed q dynamic CID, PqDCID). In both methods of excitation, the rf amplitude on the ring electrode is rapidly decreased after excitation, therefore enabling analysis of low-mass product ions. Maximum fragmentation efficiencies of approximately 20% can be obtained with pulsed CID with both regular and high-order frequency excitation, while pulsed DCID offers maximum efficiencies of approximately 12%. All the excitation methods studied offer increased internal energy depositions when compared to conventional CID, as measured by the a4/b4 product ion ratios of leucine enkephalin. These ratios were as high as 13:1 for pulsed CID and 8:1 for PqDCID. Successful mass analysis of the low-mass ions is observed with both pulsed CID and PqDCID. The combined benefit of high internal energy deposition and wider dynamic mass range offers the possibility of increased sequence coverage and the identification of unique internal fragments or high-energy product ions which may provide complementary information to biological applications of conventional CID. This is the first report on deliberate fragmentation of precursor ions at a higher-order component of the ion secular frequency combined with a successful mass analysis of the low-mass ions through pulsed CID and PqDCID.     

Simplified application of quadrupolar excitation in Fourier transform ion cyclotron resonance mass spectrometry

A new method for application of quadrupolar excitation to the trapped ion cell of a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer is presented. Quadrupolar excitation is conventionally applied to the two pairs of opposed electrodes that normally perform the excitation and detection functions in the FTICR experiment. Symmetry arguments and numerically calculated isopotential contours within the trapped ion cell lead to the conclusion that quadrupolar excitation can be applied to a single pair of opposed side electrodes. Examples of effective quadrupolar axialization via this method include a sevenfold signal-to-noise enhancement derived from 50 remeasurements of a single population of trapped bovine insulin ions and the selective isolation of a single charge state of horse heart myoglobin after an initial measurement that revealed the presence of 14 charge states.     

Excitation modes for fourier transform-ion cyclotron resonance mass spectrometry

Various geometric configurations for the excitation of coherent ion motion in Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR/MS) are analyzed (in some cases for the first time) with unified notation. The instantaneous power absorption, F v, in which v is ion velocity and F the force produced by the applied excitation electric field (harmonic, single frequency, on-resonance, in-phase), is time averaged and then set equal to the time rate of change of ion total (cyclotron + magnetron + trapping) energy, to yield a differential equation that is readily solved for the (time-dependent) amplitude of each of the various ion motions. The standard FT-ICR excitation (namely, radial dipolar) is reviewed. The effects of quadrature and radial quadrupolar excitation on ion radial (cyclotron and magnetron) motions are also reviewed. Frictional damping is shown to decrease the ion cyclotron orbital radius and trapping amplitude but increase the magnetron radius. Feedback excitation (i.e., excitation at the simultaneously detected ion cyclotron orbital frequency of the same ion packet) is introduced and analyzed as a means for exciting ions whose cyclotron frequency changes during excitation (as for relativistically shifted low-mass ions). In contrast to conventional radial dipolar excitation, axial dipolar excitation of the trapping motion leads to a mass-dependent ion motional amplitude. Parametric (i.e., axial quadrupolar) excitation is shown to produce an exponential increase in the ion motional amplitudes (hyperbolic sine and hyperbolic cosine amplitude for cyclotron and magnetron radii, respectively). More detailed consideration of parametric excitation leads to an optimal ion initial radial position in parametric-mode FT-ICRjMS.     

High amplitude short time excitation: A method to form and detect low mass product ions in a quadrupole ion trap mass spectrometer

Collision induced dissociation (CID) in a quadrupole ion trap mass spectrometer using the conventional 30 ms activation time is compared with high amplitude short time excitation (HASTE) CID using 2 ms and 1 ms activation times. As a result of the shorter activation times, dissociation of the parent ions using the HASTE CID technique requires resonance excitation voltages greater than conventional CID. After activation, the rf trapping voltage is lowered to allow product ions below the low mass cut-off to be trapped. The HASTE CID spectra are notably different from those obtained using conventional CID and can include product ions below the low mass cut-off for the parent ions of interest. The MS/MS efficiencies of HASTE CID are not significantly different when compared with the conventional 30 ms CID. Similar results were obtained with a two-dimensional (linear) ion trap and a three-dimensional ion trap.     

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 adsorption 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 (q_z and a_z values), ion population, and storage time are discussed.     

"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.     

Investigation of some pentasubstituted 1,4-dihydropyridines by means of fast ion bombardment,chemical ionization and electron impact mass spectrometry

Positive fast ion bombardment, positive chemical ionization (CI⁺) and positive electron impact (EI) ionization mass spectrometry were used to investigate a number of relatively large and structurally related organic molecules. Some of the major dissociation pathways observed in the CH₄-CI⁺ mass spectra are not present under NH₃-CI⁺ conditions, but are obtained in the collision-induced dissociation (CID) spectrum of the 50 eV MH⁺ molecular ion, formed in the latter reaction. The resemblance between the EI mass spectra and their fast ion bombardment counterparts, the effect of changing the energy of the bombarding Cs⁺ ion beam over the range 2–16 keV and the different degrees of internal excitation of ions formed in different CI reagent gases are discussed.     

Plasma source ion trap mass spectrometry: Enhanced abundance sensitivity by resonant ejection of atomic ions

An experimental study of resonant ion excitation in an rf quadrupole ion trap is reported. Atomic ions are generated in an inductively coupled plasma and injected into the ion trap where, after collisional cooling, they are irradiated by a low-voltage, dipole coupled waveform. Single frequency, narrowband, and broadband excitation pulses have been used. Absorption lineshapes (plots of observed ion signal versus excitation frequency) are shown for variations in buffer gas pressure and the amplitude and duration of the single frequency pulses. The absorption lineshapes are usually asymmetric and tail toward lower frequencies. At sufficiently low buffer gas pressure or potential well depth, the lineshapes broaden and become more asymmetric to the point that absorption by ions with adjacent mass-to-charge ratios overlaps. This overlapping absorption reduces the selectivity with which a single mass-to-charge ratio ion can be excited and ejected relative to nearby mass-to-charge ratio ions. The rate of ion ejection is different on the low versus high frequency edges of the absorption lines. This difference in ejection rates provides an important key to understanding the shape of the absorption lines. All of these observations are explained in terms of the known kinematic behavior of ions in real traps, that is, traps with substantial higher order symmetry components in the trapping field (“nonlinear” fields). The importance of the nonlinearity of the trapping field in understanding the observed lineshapes and their time dependencies is discussed. We also report resonant ejection results obtained using multiple frequency (narrow or broad bandwidth) excitation. Multiple frequency excitation allows ions with different mass-to-charge ratio values to be ejected from the trap using one excitation waveform. The finite ion storage capacity of the ion trap is thereby reserved for the ion(s) of interest. We show that ejection of ⁸⁹Y ions can be ～ 10⁵ times more efficient than ejection of ions at either m/z 88 or 90.     

Axial CID and high pressure resonance CID in a miniature ion trap mass spectrometer using a discontinuous atmospheric pressure interface

Axial collision induced dissociation (CID) and high-pressure resonance CID were implemented and compared with normal low-pressure resonance CID in a miniature ion trap mass spectrometer to obtain more complete fragmentation spectra. Axial CID was realized simply by applying a potential to the discontinuous atmospheric pressure interface (DAPI) capillary without performing parent ion isolation before dissociation. High-pressure resonance CID employed a double-introduction pulse scan function, by means of which precursor ions isolated at low-pressure (<10⁻³ torr) were dissociated at high-pressure (0.1 torr-1 torr) with higher excitation energy, so that tandem MS of isolated precursor ions was achieved and extensive fragmentation was obtained. A simple peptide (Leu-enkephalin) and dye molecule (rhodamine B) ionized by ESI were used to investigate both methods and compare them with normal low-pressure resonance CID.     

Matrix-shimmed ion cyclotron resonance ion trap simultaneously optimized for excitation, detection, quadrupolar axialization, and trapping

A different symmetry is required to optimize each of the three most common Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) electric potentials in a Penning (ICR) ion trap: one-dimensional dipolar ac for excitation (or detection), two-dimensional azimuthal quadrupolar ac excitation for ion axialization, and three-dimensional axial quadrupolar dc potential for ion axial confinement (trapping). Since no single trap shape simultaneously optimizes all three potentials, many trap configurations have been proposed to optimize the tradeoffs between the three requirements for a particular experiment. A more general approach is to divide each electrode into small segments and then apply the appropriate potential to each segment. Here, we extend segmentation to its logical extreme, by constructing a “matrix-shimmed” trap consisting of a cubic trap, with each side divided into a 5 × 5 grid of electrodes for a total of 150 electrodes. Theoretically, only 48 independent voltages need be applied to these 150 electrodes to generate all three desired electric potential fields simultaneously. In practice, it is more convenient to employ 63 independent voltages due to construction constraints. Resistive networks generate the potentials required for optimal quadrupolar trapping and quadrupolar excitation. To avoid resistive loss of excitation amplitude and detected signal, dipolar excitation/detection voltages are generated with a capacitive network. Theoretical Simion 6. 0 simulations confirm the achievement of near-ideal potentials of all three types simultaneously. From a proof-of-principle working model, several experimental benefits are demonstrated, and proposed future improvements are discussed.     

A general method for precalculation of parameters for sustained off resonance irradiation/collision-induced dissociation

Sustained off resonance irradiation (SORI) collision-induced dissociation (CID) is a commonly used method of collisionally activating ions for fragmentation in Fourier transform mass spectrometric experiments. To achieve the degree of fragmentation desired, both the irradiation frequency and amplitude must be optimized. This is a time-consuming procedure, particularly when the m/z values of the precursor ions vary over a broad range. We present an approach that simplifies this optimization by precalculating the irradiation frequency of the ions to be fragmented as a constant percentage of the reduced cyclotron frequency. Using this approach, the optimal amplitude was found to be significantly less dependent on the m/z value of the precursor ion, and therefore required little or no adjustment. This method considerably simplified optimization of SORI-CID for analysis of carbohydrates, glycoconjugates, and peptides over the mass range m/z 300-3500, requiring optimization of only a single experimental parameter, the irradiation amplitude, and only for the first MS/MS stage.     

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.     

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%.     

Electron capture dissociation mass spectrometry of metallo-supramolecular complexes

The electron capture dissociation (ECD) of metallo-supramolecular dinuclear triple-stranded helicate Fe₂L₃⁴⁺ ions was determined by Fourier transform ion cyclotron resonance mass spectrometry. Initial electron capture by the di-iron(II) triple helicate ions produces dinuclear double-stranded complexes analogous to those seen in solution with the monocationic metal centers Cu^I or Ag^I. The gas-phase fragmentation behavior [ECD, collision-induced dissociation (CID), and infrared multiphoton dissociation (IRMPD)] of the di-iron double-stranded complexes, (i.e., MS³ of the ECD product) was compared with the ECD, CID, and IRMPD of the Cu^I and Ag^I complexes generated from solution. The results suggest that iron-bound dimers may be of the form Fe₂^IL₂²⁺ and that ECD by metallo-complexes allows access, in the gas phase, to oxidation states and coordination chemistry that cannot be accessed in solution.     

On the time scale of internal energy relaxation of AP-MALDI and nano-ESI Ions in a quadrupole ion trap

Recently reported results (Konn et al. [14]) on the collisional cooling of atmospheric pressure matrix assisted laser desorption ionization (AP-MALDI) and nano-electrospray ionization (nano-ESI) generated ions in a quadrupole ion trap mass spectrometer (QITMS) are inconsistent with measured collisional cooling rates. The work reported here presents a re-examination of those previous results. Collision induced dissociation (CID) has been used to probe various properties of ions contained in a QITMS. It is shown experimentally that when trapping large numbers of ions, an effective dc trapping voltage is induced that varies with changes in the size of the ion cloud. A decrease in the resonant frequency for maximum CID efficiency is observed as the cool time between parent ion isolation and CID is increased. Ion trajectories in a QITMS are simulated to demonstrate how ion density changes over the course of parent ion isolation. The effect of space charge on ion motion is simulated, and Fourier transformations of ion axial motion plus simple calculations corroborate the experimentally observed transient frequency shifts. The relative stability of ions formed by AP-MALDI and nano-ESI is compared under low charge density conditions. These data show that the ions have reached equilibrium internal energy and, thus, that differences in dissociation onsets and “50% fragmentation efficiency points” between the ionization mechanisms are due to the formation of distinct ion conformations as previously shown in reference [28]. The conclusions of Konn et al. [14] are based on invalid experimental procedures as well as inappropriate comparisons of QITMS data to low-pressure FT-ICR data.     

Application of nonresonance excitation to ion trap tandem mass spectrometry and selected ejection chemical ionization

Nonresonance excitation is a universal ion excitation and ejection method in which increased ion kinetic energy is achieved by the combination of an axial dc dipole and the rf trapping fields. The method does not require the applied excitation frequency to match with the secular frequency of the precursor ions to effect collision-induced dissociation (CID) for tandem mass spectrometry applications. Therefore, it is free of the effects of secular frequency changes caused by space-charge and simplifies the optimization of tandem mass spectrometry parameters when combined with gas chromatography-tandem mass spectrometry (GC-MS/MS). Computer simulations show that in contrast to the resonance excitation process, the nonresonance excitation process is able to accelerate thermal ions to kinetic energies in excess of 40 eV in a few microseconds. Based on simulations, we expect that the rapid deposition of energy by this method may allow the study, in ion traps, of high energy decomposition channels of precursor ions with multiple decomposition channels. Furthermore, the method is able to simultaneously excite multiple precursor ions, for example, excite both analyte and its coeluting isotopically labeled internal standard for GC-MS/MS analysis. A GC-MS/MS analysis of 100 pg of n-butylbenzene is demonstrated with a signal-to-noise ratio of 3624, which is over an order of magnitude higher than the signal-to-noise ratio of 345 obtained by full scan gas chromatography-mass spectrometry. In addition, the nonresonance excitation method can be used as a low pass mass filter in the chemical ionization (CI) mode to eject undesired fragment ions that result from direct electron ionization. This new CI method, selected ejection chemical ionization, can produce a CI spectrum without contamination of sample fragment ions from electron ionization.