Dynamic collision-induced dissociation (DCID) in a quadrupole ion trap using a two-frequency excitation waveform: I. Effects of excitation frequency and phase angle

This study describes the application of a two-frequency excitation waveform to the end-cap electrodes of a quadrupole ion trap (QIT) during the mass acquisition period to deliberately fragment selected precursor ions. This approach obviates the need for a discrete excitation period and guarantees on-resonant excitation conditions without any requirement for resonant tuning; it is therefore faster than the conventional approach to collision-induced dissociation (CID) in QITs. The molecular ion of n-butylbenzene is used as thermometer molecule to determine the energetics of the new excitation procedure. The excitation waveform, consisting of two closely spaced sinusoidal frequencies, has an interference pattern that displays nodes and crests in the time domain. The energetics (determined by the product ion ratios of 91/92 Th) and CID efficiencies are highly dependent on the excitation amplitude, the relative position of the excitation frequencies in the Mathieu stability diagram, and whether the ions come into resonance during a node or crest of the excitation waveform. Under highly energetic conditions, ratios of 91/92 as large as 15 can be obtained at concomitant CID efficiencies of 10%, indicating internal energies in excess of 10 eV at the time of fragmentation. These extremely high internal energies far exceed the energetics achievable using conventional on-resonance excitation in QITs, indicating that the collisional heating rate is very fast in the new approach. Under less energetic conditions CID efficiencies as high as 70% are possible, which compares favorably with results obtained by conventional on-resonance excitation. Correlation analyses are used to determine the conditions that simultaneously optimize energetic and efficient fragmentation conditions.     

Phase-enhanced selective ion ejection in an orbitrap mass spectrometer

The mass resolution achieved in selective ion isolation using resonance excitation is usually limited by the frequency resolution of the ac waveform and by unintended off-resonance excitation. A new method of phase-enhanced selective ion ejection based on broadband dipolar excitation and ion ejection applicable to the Orbitrap is described and shown to allow an isolation resolution of 28,400. The method is calculated to be able to provide a mass resolution for ion ejection of up to 100,000.     

Simulated ion trajectory and induced signal in ion cyclotron resonance ion traps. Effect of ion initial axial position on ion coherence,induced signal,and radial or z ejection in a cubic trap

The effects of ion initial axial position on coherence of ion motion, induced ion cyclotron resonance (ICR) signal. and radial and z ejection have been evaluated by numerical simulation for a cubic Fourier transform-ion cyclotron resonance ion trap. For a given initial ion cyclotron phase and radius, ions of different initial z position are shown to be excited to significantly different ion cyclotron radii (and ultimately radially ejected at significantly different excitation amplitude-duration products). Ion initial z displacement from the trap midplane affects observed ICR signal magnitude in two ways: (1) for the same postexcitation cyclotron radius, an ion with larger initial z displacement induces a smaller ICR signal and (2) an ion with larger initial z displacement is excited to a smaller cyclotron radius. We also evaluate the induced ICR signal as a function of excitation amplitude-duration product for spatially uniform or Gaussian ion initial z distributions. In general, if the excitation waveform contains components at frequency, 2 ω_z or (ω₊ + 2 ω_z, in which ω_z is the axial C“trapping”) oscillation frequency, then ejection occurs axially. However, the resulting excitation amplitude-duration product for such axial ejection is significantly higher (factor of, ～ 4) than that required for radial ejection (at ω₊) for ions of small initial radius. The present results offer the first explanation of how, even if the ion is initially at rest on the z axis (i.e., zero excitation electric field amplitude on the z axis), z ejection (axial ejection) may nevertheless occur if the excitation waveform contains frequency components at ω₊ + 2ω_z and/or 2_{w z} Namely, our simulations reveal that off-resonant excitation pushes ions away from the z axis, after which the ions are exposed to z excitation and eventual z ejection.     

Dipole excitation of ions in linear radio frequency quadrupole ion traps with added multipole fields

Ion motion with auxiliary dipole excitation and collisional damping in a linear radiofrequency quadrupole ion trap incorporating small amounts of even higher order multipoles is studied analytically. The ion motion is modeled in a pseudopotential that is mostly quadratic with small amounts of higher spatial harmonics. Ion motion along x and y axes is characterized by two uncoupled forced and damped anharmonic oscillator equations. A multiple time scales method is used to solve the equations of motion of ions with a first order perturbation correction. Analytical relations between the oscillation amplitudes at steady state (the stationary amplitudes) and excitation frequency are calculated. The frequency response curves show that in some cases bistable behavior might be obtained, i.e., there are two stable stationary amplitudes for a given excitation frequency.     

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.     

Dynamic collision-induced dissociation (DCID) in a quadrupole ion trap using a two-frequency excitation waveform: II. Effects of frequency spacing and scan rate

Dynamic CID of selected precursor ions is achieved by the application of a two-frequency excitation waveform to the end-cap electrodes during the mass instability scan of a quadrupole ion trap (QIT) mass spectrometer. This new method permits a shorter scanning time when compared with conventional on-resonance CID. When the excitation waveform consists of two closely-spaced frequencies, the relative phase-relationship of the two frequencies plays a critical role in the fragmentation dynamics. However, at wider frequency spacings (>10 kHz), these phase effects are diminished, while maintaining the efficacy of closely-spaced excitation frequencies. The fragmentation efficiencies and energetics of n-butylbenzene and tetra-alanine are studied under different experimental conditions and the results are compared at various scan rate parameters between 0.1 and 1.0 ms/Th. Although faster scan rates reduce the analysis time, the maximum observed fragmentation efficiencies rarely exceed 30%, compared with values in excess of 50% achieved at slower scan rates. The internal energies calculated from the simulations of n-butylbenzene at fast scan rates are approximately 4 eV for most experimental conditions, while at slow scan rates, internal energies above 5.5 eV are observed for a wide range of conditions. Extensive ITSIM simulations support the observation that slowing the scan rate has a similar effect on fragmentation as widening the frequency spacing between the two excitation frequencies. Both approaches generally enhance CID efficiencies and make fragmentation less dependent upon the relative phase angle between the excitation waveform and the ion motion.     

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.     

Simulation of the simultaneous dual‐frequency resonance excitation of ions in a linear ion trap

The process of ion resonance dipolar excitation in a linear ion trap by 2 ejection waveforms with close frequencies is studied. The physical mechanism of increasing the resolving power using the ion excitation is a nonlinearity of the electric radio frequency fields caused by space charge. Using 2 resonance forces with 2 close frequencies leads to the completion of 2 excitation processes. In the case of the perfect quadrupole electric field, the ion motion equations are linear, and as a result, the respondent ion ensemble is also a linear and valid superposition principle. Nevertheless, the resolution increases (20%) in the case of lack of a space charge in an operating mode with a dual‐frequency. The numerical simulations show that the mass shift is removed, and the mass resolution is increased via dual‐frequency resonance excitation when the frequency difference (approximately 2.5 kHz) is relatively small and the phase difference of 2 harmonic signals is even at a high linear ion density of up to 50 000 ions per radius field r₀ .     

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.     

Peak deconvolution in high-field asymmetric waveform ion mobility spectrometry (FAIMS) to characterize macromolecular conformations

Protonated poly(ethylene glycol), produced by electrospray ionization (ESI), with molecular weights ranging from 0.3 to 5 kDa and charge states from 1+ to 7+ were characterized using high-field asymmetric waveform ion mobility spectrometry (FAIMS). Results for all but some of the 3+ and 4+ charge states are consistent with a single gas-phase conformer or family of unresolved conformers for each of these charge states. The FAIMS compensation voltage scans resulted in peaks that could be accurately fit with a single Gaussian for each peak. The peak widths increase linearly with compensation voltage for maximum ion transmission but do not depend on m/z or molecular weight. Fitting parameters obtained from the poly(ethylene glycol) data were used to analyze conformations of oxidized and reduced lysozyme formed from different solutions. For oxidized lysozyme formed from a buffered aqueous solution, a single conformer (or group of unresolved conformers) was observed for the 7+ and 8+ charge states. Two conformers were observed for the 9+ and 10+ charge states formed from more denaturing solutions. Data for the fully reduced form indicate the existence of up to three different conformers for each charge state produced directly by ESI and a general progression from a more extended to a more folded structure with decreasing charge state. These results are consistent with those obtained previously by proton-transfer reactivity and drift tube ion mobility experiments, although more conformers were identified for the fully reduced form of lysozyme using FAIMS.     

Experimental studies of charge transfer reactions between argon and the third row metals calcium through copper in the inductively coupled plasma

The effect of charge transfer reactions on analyte excitation and ionization in the inductively coupled plasma was studied by two independent techniques. In one technique, pulsed lasers were used to either deplete the ground state of neutral analyte atoms or enhance the population of selected states of the singly charged ion. In both cases the perturbed species were collision partners with argon in potential charge transfer reactions. The effects of charge transfer collisions could be detected in the form of changes in emission from product species. In the second technique, a simple correlation method was used to detect the link via charge transfer of neutral atom ground states and highly excited ionic levels. In the presence of charge transfer collisions, the populations of such linked levels show strong positive correlations. The two techniques were used to study the effects of charge transfer reactions on the third row elements Ca–Cu. With the exception of Cr and Mn, all of the elements studied showed positive evidence of excitation and ionization by charge transfer collision with argon.     

Wavelet-Based Method for Time-Domain Noise Analysis and Reduction in a Frequency-Scan Ion Trap Mass Spectrometer

We adopt an orthogonal wavelet packet decomposition (OWPD) filtering approach to cancel harmonic interference noises arising from an AC power source in time domain and remove the resulting rf voltage interference noise from the mass spectra acquired by using a charge detection frequency-scan quadrupole ion trap mass spectrometer. With the use of a phase lock resampling technique, the transform coefficients of the rf interference in signals become a constant, exhibiting a shift of the baseline in different rf phases. The rf interference is therefore removable by shifting the baselines back to zero in OWPD coefficients. The approach successfully reduces the time-domain background noise from 1367 electrons (rms) to 408 electrons (rms) (an improvement of 70?%) and removes the high frequency noise components in the charge detection ion trap mass spectrometry. Unlike other smoothing or averaging methods commonly used in the mass-to-charge (m/Ze) domain, our approach does not cause any distortion of original signals.     

High-resolution ion isolation with the ion cyclotron resonance capacitively coupled open cell

For ion cyclotron resonance, a capacitively coupled open cell variant with fourfold radial symmetry was constructed and tested for axial excitation-ejection of large ions at high resolution. With a reverse of frequency sweep direction, this cell gave substantial improvements in signal-to-noise ratio due to linearization of the excitation electric field. Single isotopic peaks of ubiquitin (8.6-kDa) and carbonic anhydrase (29-kDa) molecular ions could be isolated by selective stored waveform inverse Fourier transform excitation, which yielded an order of magnitude higher isolation resolving power than previously achieved at high mass-to-charge ratio values.     

Linear response theory of ion excitation for Fourier transform mass spectrometry

A linear relation between the voltage density or magnitude spectrum of an excitation waveform and the corresponding ion orbital radius is derived for Fourier transform mass spectrometry (FTMS). This provides a theoretical foundation for the stored waveform inverse Fourier transform excitation method. The result is also useful for the design of optimal excitation signals as well as for the estimation of the kinetic energy of ions after an excitation event in collision-induced dissociation experiments. When the linear relation is applied to two-dimensional FTMS excitation, an analytical expression for ion speed modulation is obtained.     

Multi-charged oligonucleotide ion formation in sonic spray ionization.

An oligonucleotide tends to release hydrogen atoms from a phosphoric acid group and to form negative ions that can be detected by mass spectrometry. Usually, with a solution-spray based ionization technique, the negative ions are present in different charge states. Ion formation for the nucleotide is quite complicated and is easily influenced by matrix and other constituents in a sample solution, as well as by the operating parameters for a mass spectrometer. In this work, we studied oligonucleotide ion formation by using an ion trap mass spectrometer combined with a sonic spray ionization (SSI) source. An oligonucleotide with 20 bases was measured. Effects from contaminants and parameters affecting the ion production, such as a high voltage applied to the ionization source and sample solution-flow rate, were investigated. Our results showed that an ion with about one charge for every three bases was most abundant. However, the signal intensity and the mass spectrum pattern were sensitive to the matrix and operating parameters. One of the reasons for such sensitivity is that there are various ion states for an oligonucleotide. Any change in the matrix or an operating parameter may shift the balances between the ion states. Adding Tris, or (hydroxymethyl)aminomethane, enhanced the signal intensity of the oligonucleotide and promoted formation of the oligonucleotide ion with higher charges, while adding acetic acid favored the ions with lower charges, compared with that obtained in the medium without adding Tris and acetic acid. The effects on charged droplets and chemical enhancement were investigated. The mechanism for oligonucleotide ion formation is discussed.     

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.     

Matrix methods for the calculation of stability diagrams in quadrupole mass spectrometry

The theory of the computer calculation of the stability of ion motion in periodic quadrupole fields is considered. A matrix approach for the numerical solution of the Hill equation and examples of calculations of stability diagrams are described. The advantage of this method is that it can be used for any periodic waveform. The stability diagrams with periodic rectangular waveform voltages are calculated with this approach. Calculations of the conventional stability diagram of the 3-D ion trap and the first six regions of stability of a mass filter with this method are presented. The stability of the ion motion for the case of a trapping voltage with two or more frequencies is also discussed. It is shown that quadrupole excitation with the rational angular frequency omega = Nomega/P (where N, P are integers and omega is the angular frequency of the trapping field) leads to splitting of the stability diagram along iso-beta lines. Each stable region of the unperturbed diagram splits into P stable bands. The widths of the unstable resonance lines depend on the amplitude of the auxiliary voltage and the frequency. With a low auxiliary frequency splitting of the stability diagram is greater near the boundaries of the unperturbed diagram. It is also shown that amplitude modulation of the trapping RF voltage by an auxiliary signal is equivalent to quadrupole excitation with three frequencies. The effect of modulation by a rational frequency is similar to the case of quadrupole excitation, although splitting of the stability diagram differs to some extent. The methods and results of these calculations will be useful for studies of higher stability regions, resonant excitation, and non-sinusoidal trapping voltages.     

Photoinduced dissociation of electrospray-generated ions in an ion trap/time-of-flight mass spectrometer using a pulsed CO2 laser

An ion trap/time-of-flight (IT/TOF) mass spectrometer was developed and applied to infrared multiphoton dissociation (IRMPD) studies of ions generated by electrospray ionization. A pulsed 10.6- micro m laser beam from a CO(2) laser was used for excitation of trapped ions. Results from IRMPD of peptide ions show that this method provides useful information related to the amino acid sequence of analyzed peptides. Comparative studies show that IRMPD spectra are similar to those obtained using a 266-nm UV laser beam for excitation. However, in contrast to multiple-pulse excitation required at 266 nm, the energy of a single laser pulse in IRMPD is sufficient to induce dissociation of peptide ions. The laser power is practically an exclusive parameter that must be controlled in order to obtain IRMPD spectra that will provide the optimal structural information. It is further demonstrated that the IRMPD IT/TOF technique has the potential to probe the structural features of larger ions that cannot be readily fragmented by collision-induced dissociation (CID). A multiply charged ion of equine cytochrome c is successfully fragmented in a single laser pulse experiment. The IRMPD IT/TOF technique is also shown to be a promising tool for studying dissociation kinetics of peptide and protein ions. Unlike other methods that usually monitor the dissociation ion kinetics in a dissociation time frame of greater than milliseconds, the IT/TOF can promptly detect all product ions generated by the dissociation process, and thus monitor the dissociation process of peptides and proteins in a sub-millisecond time frame. This instrument allows us to determine the dissociation rates of cytochrome c ions using high-energy photoexcitation. It is found that the charge state of the protein ion has a significant effect on dissociation kinetics, which is consistent with that found under low-energy excitation experiments. It is shown that the increase in energy of a laser pulse from 130 to 180 mJ changes the dissociation rate constant for the +12 ion from k = 2.4 x 10(3) x s(-1) to k = 7.3 x 10(4) x s(-1). The +8 ion following excitation at 130 mJ dissociates slower with a rate constant of k = 2.6 x 10(2) x s(-1). The rate difference observed is attributed to conformational differences among the ions with different charge states.     

Investigation of bovine ubiquitin conformers separated by high-field asymmetric waveform ion mobility spectrometry: Cross section measurements using energy-loss experiments with a triple quadrupole mass spectrometer

High-field asymmetric waveform ion mobility spectrometry (FAIMS) was used to separate gas-phase conformers of bovine ubiquitin produced by electrospray ionization. These conformers were sampled by a triple quadrupole mass spectrometer where energy-loss experiments, following the work of Douglas and co-workers, were used to determine their cross sections. The measured cross sections for some conformers were readily altered by the voltages applied to the interface ion optics, therefore very gentle mass spectrometer interface conditions were required to preserve gas-phase conformers separated by FAIMS. Cross sections for 19 conformers (charge states +5 through +13) were measured. Two conformers for the +12 charge state, which were readily separated in FAIMS, were found to have similar cross sections. Based on a method to calibrate the collision gas thickness, the cross sections measured using the FAIMS/energy-loss method were compared with literature values determined using drift tube ion mobility spectrometry. The comparison illustrated that the conformers of bovine ubiquitin that were identified using drift tube ion mobility spectrometry were also observed using the FAIMS device.     

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.