H/D exchange of gas phase bradykinin ions in a linear quadrupole ion trap

The gas phase H/D exchange reaction of bradykinin ions, as well as fragment ions of bradykinin generated through collisions in an orifice skimmer region, have been studied with a linear quadrupole ion trap (LIT) reflectron time-of-flight (rTOF) mass spectrometer system. The reaction in the trap takes only tens of seconds at a pressure of few mTorr of D2O or CD3OD. The exchange rate and hydrogen exchange level are not sensitive to the trapping q value over a broad range, provided q is not close to the stability boundary (q = 0.908). The relative rates and hydrogen exchange levels of protonated and sodiated +1 and +2 ions are similar to those observed previously by others with a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer system. The doubly and triply protonated ions show multimodal isotopic distributions, suggesting the presence of several different conformations. The y fragment ions show greater exchange rates and levels than a or b ions, and when water or ammonia is lost from the fragment ions, no exchange is observed.     

Mass selective axial ion ejection from a linear quadrupole ion trap

The electric fields responsible for mass-selective axial ejection (MSAE) of ions trapped in a linear quadrupole ion trap have been studied using a combination of analytic theory and computer modeling. Axial ejection occurs as a consequence of the trapped ions' radial motion, which is characterized by extrema that are phase-synchronous with the local RF potential. As a result, the net axial electric field experienced by ions in the fringe region, over one RF cycle, is positive. This axial field depends strongly on both the axial and radial ion coordinates. The superposition of a repulsive potential applied to an exit lens with the diminishing quadrupole potential in the fringing region near the end of a quadrupole rod array can give rise to an approximately conical surface on which the net axial force experienced by an ion, averaged over one RF cycle, is zero. This conical surface has been named the cone of reflection because it divides the regions of ion reflection and ion ejection. Once an ion penetrates this surface, it feels a strong net positive axial force and is accelerated toward the exit lens. As a consequence of the strong dependence of the axial field on radial displacement, trapped thermalized ions can be ejected axially from a linear ion trap in a mass-selective way when their radial amplitude is increased through a resonant response to an auxiliary signal.     

Surface-induced dissociation of molecular ions in a quadrupole ion trap mass spectrometer

A method is reported by which surface-induced dissociation is used to activate ions stored in a quadrupole ion trap mass spectrometer. The method employs a short (< 5 μs), fast-rising (< 20-ns rise time), high voltage direct current (dc) pulse, which is applied to the endcaps of a standard Paul-type quadrupole ion trap. This is in contrast to the application of an alternating current (ac) signal normally used to resonantly excite and dissociate ions in the trap. The effect of the dc pulse is to cause the ions rapidly to become unstable in the radial direction and subsequently to collide with the ring electrode. Sufficient internal energy is acquired in this collision to cause high energy fragmentations of relatively intractable molecular ions such as pyrene and benzene. The dissociations of limonene are used to demonstrate that high energy demand processes increase in relative importance in the dc pulse experiment compared with the usual resonance excitation method used to cause activation. The fragments are scanned out of the ion trap using the conventional mass-selective instability scan mode. Simulations of ion motion in the trap provide evidence that surface collisions occur at kinetic energies in the range of tens to several hundred electronvolts. The experiments also demonstrate that production of fragment ions is sensitive to the phase of the main radiofrequency drive voltage at the point when the dc is initiated.     

Fragmentation of ions in a low pressure linear ion trap

The efficiency of in-trap fragmentation in a low-pressure linear ion trap (LIT), using dipolar excitation, is dependent upon the choice of both the excitation q and the drive frequency of the quadrupole. In the work presented here, fragmentation efficiencies have been measured as a function of excitation q for drive frequencies of 816 kHz and 1.228 MHz. The experiments were carried out by fragmenting reserpine (609.23-->448.20 Th and 397.21-->365.19 Th transitions) and caffeine (195-->138 Th and 138-->110 Th transitions). The data showed that the onset of efficient fragmentation occurred at a lower Mathieu q for the LIT operated at 1.228 MHz when compared with the LIT operated at 816 kHz. A comparison of the fragmentation efficiency curves as a function of pseudo-potential well depth showed that the onset of fragmentation is independent of the drive frequency. In addition, a comparison of the fragmentation efficiency curves showed that all four of the precursor ions fragmented within a range of four V of pseudo-potential well depth. The choice of an appropriate excitation q can then be determined based upon a minimum pseudo-potential well depth, quadrupole field radius, drive frequency, and the mass of interest. Fragmentation efficiencies were also found to be significantly greater when using the higher drive frequency.     

High-resolution excitation of ions in a low-pressure linear ion trap

An exploration of the parameters necessary to obtain high‐resolution excitation, using dipolar excitation, of an ion in a linear ion trap has been undertaken in this study. These parameters included ion trap pressure, excitation amplitude, excitation period, drive frequency of the ion trap, Mathieu q value and the mass of the ion of interest. An understanding of how these parameters play a role in high‐resolution excitation is necessary to the development of a method for the targeted tandem mass spectrometric (MS/MS) analysis of ions with the same nominal mass. Resonance excitation profiles with full width half maxima as narrow as 0.015 m/z units could be obtained, under the right conditions, for an ion from a homogenously substituted triazatriphosphorine at m/z 322.049, which translates into a mass resolution of >21 500. In this particular case the requirement for high resolution was a low trap pressure (3.8 × 10^?5 Torr), low excitation amplitude (3 mV), long excitation period (100 ms) and a high Mathieu q value(0.8) when using a drive frequency of 1.228 MHz. Similar conditions were used to demonstrate the isolation of individual [M + H]⁺ component ions from mixtures of bromazepam (m/z 316.008)/chlorprothixene (m/z 316.0921)/fendiline (m/z 316.206) and chlorprothixene (m/z 316.0921)/oxycodone (m/z 316.1543)/fendiline (m/z 316.206) prior to obtaining product ion spectra with excitation at q = 0.236. In the former mixture the individual components were isolated with near 100% efficiency while in the latter mixture the isolation efficiency dropped to near 50% for the oxycodone component and to 80% for the other components. Copyright © 2010 John Wiley & Sons, Ltd.     

Ultraviolet photodissociation of protonated pharmaceuticals in a pressurized linear quadrupole ion trap

Ultraviolet photodissociation (UVPD) was evaluated as a technique for generating ion fragmentation information that is alternative and/or complementary to the information obtained by collision‐induced dissociation (CID). Ions trapped in a pressurized linear ion trap were dissociated using a 355 nm or a 266 nm pulsed laser. Comparisons of UVPD and CID spectra using a set of aromatic chromophore‐containing compounds (desmethyl bosentan, haloperidol, nelfinavir) demonstrated distinct characteristic fragmentation patterns resulting from photodissociation. The wavelength of light and the pressure of the buffer gas in the UVPD cell are important parameters that control fragmentation pathways. The wavelength effect is related to the absorption cross section, location of the chromophore and the energy carried by one photon. Thus, UV irradiation wavelength affects fragmentation pathways as well as the fragmentation rate. The pressure effect can be explained by collisional quenching of ‘slow’ fragmentation pathways. We observed that higher pressure of the buffer gas during UVPD experiments highlights unique fragment ions by suppressing slow fragmentation pathways responsible for CID‐like fragmentation patterns. Copyright © 2010 John Wiley & Sons, Ltd.     

Observation of higher order quadrupole excitation frequencies in a linear ion trap

The resonant frequencies for quadrupole excitation of ions confined with a buffer gas in a linear quadrupole ion trap with Mathieu parameters a = 0 and q ∼ 0.36 have been measured. The resonances are predicted to occur at angular frequencies ω _n ^K given by ω _n ^K = (Ώ/K)|n + β| without the presence of a buffer gas where ϒ is the angular frequency of the trapping radio frequency, K = 1,2,3 … is the order of the resonance calculated with perturbation theory, and n = 0, ±1, ±2, ±3 …. The resonances are measured through fragmentation of protonated reserpine. The observed frequencies agree closely with the theoretical values but there are small differences which vary from +0.6% at K = 2 to −2.7% at K = 6. This is believed to be the result of the dependence of the resonant frequencies upon the buffer gas density and/or the excitation amplitude. The resolution of the resonances (measured from the depletion of precursor and formation of fragment ions) increased by a factor of 2 as K increased from 1 to 6. This increase in resolution warrants further investigation into the use of higher order resonances for isolation and excitation of trapped ions.     

High-performance liquid chromatography-tandem mass spectrometry with a new quadrupole/linear ion trap instrument

The use of a new hybrid quadrupole/linear ion trap known as the Q TRAP offers unique benefits as a LC-MS-MS detector for both small and large molecule analyses. The instrument combines the capabilities of a triple quadrupole mass spectrometer and ion trap technology on a single platform. Product ion scans are conducted in a hybrid fashion with the fragmentation step accomplished via acceleration into the collision cell followed by trapping and mass analysis in the Q3 linear ion trap. This results in triple quadrupole fragmentation patterns with no inherent low molecular mass cutoff. In-trap fragmentation is also possible in order to provide triple MS (MS3) capabilities. There are also several scan modes that are not possible on conventional instruments that enable identification of analytes within complex biological matrixes for subsequent high sensitivity product ion scans. This report will describe the new hybrid instrument and the principles of operation, and also provide examples of the unique scan modes and capabilities of the Q TRAP for LC-MS-MS detection in metabolism identification.     

Evidence for ionization-related conformational differences of peptide ions in a quadrupole ion trap

The differences in boundary-activated dissociation (BAD) onsets have been investigated for peptide ions that were generated by two different ionization techniques, nanoflow electrospray ionization (nanoESI) and liquid secondary-ion mass spectrometry (LSIMS). BAD onsets of these ions were determined to compare the relative internal energies of the ions. Protonated peptide ions formed by nanoESI had lower BAD onsets than ions formed by LSIMS. The BAD onsets of peptides derivatized to have a fixed charge on the N-terminus also were lower for those generated by nanoESI than those generated by LSIMS. The BAD onsets of ions formed by nanoESI did not change with the variation of collisional cooling periods after gating ions into the ion trap and after isolating them prior to dissociation, indicating that the ions formed by the two ionization techniques would not adopt the same energy distributions. It is proposed that the ions formed by the two techniques differ in secondary structure, and the LSIMS ions are collisionally cooled to a lower local minimum along the potential energy surface than the nanoESI ions. Ions formed by both techniques show the same dissociation patterns, so assuming the absolute energy required for dissociation is the same, the LSIMS ions possess a higher critical energy of dissociation. This leads to the observation of the higher BAD onset.     

Dissociation of peptide ions by fast atom bombardment in a quadrupole ion trap

A new technique for fragmentation of cations and anions of peptides stored in ion traps including radiofrequency devices is described. The technique involves irradiation of peptide ions by a beam of particles generated by a fast atom bombardment (FAB) gun. This irradiation leads to fragmentation of N--C(alpha) backbone bonds (c- and z-fragments) and S--S bonds for cations and C(alpha)-C backbone bonds (a- and x-fragments) for anions of peptides. The fragmentation patterns observed are hypothesized to be due to the interaction of peptide ions with metastable, electronically excited species generated by the FAB gun. Interaction of a metastable atom A* with a peptide n-cation M(n+) leads to the electron transfer from the metastable atom to the polycation through the formation of an ion-pair collision complex A(+.) . . . M((n-1)+.) and subsequent fragmentation of the peptide cation. Thus, for polycations, this metastable-induced dissociation of ions (MIDI) is similar to the phenomenon of electron capture dissociation (ECD). Interaction of A* with an anion leads to the deexcitation of the metastable species and detachment of an electron from the anion. This in turn leads to backbone fragmentation similar to that in electron detachment dissociation (EDD). The MIDI technique is robust and efficient, and it is applicable to peptides in as low charge states as 2+ or 2-.     

Origin of product ions in the MS/MS spectra of peptides in a quadrupole ion trap

Stored waveform inverse Fourier transform and double resonance techniques have been used in conjunction with a quadrupole ion trap to study the dissociation patterns of peptide ions. These experiments provide insight into the origin of individual product ions in an MS/MS spectrum. Results show for a series of leucine enkephalin analogues with five amino acid residues that the b ₄ ion is the main product ion through which many other product ions arise. It was also observed that the percentage of the a ₄ product ions that are formed directly from the protonated molecule (M+H)⁺ depends on the nature of the fourth amino acid residue. In addition, it was determined that in the peptides studied here lower series b ions (e.g., b ₃ arise from direct dissociation of higher series b ions (e.g., b ₄ only about 50% of the time.     

Improving IRMPD in a quadrupole ion trap

A focused laser is used to make infrared multiphoton photodissociation (IRMPD) more efficient in a quadrupole ion trap mass spectrometer. Efficient (up to 100%) dissociation at the standard operating pressure of 1 × 10⁻³ Torr can be achieved without any supplemental ion activation and with shorter irradiation times. The axial amplitudes of trapped ion clouds are measured using laser tomography. Laser flux on the ion cloud is increased six times by focusing the laser so that the beam waist approximates the ion cloud size. Unmodified peptide ions from 200 Da to 3 kDa are completely dissociated in 2.5–10 ms at a bath gas pressure of 3.3 × 10⁻⁴ Torr and in 3–25 ms at 1.0 × 10⁻³ Torr. Sequential dissociation of product ions is increased by focusing the laser and by operating at an increased bath gas pressure to minimize the size of the ion cloud.     

Field-modulated selective ion storage in a quadrupole ion trap

A new method of selective ion storage in a quadrupole ion trap is described. Broadband waveforms were applied to the endcaps of an ion trap to eject unwanted ions by resonance excitation, which enhanced the storage of selected target ions. A unique trapping field amplitude modulation technique allowed the use of waveforms with fewer frequency components. The requirements and methods of calculations for frequency-optimized wave-forms are discussed. Advantages of this method include the reduction of target ion loss that results from collision-activated dissociation. In other applications, equivalent performance, relative to methods that use nonmodulated trapping fields combined with waveforms that have a higher frequency density, was shown.     

Origin of mass shifts in the quadrupole ion trap: dissociation of fragile ions observed with a hybrid ion trap/mass filter instrument

A novel hybrid tandem mass analyzer, coupling a quadrupole ion trap with a quadrupole mass filter, has been constructed to permit mass analysis of ions ejected from the ion trap. The initial application of this instrument is the investigation of the origin of mass shifts in the ion trap due to ion fragility. We hypothesize that fragile ions undergo mass shifts, characterized by peak fronting, due to early ejection from the quadrupole ion trap. As these ions come into resonance with the ejection frequency, they gain kinetic energy, collide with buffer gas molecules and thus can dissociate to produce fragment ions. These fragment ions will not be stable within the ion trap as they are situated past the stability boundary at q(z) = 0. 908. Consequently the fragment ions are ejected prematurely. This results in an apparent mass shift due to peak fronting. The experiments reported here clearly document the production of fragment ions as the origin of mass shifts during the resonant ejection of fragile ions. Copyright 2000 John Wiley & Sons, Ltd.     

Space-charge effects with mass-selective axial ejection from a linear quadrupole ion trap

Methods to reduce mass shifts caused by space charge with mass‐selective axial ejection from a linear quadrupole ion trap are investigated. For axial ejection, dipole excitation is applied to excite ions at q ≈ 0.85. The trapping radiofrequency (rf) voltage is scanned to bring ions of different m/z values into resonance for excitation. In the fringing field at the quadrupole exit, excited ions gain axial kinetic energy, overcoming the trapping potential, and are ejected from the trap. Space charge causes the frequencies of ion oscillation to decrease. Thus, greater rf voltages are required to bring ions into resonance for excitation and ejection, and the ions shift to higher apparent masses in a mass spectrum. At the same time, the peaks broaden, lowering resolution. The effects of injection q value, ejection q value, excitation amplitude, quadrupole dc voltages applied to the electrodes, applying an rf voltage to the exit lens, and scan speed, on mass shifts have been studied experimentally. Most experiments were done with only ions of protonated reserpine (m/z 609.3 and its isotopic peaks) in the trap. Some experiments were done with ions of protonated reserpine and ions of m/z 622 in the trap. In general, the mass shifts are reduced with higher ejection q values, higher excitation amplitudes, with quadrupole dc applied, and at higher scan speeds. The application of quadrupole dc appears to increase the ion cloud temperature, which lowers mass shifts. Thus, a proper choice of operating conditions can reduce, but not eliminate, mass shifts caused by space charge. Copyright © 2011 John Wiley & Sons, Ltd.     

Ion excitation in a linear quadrupole ion trap with an added octopole field

Modeling of ion motion and experimental investigations of ion excitation in a linear quadrupole trap with a 4% added octopole field are described. The results are compared with those obtained with a conventional round rod set. Motion in the effective potential of the rod set can explain many of the observed phenomena. The frequencies of ion oscillation in the x and y directions shift with amplitude in opposite directions as the amplitudes of oscillation increase. Excitation profiles for ion fragmentation become asymmetric and in some cases show bistable behavior where the amplitude of oscillation suddenly jumps between high and low values with very small changes in excitation frequency. Experiments show these effects. Ions are injected into a linear trap, stored, isolated, excited for MS/MS, and then mass analyzed in a time-of-flight mass analyzer. Frequency shifts between the x and y motions are observed, and in some cases asymmetric excitation profiles and bistable behavior are observed. Higher MS/MS efficiencies are expected when an octopole field is added. MS/MS efficiencies (N(2) collision gas) have been measured for a conventional quadrupole rod set and a linear ion trap with a 4% added octopole field. Efficiencies are chemical compound dependent, but when an octopole field is added, efficiencies can be substantially higher than with a conventional rod set, particularly at pressures of 1.4 x 10(-4) torr or less.     

Substitution reactions of gaseous ions in a three‐dimensional quadrupole ion trap

Substitution reactions between gaseous ions and neutral substrate molecules are of ongoing high interest. To investigate these processes in a qualitative and quantitative manner, we have constructed a device, with which a defined amount of a volatile substrate can be mixed with a defined amount of helium gas and added into a three‐dimensional quadrupole ion trap. From the known inner volume of the device, the known ratio n_substrate:n_He of the mixture, and the determined absolute partial pressure of helium in the ion trap, we can derive the partial pressure of the substrate in the ion trap and, thus, convert the directly observable pseudo–first‐order rate constants of the substitution reactions into absolute bimolecular rate constants. We have tested the device by investigating a series of S_N2 reactions of Br ^? and CF₃CH₂O ^? anions as well as ligand exchange reactions of ligated Na⁺ cations. As the obtained results suggest, the described device makes it possible to determine the bimolecular rate constants of substitution reactions as well as other ion‐molecule reactions with satisfactory accuracy and reliability.     

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.