A novel electric ion resonance cell design with high signal-to-noise ratio and low distortion for Fourier transform mass spectrometry

Performing wideband ion image current detection mass spectrometry experiments with an electric ion trap—e. g., the Paul trap—is a difficult task, as there is a strong crosstalk current induced by the high voltages of the radio frequency (rf) storage field. In a classic Paul trap the metallic hyperbolic electrodes (a ring electrode and two end cap electrodes) are shaped following the isopotential lines of the quadrupole potential distribution. In our new design the ring electrode is replaced by a cylindrical series of ring electrodes with a parabolic potential distribution, whereas the end cap electrodes are used without modification. Thus the quadrupole field within the trap remains unchanged but the capacitances between the electrodes and therefore the crosstalk currents are significantly reduced. The remaining crosstalk is balanced out by an electronic compensation technique. As a consequence the weak signals of the ion-induced charge can be detected with a wideband low-noise amplifier to perform Fourier transform mass spectrometry experiments with improved signal-to-noise ratio.     

Analysis of non-covalent protein complexes up to 290 kDa using electrospray ionization and ion trap mass spectrometry

Non-covalently-bound subunit complexes of proteins have been measured by an ion trap mass spectrometer equipped with an orthogonal electrospray ionization source. For the analysis of the generated molecular ions with high mass/charge ratios, the mass/charge range of the ion trap was extended by increasing its radio frequency (rf) voltage to 15 kV (V(0-p)) and by resonant ion ejection. Ions of the non-covalent dimer of bovine serum albumin (BSA), as well as of subunit complexes of alcohol dehydrogenase (ADH) from bakers' yeast and from horse liver, have been detected at mass/charge values between 3000-9000 Th. The maximum observed molecular weight was that of a non-covalently-bound subunit-octamer of bakers' yeast ADH (two non-covalently-bound subunit-tetramers) at ca. 290 kDa.     

Controlled ion fragmentation in a 2-D quadrupole ion trap for external ion accumulation in ESI FTICR mass spectrometry

Undesired fragmentation of electrospray generated ions in an rf multipole traps can be problematic in many applications. Of special interest here is ion dissociation in a 2-D quadrupole ion trap external to a Fourier transform ion cyclotron resonance mass spectrometer (FTICR MS) used in proteomic studies. In this work, we identified the experimental parameters that determine the efficiency of ion fragmentation. We have found that under the pressure conditions used in this study there is a specific combination of the radial and axial potential well depths that determines the fragmentation threshold. This combination of rf and dc fields appears to be universal for ions of different mass-to-charge ratios, molecular weights, and charge states. Such universality allows the fragmentation efficiency of the trapped ions in the course of capillary liquid chromatography (LC) separation studied to be controlled and can increase the useful duty cycle and dynamic range of a FTICR mass spectrometer equipped with an external rf only 2-D quadrupole ion trap.     

A combined linear ion trap for mass spectrometry

We propose a novel ion cyclotron resonance ion trap capable of confining ions even at high pressure. The trap consists of three capacitively coupled axial sections, each composed of four circular cross-section rods parallel to the magnetic field axis. Ion confinement along the magnetic field direction is provided by applying the same static voltage to each set of “endcap” rods. As for a two-dimensional quadrupole mass filter, a sufficiently high rf frequency (several MHz) leads to an “effective” electrostatic “pseudopotential” well with a minimum on the trap central axis. Ions are confined radially by the combination of an applied axial static magnetic field and a radially inward-directed electric field resulting from differential rf voltages applied to each set of four rods. Ion confinement properties are revealed from a Paul traplike “stability diagram,” whereas ion trajectories are analyzed in terms of Penning-type ion cyclotron rotation, magnetron rotation, and axial oscillation motional modes. Ion cyclotron frequency increases with the strength of the rf trapping field. Ion magnetron motion becomes stable if the rf voltage is high enough. Therefore, ion trajectories can be stable even in the presence of ion-neutral collisions. Adding an ac potential to a Penning trap should dramatically increase the upper mass detection limit.     

Characterization of an Electron Ionization Source Trap Operating in the Presence of a Magnetic Field Through Computer Simulation

We explore the feasibility of conducting electron ionization (EI) in a radio-frequency (rf) ion source trap for mass spectrometry applications. Electrons are radially injected into a compact linear ion trap in the presence of a magnetic field used essentially to lengthen the path of the electrons in the trap. The device can either be used as a stand-alone mass spectrometer or can be coupled to a mass analyzer. The applied parallel magnetic field and the oscillating rf electric field produced by the trap give rise to a set of coupled Mathieu equations of motion. Via numerical simulations, electron trajectories are studied under varying intensities of the magnetic field in order to determine the conditions that enhance ion production. Likewise, the dynamic behavior of the ions are investigated in the proposed EI source trap and the fast Fourier transform FFT formalism is used to obtain the frequency spectrum from the numerical simulations to study the motional frequencies of the ions which include combinations of the low-frequency secular and the high-frequency micromotion with magnetron and cyclotron frequencies. The dependence of these motional frequencies on the trapping conditions is examined and particularly, the limits of applying a radial magnetic field to the EI ion trap are characterized.

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.     

A segmented ring,cylindrical ion trap source for time-of-flight mass spectrometry

An ion trap source has been designed for use with time-of-flight (TOF) mass analysis. Two thin diaphragms make up a segmented ring electrode; the end cap electrodes are planar wire mesh. The potential field produced by the rf voltage applied between the ring and end cap electrodes resembles that of the cylindrical ion trap. The trapped ion population for ions created by electron impact exhibits linear growth against a first-order loss that has a time constant of about 50 µs; no ion loss occurs when the electron beam is off. The observed value of q _z at low-mass cutoff for rf ion storage is ?0.84. Pulsed extraction of all ions is accomplished by switching the trap electrodes from rf to voltages required to provide a linear dc extraction field. The TOF flight path includes a wide energy range reflectron. Better than unit mass resolution is achieved through m/z 500 without collisional ion cooling. With an extraction rate of 1 kHz and a recording rate of 4 spectra per second, a linear working curve is obtained between 36 pg and 18 ng of chlorobenzene delivered chromatographically. The system has demonstrated the potential to achieve a very high sample utilization efficiency at high spectral generation rates.     

Langevin equation for the parametric oscillator: a model for ion confinement in a radio frequency trap

We have calculated 〈x ²〉 and 〈v ²〉 for an ion in a rf trap being cooled by a stochastic force. The results agree with earlier work (using a Fokker-Planck equation) as long as there is white noise. However, there is an appreciable reduction for both quantities, if non-Markovian processes are included.     

Quantitative analysis of crude plasma extracts by ion trap tandem mass spectrometry

The ion trap mass spectrometer is a tandem-in-time instrument that has promise as an extremely sensitive device for practical tandem mass spectrometry assays. An approach for the quantitative analysis of unknown drug levels in crude extracts, using combined capillary gas chromatography and the ion trap mass spectrometer in the tandem mode, is described. One-gram plasma samples were spiked with an anti-inflammatory drug at levels of 1–100 ng, and with 50 ng of a chemical analog internal standard. Crude extracts of the plasma samples are analyzed by using scan functions that utilize combined radiofrequency (rf) and de voltages. The need for combined rf- and de-voltage sequences for analysis of such extracts is demonstrated by comparison to attempted analyses using only rf voltages. Limitations of the method are: (1) the need for accurate calibration of ionization times to obtain linear calibration lines, and (2) the lack of automatic gain control for scans using combined rf and dc voltages to control and optimize parent ion populations and to allow a simpler analysis of “unknowns. ”     

Miniature toroidal radio frequency ion trap mass analyzer

A miniature ion trap mass analyzer is reported. The described analyzer is a 1/5-scale version of a previously reported toroidal radio frequency (rf) ion trap mass analyzer. The toroidal ion trap operates with maximum rf trapping voltages about 1 kVp-p or less; however despite the reduced dimensions, it retains roughly the same ion trapping capacity as conventional 3D quadrupole ion traps. The curved geometry provides for a compact mass analyzer. Unit-mass resolved mass spectra for n-butylbenzene, xenon, and naphthalene are reported and preliminary sensitivity data are shown for naphthalene. The expected linear mass scale with rf amplitude scan is obtained when scanned using a conventional mass-selective instability scan mode combined with resonance ejection.     

Dipolar DC Collisional Activation in a “Stretched” 3-D Ion Trap: The Effect of Higher Order Fields on rf-Heating

Applying dipolar DC (DDC) to the end-cap electrodes of a 3-D ion trap operated with a bath gas at roughly 1 mTorr gives rise to ‘rf-heating’ and can result in collision-induced dissociation (CID). This approach to ion trap CID differs from the conventional single-frequency resonance excitation approach in that it does not rely on tuning a supplementary frequency to coincide with the fundamental secular frequeny of the precursor ion of interest. Simulations using the program ITSIM 5.0 indicate that application of DDC physically displaces ions solely in the axial (inter end-cap) dimension whereupon ion acceleration occurs via power absorption from the drive rf. Experimental data shows that the degree of rf-heating in a stretched 3-D ion trap is not dependent solely on the ratio of the dipolar DC voltage/radio frequency (rf) amplitude, as a model based on a pure quadrupole field suggests. Rather, ion temperatures are shown to increase as the absolute values of the dipolar DC and rf amplitude both decrease. Simulations indicate that the presence of higher order multi-pole fields underlies this unexpected behavior. These findings have important implications for the use of DDC as a broad-band activation approach in multi-pole traps.     

Negative chemical ionization in quadrupole ion trap mass spectrometry: Effects of applied voltages and reaction times

The effects of applied voltages and reaction times on negative ion chemical ionization in the quadrupole ion trap are investigated. Mass-selected ejection of undesired reagent ions and selective mass storage of only negative ions are required for practical negative ion chemical ionization. This is achieved by application of rf and dc voltages to the ring electrode to control the mass-to-charge ratios one polarity) of ions stored, as well as by application of a supplemental rf voltage applied across the endcap electrodes to selectively eject ions of a particular mass-to-charge ratio. Even with careful control of these parameters, negative chemical ionization is not as sensitive as electron ionization and positive chemical ionization because of the lack of thermal electrons in the ion trap. Mass selection of the hydroxide anion as a reagent ion and exclusion of all positive ions provide [M ? H]^? ions with little or no fragmentation for a wide variety of compounds.     

Adaptation of a 3-D Quadrupole Ion Trap for Dipolar DC Collisional Activation

Means to allow for the application of a dipolar DC pulse to the end-cap electrodes of a three-dimensional (3-D) quadrupole ion trap for as short as a millisecond to as long as hundreds of milliseconds are described. The implementation of dipolar DC does not compromise the ability to apply AC waveforms to the end-cap electrodes at other times in the experiment. Dipolar DC provides a nonresonant means for ion acceleration by displacing ions from the center of the ion trap where they experience stronger rf electric fields, which increases the extent of micro-motion. The evolution of the product ion spectrum to higher generation products with time, as shown using protonated leucine enkephalin as a model protonated peptide, illustrates the broad-band nature of the activation. Dipolar DC activation is also shown to be effective as an ion heating approach in mimicking high amplitude short time excitation (HASTE)/pulsed Q dissociation (PQD) resonance excitation experiments that are intended to enhance the likelihood for observing low m/z products in ion trap tandem mass spectrometry.     

A novel approach for identification and characterization of glycoproteins using a hybrid linear ion trap/FT-ICR mass spectrometer

Combining source collision-induced dissociation (CID) and tandem mass spectral acquisition in a pseudo-MS(3) experiment using a linear ion trap results in a highly selective and sensitive approach to identifying glycopeptide elution from a protein digest. The increased sensitivity is partially attributed to the nonselective nature of source CID, which allows simultaneous activation of all charge states and coeluting glycoforms generating greater ion abundance for the mass-to-charge (m/z) 204 and/or 366 oxonium ions. Unlike source CID alone, a pseudo-MS(3) approach adds selectivity while improving sensitivity by eliminating chemical noise during the tandem mass spectral acquisition of the oxonium ions in the linear ion trap. Performing the experiments in the hybrid linear ion trap/Fourier transform-ion cyclotron resonance (FT-ICR) enables subsequent high-resolution/high-mass accuracy full-scan mass spectra (MS) and parallel acquisition of MS/MS in the linear ion trap to be completed in 2 s directly following the pseudo-MS(3) scan to collate identification and characterization of glycopeptides in one experimental scan cycle. Analysis of bovine fetuin digest using the combined pseudo-MS(3), high-resolution MS, and data-dependent MS/MS events resulted in identification of four N-linked and two O-linked glycopeptides without enzymatic cleavage of the sugar moiety or release of the sialic acids before analysis. In addition, over 95% of the total protein sequence was identified in one analytical run.     

Characterization of a serial array of miniature cylindrical ion trap mass analyzers

Two small (5 mm internal radius) cylindrical ion traps (CITs) are arranged in series and operated using a single ion source, detector and radio frequency (rf) trapping signal. Ions are trapped in the first CIT and later transferred to the second by applying a direct current (dc) pulse to the endcap electrode of the first trap. This process is facilitated if a second, appropriately timed, retarding dc pulse is applied to the exit endcap electrode of the second trap. Mesh endcaps are used for the CITs to increase the number of ionizing electrons entering the trap and to maximize the transfer efficiency and detected signal. The transfer efficiency is dependent on the amplitude of the dc potential applied to eject the ions from the first trap, the amplitude of the dc potential applied to retain the ions in the second trap, and the period during which the retarding potential is applied. The amplitude and phase of the rf also affect the transfer process. Ions that readily dissociate upon collision have low transfer efficiencies; more stable ions can be transferred with up to 50% efficiency. Copyright 1999 John Wiley & Sons, Ltd.     

Charge Detection Mass Spectrometry with Resolved Charge States

Charge detection mass spectrometry (CDMS) measurements have been performed for cytochrome c and alcohol dehydrogenase (ADH) monomer using a modified cone trap incorporating a cryogenically cooled JFET. Cooling the JFET increases its transconductance and lowers thermal noise, improving the signal to noise (S/N) ratio. Single ions with as few as 9 elementary charges (e) have been detected. According to simulations, the detection efficiency for ions with a charge of 13 e is 75 %, and for charges above 13 e the detection efficiency rapidly approaches 95 %. With the low limit of detection achieved here, adjacent charge states are easily resolved in the m/z spectrum, so the accuracy and precision of the image charge measurements can be directly evaluated by comparing the measured image charge to the charge deduced from the m/z spectrum. For ADH monomer ions with 32 to 43 charges, the root mean square deviation of the measured image charge is around 2.2 e. Ions were trapped for over 1500 cycles. The number of cycles detected appears to be limited mainly by collisions with the background gas.

Simultaneous quantitative cassette analysis of drugs and detection of their metabolites by high performance liquid chromatography/ion trap mass spectrometry

A method using high performance liquid chromatography (HPLC) coupled with ion trap mass spectrometry (MS) for simultaneous quantification of multiple drugs and detection of their metabolites is described. The new approach offers a significant increase in analytical throughput and is illustrated with analysis of the in vitro metabolism of 19 alpha-1a receptor antagonists. The compounds were separated into four cassette groups by using a computer program as well as by manual examination. The samples from incubation with dog liver microsomes were pooled into the designed cassette groups and analyzed by HPLC/electrospray (ESI) ion trap MS in full-scan mode. The metabolic stability of the drugs was determined by comparing their signals after incubation for 0 and 60 min, respectively. The quantitative results from the cassette analysis procedure agreed well with those obtained from conventional discrete analysis. In addition, the technique allowed simultaneous detection of metabolites formed during the same incubation without having to reanalyze the samples. The metabolites were first characterized by nominal mass measurement of the corresponding protonated molecules. Subsequent multi-stage tandem mass spectrometry (MS(n)) on the ion trap instrument allowed confirmation of the detected metabolites.     

Compressive Mass Analysis on Quadrupole Ion Trap Systems

Conventionally, quadrupole ion trap mass spectrometers eject ions of different mass-to-charge ratio (m/z) in a sequential fashion by performing a scan of the rf trapping voltage amplitude. Due to the inherent sparsity of most mass spectra, the detector measures no signal for much of the scan time. By exploiting this sparsity property, we propose a new compressive and multiplexed mass analysis approach—multi Resonant Frequency Excitation (mRFE) ejection. This new approach divides the mass spectrum into several mass subranges and detects all the subrange spectra in parallel for increased mass analysis speed. Mathematical estimation of standard mass spectrum is demonstrated while statistical classification on the parallel measurements remains viable because of the sparse nature of the mass spectra. This method can reduce mass analysis time by a factor of 3–6 and increase system duty cycle by 2×. The combination of reduced analysis time and accurate compound classification is demonstrated in a commercial quadrupole ion trap (QIT) system.

Determining Energies and Cross Sections of Individual Ions Using Higher-Order Harmonics in Fourier Transform Charge Detection Mass Spectrometry (FT-CDMS)

A general method for in situ measurements of the energy of individual ions trapped and weighed using charge detection mass spectrometry (CDMS) is described. Highly charged (>?300 e), individual polyethylene glycol (PEG) ions are trapped and oscillate within an electrostatic trap, producing a time domain signal. A segmented Fourier transform (FT) of this signal yields the temporal evolution of the fundamental and harmonic frequencies of ion motion throughout the 500-ms trap time. The ratio of the fundamental frequency and second harmonic (HAR) depends on the ion energy, which is an essential parameter for measuring ion mass in CDMS. This relationship is calibrated using simulated ion signals, and the calibration is compared to the HAR values measured for PEG ion signals where the ion energy was also determined using an independent method that requires that the ions be highly charged (>?300 e). The mean error of 0.6% between the two measurements indicates that the HAR method is an accurate means of ion energy determination that does not depend on ion size or charge. The HAR is determined dynamically over the entire trapping period, making it possible to observe the change in ion energy that takes place as solvent evaporates from the ion and collisions with background gas occur. This method makes it possible to measure mass changes, either from solvent evaporation or from molecular fragmentation (MSⁿ), as well as the cross sections of ions measured using CDMS.

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Graphical Abstract

     

Computer simulation of the gap-tripole ion trap with linear injection, 3D ion accumulation,and versatile packet ejection

The behavior of a completely new ion trap is shown with SIMION 7.0 simulations. The simulated trap, which was a mix of a linear and a 3D trap, was made by axially setting two ion guides with a gap between them. Each guide consisted of three rods with three symmetrically delayed radio frequency (rf) voltages (tripole). The "injected" ions were linearly contained by pulsed potentials on the entrance and exit plates. Then the three-dimensional (3D) rf field in the gap, which was created by the tripole special rod arrangement, could trap the ions when the translational energy was dampened by collisions with low-pressure nitrogen. Because the injected ions were trapped in the small gap, the trapping cycle could be repeated many times before ion ejection, so a high concentrated ion cloud could be obtained. This trapping and accumulation methodology is not possible in most conventional multipole linear traps with even number of poles. Compared with quadrupole linear trap at the same rf amplitude, tripole lost more ions due to strong charge repulsion in the ion cloud. However, tripole could catch up the ions at higher voltage. Radial and axial mass-independent ejection of the ions localized in the tripole gap was very simple, compared with conventional linear ion traps that need extra and complicated electrodes for effective axial ejection.