Three-dimensional Quadrupole Ion Trap Research Articles

An ion mobility mass spectrometer coupled with a cryogenic ion trap for recording electronic spectra of charged, isomer-selected clusters.

Infrared and electronic spectra are indispensable for understanding the structural and energetic properties of charged molecules and clusters in the gas phase. However, the presence of isomers can potentially complicate the interpretation of spectra, even if the target molecules or clusters are mass-selected beforehand. Here, we describe an instrument for spectroscopically characterizing charged molecular clusters that have been selected according to both their isomeric form and their mass-to-charge ratio. Cluster ions generated by laser ablation of a solid sample are selected according to their collision cross sections with helium buffer gas using a drift tube ion mobility spectrometer and their mass-to-charge ratio using a quadrupole mass filter. The mobility- and mass-selected target ions are introduced into a cryogenically cooled, three-dimensional quadrupole ion trap where they are thermalized through inelastic collisions with an inert buffer gas (He or He/N2 mixture). Spectra of the molecular ions are obtained by tagging them with inert atoms or molecules (Ne and N2), which are dislodged following resonant excitation of an electronic transition, or by photodissociating the cluster itself following absorption of one or more photons. An electronic spectrum is generated by monitoring the charged photofragment yield as a function of wavelength. The capacity of the instrument is illustrated with the resonance-enhanced photodissociation action spectra of carbon clusters (Cn +) and polyacetylene cations (HC2nH+) that have been selected according to the mass-to-charge ratio and collision cross section with He buffer gas and of mass-selected Au2 + and Au2Ag+ clusters.

Enabling Isotope Ratio Measurements on an Ion Trap Mass Spectrometer.

For portable, remotely operated systems in space and defense, relaxed vacuum requirements are a strong advantage of ion trap mass analyzers. However, ion traps are believed to have insufficient capability for isotope ratio measurement because they fundamentally restrict sampling capacity. Focusing on modifications to the detection sequence of a digitally driven 3D quadrupole ion trap, operating in resonance ejection mode, we investigated improved performance for isotope ratio precision and accuracy. Due to xenon's inert nature and wide span of isotopes, xenon isotope ratios provide an excellent marker of processes (e.g. radioactive decay and planetary atmospheric escape) which would be ideally measured by in situ mass spectrometry. To target xenon isotope ratio analysis specifically, we implemented data acquisition system modifications for enhanced y-axis resolution measurements and signal filtering. In this manner, we show measurement precision improvements from ~±100 0/00 to ~±0.1 0/00 and accuracy improvements from ~30 0/00 to ~0.5 0/00 for our targeted isotopes of interest.

Temperature evolution of ions in a Paul trap driven by various radio-frequency waveforms

In this study, temperature evolution of an ion ensemble in a three-dimensional quadrupole ion trap is explored. Four different radio-frequency (RF) waveforms have been used to drive the trap. It has been found that for the given period of the RF waveforms (rectangular, sine, triangular, and sawtooth), there have been obtained various ion temperatures for each waveform. The temperature evolution of ions was obtained using by the PyDIT code. Trapped ion temperature is affected by the motion of ions which consist of secular motion and micro-motion. It was found that temperature of ion ensemble is different at each of the four waveforms. This kind of investigation might be useful to select one of these RF waveforms which would be appropriate for specific applications. Furthermore, various octopole field contributions, and nonlinear Mathieu parameter (q), and initial condition effects on the ion ensemble temperature have also been investigated.

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 nsubstrate :nHe 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 SN 2 reactions of Br- and CF3 CH2 O- 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.

Applications of the fractional calculus to study the physical theory of ion motion in a quadrupole ion trap.

In this article, fractional calculus has been applied to study the motion of ions in a three-dimensional radio frequency quadrupole ion trap; we have called this arrangement a fractional quadrupole ion trap. The main purpose of the article is to show that by controlling the fractional parameter of a trapped ion, one can gain a more efficient mass separation. In what follows, we will see that with decreasing the fractional parameter, we can achieve a smaller first stability region. Note that a small stability diagram will result in a good and acceptable mass separation. Various methods can be proposed to obtain a desired ion acceleration with a sufficient accuracy for good mass separation, which is similar to the one obtained by a fractional ion trap. Some of these methods are using the effects of a damping force, a magnetic field or both on the confinement of particles in the quadrupole ion trap. The first stability regions are plotted for all of the aforementioned methods, and simulation results are provided to compare them with those for the fractional case.

High-cooling-efficiency cryogenic quadrupole ion trap and UV-UV hole burning spectroscopy of protonated tyrosine

The cooling efficiency of a cryogenic three-dimensional quadrupole ion trap (QIT) is drastically improved by using copper electrodes instead of conventional stainless-steel ones. The temperature of trapped ions (protonated tyrosine TyrH+) was estimated based on the ultraviolet (UV) photo-dissociation spectra. The UV spectrum of TryH+ shows almost no hot bands, and thus the high cooling efficiency of the copper ion trap was proven. The temperature was also estimated by simulating the observed band contour in the UV spectra, which is determined by the population in the rotationally excited levels. From the simulations, the temperature of TryH+ was estimated to be ∼13K, while that in the stainless-steel QIT was 45–50K. In addition, to demonstrate the advantage of the copper QIT, UV-UV hole burning (HB) spectra, i.e. conformation-selected UV spectra, were measured. It was confirmed that four different conformers, A∼D, coexist in the ultra-cold protonated tyrosine. By comparing with the calculated Franck-Condon spectra, their structural assignments were discussed, including the orientation of the OH group.

Laser desorption lamp ionization source for ion trap mass spectrometry.

A two-step laser desorption lamp ionization source coupled to an ion trap mass spectrometer (LDLI-ITMS) has been constructed and characterized. The pulsed infrared (IR) output of an Nd:YAG laser (1064 nm) is directed to a target inside a chamber evacuated to ~15 Pa causing desorption of molecules from the target's surface. The desorbed molecules are ionized by a vacuum ultraviolet (VUV) lamp (filled with xenon, major wavelength at 148 nm). The resulting ions are stored and detected in a three-dimensional quadrupole ion trap modified from a Finnigan Mat LCQ mass spectrometer operated at a pressure of ≥ 0.004 Pa. The limit of detection for desorbed coronene molecules is 1.5 pmol, which is about two orders of magnitude more sensitive than laser desorption laser ionization mass spectrometry using a fluorine excimer laser (157 nm) as the ionization source. The mass spectrum of four standard aromatic compounds (pyrene, coronene, rubrene and 1,4,8,11,15,18,22,25-octabutoxy-29H,31H-phthalocyanine (OPC)) shows that parent ions dominate. By increasing the infrared laser power, this instrument is capable of detecting inorganic compounds.

Radio frequency quadrupole technology: Evolution and contributions to mass spectrometry

Just as 2013 marks the centenary of the birth of mass spectrometry through the publication of Thomson’s classic book ‘Rays of Positive Electricity and Their Application to Chemical Analyses’, it is also exactly six decades since Paul and Steinwedel filed their first German patent ‘Verfahren zur Trennung bzw. Zum getrennten Nachweis von Ionen verschiedener spezifischer Ladung’ (‘Method for separating or separately detecting ions of different specific charges’) on 24th December, 1953. This patent described the quadrupole mass filter (QMF) and the three-dimensional quadrupole ion trap (3D-QIT), both of which operate by confining ions mass-selectively through the application of radio frequency quadrupolar potentials to appropriate electrode structures. In the ensuing 60 years since the initial description of these devices the impact of quadrupole technology upon mass spectrometry as a whole has been truly remarkable, especially when combined with chromatographic separation methods and/or other types of mass analysers. This retrospective article will aim to trace the principal milestones in the evolution of transmission quadrupoles (the QMF, quadrupole beam guides, and triple quadrupole tandem instruments) and of trapping quadrupoles (the 3D-QIT and, the more recent, linear quadrupole ion trap (LQIT)), both as stand-alone instruments and in various hybrid configurations. Recent research advances into quadrupole technology itself will be discussed; an account of ion trapping in the Kingdon trap and the Orbitrap™ mass spectrometer is included in the Supplementary Information for comparison.

Ion trap electric field characterization using slab coupled optical fiber sensors.

This paper presents a method for characterizing electric field profiles of radio frequency (rf) quadrupole ion trap structures using sensors based on slab coupled optical-fiber sensor (SCOS) technology. The all-dielectric and virtually optical fiber-sized SCOS fits within the compact environment required for ion traps and is able to distinguish electric field orientation and amplitude with minimal perturbation. Measurement of the fields offers insight into the functionality of traps, which may not be obtainable solely by performing simulations. The SCOS accurately mapped the well-known field profiles within a commercially available three-dimensional quadrupole ion trap (Paul trap). The results of this test allowed the SCOS to map the more complicated fields within the coaxial ion trap with a high degree of confidence as to the accuracy of the measurement. Figure ᅟ

Femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) of deprotonated phosphopeptide anions

Radical-directed dissociation techniques provide structural information which is complementary to that from conventional collision-induced dissociation (CID). The analysis of phosphopeptide anions is warranted due to their relatively acidic character. As femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) is uniquely initiated by field ionization, an investigation is warranted to determine whether fsLID may provide novel analytical utility for phosphopeptide anions. Twenty-three synthetic deprotonated phosphopeptide anions were introduced into a three-dimensional quadrupole ion trap mass spectrometer via electrospray ionization. The ion trap was interfaced with a near-IR (802 nm) ultrashort-pulsed (35 fs FWHM) ultrahigh-powered (peak power ~10(14) W/cm(2)) laser system. Performance comparisons are made with other techniques applied to phosphopeptide anion analysis, including CID, electron detachment dissociation (EDD), negative electron transfer dissociation (NETD), activated electron photodetachment dissociation (activated-EPD), and ultraviolet photodissociation (UVPD). FsLID-MS/MS of multiply deprotonated phosphopeptide anions provides sequence information via phosphorylation-intact a/x ions in addition to other sequence ions, satellite ions, and side-chain losses. Novel fragmentation processes include selective c-ion formation N-terminal to Ser/Thr and a phosphorylation-specific correlation between xn -98 ion abundances and phosphorylation at the n(th) residue. Sequencing-quality data required about 30 s of signal averaging. fsLID-MS/MS of singly deprotonated phosphopeptides did not yield product anions with stable trajectories, despite significant depletion of the precursor. Multiply deprotonated phosphopeptide anions were sequenced via negative-mode fsLID-MS/MS, with phosphosite localization facilitated by a/x ion series in addition to diagnostic x(n)-98 ions. fsLID-MS/MS is qualitatively competitive with other techniques. Further efficiency enhancements (e.g., implementation on a linear trap or/and higher pulse frequencies) may permit sequence analyses on chromatographic timescales.

Analysis of High Mass-to-Charge Ions in a Quadrupole Ion Trap Mass Spectrometer via an End-Cap Quadrupolar Direct Current Downscan

A method for performing mass-selective instability analysis in a three-dimensional (3-D) quadrupole ion trap is described that involves scanning a direct current (dc) voltage applied to the end-cap electrodes while holding the radio frequency (rf) potential at a fixed value. Rather than eject at the ß(z) = 1 instability line by ramping the amplitude of the drive rf potential applied to the ring electrode, as with the original mass-selective instability scan, this approach effects ion ejection along the ß(z) = 0 instability line in a process identical in principle (though it varies in its method of implementation) to the previously termed "downscan" ( Todd , J. F. J. ; Penman , A. D. ; Smith , R. D. Int. J. Mass Spectrom. Ion Processes 1991 , 106 , 117 - 135 ). A linear scan of the dc amplitude results in a nonlinear mass scale, unlike the conventional resonance ejection scan with a linear scan of the rf amplitude, and the ejection of ions in the direction of high mass-to-charge (m/z) to low m/z. However, the downscan offers some advantages over the traditional rf scan for ions of high m/z values. These include a larger scannable mass range, as well as the opportunity for improved resolution at high mass. These characteristics are demonstrated with ions of m/z 10(4)-10(5).

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.

Sensitivity and amplitude calibration of a Fourier transform 3D quadrupole ion trap mass spectrometer

With a three-dimensional (3D) quadrupole ion trap running in a Fourier transform operating mode, the detected signal is an image of the collective motion of the confined ions. Consequently, it is assumed that the image signal is the sum of the axial trajectories of the simultaneously confined ions. The resulting frequency spectrum after Fourier transformation comprises frequency peaks at the axial secular frequencies of the confined species according to their mass/charge ratio. With a singly confined species, the maximal amplitude of the image signal is proportional to the amplitude of the secular axial frequency peak. The matrix method is employed to express the axial trajectory sampled at the confinement field period. In that case, the expression of the image signal, as well as its maximal amplitude, is calculated as a function of the trap operating conditions and initial axial positions and axial velocities of the ions. The initial position and velocity distributions are connected to the injection mode. With the steady ion flow injection mode (SIFIM) and an initial phase of the confinement field equal to kπ, the maximal amplitude of the image signal is proportional to either the sum of the initial axial positions or the number of confined ions and the mean value of the initial axial positions. By simulation, amplitude fluctuation of the frequency peak is then calculated for a number of ions ranging between some tens to some thousands of ions injected by SIFIM. The peak amplitude fluctuations induced by the fluctuations of the number of ions are seven times greater than those induced by the fluctuations of the distribution of the initial axial positions.

Note: A simple dual polarity dual nanoelectrospray ionization source for ion/ion reactions

A continuously operated dual polarity dual nanoelectrospray ionization source has been constructed and tested. A commercial quadrupole ion trap mass spectrometer was modified to accumulate and trap ions of opposite charge. All changes to the commercial three-dimensional quadrupole ion trap have been made external to the instrument outside of the vacuum system. Few hardware modifications were required because the two emitters send ion beams through the same transmission guides. Computer controlled source voltage polarities are switched quickly and efficiently to transmit one of two continuously generated ion beams. With customized software, this design has proved simple to implement and to operate.

Development and characterization of an ion trap mass spectrometer for the on-line chemical analysis of atmospheric aerosol particles

A novel Ion Trap Aerosol Mass Spectrometer (IT-AMS) for atmospheric particles has been developed and characterized. With this instrument the chemical composition of the non-refractory component of aerosol particles can be measured quantitatively. The set-up makes use of the well-characterized inlet and vaporization/ionization system of the Aerodyne Aerosol Mass Spectrometer (AMS). While the AMS uses either a linear quadrupole mass filter (Q-AMS) or a time-of-flight mass spectrometer (ToF-AMS) as the mass analyzer, the IT-AMS utilizes a three-dimensional quadrupole ion trap. The main advantages of an ion trap are the possibility of performing MS n-experiments as well as ion/molecule reaction studies. The mass analyzer has been built in-house together with major components of the electronics. The IT-AMS is operated under full PC control and can be used as a field instrument due to its compact size. A detailed description of the set-up is presented. Experiments show that a mass resolving power larger than 1500 can be reached. This value is high enough to separate different organic species at m/ z 43. Calibrations with laboratory-generated aerosol particles indicate a linear relationship between signal response and aerosol mass concentration. These studies, together with estimates of the detection limits for particulate sulfate (0.65 μg/m 3) and nitrate (0.16 μg/m 3) demonstrate the suitability of the IT-AMS to measure atmospheric aerosol particles. An inter-comparison between the IT-AMS and a Q-AMS for nitrate in urban air yields good agreement. For laboratory-generated polystyrene latex particles a MS/MS-study using collision-induced dissociation (CID) with a daughter/parent ion yield of more than 60% has been performed. In the future, similar MS/MS-studies can be conducted for atmospheric particles and for the study of secondary aerosol formation in smog chamber experiments.

Electron transfer ion/ion reactions in a three-dimensional quadrupole ion trap: reactions of doubly and triply protonated peptides with SO2*-.

Ion-ion reactions between a variety of peptide cations (doubly and triply charged) and SO2 anions have been studied in a 3-D quadrupole ion trap, resulting in proton and electron transfer. Electron transfer dissociation (ETD) gives many c- and z-type fragments, resulting in extensive sequence coverage in the case of triply protonated peptides with SO2*-. For triply charged neurotensin, in which a direct comparison can be made between 3-D and linear ion trap results, abundances of ETD fragments relative to one another appear to be similar. Reactions of doubly protonated peptides with SO2*- give much less structural information from ETD than triply protonated peptides. Collision-induced dissociation (CID) of singly charged ions formed in reactions with SO2*- shows a combination of proton and electron transfer products. CID of the singly charged species gives more structural information than ETD of the doubly protonated peptide, but not as much information as ETD of the triply protonated peptide.

Electron capture dissociation of polypeptides in a three-dimensional quadrupole ion trap: Implementation and first results

The adverse influence of the radio frequency (RF) voltage on electrons has been the main obstacle for the implementation of electron capture dissociation (ECD) in three-dimensional quadrupole ion traps (3D QITs). Here we demonstrate that the use of axial magnetic field, together with the injection of low-energy (<5 eV) electrons, in the beginning of the positive RF semi-period achieves trapping of electrons for a period of time comparable with the semi-period duration. Importantly, the energy of the electrons remains low during most of the trapping period. With this technique, which we call "magnetized electrons, in-phase injection" (MEPhI), ECD and other ion-electron reactions have become possible in a 3D QIT. Initial ECD results, including single-scan data, were obtained with dications of Substance P. The observed secondary fragmentation of ECD fragments indicates that the trapped electrons are still somewhat hotter than desired.

Protein and Synthesized Peptide pI Marker Analysis by Capillary Isoelectric Focusing Separation/Mass Spectrometry Using Sonic Spray Ionization.

Protein and synthesized-peptide pI marker analysis by using capillary isoelectric focusing separation/mass spectrometry (CIEF/MS) with a sonic spray ionization (SSI) interface, which has a buffer reservoir between the ion source and the separation capillary, has been demonstrated. Various proteins have often been used as pI markers for CIEF; however, they were unstable, so their pI could be changed from their expected ones. Therefore synthetic peptide pI markers are useful because of their higher stability and purity. However, the m/z of peptide pI markers are in the same range with those of the ions of polymers with a wide range of molecular weights due to ampholytes used for CIEF. As a result, detecting the protonated molecules of the peptide pI markers was difficult. In our work, we have optimized the scanning m/z range of a three-dimensional quadrupole (3DQ) ion-trap mass spectrometer to analyze of peptide pI markers and proteins, respectively, and to scan intensities of two ranges at the same time. Specifically, we separated the scanning range from 300 to 500 and from 700 to 1900. Using this method, carbonic anhydrase II, myoglobin, cytochrome-c, and four peptide pI markers were analyzed simultaneously by using CIEF/MS with an SSI interface, and these proteins were observed with reasonable pI values within the limit of the separation-power of this system.

Ion trap mass spectrometry: a personal perspective

This paper is a personal perspective of the commercial development of the three-dimensional quadrupole ion trap mass spectrometer. Early ion trap invention and development which dates back to 1953, is described. The development of the ion trap is traced through three ages with the last age being where commercial development takes place. Key technical breakthroughs in ion trap technology and commercialization are presented and described up to the present time.

Ion parking during ion/ion reactions in electrodynamic ion traps.

Under appropriate ion density conditions, it is possible to selectively inhibit rates of ion/ion reactions in a quadrupole ion trap via the application of oscillatory voltages to one or more electrodes of the ion trap. The phenomenon is demonstrated using dipolar resonance excitation applied to the end-cap electrodes of a three-dimensional quadrupole ion trap. The application of a resonance excitation voltage tuned to inhibit the ion/ion reaction rate of a specific range of ion mass-to-charge ratios is referred to as "ion parking". The bases for rate inhibition are (i) an increase in the relative velocity of the ion/ion reaction pair, which reduces the cross section for ion/ion capture and, at least in some cases, (ii) reduction in the time of physical overlap of positively charged and negatively charged ion clouds. The efficiency and specificity of the ion parking experiment is highly dependent upon ion densities, trapping conditions, ion charge states, and resonance excitation conditions. The ion parking experiment is illustrated herein along with applications to the concentration of ions originally present over a range of charge states into a selected charge state and in the selection of a particular ion from a set of ions derived from a simple protein mixture.