Resonant excitation in a low-pressure linear ion trap

Square Parametric Excitation: A Digital Resonant Method for the Quadrupole Ion Trap

Digital ion trap technology is an alternate method for driving quadrupole ion traps and mass filters using variable frequency, fixed amplitude RF square waves in place of variable amplitude, fixed frequency RF sine waves. This technique offers some advantages such as an increase in the high mass analysis range by varying frequency and lower overall voltage requirements. Here, we present a complex square waveform developed for resonant parametric excitation in a quadrupole linear ion trap. Unlike traditional resonance methods, the driving RF square wave and auxiliary square wave are coupled using the same digital circuitry without the need for transformer coupling. In this work, we use this complex waveform to selectively excite the first order parametric resonances of ion motion. The square parametric excitation method presented here employs a simple and repetitive circuit design consisting of a low-voltage waveform generator followed by a series of high-voltage MOSFET switches. This design allows for resonance methods to be easily implemented in the all-digital quadrupole. The complex square waveform can perform the same useful functions as sine wave auxiliary signals, such as selective mass elimination and mass isolation. We also demonstrate that the mass resolution performance and S/N of our digital mass spectrometer is improved by applying the complex square waveform during ion ejection.

Ion scanning or ion trapping: Why not both?

The present contribution describes analogies and differences between the quadrupolar ion trap (QIT) and the quadrupole mass analyzers, shows the potentialities of their combination in a single instrument and presents a review of applications of such a technology in different fields. The first section describes the quadrupole mass filter (QMF), outlining its principles of operation and the ion sorting procedure according to the use of oscillating electric fields inducing stable trajectories to the ions allowing them to reach the detector. Multiple quadrupole systems (normally triple quadrupoles) are then explained, showing their use in tandem mass spectrometry in space experiments (MS/MS-in-space). QIT principles of operation are then examined, pointing out that in this case the use of the same combination of oscillating electric fields takes advantage of unstable ion trajectories for their sorting. Substantially, analogies and differences between QMF and QIT come out, which consist in the fact that QMF is a scanning mass analyzer, whereas QIT is a sequential mass analyzer. In addition, the section underlines that QIT is capable to perform tandem mass spectrometry in time experiments (MS/MS-in-time). Later, the possibility to use a quadrupole as a trapping system with a prevailing dimension (linear ion trap [LIT]) is taken into consideration, and the possibility to combine both QMF and LIT in a single instrument, a QTrap mass spectrometer, is illustrated. In this frame, a lot more experiment types are possible with respect to both standalone triple quadrupoles and LIT, and they are described as well. Several combinations of these QTrap features can be used in information dependent acquisition (IDA) mode, allowing the high versatility of this instrumental configuration. The second section deals with a review of applications in different fields. These are organized by kind of QTrap and IDA features and cover different topics in biological, medical, agrochemical, nutritional and environmental fields.

Modelling of a linear ion trap operation in the second stability region

Ion trajectory numerical simulation is used to find the linear ion trap excitation contour in the second stability region. The effects of initial conditions, the ejection Mathieu parameter, scan speed, dipole excitation voltage and gas damping are studied. Modeling shows that in the stability region center the resolution power is ≈ 200 000 (at full width half height of a peak, FWHM) at pressure 0.1 mTorr and 100 % excitation efficiency (not taking into account the space charge).

The Resonant Excitation Process in Commercial Quadrupole Ion Traps Revisited

The collision-induced resonant excitation process in real quadrupole ion traps is revisited theoretically and experimentally by explicitly including in the discussion the influence of higher order potential impurities. This includes mainly the dependence of the secular oscillation frequency f_ion on the ion's oscillation amplitude z_max. Due to frequency calibration, commercial ion traps use excitation frequencies f_exc that are higher than the theoretical secular oscillation frequency f_ion. This may lead to switching in frequency order between f_exc and f_ion that can allow ions to stay longer in on-resonance. It is also found that there is a most efficient but also a harshest excitation frequency, which are not identical. These phenomena are explained and described with a simple harmonic oscillator model and precise numerical calculations, using the trajectory simulation program ITSIM 5.0. Experimental MS² have been performed with the thermometer ion leucine-enkephalin, which are then in line with expectations from the trajectory calculations. The important difference to the existing literature is that, here, overexcitation is characterized by the observed a₄/b₄ fragment-ion ratio, while the fragmentation efficiency was kept constant. By slightly increasing the excitation frequency one can obtain drastically different effective collisional temperatures. This knowledge gives even commercial ion traps, without instrument adjustments, the possibility of producing energetically versatile fragment ion spectra. It is also shown that the damped driven harmonic oscillator cannot be used as a simplified model of the motion during the resonant excitation process in real ion traps.

Measurement of the effective electric field radius on digital ion trap spectrometer

The effective electric field radius is a fundamental parameter of ion traps, and it has a significant influence on ion-trapping capability, signal intensity, mass range and some other properties of the ion trap. For a quadrupole ion trap built with ideal hyperbolic electrodes, its effective electric field radius can be obtained by its geometrical size, while it is very difficult to obtain the effective electric field radius for a non-hyperbolic ion trap. In this study, the effective electric field radius of a linear ion trap and some ceramic rectilinear ion traps (cRITs) were investigated via the digital ion trap technology. The dipole frequency of supplementary AC for excitation was locked at a certain value of the main RF trapping wave, and the characteristic q values for excitation could be determined accordingly. The q values could be further used to calculate the effective electric field radius through theoretical calculations. A linear equation had been fitted between the q values for excitation and the square of period T2 through experiments subsequently. The relative deviation between the measured electric field radius and the simulative electric field radius is less than 2%. The simulation results and experimental validation show that the approach has predictive power for modeling and measuring the effective field radius of non-hyperbolic ion traps. It is certainly significant for further understanding the performances of non-hyperbolic quadrupole systems.

A simulation study of excitation contour of a linear trap with spatial harmonics

The process of nonlinear resonant excitation of ion oscillations in a linear trap is studied. There is still no detailed simulation of the resonance peak in the literature. We propose to use the excitation contour to describe the collective ion resonance. The excitation contour is a resonant mass peak obtained by the trajectory method with the Gaussian distribution of the initial coordinates and velocities. The following factors are considered: excitation time, low order hexapole and octopole harmonics with amplitudes A₃ and A₄, the depth of the initial ion cloud position. These multipoles are used for selective ion ejection from linear ion trap. All these factors affect the ion yield and the shape of the contours. Obtained data can be useful for control of such processes as ion fragmentation, ion isolation, ion activation, and ion ejection. Simulated resonance peaks are important for the theoretical description of the ion collective nonlinear resonances.

Two-dimensional mass spectrometry in a linear ion trap, an in silico model

RATIONALE

Two-dimensional mass spectrometry (2D MS) is a technique that correlates precursor and product ions in a sample without requiring prior ion isolation. Until now, this technique has only been implemented on Fourier transform ion cyclotron resonance mass spectrometers. By coupling 2D MS techniques in linear ion traps (LITs) with a mass analyser with a fast duty cycle (e.g. time-of-flight), data-independent tandem mass spectrometry techniques can be compatible on a liquid chromatography (LC) or gas chromatography (GC) timescale.

METHODS

The feasibility of 2D MS in a LIT is explored using SIMION ion trajectory calculations.

RESULTS

By applying stored waveform inverse Fourier transform techniques for radial excitation on a LIT, the sizes of ion clouds were found to be modulated according to the ions' resonant frequencies in the LIT. By simulating a laser-based fragmentation at the centre of the LIT after the radius modulation step, product ion abundances were found to be modulated according to the resonant frequency of their precursor.

CONCLUSIONS

A 2D mass spectrum could be obtained using the results from the simulation. This in silico model shows the feasibility of 2D MS on a LIT. 2D MS in a LIT allows for tandem mass spectrometry without ion isolation. Copyright © 2017 John Wiley & Sons, Ltd.

Linear ion trap mass selectivity with impulse power supply and sinusoidal dipolar excitation

RATIONALE

An ion trap mass analyzer can be operated by either a sinusoidal waveform power supply or an impulse waveform power supply. The optimal conditions for the performance of ion trap which is driven by an impulse waveform power supply with sinusoidal dipolar voltage were investigated theoretically, and further verified by experiments.

METHODS

The analytical relationship between β and q values is derived theoretically for optimal performance, and the dependencies β(q) for different trapezoidal waveforms are studied. To explain the dependence of resolution with working point q, the derivative dβ/dq is also derived analytically for the case of a rectangular waveform power supply. The theoretical results are further verified by experiments.

RESULTS

The results from both theoretical calculations and experiments are in very good agreement. The behaviour resolution with q is controlled by the dispersion dβ/dq that was also confirmed by experiments, when the resolution increases with q.

CONCLUSIONS

The optimal conditions of β, q_ex values and required excitation time n are when S(q) is close to 1 for an ion trap driven by trapezoidal waveform voltage with sinusoidal dipolar voltage. It shown that with increasing impulse parameter τ the dispersion dβ/dq decreases and the mass resolution also decreases as result. In the case of applying a rectangular waveform shape voltage, the mass selectivity is the same as for the sinusoidal wave shape. Copyright © 2016 John Wiley & Sons, Ltd.

Dipole Excitation: A New Method for Mass Analysis with a Quadrupole Mass Filter

Trajectory calculations are used to investigate peak shapes and ion transmission with a proposed new method of mass analysis with a quadrupole mass filter. Dipole excitation is applied to either the x or the y electrodes, or both, to create bands of instability within the first stability region. With excitation between the y electrodes (near β y  = 0), ions are removed from the low mass side of a peak, and with ion excitation in x (near β x  = 1), ions are removed from the high mass side. The mass resolution can be approximately doubled with comparatively little loss in ion transmission. Ion motion in an ideal quadrupole field and in the field of a quadrupole constructed with round rods has been studied. With an ideal quadrupole field, excitation in y is found to give better peak shape and resolution than excitation in x. With quadrupoles constructed with round rods, excitation in y is found to remove ions from both the low and high mass sides of a peak. The additional higher order multipoles introduced to the quadrupole potential by the use of round rods couple the x motion to the y motion so that exciting the y motion also excites ions in x. Thus, only excitation in y is necessary. Both with an ideal quadrupole field and quadrupoles constructed with round rods, the resolution can be increased ca. ×2 with little loss of transmission. Graphical Abstract ᅟ.

Quantification of emerging micropollutants in an amphipod crustacean by nanoliquid chromatography coupled to mass spectrometry using multiple reaction monitoring cubed mode

An innovative analytical method has been developed to quantify the bioaccumulation in an amphipod crustacean (Gammarus fossarum) of three micropollutants regarded as anthropic-pollution markers: carbamazepine, oxazepam, and testosterone. A liquid-liquid extraction assisted by salts, known as QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) was miniaturised and optimised, so it could be adapted to the low mass samples (approximatively 5mg dry weight). For this same reason and in order to obtain good sensitivity, ultra-trace analyses were carried out by means of nanoliquid chromatography. A preconcentration system by on-column trapping was optimised to increase the injection volume. In order to improve both sensitivity and selectivity, the multiple reaction monitoring cubed mode analyses (MRM(3)) were carried out, validated and compared to the classic MRM. To the best of our knowledge, this is the first time that MRM(3) is coupled to nanoliquid chromatography for the analysis and detection of organic micropollutants <300Da. The optimised extraction method exhibited recoveries superior to 80%. The limits of quantification of the target compounds were 0.3, 0.7 and 4.7ng/g (wet weight) for oxazepam, carbamazepine and testosterone, respectively and the limits of detection were 0.1, 0.3 and 2.2ng/g (wet weight), respectively. The intra- and inter-day precisions were inferior to 7.7% and 10.9%, respectively, for the three levels of concentration tested. The analytical strategy developed allowed to obtain limits of quantification lower than 1ng/g (wet weight) and to establish the kinetic bioconcentration of contaminants within G. fossarum.

Theoretical Study of Dual-Direction Dipolar Excitation of Ions in Linear Ion Traps

The ion enhanced activation and collision-induced dissociation (CID) by simultaneous dipolar excitation of ions in the two radial directions of linear ion trap (LIT) have been recently developed and tested by experiment. In this work, its detailed properties were further studied by theoretical simulation. The effects of some experimental parameters such as the buffer gas pressure, the dipolar excitation signal phases, power amplitudes, and frequencies on the ion trajectory and energy were carefully investigated. The results show that the ion activation energy can be significantly increased by dual-direction excitation using two identical dipolar excitation signals because of the addition of an excitation dimension and the fact that the ion motion radius related to ion kinetic energy can be greater than the field radius. The effects of higher-order field components, such as dodecapole field on the performance of this method are also revealed. They mainly cause ion motion frequency shift as ion motion amplitude increases. Because of the frequency shift, there are different optimized excitation frequencies in different LITs. At the optimized frequency, ion average energy is improved significantly with relatively few ions lost. The results show that this method can be used in different kinds of LITs such as LIT with 4-fold symmetric stretch, linear quadrupole ion trap, and standard hyperbolic LIT, which can significantly increase the ion activation energy and CID efficiency, compared with the conventional method.

Enhancement of Ion Activation and Collision-Induced Dissociation by Simultaneous Dipolar Excitation of Ions in x- and y-Directions in a Linear Ion Trap

Collision-induced dissociation (CID) in linear ion traps is usually performed by applying a dipolar alternating current (AC) signal to one pair of electrodes, which results in ion excitation mainly in one direction. In this paper, we report simulation and experimental studies of the ion excitation in two coordinate directions by applying identical dipolar AC signals to two pairs of electrodes simultaneously. Theoretical analysis and simulation results demonstrate that the ion kinetic energy is higher than that using the conventional CID method. Experimental results show that more activation energy (as determined by the intensity ratio of the a4/b4 fragments from the CID of protonated leucine enkephalin) can be deposited into parent ions in this method. The dissociation rate constant in this method was about 3.8 times higher than that in the conventional method under the same experimental condition, at the Mathieu parameter qu (where u = x, y) value of 0.25. The ion fragmentation efficiency is also significantly improved. Compared with the conventional method, the smaller qu value can be used in this method to obtain the same internal energy deposited into ions. Consequently, the "low mass cut-off" is redeemed and more fragment ions can be detected. This excitation method can be implemented easily without changing any experimental parameters.

Reactions of hydroxyalkyl radicals with cysteinyl peptides in a nanoESI plume

In biological systems, carbon-centered small molecule radicals are primarily formed via external radiation or internal radical reactions. These radical species can react with a variety of biomolecules, most notably nucleic acids, the consequence of which has possible links to gene mutation and cancer. Sulfur-containing peptides and proteins are reactive toward a variety of radical species and many of them behave as radical scavengers. In this study, the reactions between alkyl alcohol carbon-centered radicals (e.g., •CH2OH for methanol) and cysteinyl peptides within a nanoelectrospray ionization (nanoESI) plume were explored. The reaction system involved ultraviolet (UV) irradiation of a nanoESI plume using a low pressure mercury lamp consisting of 185 and 254 nm emission bands. The alkyl alcohol was added as solvent into the nanoESI solution and served as the precursor of hydroxyalkyl radicals upon UV irradiation. The hydroxyalkyl radicals subsequently reacted with cysteinyl peptides either containing a disulfide linkage or free thiol, which led to the formation of peptide-S-hydroxyalkyl product. This radical reaction coupled with subsequent MS/MS was shown to have analytical potential by cleaving intrachain disulfide linked peptides prior to CID to enhance sequence information. Tandem mass spectrometry via collision-induced dissociation (CID), stable isotope labeling, and accurate mass measurement were employed to verify the identities of the reaction products.

Mass selectivity of dipolar resonant excitation in a linear quadrupole ion trap

RATIONALE

For mass analysis, linear quadrupole ion traps operate with dipolar excitation of ions for either axial or radial ejection. There have been comparatively few computer simulations of this process. We introduce a new concept, the excitation contour, S(q), the fraction of the excited ions that reach the trap electrodes when trapped at q values near that corresponding to the excitation frequency.

METHODS

Ion trajectory calculations are used to calculate S(q). Ions are given Gaussian distributions of initial positions in x and y, and thermal initial velocity distributions. To model gas damping, a drag force is added to the equations of motion. The effects of the initial conditions, ejection Mathieu parameter q, scan speed, excitation voltage and collisional damping, are modeled.

RESULTS

We find that, with no buffer gas, the mass resolution is mostly determined by the excitation time and is given by R~dβ/dq qn, where β(q) determines the oscillation frequency, and n is the number of cycles of the trapping radio frequency during the excitation or ejection time. The highest resolution at a given scan speed is reached with the lowest excitation amplitude that gives ejection. The addition of a buffer gas can increase the mass resolution. The simulation results are in broad agreement with experiments.

CONCLUSIONS

The excitation contour, S(q), introduced here, is a useful tool for studying the ejection process. The excitation strength, excitation time and buffer gas pressure interact in a complex way but, when set properly, a mass resolution R0.5 of at least 10,000 can be obtained at a mass-to-charge ratio of 609.

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.

In-source fragmentation technique for the production of thermalized ions

Our electrospray ionization-ion funnel-rf hexapole (ESI-IF-6P) source is designed to produce ions for threshold collision-induced dissociation (TCID) studies in a guided ion beam mass spectrometer. This ion source forms an initial distribution of Ca2+(H2O)x ions where x is 6-9. A new in-source fragmentation technique within the hexapole ion guide of the source is described, which is easy to implement and of modest machining and electrical costs, and is able to generate smaller Ca2+(H2O)x complexes, where x = 2-5. Fragmentation is achieved by biasing an assembly of six 0.25 in. long electrodes that are inserted between the hexapole rods. The assembly is positioned in the high-pressure region of the source such that newly formed Ca2+(H2O)x ions undergo enough collisions to become thermalized, as verified by TCID studies. From the initial distribution of ions, fragmentation proceeds along the lowest energy pathway, which corresponds to sequential water loss for most complexes. However, the Ca2+(H2O) complex cannot be formed using this method because charge separation into CaOH+ and H3O+ becomes the lowest energy pathway from the Ca2+(H2O)2 complex. Therefore, this fragmentation technique can be used to identify the critical size complex for M2+(H2O)x systems, which we define as the complex size (x) at which charge separation becomes a lower energy pathway compared with simple ligand loss.

Off-resonance excitation in a linear ion trap

Off-resonance excitation coupled with mass-selective axial ejection of ions in a linear ion trap is shown to allow coherent control of a trapped ion population. Oscillations of the detected ion current have been found to correspond to the degree of detuning of the excitation field from the resonance frequency. Under appropriate excitation conditions coherent oscillations at the excitation frequency are seen that evolve into the ions' secular frequency on termination of the excitation field. Termination of the excitation field at various points during the off-resonance excitation profile leaves the ions with different degrees of radial excitation. The degree of radial excitation can be controlled by the coherent excitation field and is demonstrated to be useful for collision-induced dissociation.

Fragmentation of singly protonated peptides via interaction with metastable rare gas atoms

The effects of metastable energy level and peptide sequence on the fragmentation patterns of singly charged peptide ions dissociated in collisions with metastable rare gas atoms were studied. Fragmentation spectra of singly charged peptide ions were shown to be more structure-informative and very different from those obtained in low-energy collision-induced dissociation. Unusual odd-electron radical a- and x-ions were observed. Several fragment ions corresponding to a side-chain loss were also observed, which allowed differentiation between leucine and isoleucine. The fragmentation mechanism depends on electronic energy transferred during interaction with metastable gas atoms and proceeds either via Penning ionization with formation of radical odd-electron doubly charged molecular cation or via high-energy excitation of internal degrees of freedom of the peptide cation.

The tripole linear ion trap with highly efficient orthogonal ion ejection designed by computer simulations

An ion guide, consisting of three rods carrying three alternating current (AC) voltages symmetrically delayed, called a tripole, was used as a linear ion trap (LIT) and studied by computer simulations. Radial containment of ions was also demonstrated with the pseudopotential which was calculated by approximating the tripole electric potential to the multipoles expansion. This work found a new analyte concentrator, which performs effective ion ejection, and is suitable for use with time-of-flight mass spectrometry. The efficiency of the overall process from the trapping until the ejection was higher than 90%, although some degree of ion spatial and kinetic energy spread which can be corrected with a reflectron was obtained. The reason for the ejection of this tripole linear ion trap (tLIT) lies in the high space available between the rods. The ejection is optimized with the application of focusing voltages, especially suitable for a tripole symmetry (one electrode has a pulse offset voltage and the other two have a fraction of that pulse). The beam is finally well parallelized with a rectangular Einzel lens.

Quadrupole excitation of ions in linear quadrupole ion traps with added octopole fields

Modeling and experimental studies of quadrupole excitation of ions in linear quadrupole traps with added octopole fields are described. An approximate solution to the equations of motion of ions trapped in a quadrupole with added octopole and dodecapole fields, with quadrupole excitation and damping is given. The solutions give the steady-state or stationary amplitudes of oscillation with different excitation frequencies. Trajectory calculations of the oscillation amplitudes are also presented. The calculations show that there can be large changes in the amplitude of ion oscillation with small changes in excitation frequency, on both the low and high-frequency sides of a resonance. Results of experiments with quadrupole excitation of reserpine ions in linear quadrupole traps with 2.0%, 2.6%, and 4.0% added octopole fields are given. It is found that as the excitation frequency is changed, two resonances are generally observed, which are attributed to the motion in the x and y directions. The two resonances can have quite different intensities. Sudden jumps or sharp sided resonances are not observed, although in some cases asymmetric resonances are seen. The calculated frequency differences between the two resonances are in approximate agreement with the experiments.

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.

Mass analysis in islands of stability with linear quadrupoles with added octopole fields

Mass analysis with linear quadrupole mass filters is possible by forming "islands" in the stability diagram with auxiliary quadrupole excitation. In this work, computer simulations are used to calculate stability boundaries, island positions, and peak shapes and ion transmission for mass analysis with linear quadrupole mass filters that have added octopole fields of about 2 to 4%. Rod sets with exact geometries that have quadrupole and octopole fields only in the potential, and round rod sets, with multipoles up to N = 10 (the twenty pole term) included in the calculations, show the same stability boundaries, island positions, and peak shapes. With the DC voltage applied to the rods so that the Mathieu parameter a < 0, conventional mass analysis is possible without the use of an island. With the DC polarity reversed so that a > 0, the resolution and transmission are poor preventing conventional mass analysis. In principle, mass analysis in an island is possible with operation at either of two tips. Provided the correct island tip is chosen for mass analysis, peak shapes comparable to those with a > 0 and no excitation are possible, both with a > 0 and with a < 0. In the latter case, the use of an island of stability allows mass analysis when the added octopole otherwise prevents conventional mass analysis.

Study of the enhancement of dipolar resonant excitation by linear ion trap simulations

Resolution improvements in dipolar resonant excitation have been examined in a round-rod quadrupolar collision cell for values of the Mathieu characteristic exponent beta equal to n/p, where n and m are small integers (prime beta values) versus other beta values where n and p are not small (ordinary beta values). The trajectories of ions moving in the time-varying electric fields of a quadrupole with and without buffer-gas molecules were calculated to determine the relationship of prime and ordinary beta values to frequency resolution for resonant ion excitation and ejection. For prime beta values, the ion trajectory in the hyperbolic quadrupole field will be exactly periodic with a period of at most 4 pi p/Omega, where Omega is the angular frequency of the main drive radio-frequency (RF) potential. Ion trajectory simulations with prime beta versus ordinary beta values show that the motion of ions with prime beta values have simpler trajectories of shorter periods. Frequency response profiles (FRPs) for round-rod quadrupoles at zero pressure show that dipolar resonant excitations with prime beta values exhibit significantly narrower bandwidths than those with ordinary beta values. Simulations show that at 0.05 to 0.8 mTorr of nitrogen, it is possible to reduce the FRP bandwidth by 20% (measured at 50% depth).

Protein identification using mass spectrometry: a method overview

With the introduction of soft ionization techniques such as Matrix Assisted Laser Desorption Ionization (MALDI), and Electrospray Ionization (ESI), proteins have become accessible to mass spectrometric analyses. Since then, mass spectrometry has become the method of choice for sensitive, reliable and inexpensive protein and peptide identification. With the increasing number of full genome sequences for a variety of organisms and the numerous protein databases constructed thereof, all the tools necessary for the high-throughput protein identification with mass spectrometry are in place. This chapter highlights the different mass spectrometric techniques currently applied in proteome research by giving a brief overview of methods for identification of posttranslational modifications and discussing their suitability of strategies for automated data analysis.

Membrane proteome in Escherichia coli probed by MS3 mass spectrometry: a preliminary report

Characterization of the membrane proteome is particularly intriguing since a better knowledge in this field might lead to new insights into the function of different membrane systems. Despite the biological relevance of surface proteins however, their characterization still remains a challenging task. Outer membrane proteins (OMPs) of Gram-negative bacteria are key molecules that interface the cell with the environment. Hence, surface proteins of Gram-negative bacteria contain proteins that might be good targets for drugs, antimicrobials or detection systems and they may become components of effective vaccines. In this respect, Escherichia coli has been chosen as a model organism for several structural and functional studies aimed at understanding the biophysical and biochemical organization of proteins in Gram-negative cell walls. Here we present first results for the identification of bacterial surface exposed proteins in E. coli K12 based on the use of dansyl chloride labelling coupled with bidimensional tandem mass spectrometry exploiting the advantage of precursor ion/MS3 scan modes. This procedure resulted in a promising, simple, and rapid strategy for the identification of membrane proteins in E. coli as model organism, thus avoiding time-consuming procedures based on two-dimensional liquid chromatography and electrophoresis. The proteins identified could be grouped into five major families: outer membrane (29 proteins), lipoproteins (6 proteins), transmembrane (43 proteins) families.

Linear quadrupoles with added hexapole fields

Linear quadrupoles with added hexapole fields are described. The shifts in ion oscillation frequency caused by the addition of a hexapole field are calculated within the effective potential model. Methods to construct linear quadrupoles with added hexapole fields with exact electrode geometries and with round rods are discussed. A quadrupole with added hexapole field can be constructed with round rods by rotating two rods (say the y rods) towards an x rod. Computer simulations are used to investigate the possibility of mass analysis with quadrupoles with added hexapole fields. We find that a quadrupole with an added hexapole field in the range 2-12% can provide mass analysis provided the dc is applied with the correct polarity and value. When a rod set is constructed with round rods, other multipoles in the potential degrade the peak shape, resolution and transmission. The largest of these after the quadrupole and hexapole are a dipole and octopole term. With round rod sets, the peak shape can be improved by using different diameters for the x and y rod pairs to minimize the octopole term in the potential and by injecting ions at the field center where the dipole term is zero. Calculations of the boundaries of the stability diagram for this case show the boundaries move out, relative to those of a pure quadrupole field, but remain sharp.

Positive ion transmission mode ion/ion reactions in a hybrid linear ion trap

A triple quadrupole mass spectrometer capable of ion trapping experiments has been adapted for ion/ion reaction studies. The instrument is based on a commercially available linear ion trap (LIT) tandem mass spectrometer (i.e., an MDS SCIEX 2000 Q TRAP) that has been modified by mounting an atmospheric sampling glow discharge ionization (ASGDI) source to the side of the vacuum manifold for production of singly charged anions. The ASGDI source is located line of sight to the side of the third quadrupole of the triple quadrupole assembly (Q3). Anions are focused into the side of the rod array (i.e., anion injection occurs orthogonal to the normal ion flight path). A transmission mode method to perform ion/ion reactions has been developed whereby positive ions are transmitted through the pressurized collision quadrupole (Q2) while anions are stored in Q2. The Q2 LIT is used to trap negative ions whereas the Q3 LIT is used to accumulate positive ions transmitted from Q2. Anions are injected to Q3 and transferred to Q2, where they are stored and collisionally cooled. Multiply charged protein/peptide ions, formed by electrospray, are then mass selected by the first quadrupole assembly (Q1) operated in the rf/dc mode and injected into Q2. The positive ions, including the residual precursor ions and the product ions arising from ion/ion proton-transfer reactions, are accumulated in Q3 until they are analyzed via mass-selective axial ejection for mass analysis. The parameters that affect ion/ion reactions are discussed, including pressure, nature of the gas in Q2, and operation of Q2 as a linear accelerator. Ion/ion reactions in this mode can be readily utilized to separate ions with the same m/z but largely different mass and charge, e.g., +1 bradykinin and +16 myoglobin, in the gas phase.

Hybrid triple quadrupole-linear ion trap mass spectrometry in fragmentation mechanism studies: application to structure elucidation of buspirone and one of its metabolites

The use of a hybrid triple quadrupole-linear ion trap (QqQ(LIT)) mass spectrometer system for a comprehensive study of fragmentation mechanisms is described. The anxiolytic drug, buspirone, was chosen as a model compound for this study. With the advent of a QqQ(LIT) instrument, both the traditional quadrupole and the new linear ion trap scans (LIT) could be performed in a single LC run. In the past, a sample had to be run on two different instruments, namely, a triple quadrupole instrument (QqQ) and a 3D ion trap (3D IT) to obtain similar information. With the new QqQ(LIT) technology, collision-induced dissociation (CID) occur in a quadrupole collision cell, q2, and fragment ions are trapped and analyzed in Q3 operated in LIT mode. In this work, high-sensitivity product ion spectra of buspirone were obtained from the one-stage 'Enhanced Product Ion' scan (EPI) with rich product ions and no low mass cut-off. Furthermore, detailed fragmentation pathways were elucidated by further dissociation of each of the fragment ions in the EPI spectrum using MS(3) mode in the same run. The MS(3) scan was performed by incorporating CID in q2, and trapping, cooling, isolation, and resonance-excitation in Q3 when operating in LIT mode. This approach allowed unambiguous assignment of all fragment ions quickly with fewer experiments and easier interpretation than the previous approach. The overall sensitivity for obtaining complete fragment ion data was significantly improved for QqQ(LIT) as compared with that of QqQ and 3D IT mass spectrometers. This is beneficial for structure determination of unknown trace components. The method allowed structure determination of metabolites of buspirone in rat microsomes at 1 microM concentration, which was a 10-fold lower concentration than was needed for QqQ or 3D IT instruments. The QqQ(LIT) instrument provided a simple, rapid, sensitive and powerful approach for structure elucidation of trace components.

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.

Dual linear ion trap/orthogonal acceleration time-of-flight mass spectrometer with improved precursor ion selectivity

A new hybrid mass spectrometer based on dual linear ion traps (LITs) and an orthogonal acceleration time-of-flight mass spectrometer (oaTOF), that can achieve MS(n) analysis and high-mass-accuracy detection with high sensitivity, has been developed. Dual-LIT was necessary because, in a single LIT plus oaTOF combination, the LIT pressure favorable for high precursor selectivity in MS(n) analysis (less than 1 mTorr) was far different from an optimum damping pressure (50-100 mTorr) for efficient connection to the TOF mass spectrometer. A dual-LIT solved this problem of inconsistency of the optimum pressures by using the first LIT for MS(n) analysis and the second LIT for collisional damping. This dual-LIT/TOF instrument achieved high-sensitivity MS(n) analysis with high precursor-ion selectivity.

Mutual storage mode ion/ion reactions in a hybrid linear ion trap

Ion/ion proton transfer reactions involving mutual storage of both ion polarities in a linear ion trap (LIT) that comprises part of a hybrid triple quadrupole/linear ion trap mass spectrometer have been effected. Mutual ion storage in the x- and y-dimensions arises from the normal operation of the oscillating quadrupole field of the quadrupole array, while storage in the z-dimension is enabled by applying unbalanced radio-frequency amplitudes to opposing sets of rods of the array. Efficient trapping (>90%) is achieved for thermalized ions over periods of several seconds. Reactions were demonstrated for multiply charged protein/peptide cations formed by electrospray with anions derived from glow discharge ionization of perfluoro(methyldecalin) (PMD) introduced from the side of the LIT rod array. Doubly and singly charged protein ions are readily formed via ion/ion reactions. The parameters that affect ion/ion reactions are discussed, including the degree of RF unbalance on the LIT rods, vacuum pressure, nature of the buffer gas, reaction time, anion abundance, and the low mass cutoff for ion/ion reaction. The present system has a demonstrated upper mass-to-charge ratio limit of at least 33,000. The system also has high flexibility with respect to defining MS(n) experiments involving both collision-induced dissociation (CID) and ion/ion reactions. Experiments are demonstrated involving beam-type CID in the pressurized collision quadrupole (Q2) followed by ion/ion reactions involving the product ions in the LIT. Ion parking experiments are also demonstrated using the mutual storage ion/ion reaction mode in the LIT, with a parking efficiency over 60%.

Linear ion traps in mass spectrometry

Linear ion traps are finding new applications in many areas of mass spectrometry. In a linear ion trap, ions are confined radially by a two-dimensional (2D) radio frequency (RF) field, and axially by stopping potentials applied to end electrodes. This review focuses on linear ion trap instrumentation. Potentials and ion motion in linear multipole fields and methods of ion trapping, cooling, excitation, and isolation are described. This is followed by a description of various mass discrimination effects that have been reported with linear ion traps. Linear ion traps combined in various ways with three-dimensional (3D) traps, time-of-flight (TOF) mass analyzers, and Fourier transform ion cyclotron resonance mass spectrometers are then given. Linear ion traps can be used as stand alone mass analyzers, and their use for mass analysis by Fourier transforming image currents, by mass selective radial ejection, and by mass selective axial ejection are reviewed.

Establishing low-energy sequential decomposition pathways of leucine enkephalin and its N- and C-terminus fragments using multiple-resonance CID in quadrupolar ion guide

The simultaneous resonant low-energy excitation of leucine enkephalin and its fragment ions was demonstrated in a collision cell of the multipole-quadrupole time-of-flight instrument. Using low-amplitude multiple-resonance excitation CID, we were able to show the exclusive sequential fragmentation of N- and C-terminus fragments all the way to the final fragments--immonium ions of phenylalanine or tyrosine. In this CID mode the single-channel dissociation of each new generation of fragments followed the lowest energy decomposition pathways observable on the time scale of our experiment. Up to six generations of sequential dissociation were carried out in multiple-resonance CID experiments. The direct qualitative comparison of fragmentation of axial-acceleration versus resonant (radial) CID was performed in the same instrument. In both activation methods, fragmentation patterns suggested complex decomposition mechanisms attributable to dynamic competition between sequential and parallel dissociation channels.

Recent trends in mass spectrometer development

Trends in mass analyzer development are reviewed here with an emphasis on tandem mass spectrometers. The move toward "hybridization" of conventional mass analyzers to allow additional instrument functionality in tandem mass spectrometry is discussed.

Excitation of ions by high-harmonic frequency components in Paul and Penning traps and ion guides. I. Selective simultaneous dipolar excitation of high charge states with clipped sinusoidal and non-harmonic waveforms in a linear quadrupole ion guide

This article presents a method for simultaneous excitation of multiple high charge states of a molecular ion in Paul or Penning trap. Using a linear quadrupolar ion guide we validate the method by using a variety of time- domain excitation waveforms with high harmonics of the first charge state's resonant frequency. The proposed way of inducing harmonics is the deliberate distortion of the excitation waveform from its sinusoidal form. In order to facilitate interference of the harmonics, a superposition of two sinusoids different by a frequency factor of two is used. The simplest form of distortion - amplitude restriction - of such waveform produces interference of the harmonics and results in selective excitation of charge states. Multiple protonation states of melittin were used as a model in this study.

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.

Quadrupole mass filters with octopole fields

The performance of quadrupole mass filters with added octopole fields in the range 2.0-4.0% has been investigated. The added fields are much greater than those normally added to conventional rod sets by mechanical tolerances or construction errors. Quadrupole rod sets with added octopole fields were constructed with round rods by making one pair of rods greater in diameter than the other pair. For positive ions, resolution at half height of only about 200 is possible if the negative direct current (dc) output of the quadrupole power supply is connected to the smaller rods. If the positive dc output of the quadrupole power supply is connected to the smaller rods, the resolution improves dramatically; a resolution at half height of 5800 has been observed with a rod set with 2.6% added octopole field. For negative ions the best resolution is obtained with the polarity of the dc reversed, i.e. with the negative dc applied to the smaller rods. These findings are unexpected in view of the literature that argues that to obtain high mass resolution with quadrupole mass filters, higher order multipoles must be kept as small as possible. Numerical simulations of peak shapes agree qualitatively with experiments. Simulation of the boundaries of the first stability region for positive ions shows that when the positive dc is applied to the smaller rods, the addition of a 2.0% octopole field causes the boundaries to shift slightly but the boundaries are well defined, and the tip of the stability region remains sharp. When the positive dc is applied to the larger rods, the boundaries of the stability region move out and become diffuse. For instruments that require a rod set that can be used both as a linear trap and a mass filter, these rod sets may offer improved trap performance while still being capable of providing conventional mass analysis.