For Fourier Transform Ion Cyclotron Resonance Research Articles

Dynamic binning peak detection and assessment of various lipidomics liquid chromatography-mass spectrometry pre-processing platforms

Liquid chromatography-mass spectrometry (LC-MS)-based lipidomics generates large datasets that need to be interpreted using high-performance data pre-processing tools such as XCMS, mzMine, and Progenesis. These pre-processing tools rely heavily on accurate peak detection, which depends on proper setting of the peak detection mass tolerance (PDMT). The PDMT is usually set with a fixed value in either ppm or Da units. However, this fixed value may result in duplicates or missed peak detection and inaccurate peak quantification. To improve the accuracy of peak detection, we developed the dynamic binning method, which considers peak broadening described by the physics of ion separation and sets the PDMT dynamically in function of m/z. In our method, the PDMT is proportional to (mz)2 for Fourier-transform ion cyclotron resonance (FTICR), to (mz)1.5 for Orbitrap and to m/z for Quadrupole time-of-flight (Q-TOF), and is a constant for Quadrupole mass analyzer. The dynamic binning method was implemented in XCMS [1,2], and the adopted source code is available in GitHub at https://github.com/xiaodfeng/DynamicXCMS. We have compared the performance of the XCMS implemented dynamic binning with different popular lipidomics pre-processing tools to find differential compounds. We generated set samples with 43 lipid internal standards that were differentially spiked to aliquots of one human plasma lipid sample using Orbitrap LC-MS/MS. The performance of various pipelines using matched parameter sets was quantified by a quality score system that reflects the ability of a pre-processing pipeline to detect differential peaks spiked at various concentrations. The quality score indicated that our dynamic binning method improves the quantification performance of XCMS (maximum p-value 9.8·10−3 of two-sample Wilcoxon test) over its original implementation. We also showed that the XCMS with dynamic binning found differential spiked-in lipids better or with similar performance as mzMine and Progenesis do.

Positive Ion Electrospray Ionization Suppression in Petroleum and Complex Mixtures

Since the emergence of high resolving power crude oil mass spectrometry two decades ago, hundreds of publications and presentations have detailed petroleum complex mixtures by electrospray ionization (ESI) mass spectrometry (MS). None of these works have reported or detailed ion suppression (also referred to as ionization biasing or matrix effects) which is a well-known feature of ESI. Here, we show the extreme consequences of ionization biasing within a narrow, 1 order of magnitude concentration range for crude oil mixture direct infusion experiments in positive ion (+) ESI. An oil spill contaminant, a crude oil, and an equimolar model compound mixture were electrosprayed at various analyte and acid modifier concentrations for Fourier transform ion cyclotron resonance (FT-ICR) and time-of-flight (TOF) MS analysis. A 3-fold increase in the number of elemental compositions is achieved by optimization of analyte and acid concentration. At high analyte concentration, oxygen heteroatom class (i.e., CcHhOx spe...

Absorption Mode Fourier Transform Electrostatic Linear Ion Trap Mass Spectrometry

In Fourier transform mass spectrometry, it is well-known that plotting the spectrum in absorption mode rather than magnitude mode has several advantages. However, magnitude spectra remain commonplace due to difficulties associated with determining the phase of each frequency at the onset of data acquisition, which is required for generating absorption spectra. The phasing problem for electrostatic traps is much simpler than for Fourier transform ion cyclotron resonance (FTICR) instruments, which greatly simplifies the generation of absorption spectra. Here, we present a simple method for generating absorption spectra from a Fourier transform electrostatic linear ion trap mass spectrometer. The method involves time shifting the data prior to Fourier transformation in order to synchronize the onset of data acquisition with the moment of ion acceleration into the electrostatic trap. Under these conditions, the initial phase of each frequency at the onset of data acquisition is zero. We demonstrate that absorption mode provides a 1.7-fold increase in resolution (full width at half maximum, fwhm) as well as reduced peak tailing. We also discuss methodology that may be applied to unsynchronized data in order to determine the time shift required to generate an absorption spectrum.

Determination of a correction to improve mass measurement accuracy of isotopically unresolved polymerase chain reaction amplicons by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

The experimental determination of average mass by mass spectrometry is limited for large molecules due to the negative bias introduced by the natural distribution of isotopic abundances. This results in the measurement of the top-of-centroid (ToC) as opposed to the true centroid. We have developed a practical correction factor that is applied to the ToC measurement to largely remove the systematic bias introduced by nature. The correction factor is calculated easily using the average molecular mass (<100 kDa) of the analyte molecule and the full-width half maximum resolving power (<3,500) of the measurement. In addition, an approach to calculating resolving power is described that accurately predicts resolving power achievable for Fourier transform ion cyclotron resonance (FT-ICR) mass analysis of large molecules. A combination of internal calibration with a dual-electrospray source and application of the correction factor to average mass measurements improved the mass error from 192.5 to -35.0 ppm for a 44 kDa PCR amplicon.

Frequency shifts due to the interference of resolved peaks in magnitude-mode fourier-transform ion cyclotron resonance mass spectra

We have obtained relationships for frequency shifts resulting from the interference of spectral components for the magnitude mode Fourier transform. The approximation of a weak perturbation of well resolved peaks has been used. Both the low- and high-pressure limits for Fourier-transform ion cyclotron resonance (FTICR) operation have been considered. We have found that the shifts can be either negative or positive, depending on the initial phase and/or the choice of the time-domain interval. The magnitude of shifts generally does not exceed the peak width. In the approximation of small perturbations the shifts produced by multiple peaks are additive. We have compared theoretical results with experimental shifts for isotopic clusters of multiply charged insulin. Up to 1 ppm frequency variations were experimentally observed for the insulin 5+ charge state, consistent with theoretical estimates. The peak interference is of particular significance in the case of bio-molecular mass spectra having a large number of peaks and covering a considerable dynamic range (i.e., relative abundance). We conclude that the common mass measurement procedure based on the location of the magnitude mode maxima of well resolved peaks can result in systematic mass measurement errors. The relationships obtained provide corrections for the frequency shifts and thus improve the mass measurement accuracy.

Dynamically assisted gated trapping for Fourier transform ion cyclotron mass spectrometry.

An efficient approach for trapping ions and enhancing signal based on 'adiabatic amplitude reduction' for Fourier transform ion cyclotron resonance (FTICR) mass spectrometry is described and evaluated. This method is a modification to the widely used gated trapping technique in which the trapping potential is raised adiabatically rather than instantaneously (non-adiabatically). Compared with non-adiabatic gated trapping, the final amplitudes of ion axial oscillations and energies are lower in the proposed method. All performance aspects of the FTICR spectrum (e.g., peak intensities, mass resolution, and mass accuracy) improve significantly compared to the conventional gated trapping technique.

Central ring electrode for trapping and excitation/detection in Fourier transform ion cyclotron resonance mass spectrometry

The use of a central trapping ring electrode for Fourier transform ion cyclotron resonance (FTICR) mass spectrometry is demonstrated. Ions are trapped with an oppositely biased static potential superimposed on both the excite and detect electrodes and maintained throughout the experiment, including the application of a dipolar rf excite waveform and the image current ion detection event. The use of a central trapping electrode for FTICR coupled with an open cell design retains the advantages of high ion throughput and gas conductance, while simplifying the electrode geometry and reducing the overall dimensions of the cell. This allows the central trapping electrode to be of utility in volume-limited vacuum chambers including FTICR instrument miniaturization. Presented here are the preliminary experimental results using the central trapping electrode as an FTICR cell in which the excitation and detection electrodes also create a trapping depression to constrain the z-axis motion of the ions. The cell overcomes the principle limitation of an earlier single trapping electrode design by producing a 91% effective potential well depth compared to 19% for the single trapping electrode and 33% for standard open cells. This allows the central trapping electrode configuration to achieve an order of magnitude improvement in ion capacity compared to more conventional open cell designs.

Linearity and quadrupolarity of tetragonal and cylindrical penning traps of arbitrary length-to-width ratio

The two most popular Penning traps in use for Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry are tetragonal (i. e., orthorhombic with square cross section) and cylindrical. Here we compare tetragonal and cylindrical traps as a function of aspect (length-to-width) ratio and position within the trap, by comparing the numerically computed (from Simion 6.0) electric potential field of a given trap relative to each of three idealized potentials required for FT-ICR experiments: dipolar one-dimensional potential for alternating current (ac) excitation/detection of cyclotron motion, azimuthal two-dimensional quadrupolar potential for ac excitation for ion axialization, and axial three-dimensional quadrupolar potential for direct current axial confinement of ions. Our numerically computed results agree well with those previously derived analytically. The numerical approach provides a simpler and more accessible means for analyzing the aforementioned potentials. Moreover, the numerical approach (unlike the analytical approach) readily extends to traps of lower symmetry. Finally, even when analytical solutions are available, the numerical method presented here is complementary, since it provides a useful check on the validity of the derived equations.

Sharing a Pair of Electrodes between Excitation and Detection in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

Time-sharing of electrodes between excitation and detection for Fourier transform (FT) study of the coherent cyclotron motion of ions is discussed, together with the choice of a suitable commutation device. A practical implementation is described, and the application to an open-end, flat, ion cyclotron resonance cell presented. In addition, the switching technique described is useful to minimise ion losses due to resistive damping at the magnetron frequencies, and could also be used in conventional FT ion cyclotron resonance cells for quadrupolar excitation and detection, and for ion axialization.

Multiply pulsed collision gas for ion axialization in Fourier-transform ion cyclotron resonance mass spectrometry.

We present a new multiply pulsed collision-gas technique for ion axialization for Fourier-transform ion cyclotron resonance (FTICR) high-resolution mass analysis. Ions are axialized in the source trap of a dual-trap FTICR spectrometer by azimuthal quadrupolar irradiation for several tens of seconds at a steady-state pressure maintained by repeated pulses of collision gas (argon), followed by removal of the collision gas and detection at a much lower pressure after transfer to the analyzer trap. Magnitude-mode FTICR mass resolving power, m/delta m approximately 1,770,000, for [M+K]+ ions from laser-desorbed/ionized leucine enkephalin at m/z 594 is demonstrated. This mass resolving power is the highest yet reported for a peptide with any type of laser desorption/ionization mass analyzer.

Quadrupolar excitation and collisional cooling for axialization and high pressure trapping of ions in Fourier transform ion cyclotron resonance mass spectrometry

A recently developed technique for axialization of ions in a Penning (i.e. hyperbolic) trap has been adapted for Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry in a dual cubic trap instrument. A resonant alternating electric azimuthal quadrupolar field at the combination frequency, ω c = ω + + ω −, converts ion magnetron motion into collision-damped cyclotron motion. The usual collision- induced drift of ions from the center of the trap under the influence of the radially outward-directed electric force of the trapping field is thereby effectively inverted, so that ions with off-axis ICR orbit centers may be driven back to on-axis low radius ion cyclotron orbits. This effect is frequency-dependent and therefore mass-selective. The experiment requires only minor wiring modifications to an existing cubic, tetragonal, or cylindrical ICR ion trap. With this technique, we have been able to store benzene molecular ions for several seconds at high pressure (> 1 x 10 −5 mbar) in one half of a dual trap, as demonstrated by subsequent transfer of these ions to the other half of the dual trap for ICR excitation and detection. We also report simultaneous axialization and extended trapping of ions of different mass-to-charge ratios by use of multiple-frequency stored-waveform inverse Fourier transform excitation. Proposed applications include axialization and cooling for improved detection of product ions in MSMS experiments, ion trapping at high pressure for extended periods for measurement of slow ion/molecule reaction rates, and increased sensitivity for detection of externally injected ions.

Quadrupole-detection FT-ICR mass spectrometry

A new detection scheme for Fourier transform-ion cyclotron resonance (FT-ICR) studies is proposed and initial experimental results are presented. While in conventional FT-ICR the difference of the transient signals from two opposite electrodes yields a signal at the reduced cyclotron frequency v +, which depends on the applied trapping voltage and space charge, it is also possible to use the difference of the sum of these signals and the sum of a similar set of electrodes perpendicular to the first. In this way resonances are observed at the harmonic of the reduced cyclotron frequency, 2· ν +, as well as at ( v + + v -). The latter is interesting in respect of accurate mass measurements, since ( v + + v -) does not depend on the trapping voltage.

Parametric-mode-excitation/dipole-mode-detection Fourier-transform–ion-cyclotron-resonance spectrometry

A new excitation/detection scheme for Fourier-transform–ion-cyclotron-resonance (FT-ICR) studies is described. The ions are created in the center of a hyperbolic Penning trap and excited to a large magnetron radius. Parametric-mode excitation is used to drive the cyclotron motion. The ions are detected in the conventional dipole-mode detection scheme by use of a segmented ring electrode. Since the resonance frequencies of excitation (ν+−ν−) and detection (ν+, the reduced cyclotron frequency) differ by the magnetron frequency (ν−), this method allows the simultaneous excitation and detection of the ion motion.

フーリエ変換イオンサイクロトロン共鳴分析におけるイオンの選択的励起

Recent progress in electronics has made it possible for us to utilize commercial instruments in building an excitation and data sampling system for Fourier transform ion cyclotron resonance (FT-ICR) spectrometry.An arbitrary waveform generator was used to excite mass-selected ions trapped in an FT-ICR cell and a digital oscilloscope was used to sample and process signals of resonant ions. Excitation waveforms were synthesized from sinusoidal waves of specific frequencies to excite the ions of various mass-to-charge ratios. Simultaneous excitation/ejection experiment was performed by varying amplitude of each frequency component in the excitation waveform. The arbitrary waveform generator has been proved to be useful for SWIFT (stored waveform inverse Fourier transform) experiment as an interface between the computer and the FT-ICR spectrometer.

A new detection scheme for Fourier transform-ion cyclotron resonance spectrometry in Penning traps

A new detection scheme for Fourier transform-ion cyclotron resonance (FT-ICR) studies is proposed and initial experimental results are presented. While in conventional FT-ICR, the difference of the transient signals from two opposite electrodes is recorded and Fourier transformed, it is also possible to use the sum of these signals. In this way resonances are observed at the harmonic of the reduced cyclotron frequency 2 ν+ as well as ν+−ν− and ν++ν−, the later being important for accurate mass measurements. The experiments were performed with a Penning trap in an electromagnet.

A "screened" electrostatic ion trap for enhanced mass resolution, mass accuracy, reproducibility, and upper mass limit in Fourier transform ion cyclotron resonance mass spectrometry.

Until now, it was thought that the optimal static electromagnetic ion trap for Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry should be designed to produce a quadrupolar electrical potential, for which the ion cyclotron frequency is independent of the ion's preexcitation location within the trap. However, a quadrupolar potential results in a transverse (to the magnetic field) electric field that increases linearly with distance from the center of the trap. That radially linear electric field shifts the observed ICR frequency, increases the ICR orbital radius, and ultimately limits the highest mass-to-charge ratio ion that can be contained within the trap. In this paper, we propose a new static electromagnetic ion "trap" in which grounded screens placed just inside the usual "trapping" plates produce a good approximation to a "particle-in-a-box" potential (rather than the quadrupolar "harmonic oscillator" potential). SIMION calculations confirm that the electric potential of the screened trap is near zero almost everywhere within the trap. For our screened orthorhombic (2.5 in. X 2 in. X 2 in.) trap, the experimental ICR frequency shift due to trapping voltage is reduced by a factor of approximately 100, and the experimental variation of ICR frequency with ICR radius is reduced by a factor of approximately 10 compared to a conventional (unscreened) 2-in. cubic ion trap.(ABSTRACT TRUNCATED AT 250 WORDS)

マイクロコンピュータを用いたフーリエ変換イオンサイクロトロン共鳴（ＦＴ‐ＩＣＲ）質量分析計のデータ処理システム

This paper reports a microcomputer based data acquisition system for Fourier transform ion cyclotron resonance (FT-ICR) mass spectroscopy. The system has been developed for a prototype spectrometer constructed with a permanent magnet whose magnetic field strength is 6,200 gauss. The system cosists of two-channel sampling ports with sample-hold circuits, a multiplexer, an A-D converter, an I/O port and a logic circuit. The logic circuit starts data acquisition synchronizing with an external trigger pulse. The acquisition is then repeated for preset number of times to accumulate data for signal averaging. An operating program for the system was written in an assembly language in order to execute high-speed data acquisition and a program for FT-ICR experiments was written using BASIC. Resolution of 40,000 was obtained with CO+ ion in residual gas.

Detection theory of ion cyclotron resonance phenomena

A formalism describing the signal voltage induced by charged particles in ion cyclotron resonance detector circuits is developed from first principles. Two detector circuits, one for Fourier-transform ion cyclotron resonance (FT-ICR) and the other a marginal oscillator detector, are analyzed. Signal and noise characteristics are discussed in relation to circuit parameters of the FT-ICR detector. The signal voltage obtained for the marginal oscillator from the present theory is compared with that from tile usual ldequivalent parallel resistance modelrd and the treatments are shown to be consistent.

Relaxation and spectral line shape in Fourier transform ion resonance spectroscopy

Analytical expressions for Fourier transform ion cyclotron resonance (FT-ICR) line shape [absorption mode, dispersion mode, and magnitude (absolute value) mode] are derived for coherently excited ions that undergo both reactive and nonreactive ion–molecule collisions. The expressions are valid at arbitrary sample pressure, and reduce to particularly simple form in the ’’zero-pressure’’ limit (essentially no ion–molecule collisions during the data acquisition period) or ’’high-pressure’’ limit (many ion–molecule collisions during the data acquisition period). The zero-pressure line shape has been analyzed in earlier papers; in this paper, various useful properties of the high-pressure line shape (e.g., linewidth, mass resolution, and upper mass limit) are tabulated for various choices of the fraction of maximal absorption (or magnitude) peak height at which linewidth is to be measured. Absorption, dispersion, and magnitude spectra are plotted for zero-pressure and high-pressure limits, and also for an intermediate pressure. Convenient reference graphs of high-pressure FT-ICR linewidth, mass resolution, and upper mass limit as functions of ionic mass and time-domain ICR half-life for singly charged ions at magnetic field strength of 2 T are included. Finally, the intermediate-pressure resolution is calculated as a function of acquisition period at fixed pressure, to shown that near-optimal mass resolution (to within 90% of maximal absorption-mode resolution, or 95% of maximal magnitude-mode resolution) is achieved by truncating the FT-ICR time-domain signal after just three relaxation times. The particularly simple trade-off between signal-to-noise ratio and mass resolution in FT-ICR spectroscopy is noted and explained. Good agreement between experimental and theoretical line shape (and thus mass resolution) is demonstrated.