Image charge-induced ion cyclotron orbital frequency shift for orthorhombic and cylindrical FT-ICR ion traps

Experimental and Theoretical Brownian Dynamics Analysis of Ion Transport During Cellular Electroporation of E. coli Bacteria

Escherichia coli bacterium is a rod-shaped organism composed of a complex double membrane structure. Knowledge of electric field driven ion transport through both membranes and the evolution of their induced permeabilization has important applications in biomedical engineering, delivery of genes and antibacterial agents. However, few studies have been conducted on Gram-negative bacteria in this regard considering the contribution of all ion types. To address this gap in knowledge, we have developed a deterministic and stochastic Brownian dynamics model to simulate in 3D space the motion of ions through pores formed in the plasma membranes of E. coli cells during electroporation. The diffusion coefficient, mobility, and translation time of Ca2+, Mg2+, Na+, K+, and Cl- ions within the pore region are estimated from the numerical model. Calculations of pore's conductance have been validated with experiments conducted at Gustave Roussy. From the simulations, it was found that the main driving force of ionic uptake during the pulse is the one due to the externally applied electric field. The results from this work provide a better understanding of ion transport during electroporation, aiding in the design of electrical pulses for maximizing ion throughput, primarily for application in cancer treatment.

Dynamic Energy Measurements in Charge Detection Mass Spectrometry Eliminate Adverse Effects of Ion-Ion Interactions

Ion-ion interactions in charge detection mass spectrometers that use electrostatic traps to measure masses of individual ions have not been reported previously, although ion trajectory simulations have shown that these types of interactions affect ion energies and thereby degrade measurement performance. Here, examples of interactions between simultaneously trapped ions that have masses ranging from ca. 2 to 350 MDa and ca. 100 to 1000 charges are studied in detail using a dynamic measurement method that makes it possible to track the evolution of the mass, charge, and energy of individual ions over their trapping lifetimes. Signals from ions that have similar oscillation frequencies can have overlapping spectral leakage artifacts that result in slightly increased uncertainties in the mass determination, but these effects can be mitigated by the careful choice of parameters used in the short-time Fourier transform analysis. Energy transfers between physically interacting ions are also observed and quantified with individual ion energy measurement resolution as high as ∼950. The mass and charge of interacting ions do not change, and their corresponding measurement uncertainties are equivalent to ions that do not undergo physical interactions. Simultaneous trapping of multiple ions in CDMS can greatly decrease the acquisition time necessary to accumulate a statistically meaningful number of individual ion measurements. These results demonstrate that while ion-ion interactions can occur when multiple ions are trapped, they have negligible effects on mass accuracy when using the dynamic measurement method.

Improved Dynamic Range, Resolving Power, and Sensitivity Achievable with FT-ICR Mass Spectrometry at 21 T Reveals the Hidden Complexity of Natural Organic Matter

Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS) is the only mass analyzer that can resolve the molecular complexity of natural organic matter at the level of elemental composition assignment. Here, we leverage the high dynamic range, resolving power, resistance to peak coalescence, and maximum ion number and ion trapping duration in a custom built, 21 tesla hybrid linear ion trap /FT-ICR mass spectrometer for a dissolved organic matter standard (Suwanne River Fulvic Acid). We compare the effect of peak-picking threshold (3σ, 4σ, 5σ, and 6σ) on number of elemental composition assignments, mass measurement accuracy, and dynamic range for a 6.3 s transient across the mass range of m/z 200-1200 that comprises the highest achieved resolving power broadband FT-ICR mass spectrum collected to date. More than 36 000 species are assigned with signal magnitude greater than 3σ at root-mean-square mass error of 36 ppb, the most species identified reported to date for dissolved organic matter. We identify ¹⁸O and ¹⁷O isotopologues and resolve isobaric overlaps on the order of a few electrons across a wide mass range (up to m/z 1000) leveraging mass resolving powers (3 000 000 at m/z 200) only achievable by 21 T FT-ICR MS and increased by ∼30% through absorption mode data processing. Elemental compositions unique to the 3σ span a wide compositional range of aromaticity not detected at higher peak-picking thresholds. Furthermore, we leverage the high dynamic range at 21 T FT-ICR MS to provide a molecular catalogue of a widely utilized reference standard (SRFA) to the analytical community collected on the highest performing mass analyzer for complex mixture analysis to date. This instrument is available free of charge to scientists worldwide.

Ultra-High Mass Resolving Power, Mass Accuracy, and Dynamic Range MALDI Mass Spectrometry Imaging by 21-T FT-ICR MS

Detailed characterization of complex biological surfaces by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) requires instrumentation that is capable of high mass resolving power, mass accuracy, and dynamic range. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers the highest mass spectral performance for MALDI MSI experiments, and often reveals molecular features that are unresolved on lower performance instrumentation. Higher magnetic field strength improves all performance characteristics of FT-ICR; mass resolving power improves linearly, while mass accuracy and dynamic range improve quadratically with magnetic field strength. Here, MALDI MSI at 21T is demonstrated for the first time: mass resolving power in excess of 1 600 000 (at m/z 400), root-mean-square mass measurement accuracy below 100 ppb, and dynamic range per pixel over 500:1 were obtained from the direct analysis of biological tissue sections. Molecular features with m/z differences as small as 1.79 mDa were resolved and identified with high mass accuracy. These features allow for the separation and identification of lipids to the underlying structures of tissues. The unique molecular detail, accuracy, sensitivity, and dynamic range combined in a 21T MALDI FT-ICR MSI experiment enable researchers to visualize molecular structures in complex tissues that have remained hidden until now. The instrument described allows for future innovative, such as high-end studies to unravel the complexity of biological, geological, and engineered organic material surfaces with an unsurpassed detail.

Producing absorption mode Fourier transform ion cyclotron resonance mass spectra with non-quadratic phase correction functions

RATIONALE

Previously described methods for producing absorption mode Fourier transform ion cyclotron resonance (FTICR) mass spectra have all relied on the phase correction function being quadratic. This assumption has been found to be invalid for some instruments and spectra and so it has not been possible to produce absorption mode spectra for these cases.

METHODS

The Autophaser algorithm has been adapted to allow nth order polynomial phase correction functions to be optimized. The data was collected on a modified Thermo LTQ FTICR mass spectrometer, using electrospray ionization and a novel ICR cell design (NADEL). Peak assignment and mass calibration were undertaken using the pyFTMS framework.

RESULTS

An nth-order phase correction function has been used to produce an absorption mode mass spectrum of the maltene fraction of a crude oil sample which was not possible using the previous assumption that the phase correction function must be quadratic. Data processing for this spectrum in absorption mode has shown the expected benefits in terms of increasing the number of assigned peaks and also improving the mass accuracy (i.e. confidence) of the assignments.

CONCLUSIONS

It is possible to phase-correct time-domain data in FTICRMS to yield absorption mode mass spectra representation even when the data does not correspond to the theoretical quadratic phase correction function predicted by previous studies. This will allow a larger proportion of spectra to be processed in absorption mode.

Data processing in Fourier transform ion cyclotron resonance mass spectrometry

The Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer intricately couples advanced physics, instrumentation, and electronics with chemical and particularly biochemical research. However, general understanding of the data processing methodologies used lags instrumentation, and most data processing algorithms we are familiar with in FT-ICR are not well studied; thus, professional skill and training in FT-ICR operation and data analysis is still the key to achieve high performance in FT-ICR. This review article is focused on FT-ICR data processing, and explains the procedures step-by-step for users with the goal of maximizing spectral features, such as mass accuracy, resolving power, dynamic range, and detection limits.

Improved optimization of the Fourier transform ion cyclotron resonance mass spectrometry phase correction function using a genetic algorithm

RATIONALE

Fourier Transform Ion Cyclotron Resonance mass spectra exhibit improved resolving power, mass accuracy and signal-to-noise ratio when presented in absorption mode; a process which requires calculation of a phase correction function. Mass spectrometric images can contain many thousands of pixels; hence methods of decreasing the time required to solve for a phase correction function will result in significant improvements in this application.

METHODS

A genetic algorithm approach for optimizing the phase correction function has been developed and compared with a previously described convergent iteration technique.

RESULTS

The genetic algorithm method has been shown to offer a five-fold improvement in processing speed compared with the previous iterative approach used in the Autophaser algorithm, while maintaining the levels of accuracy. This translates to an 11 hour improvement in processing for a 20 000 pixel mass spectrometric image.

CONCLUSIONS

The genetic algorithm method described in this manuscript offers significant processing speed advantages over the previously described convergent iteration technique. This improvement is key to allowing the future routine use of absorption mode mass spectrometric images.

Autophaser: an algorithm for automated generation of absorption mode spectra for FT-ICR MS

Phase correction of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry data allows the spectra to be presented in absorption mode. Absorption mode spectra offer superior mass resolving power (up to a factor of 2), mass accuracy, and sensitivity over the conventional magnitude mode. Hitherto, the use of absorption mode in FT-ICR mass spectrometry has required either specially adapted instrumentation or a manually intensive process of phase correction or has ignored the potentially significant effects of image charge and the associated frequency shifts. Here we present an algorithm that allows spectra recorded on unadapted FT-ICR mass spectrometers to be phase corrected, their baseline deviations removed, and then an absorption mode spectrum presented in an automated manner that requires little user interaction.

Comparison of particle-in-cell simulations with experimentally observed frequency shifts between ions of the same mass-to-charge in Fourier transform ion cyclotron resonance mass spectrometry

It has been previously observed that the measured frequency of ions in a Fourier transform mass spectrometry experiment depend upon the number of trapped ions, even for populations consisting exclusively of a single mass-to-charge. Since ions of the same mass-to-charge are thought not to exert a space-charge effect among themselves, the experimental observation of such frequency shifts raises questions about their origin. To determine the source of such experimentally observed frequency shifts, multiparticle ion trajectory simulations have been conducted on monoisotopic populations of Cs(+) ranging from 10(2) ions to 10(6) ions. A close match to experimental behavior is observed. By probing the effect of ion number and orbital radius on the shift in the cyclotron frequency, it is shown that for a monoisotopic population of ions, the frequency shift is caused by the interaction of ions with their image-charge. The addition of ions of a second mass-to-charge to the simulation allows the comparison of the magnitude of the frequency shift resulting from space-charge (ion-ion) effects versus ion interactions with their image charge.

The spontaneous loss of coherence catastrophe in Fourier transform ion cyclotron resonance mass spectrometry

The spontaneous loss of coherence catastrophe (SLCC) is a frequently observed, yet poorly studied, space-charge related effect in Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS). This manuscript presents an application of the filter diagonalization method (FDM) in the analysis of this phenomenon. The temporal frequency behavior reproduced by frequency shift analysis using the FDM shows the complex nature of the SLCC, which can be explained by a combination of factors occurring concurrently, governed by electrostatics and ion packet trajectories inside the ICR cell.

Effect of post-excitation radius on ion abundance, mass measurement accuracy, and isotopic distributions in Fourier transform ion cyclotron resonance mass spectrometry

We report an evaluation of a modern Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) instrument to determine the general trend of post-excitation radius on total ion abundance, mass measurement accuracy, and isotopic distributions for internally calibrated mass spectra. The optimum post-excitation radius was determined using total ion abundance, mass measurement accuracy (MMA), and isotope ratios. However, despite the utility of internal calibration for achieving ultimate MMA, the internal calibrant ions were insufficient for compensating for sub-optimum ICR cell conditions. The findings presented herein underscore the importance of determining the optimal post-excitation radius in FT-ICR-MS to achieve high ion abundance (low limits of detection), high MMA, and valid isotopic distributions.

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.

Mass measurement errors caused by 'local" frequency perturbations in FTICR mass spectrometry

One of the key qualities of mass spectrometric measurements for biomolecules is the mass measurement accuracy (MMA) obtained. FTICR presently provides the highest MMA over a broad m/z range. However, due to space charge effects, the achievable MMA crucially depends on the number of ions trapped in the ICR cell for a measurement. Thus, beyond some point, as the effective sensitivity and dynamic range of a measurement increase, MMA tends to decrease. While analyzing deviations from the commonly used calibration law in FTICR we have found systematic errors which are not accounted for by a "global" space charge correction approach. The analysis of these errors and their dependence on charge population and post-excite radius have led us to conclude that each ion cloud experiences a different interaction with other ion clouds. We propose a novel calibration function which is shown to provide an improvement in MMA for all the spectra studied.

Fourier transform mass spectrometry-advancing years (1992-mid. 1996)

This article is one of a series of Fourier transform mass spectrometry (FTMS) reviews that has appeared in this journal at ca. 3-4 year intervals. A comprehensive review of the recent theoretical developments, instrumental developments, electrospray ionization (ESI), and MALDI is given. Ion dissociation techniques are also discussed because of their contributions to gaining insight into chemical structure. Special sections have been devoted to discussing the emerging fields of surface analysis, polymer analysis, Buckminsterfullerenes (buckyballs), and hydrogen/deuterium exchange studies. This review, although not all-inclusive, is intended to be a starting point for those wishing to learn more about the current status of FTMS, and also as a representative cross-section of the literature for those familiar with the technique. © 1997 John Wiley & Sons, Inc.

Analysis and elimination of systematic errors originating from coulomb mutual interaction and image charge in Fourier transform ion cyclotron resonance precise mass difference measurements

The effect of mutual Coulomb-mediated interactions between ions of two different mass-to-charge ratios (but equal ion cyclotron orbital radii) on their Fourier transform ion cyclotron resonance (FT/ICR) mass spectral frequency difference is derived analytically and measured experimentally. For a cylindrical ion trap, ion packets are modeled theoretically as infinitely extended lines of charge, and contributions to cyclotron frequency difference due to direct Coulomb repulsion between the lime charges as well as the forces arising from image charge induced on the trap electrodes by each line charge are calculated. A striking theoretical prediction is that the effect on ICR frequency difference of mutual Coulomb repulsion between ions in a mass doublet may be compensated by the image-charge effect. As a result, there is an optimal (calculable) ion cyclotron orbital radius at which the measured cyclotron orbital frequency difference between ions of two different mass-to-charge ratios is independent of mutual Coulomb-mediated interactions between the two components of the mass doublet! Moreover, if the two mass-doublet component ions are present in equal numbers, then the measured ion cyclotron orbital frequency difference is also independent of all Coulomb-mediated interactions between the two types of ions! Thus, the single largest systematic error in measurement of mass difference in a mass doublet by FT/ICR mass spectrometry may be virtually eliminated by appropriate control of ICR orbital radius and/or by performing measurements at various relative abundance ratios and extrapolating to equal relative abundance of the two mass-doublet components. We report experimental tests and verification of these predictions for two different mass doublets: (3)He(+)/(3)H(+) (cylindrical trap at 4.7 Tesla) and (12)C(1)H 2 (+) /(14) N(+) (cubic trap at 7.0 Tesla). From the latter measurement, we determine the mass of atomic nitrogen as m((14)N)=14.003 074 014(19) u.