Multiparticle Simulations of Quadrupolar Ion Detection in an Ion Cyclotron Resonance Cell with Four Narrow Aperture Detection Electrodes.

The current paradigm in FT-ICR cell design is to approximate the ideal three-dimensional quadratic trapping potential as closely as possible to maintain ion cloud spatial coherence and achieve long transients, either with hyperbolically shaped electrodes, shimming electrodes, or by dynamic harmonization. In sharp contrast, the FT-ICR analyzer cell with four narrow aperture detection electrodes (NADEL) introduces significant anharmonic terms to the trapping potential. This analyzer cell is capable of quadrupolar detection by which one can measure a signal that is close to the unperturbed cyclotron frequency. This is far less sensitive to trapping potential and space charge shifts than the reduced cyclotron frequency measured in conventional ICR cells. The quadrupolar mode of ion detection in NADEL cells has been examined previously by SIMION simulations of ion clouds with up to 500 ions per simulation. Here, the behavior of the NADEL analyzer cell is examined through particle-in-cell (PIC) simulations, which allows us to examine the behavior of large populations (tens of thousands) of ions with space charge considerations, and to calculate the induced charge on the NADEL detection electrodes, and thus the transient signal. PIC simulations confirm a unique spatial distribution of the ions, with a coherent motion that results in long transient signals. Dependence of the ion cloud and image current signal on cell design, ion energy, and magnetron radius are examined. Coalescence effects are compared with those found in a dynamically harmonized cell. The insensitivity of the measured cyclotron frequency to space-charge is demonstrated both with simulations and experimentally. Graphical Abstract ᅟ.

Advanced mass calibration and visualization for FT-ICR mass spectrometry imaging.

Mass spectrometry imaging by Fourier transform ion cyclotron resonance (FT-ICR) yields hundreds of unique peaks, many of which cannot be resolved by lower performance mass spectrometers. The high mass accuracy and high mass resolving power allow confident identification of small molecules and lipids directly from biological tissue sections. Here, calibration strategies for FT-ICR MS imaging were investigated. Sub-parts-per-million mass accuracy is demonstrated over an entire tissue section. Ion abundance fluctuations are corrected by addition of total and relative ion abundances for a root-mean-square error of 0.158 ppm on 16,764 peaks. A new approach for visualization of FT-ICR MS imaging data at high resolution is presented. The "Mosaic Datacube" provides a flexible means to visualize the entire mass range at a mass spectral bin width of 0.001 Da. The high resolution Mosaic Datacube resolves spectral features not visible at lower bin widths, while retaining the high mass accuracy from the calibration methods discussed.

Performance of Orbitrap mass analyzer at various space charge and non-ideal field conditions: simulation approach.

The orbital trap mass analyzer provides a number of unique analytical features along with inevitable limitations as an electrostatic instrument operating in high space charge regimes resulting in systematic measured frequency errors as an effect of stored ion clouds on the trap field and each other effect of non-ideal machining the trap electrodes, effect of injection slot, effect of real versus theoretical trap dimensions, etc. This paper deals with determining the influence of the space charge effect and imperfection of the electrostatic field on the motion of ion ensembles in the orbital trap. We examine effects of theoretically modeled non-harmonicity of the electrostatic potential and the number of confined ions on stability of coherent ion motion in the trap that determines the frequency shifts of axial ion oscillation. Three different Orbitrap geometries were considered: geometry close to preproduction Orbitrap, close to standard Orbitrap, close to high field Orbitrap. Frequency shifts for m/z = 500 and for charge state +23 of cytochrome c isotopic cluster particles with 10(4)-6*10(6) elemental charges in the trap were considered. Refined spectra were calculated using the filter diagonalization method proposed by Mandelshtam et al. and applied to mass spectrometry by O'Connor and Aizikov.

C60+ secondary ion microscopy using a delay line detector.

Buckminsterfullerene (C(60)) as a primary ion for secondary ion mass spectrometry (SIMS) has shown many benefits over classical SIMS sources in the analysis of large organic molecules including many of biological significance. One constraint has been the limited focusing capabilities of the C(60)(+) beam. Although this could be circumvented by using beam size limiting apertures at the cost of beam current, high-resolution imaging using conventional time-of-flight (TOF) instruments has been challenging and time-consuming. We present a method in which we combine the use of an unfocused C(60)(+) beam with an ion optical microscope. A delay line detector is used to obtain fully resolved hyperspectral data sets that contain both the full mass spectral and the localization information. The obtained image resolving power is 4 microm at a pixel size of 250 nm. Microscope mode C(60)(+) imaging was shown to resolve micrometer-scale features in a combined polymer-tissue sample. Our new approach demonstrates high-quality SIMS imaging using the full C(60)(+) beam current. This results in equal or better resolving power at reduced acquisition speed.

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.