Autophaser: An Algorithm for Automated Generation of Absorption Mode Spectra for FT-ICR MS

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Abstract. Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules.

Section: Control Mass Spectra and Product-ion Spectramentioning

confidence: 99%

Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Agthoven

Barrow

Chiron³

et al. 2015

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“…We have used ECD datasets to test the algorithm because ECD is well known to be an inefficient fragmentation process, which results in complex spectra characterized by signals of low S/N, ideal to test the utility of the algorithm. The spectrum was processed to absorption mode using the Autophaser method, applying a full apodization (F = 0.5) to generate a baseline deviation-free mass spectrum [20][21][22][23]. The superimposed isotopic distribution for the fragment was generated using the method described previously [24].…”

Section: Resultsmentioning

confidence: 99%

Autopiquer - a Robust and Reliable Peak Detection Algorithm for Mass Spectrometry

Kilgour

Hughes

Kilgour

et al. 2016

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Abstract. We present a simple algorithm for robust and unsupervised peak detection by determining a noise threshold in isotopically resolved mass spectrometry data. Solving this problem will greatly reduce the subjective and time-consuming manual picking of mass spectral peaks and so will prove beneficial in many research applications. The Autopiquer approach uses autocorrelation to test for the presence of (isotopic) structure in overlapping windows across the spectrum. Within each window, a noise threshold is optimized to remove the most unstructured data, whilst keeping as much of the (isotopic) structure as possible. This algorithm has been successfully demonstrated for both peak detection and spectral compression on data from many different classes of mass spectrometer and for different sample types, and this approach should also be extendible to other types of data that contain regularly spaced discrete peaks.

“…This conclusion also follows from the analysis of a crude oil fraction using NADEL ICR cell, vide infra. Application of absorption mode FT signal processing allows improving RMS mass accuracy values two times, as expected [50][51][52]. However, the observed increase in mass inaccuracy when a very wide m/z range is analyzed, Figure S7 (Supporting Information) and Table 1, needs further investigation.…”

Section: Nadel Icr Cell Performance: Mass Accuracymentioning

confidence: 88%

Ion Trap with Narrow Aperture Detection Electrodes for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Nagornov

Kozhinov

Tsybin

et al. 2015

Abstract. The current paradigm in ion trap (cell) design for Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the ion detection with wide aperture detection electrodes. Specifically, excitation and detection electrodes are typically 90°wide and positioned radially at a similar distance from the ICR cell axis. Here, we demonstrate that ion detection with narrow aperture detection electrodes (NADEL) positioned radially inward of the cell's axis is feasible and advantageous for FT-ICR MS. We describe design details and performance characteristics of a 10 T FT-ICR MS equipped with a NADEL ICR cell having a pair of narrow aperture (flat) detection electrodes and a pair of standard 90°excitation electrodes. Despite a smaller surface area of the detection electrodes, the sensitivity of the NADEL ICR cell is not reduced attributable to improved excite field distribution, reduced capacitance of the detection electrodes, and their closer positioning to the orbits of excited ions. The performance characteristics of the NADEL ICR cell are comparable with the state-of-the-art FT-ICR MS implementations for small molecule, peptide, protein, and petroleomics analyses. In addition, the NADEL ICR cell's design improves the flexibility of ICR cells and facilitates implementation of advanced capabilities (e.g., quadrupolar ion detection for improved mainstream applications). It also creates an intriguing opportunity for addressing the major bottleneck in FTMS-increasing its throughput via simultaneous acquisition of multiple transients or via generation of periodic non-sinusoidal transient signals.