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McCann A, Rappe S, La Rocca R, Tiquet M, Quinton L, Eppe G, Far J, De Pauw E, Kune C. Mass shift in mass spectrometry imaging: comprehensive analysis and practical corrective workflow. Anal Bioanal Chem 2021; 413:2831-2844. [PMID: 33517478 DOI: 10.1007/s00216-021-03174-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/22/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022]
Abstract
MALDI mass spectrometry imaging (MSI) allows the mapping and the tentative identification of compounds based on their m/z value. In typical MSI, a spectrum is taken at incremental 2D coordinates (pixels) across a sample surface. Single pixel mass spectra show the resolving power of the mass analyzer. Mass shift, i.e., variations of the m/z of the same ion(s), may occur from one pixel to another. The superposition of shifted masses from individual pixels peaks apparently degrades the resolution and the mass accuracy in the average spectrum. This leads to low confidence annotations and biased localization in the image. Besides the intrinsic performances of the analyzer, the sample properties (local composition, thickness, matrix deposition) and the calibration method are sources of mass shift. Here, we report a critical analysis and recommendations to mitigate these sources of mass shift. Mass shift 2D distributions were mapped to illustrate its effect and explore systematically its origin. Adapting the sample preparation, carefully selecting the data acquisition settings, and wisely applying post-processing methods (i.e., m/z realignment or individual m/z recalibration pixel by pixel) are key factors to lower the mass shift and to improve image quality and annotations. A recommended workflow, resulting from a comprehensive analysis, was successfully applied to several complex samples acquired on both MALDI ToF and MALDI FT-ICR instruments.
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Affiliation(s)
- Andréa McCann
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Sophie Rappe
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Raphaël La Rocca
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Mathieu Tiquet
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium.
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van Agthoven MA, Kilgour DPA, Lynch AM, Barrow MP, Morgan TE, Wootton CA, Chiron L, Delsuc MA, O'Connor PB. Phase relationships in two-dimensional mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2594-2607. [PMID: 31617086 PMCID: PMC6914722 DOI: 10.1007/s13361-019-02308-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/29/2019] [Accepted: 08/02/2019] [Indexed: 05/14/2023]
Abstract
Two-dimensional mass spectrometry (2D MS) is a data-independent tandem mass spectrometry technique in which precursor and fragment ion species can be correlated without the need for prior ion isolation. The behavior of phase in 2D Fourier transform mass spectrometry is investigated with respect to the calculation of phase-corrected absorption-mode 2D mass spectra. 2D MS datasets have a phase that is defined differently in each dimension. In both dimensions, the phase behavior of precursor and fragment ions is found to be different. The dependence of the phase for both precursor and fragment ion signals on various parameters (e.g., modulation frequency, shape of the fragmentation zone) is discussed. Experimental data confirms the theoretical calculations of the phase in each dimension. Understanding the phase relationships in a 2D mass spectrum is beneficial to the development of possible algorithms for phase correction, which may improve both the signal-to-noise ratio and the resolving power of peaks in 2D mass spectra.
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Affiliation(s)
- Maria A van Agthoven
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - David P A Kilgour
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
- School of Science and Technology, Nottingham Trent University, 50 Shakespeare Street, Nottingham, NG1 4FQ, UK
| | - Alice M Lynch
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
- Department of Computer Science, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SX, UK
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Tomos E Morgan
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Christopher A Wootton
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Lionel Chiron
- CASC4DE, Le Lodge 20 av. du Neuhof, 67100, Strasbourg, France
| | - Marc-André Delsuc
- CASC4DE, Le Lodge 20 av. du Neuhof, 67100, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM, U596, CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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van Agthoven MA, Lam YPY, O'Connor PB, Rolando C, Delsuc MA. Two-dimensional mass spectrometry: new perspectives for tandem mass spectrometry. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2019; 48:213-229. [PMID: 30863873 PMCID: PMC6449292 DOI: 10.1007/s00249-019-01348-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/24/2019] [Accepted: 02/06/2019] [Indexed: 12/11/2022]
Abstract
Fourier transform ion cyclotron resonance mass analysers (FT-ICR MS) can offer the highest resolutions and mass accuracies in mass spectrometry. Mass spectra acquired in an FT-ICR MS can yield accurate elemental compositions of all compounds in a complex sample. Fragmentation caused by ion-neutral, ion-electron, or ion-photon interactions leads to more detailed structural information on compounds. The most often used method to correlate compounds and their fragment ions is to isolate the precursor ions from the sample before fragmentation. Two-dimensional mass spectrometry (2D MS) offers a method to correlate precursor and fragment ions without requiring precursor isolation. 2D MS therefore enables easy access to the fragmentation patterns of all compounds from complex samples. In this article, the principles of FT-ICR MS are reviewed and the 2D MS experiment is explained. Data processing for 2D MS is detailed, and the interpretation of 2D mass spectra is described.
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Affiliation(s)
- Maria A van Agthoven
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV47AL, UK
| | - Yuko P Y Lam
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV47AL, UK
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV47AL, UK
| | - Christian Rolando
- MSAP USR 3290, Université Lille, Sciences et Technologies, 59655, Villeneuve d'Ascq Cedex, France
| | - Marc-André Delsuc
- Institut de Génétique, Biologie Moléculaire et Cellulaire, INSERM, U596, CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France.
- CASC4DE, 20 avenue du Neuhof, 67100, Strasbourg, France.
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van Agthoven MA, Lynch AM, Morgan TE, Wootton CA, Lam YPY, Chiron L, Barrow MP, Delsuc MA, O'Connor PB. Can Two-Dimensional IR-ECD Mass Spectrometry Improve Peptide de Novo Sequencing? Anal Chem 2018; 90:3496-3504. [PMID: 29420878 DOI: 10.1021/acs.analchem.7b05324] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two-dimensional mass spectrometry (2D MS) correlates precursor and fragment ions without ion isolation in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR MS) for tandem mass spectrometry. Infrared activated electron capture dissociation (IR-ECD), using a hollow cathode configuration, generally yields more information for peptide sequencing in tandem mass spectrometry than ECD (electron capture dissociation) alone. The effects of the fragmentation zone on the 2D mass spectrum are investigated as well as the structural information that can be derived from it. The enhanced structural information gathered from the 2D mass spectrum is discussed in terms of how de novo peptide sequencing can be performed with increased confidence. 2D IR-ECD MS is shown to sequence peptides, to distinguish between leucine and isoleucine residues through the production of w ions as well as between C-terminal ( b/ c) and N-terminal ( y/ z) fragments through the use of higher harmonics, and to assign and locate peptide modifications.
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Affiliation(s)
- Maria A van Agthoven
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Alice M Lynch
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Tomos E Morgan
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Christopher A Wootton
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Yuko P Y Lam
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Lionel Chiron
- CASC4DE, Le Lodge , 20 av. du Neuhof , 67100 Strasbourg , France
| | - Mark P Barrow
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
| | - Marc-André Delsuc
- CASC4DE, Le Lodge , 20 av. du Neuhof , 67100 Strasbourg , France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM, U596; CNRS, UMR7104 , Université de Strasbourg , 1 rue Laurent Fries , 67404 Illkirch-Graffenstaden , France
| | - Peter B O'Connor
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom
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van Agthoven MA, O'Connor PB. Two-dimensional mass spectrometry in a linear ion trap, an in silico model. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:674-684. [PMID: 28181731 DOI: 10.1002/rcm.7836] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/12/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
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.
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Affiliation(s)
- Maria A van Agthoven
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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Nikolaev EN, Kostyukevich YI, Vladimirov GN. Fourier transform ion cyclotron resonance (FT ICR) mass spectrometry: Theory and simulations. MASS SPECTROMETRY REVIEWS 2016; 35:219-58. [PMID: 24515872 DOI: 10.1002/mas.21422] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 12/16/2013] [Indexed: 05/22/2023]
Abstract
Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer offers highest resolving power and mass accuracy among all types of mass spectrometers. Its unique analytical characteristics made FT ICR important tool for proteomics, metabolomics, petroleomics, and investigation of complex mixtures. Signal acquisition in FT ICR MS takes long time (up to minutes). During this time ion-ion interaction considerably affects ion motion and result in decreasing of the resolving power. Understanding of those effects required complicated theory and supercomputer simulations but culminated in the invention of the ion trap with dynamic harmonization which demonstrated the highest resolving power ever achieved. In this review we summarize latest achievements in theory and simulation of FT ICR mass spectrometers.
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Affiliation(s)
- Eugene N Nikolaev
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k. 2, 119334, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, ul. Pogodinskaya 10, 119121, Moscow, Russia
| | - Yury I Kostyukevich
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k. 2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Gleb N Vladimirov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k. 2, 119334, Moscow, Russia
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Nagornov KO, Kozhinov AN, Tsybin OY, Tsybin YO. Ion trap with narrow aperture detection electrodes for Fourier transform ion cyclotron resonance mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:741-751. [PMID: 25773900 DOI: 10.1007/s13361-015-1089-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 06/04/2023]
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.
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Affiliation(s)
- Konstantin O Nagornov
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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Nagornov KO, Gorshkov MV, Kozhinov AN, Tsybin YO. High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry with Increased Throughput for Biomolecular Analysis. Anal Chem 2014; 86:9020-8. [DOI: 10.1021/ac501579h] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Konstantin O. Nagornov
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Mikhail V. Gorshkov
- Institute
for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141707 Dolgoprudny,
Moscow Region, Russia
| | - Anton N. Kozhinov
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Yury O. Tsybin
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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Popov IA, Nagornov K, Vladimirov GN, Kostyukevich YI, Nikolaev EN. Twelve million resolving power on 4.7 T Fourier transform ion cyclotron resonance instrument with dynamically harmonized cell--observation of fine structure in peptide mass spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:790-799. [PMID: 24604470 DOI: 10.1007/s13361-014-0846-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/28/2014] [Accepted: 01/28/2014] [Indexed: 06/03/2023]
Abstract
Resolving power of about 12,000 000 at m/z 675 has been achieved on low field homogeneity 4.7 T magnet using a dynamically harmonized Fourier transform ion cyclotron resonance (FT ICR) cell. Mass spectra of the fine structure of the isotopic distribution of a peptide were obtained and strong discrimination of small intensity peaks was observed in case of resonance excitation of the ions of the whole isotopic cluster to the same cyclotron radius. The absence of some peaks from the mass spectra of the fine structure was explained basing on results of computer simulations showing strong ion cloud interactions, which cause the coalescence of peaks with m/z close to that of the highest magnitude peak. The way to prevent peak discrimination is to excite ion clouds of different m/z to different cyclotron radii, which was demonstrated and investigated both experimentally and by computer simulations.
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Affiliation(s)
- Igor A Popov
- Talrose Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences, Moscow, Russia
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Zaikin VG, Sysoev AA. Review: mass spectrometry in Russia. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2013; 19:399-452. [PMID: 24378462 DOI: 10.1255/ejms.1248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The present review covers the main research in the area of mass spectrometry from the 1990s which was about the same time as the Russian Federation emerged from the collapse of the Soviet Union (USSR). It consists of two main parts-application of mass spectrometry to chemistry and related fields and creation and development of mass spectrometric technique. Both traditional and comparatively new mass spectrometric methods were used to solve various problems in organic chemistry (reactivity of gas-phase ions, structure elucidation and problems of identification, quantitative and trace analysis, differentiation of stereoisomers, derivatization approaches etc.), biochemistry (proteomics and peptidomics, lipidomics), medical chemistry (mainly the search of biomarkers, pharmacology, doping control), environmental, petrochemistry, polymer chemistry, inorganic and physical chemistry, determination of natural isotope ratio etc. Although a lot of talented mass spectrometrists left Russia and moved abroad after the collapse of the Soviet Union, the vitality of the mass spectral community proved to be rather high, which allowed the continuation of new developments in the field of mass spectrometric instrumentation. They are devoted to improvements in traditional magnetic sector mass spectrometers and the development of new ion source types, to analysis and modification of quadrupole, time-of-flight (ToF) and ion cyclotron resonance (ICR) analyzers. The most important achievements are due to the creation of multi-reflecting ToF mass analyzers. Special attention was paid to the construction of compact mass spectrometers, particularly for space exploration, of combined instruments, such as ion mobility spectrometer/mass spectrometer and accelerating mass spectrometers. The comparatively young Russian Mass Spectrometry Society is working hard to consolidate the mass spectrometrists from Russia and foreign countries, to train young professionals on new appliances and regularly holds conferences on mass spectrometry. For ten years, a special journal Mass-spektrometria has published papers on all disciplines of mass spectrometry.
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Affiliation(s)
- Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky prospect 29, 119991 Moscow, Russian Federation.
| | - Alexander A Sysoev
- National Research Nuclear University MEPhI, Kashirskoe Shosse 31, 115409 Moscow, Russian Federation
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Gorshkov MV, Fornelli L, Tsybin YO. Observation of ion coalescence in Orbitrap Fourier transform mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1711-1717. [PMID: 22730091 DOI: 10.1002/rcm.6289] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Similar to other mass spectrometric technologies based on ion trapping in a spatially restricted area, the performance of Orbitrap Fourier transform mass spectrometry (FTMS) is affected by the interaction between the trapped ion clouds. One of the effects associated with Coulombic interaction inside the ion trap is the ion cloud coupling, known in ion cyclotron resonance (ICR) FTMS as coalescence, or a phase-locking phenomenon. Nevertheless, the direct observation of ion coalescence has not been reported for Orbitrap FTMS yet. METHODS We have performed experiments on ion coalescence with a pair of isobaric peptides in the state-of-the-art hybrid linear ion trap high-field compact Orbitrap Elite FT mass spectrometer using both standard and advanced signal processing modes. RESULTS For the instrument configuration employed in this work we found that ion coalescence occurs when two singly charged peptides with the mass difference of 22 mDa and molecular weight of about 1060 Da have the total abundance of at least 7.5*10(4) charges. CONCLUSIONS We experimentally demonstrate the existence of the ion coalescence phenomenon in Orbitrap FTMS for peptides for a wide range of total trapped ion population. Using the applicable modeling of the phase-locking threshold we estimate the effect of ion coalescence on the performance of Orbitrap FTMS.
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Affiliation(s)
- Mikhail V Gorshkov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia.
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Gorshkov MV, Good DM, Lyutvinskiy Y, Yang H, Zubarev RA. Calibration function for the Orbitrap FTMS accounting for the space charge effect. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1846-1851. [PMID: 20696596 DOI: 10.1016/j.jasms.2010.06.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 06/23/2010] [Accepted: 06/29/2010] [Indexed: 05/29/2023]
Abstract
Ion storage in an electrostatic trap has been implemented with the introduction of the Orbitrap Fourier transform mass spectrometer (FTMS), which demonstrates performance similar to high-field ion cyclotron resonance MS. High mass spectral characteristics resulted in rapid acceptance of the Orbitrap FTMS for Life Sciences applications. The basics of Orbitrap operation are well documented; however, like in any ion trap MS technology, its performance is limited by interactions between the ion clouds. These interactions result in ion cloud couplings, systematic errors in measured masses, interference between ion clouds of different size yet with close m/z ratios, etc. In this work, we have characterized the space-charge effect on the measured frequency for the Orbitrap FTMS, looking for the possibility to achieve sub-ppm levels of mass measurement accuracy (MMA) for peptides in a wide range of total ion population. As a result of this characterization, we proposed an m/z calibration law for the Orbitrap FTMS that accounts for the total ion population present in the trap during a data acquisition event. Using this law, we were able to achieve a zero-space charge MMA limit of 80 ppb for the commercial Orbitrap FTMS system and sub-ppm level of MMA over a wide range of total ion populations with the automatic gain control values varying from 10 to 10(7).
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Affiliation(s)
- Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Mikhail E. Belov
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Navdeep Jaitly
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Richard D. Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
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Frahm JL, Velez CMC, Muddiman DC. Understanding the influence of post-excite radius and axial confinement on quantitative proteomic measurements using Fourier transform ion cyclotron resonance mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:1196-204. [PMID: 17330212 DOI: 10.1002/rcm.2957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Early studies of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) explored many of the fundamental issues surrounding the potential of the technique to provide quantitative data. Improvements in instrument technology and the analysis of larger molecules in increasingly complex mixtures warrant not only a revisit to some of these earlier studies, but a more comprehensive examination of the influence of various instrument parameters on quantitative (absolute and relative) measurements in proteomics. We present a detailed examination of the role that acquisition time, excite voltage (i.e. excite radius), trapping voltage, and the type of excitation waveform have on the ability of FT-ICR to accurately quantify biological molecules. The use of a stable-isotope-labeled and unlabeled phenyl isocyanate derivatized peptide allows us to ascribe the effects of FT-ICR-MS on quantification, thus eliminating the contribution of ionization differences to ion abundance. To adequately assess the multiple parameters in the large dataset, we develop a multiplicative quality factor that encompasses the total ion abundance, as well as the accuracy and the precision of abundance ratios. This assessment allows facile determination of optimal instrument parameters for quantitative measurements.
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Affiliation(s)
- Jennifer L Frahm
- Department of Chemistry, North Carolina State University, Dabney Hall, Campus Box 8204, Raleigh, NC 27695-8204, USA
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Nikolaev EN, Heeren RMA, Popov AM, Pozdneev AV, Chingin KS. Realistic modeling of ion cloud motion in a Fourier transform ion cyclotron resonance cell by use of a particle-in-cell approach. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:3527-3546. [PMID: 17944004 DOI: 10.1002/rcm.3234] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Using a 'Particle-In-Cell' approach taken from plasma physics we have developed a new three-dimensional (3D) parallel computer code that today yields the highest possible accuracy of ion trajectory calculations in electromagnetic fields. This approach incorporates coulombic ion-ion and ion-image charge interactions into the calculation. The accuracy is achieved through the implementation of an improved algorithm (the so-called Boris algorithm) that mathematically eliminates cyclotron motion in a magnetic field from digital equations for ion motion dynamics. It facilitates the calculation of the cyclotron motion without numerical errors. At every time-step in the simulation the electric potential inside the cell is calculated by direct solution of Poisson's equation. Calculations are performed on a computational grid with up to 128 x 128 x 128 nodes using a fast Fourier transform algorithm. The ion populations in these simulations ranged from 1000 up to 1,000,000 ions. A maximum of 3,000,000 time-steps were employed in the ion trajectory calculations. This corresponds to an experimental detection time-scale of seconds. In addition to the ion trajectories integral time-domain signals and mass spectra were calculated. The phenomena observed include phase locking of particular m/z ions (high-resolution regime) inside larger ion clouds. A focus was placed on behavior of a cloud of ions of a single m/z value to understand the nature of Fourier transform ion cyclotron resonance (FTICR) resolution and mass accuracy in selected ion mode detection. The behavior of two and three ion clouds of different but close m/z was investigated as well. Peak coalescence effects were observed in both cases. Very complicated ion cloud dynamics in the case of three ion clouds was demonstrated. It was found that magnetic field does not influence phase locking for a cloud of ions of a single m/z. The ion cloud evolution time-scale is inversely proportional to magnetic field. The number of ions needed for peak coalescence depends quadratically on the magnetic field.
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Affiliation(s)
- Eugene N Nikolaev
- The Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr.38, k.2, Moscow, Russia 119334.
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Naito Y, Inoue M. Collective motion of ions in an ion trap for Fourier transform ion cyclotron resonance mass spectrometry. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0168-1176(96)04467-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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The non-neutral plasma: an introduction to physics with relevance to cyclotron resonance mass spectrometry. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0168-1176(96)04395-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Mitchell DW, Smith RD. Cyclotron motion of two Coulombically interacting ion clouds with implications to Fourier-transform ion cyclotron resonance mass spectrometry. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 52:4366-4386. [PMID: 9963909 DOI: 10.1103/physreve.52.4366] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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Peurrung A, Kouzes R. Analysis of space-charge effects in cyclotron resonance mass spectrometry as coupled gyrator phenomena. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0168-1176(95)04221-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Peurrung AJ, Kouzes RT. Long-term coherence of the cyclotron mode in a trapped ion cloud. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 49:4362-4368. [PMID: 9961729 DOI: 10.1103/physreve.49.4362] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Chen R, Marshall AG. An off-center cubic ion trap for Fourier transform ion cyclotron resonance mass spectrometry. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/0168-1176(94)03946-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gorshkov MV, Guan S, Marshall AG. Masses of stable neon isotopes determined at parts per billion precision by Fourier transform ion cyclotron resonance mass spectrometry. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/0168-1176(93)87015-k] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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