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Two-Dimensional Mass Spectrometry in Natural Extracts and Protein Analysis

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Analytical Chemistry".

Deadline for manuscript submissions: closed (30 March 2021) | Viewed by 10491

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Special Issue Editors

Dr. Marc-Andre Delsuc

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Guest Editor

Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U596, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch-Graffenstaden, France
Interests: mass spectrometry; two-dimensional mass spectrometry; NMR spectroscopy; innovative processing methods; scientific software development

Dr. Maria van Agthoven

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Guest Editor

Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
Interests: mass spectrometry; two-dimensional mass spectrometry; fragmentation; proteins; post-translational modifications; nucleic acids; post-transcriptional modifications

Special Issue Information

Dear Colleagues,

Two-dimensional mass spectrometry (2D MS) enables tandem mass spectrometry without requiring ion isolation, and 2D MS spectra yield correlations between precursor and fragment ions. The capacity of 2D MS to separate by mass-to-charge ratio and charge state makes it an exciting alternative (or complement) to chromatographic methods.

This technique, which was pioneered in the 1980s, has really taken off as an analytical tool in the last decade. Today, 2D MS can be applied on FT-ICR mass spectrometers, quadrupole ion traps, and is in development for linear ion traps. Techniques to improve the performance of 2D MS (signal-to-noise ratio, experiment duration, sample consumption, mass resolving power, resolution, calibration, etc.) are in constant development. The possibility to analyze a complex mixture without the need of a chromatographic separation opens new analytical avenues that are yet to be explored. Already shown to be efficient in fragmentation studies, agrochemical studies, polymer studies, metabolomics, and in top–down and bottom–up proteomics, the field of applications for 2D MS is still expanding, as well as the understanding of the analytical information contained in 2D mass spectra.

The time is right for a Special Issue of Molecules, which will serve as an open forum where researchers may share their investigations and findings in two-dimensional mass spectrometry in natural extracts and protein analysis. Contributions to this issue, both in the form of original research or review articles, may cover all aspects of two-dimensional mass spectrometry; studies with multidisciplinary input, offering new methodologies or insights, are particularly welcome.

Prof. Marc-Andre Delsuc
Dr. Maria van Agthoven
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

Two-dimensional mass spectrometry
Fourier transform ion cyclotron resonance mass spectrometry
Quadrupole ion trap
Linear ion trap
Protein analysis
Natural extracts
Environmental studies
Polymer studies

Published Papers (4 papers)

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Research

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12 pages, 1614 KiB

Open AccessArticle

Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry

by Taran Driver, Nikhil Bachhawat, Leszek J. Frasinski, Jonathan P. Marangos, Vitali Averbukh and Marina Edelson-Averbukh

Molecules 2021, 26(12), 3728; https://doi.org/10.3390/molecules26123728 - 18 Jun 2021

Cited by 5 | Viewed by 2392

Abstract

The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer. Full article

(This article belongs to the Special Issue Two-Dimensional Mass Spectrometry in Natural Extracts and Protein Analysis)

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14 pages, 3270 KiB

Open AccessArticle

Phase Correction for Absorption Mode Two-Dimensional Mass Spectrometry

by Marc-André Delsuc, Kathrin Breuker and Maria A. van Agthoven

Molecules 2021, 26(11), 3388; https://doi.org/10.3390/molecules26113388 - 03 Jun 2021

Cited by 3 | Viewed by 2672

Abstract

Two-dimensional mass spectrometry (2D MS) is a tandem mass spectrometry method that relies on manipulating ion motions to correlate precursor and fragment ion signals. 2D mass spectra are obtained by performing a Fourier transform in both the precursor ion mass-to-charge ratio (m/z) dimension and the fragment ion m/z dimension. The phase of the ion signals evolves linearly in the precursor m/z dimension and quadratically in the fragment m/z dimension. This study demonstrates that phase-corrected absorption mode 2D mass spectrometry improves signal-to-noise ratios by a factor of 2 and resolving power by a factor of 2 in each dimension compared to magnitude mode. Furthermore, phase correction leads to an easier differentiation between ion signals and artefacts, and therefore easier data interpretation. Full article

(This article belongs to the Special Issue Two-Dimensional Mass Spectrometry in Natural Extracts and Protein Analysis)

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22 pages, 699 KiB

Open AccessArticle

Application of Optimal Control Theory to Fourier Transform Ion Cyclotron Resonance

by Vardan Martikyan, Camille Beluffi, Steffen J. Glaser, Marc-André Delsuc and Dominique Sugny

Molecules 2021, 26(10), 2860; https://doi.org/10.3390/molecules26102860 - 12 May 2021

Cited by 2 | Viewed by 2832

Abstract

We study the application of Optimal Control Theory to Ion Cyclotron Resonance. We test the validity and the efficiency of this approach for the robust excitation of an ensemble of ions with a wide range of cyclotron frequencies. Optimal analytical solutions are derived in the case without any pulse constraint. A gradient-based numerical optimization algorithm is proposed to take into account limitation in the control intensity. The efficiency of optimal pulses is investigated as a function of control time, maximum amplitude and range of excited frequencies. A comparison with adiabatic and SWIFT pulses is done. On the basis of recent results in Nuclear Magnetic Resonance, this study highlights the potential usefulness of optimal control in Ion Cyclotron Resonance. Full article

(This article belongs to the Special Issue Two-Dimensional Mass Spectrometry in Natural Extracts and Protein Analysis)

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20 pages, 3134 KiB

Open AccessPerspective

Early Days of Two-Dimensional Ion Cyclotron Resonance

by Geoffrey Bodenhausen

Molecules 2021, 26(11), 3381; https://doi.org/10.3390/molecules26113381 - 03 Jun 2021

Cited by 1 | Viewed by 1766

Abstract

This contribution is an attempt to evoke the favorable atmosphere that prevailed in Lausanne around 1986 and provided the backdrop of our invention of two-dimensional ion cyclotron resonance mass spectroscopy (2D ICR-MS). To avoid a self-centered histoire d’ancien combattant, we shall try to emphasize the context: the contributions of key players within our nascent research group at UNIL and the established group of Tino Gäumann at EPFL, the role of external speakers, and the open atmosphere that was not yet polluted by bibliometrics, obsessive concern with impact factors, and top–down management of research. We shall also explain why the idea of 2D ICR-MS has been ignored for many years and still has a limited impact: different scientific cultures in the ICR and NMR communities, different concerns with fundamental vs. applied research, different status of theory and numerical simulations, different levels of commitment of instrument manufacturers, not to mention many theoretical problems that appear to be at least as challenging in ICR as in NMR. Full article

(This article belongs to the Special Issue Two-Dimensional Mass Spectrometry in Natural Extracts and Protein Analysis)

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