1
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Bell RJ, Hage DS, Dodds ED. Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of N-Linked Glycopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1208-1216. [PMID: 38713472 DOI: 10.1021/jasms.4c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Glycosylation is a common modification across living organisms and plays a central role in understanding biological systems and disease. Our ability to probe the gylcome has grown exponentially in the past several decades. However, further improvements to the analytical toolbox available to researchers would allow for increased capabilities to probe structure and function of biological systems and to improve disease treatment. This article applies the developing technique of two-dimensional Fourier transform ion cyclotron resonance mass spectrometry to a glycoproteomic workflow for the standard glycoproteins coral tree lectin (CTL) and bovine ribonuclease B (BRB) to demonstrate its feasibility as a tool for glycoproteomic workflows. 2D infrared multiphoton dissociation and electron capture dissociation spectra of CTL reveal comparable structural information to their 1D counterparts, confirming the site of glycosylation and monosaccharide composition of the glycan. Spectra collected in 2D of BRB reveal correlation lines of fragment ion scans and vertical precursor ion scans for data collected using infrared multiphoton dissociation and diagonal cleavage lines for data collected by electron capture dissociation. The use of similar techniques for glycoproteomic analysis may prove valuable in instances where chromatographic separation is undesirable or quadrupole isolation is insufficient.
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Affiliation(s)
- Richard J Bell
- Department of Chemistry and University of Nebraska─Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - David S Hage
- Department of Chemistry and University of Nebraska─Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Eric D Dodds
- Department of Chemistry and University of Nebraska─Lincoln, Lincoln, Nebraska 68588-0304, United States
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2
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Bell RJ, Hage DS, Dodds ED. Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry by Matrix-Assisted Laser Desorption Ionization. Anal Chem 2024; 96:6584-6587. [PMID: 38619932 DOI: 10.1021/acs.analchem.3c05601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Two-dimensional Fourier transform ion cyclotron resonance (2D FTICR) mass spectrometry is a developing form of data-independent acquisition that allows for the simultaneous fragmentation and correlation of fragment ions to their precursors across a range of m/z values. The modern usage of 2D FTICR is performed using electrospray ionization (ESI) as the dried droplet preparation for matrix-assisted laser desorption ionization (MALDI) does not produce a consistent packet of ions over a number of scans. This work uses pneumatic spray techniques from mass spectrometry imaging to create a homogeneous surface for use with MALDI as an ionization source for 2D FTICR. A mixture of peptides and matrix was deposited onto a glass slide using an HTX pneumatic sprayer. MALDI was then used to ionize the peptide mixture for use with a standard 2D FTICR pulse sequence. The generated 2D spectrum reveals comparable structural information to spectra collected in a 1D experiment. Artifacts observed in the collected 2D MALDI spectra do not significantly differ from those expected from 2D ESI spectra.
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Affiliation(s)
- Richard J Bell
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Eric D Dodds
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
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3
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Rahman M, Marzullo B, Holman SW, Barrow M, Ray AD, O’Connor PB. Advancing PROTAC Characterization: Structural Insights through Adducts and Multimodal Tandem-MS Strategies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:285-299. [PMID: 38197777 PMCID: PMC10853971 DOI: 10.1021/jasms.3c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/11/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are specialized molecules that bind to a target protein and a ubiquitin ligase to facilitate protein degradation. Despite their significance, native PROTACs have not undergone tandem mass spectrometry (MS) analysis. To address this gap, we conducted a pioneering investigation on the fragmentation patterns of two PROTACs in development, dBET1 and VZ185. Employing diverse cations (sodium, lithium, and silver) and multiple tandem-MS techniques, we enhanced their structural characterization. Notably, lithium cations facilitated comprehensive positive-mode coverage for dBET1, while negative polarity mode offered richer insights. Employing de novo structure determination on 2DMS data from degradation studies yielded crucial insights. In the case of VZ185, various charge states were observed, with [M + 2H]2+ revealing fewer moieties than [M + H]+ due to charge-related factors. Augmenting structural details through silver adducts suggested both charge-directed and charge-remote fragmentation. This comprehensive investigation identifies frequently dissociated bonds across multiple fragmentation techniques, pinpointing optimal approaches for elucidating PROTAC structures. The findings contribute to advancing our understanding of PROTACs, pivotal for their continued development as promising therapeutic agents.
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Affiliation(s)
- Mohammed Rahman
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
- Department
of Physics, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Bryan Marzullo
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Stephen W. Holman
- Chemical
Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 4TF, U.K.
| | - Mark Barrow
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Andrew D. Ray
- New
Modalities and Parenteral Development, Pharmaceutical Technology &
Development, Operations, AstraZeneca, Macclesfield, SK10 4TF, U.K.
| | - Peter B. O’Connor
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
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4
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Polák M, Palasser M, Kádek A, Kavan D, Wootton CA, Delsuc MA, Breuker K, Novák P, van Agthoven MA. Top-Down Proteoform Analysis by 2D MS with Quadrupolar Detection. Anal Chem 2023; 95:16123-16130. [PMID: 37877738 PMCID: PMC10633810 DOI: 10.1021/acs.analchem.3c02225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023]
Abstract
Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that does not rely on ion isolation to correlate the precursor and fragment ions. On a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), 2D MS instead uses the modulation of precursor ion radii inside the ICR cell before fragmentation and yields 2D mass spectra that show the fragmentation patterns of all the analytes. In this study, we perform 2D MS for the first time with quadrupolar detection in a dynamically harmonized ICR cell. We discuss the advantages of quadrupolar detection in 2D MS and how we adapted existing data processing techniques for accurate frequency-to-mass conversion. We apply 2D MS with quadrupolar detection to the top-down analysis of covalently labeled ubiquitin with ECD fragmentation, and we develop a workflow for label-free relative quantification of biomolecule isoforms in 2D MS.
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Affiliation(s)
- Marek Polák
- Institute
of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
- Faculty
of Science, Charles University, Prague 12843, Czech Republic
| | - Michael Palasser
- Center
for Chemistry and Biomedicine, University
of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Alan Kádek
- Institute
of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Daniel Kavan
- Institute
of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
- Faculty
of Science, Charles University, Prague 12843, Czech Republic
| | | | - Marc-André Delsuc
- Institut
de Génétique et de Biologie Moléculaire et Cellulaire,
INSERM, U596, CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France
| | - Kathrin Breuker
- Center
for Chemistry and Biomedicine, University
of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Petr Novák
- Institute
of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
- Faculty
of Science, Charles University, Prague 12843, Czech Republic
| | - Maria A. van Agthoven
- Institute
of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
- Center
for Chemistry and Biomedicine, University
of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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5
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Palasser M, Heel SV, Delsuc MA, Breuker K, van Agthoven MA. Ultra-Accurate Correlation between Precursor and Fragment Ions in Two-Dimensional Mass Spectrometry: Acetylated vs Trimethylated Histone Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:608-616. [PMID: 36930827 PMCID: PMC10080674 DOI: 10.1021/jasms.2c00319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/23/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Two-dimensional mass spectrometry (2D MS) is a method for tandem mass spectrometry in which precursor and fragment ions are correlated by manipulating ion radii rather than by ion isolation. A 2D mass spectrum contains the fragmentation patterns of all analytes in a sample, acquired in parallel. We report ultrahigh-resolution narrowband 2D mass spectra of a mixture of two histone peptides with the same sequence, one of which carries an acetylation and the other a trimethylation (m/z 0.006 difference). We reduced the distance between data points in the precursor ion dimension and compared the accuracy of the precursor-fragment correlation with the resolving power. We manage to perform label-free quantification on the histone peptide mixture and show that precursor and fragment ions can be accurately correlated even though the precursor ions are not resolved. Finally, we show that increasing the resolution of a 2D mass spectrum in the precursor ion dimension too far can lead to a decline in the signal-to-noise ratio.
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Affiliation(s)
- Michael Palasser
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
| | - Sarah V. Heel
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
| | - Marc-André Delsuc
- Institut
de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, UMR 7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France
- CASC4DE, Pôle API, 300 Bd. Sébastien
Grant, 67400 Illkirch-Graffenstaden, France
| | - Kathrin Breuker
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
| | - Maria A. van Agthoven
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
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6
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Zemaitis KJ, Zhou M, Kew W, Paša-Tolić L. 193 nm Ultraviolet Photodissociation for the Characterization of Singly Charged Proteoforms Generated by MALDI. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:328-332. [PMID: 36622763 PMCID: PMC10084724 DOI: 10.1021/jasms.2c00302] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
MALDI imaging allows for the near-cellular profiling of proteoforms directly from microbial, plant, and mammalian samples. Despite detecting hundreds of proteoforms, identification of unknowns with only intact mass information remains a distinct challenge, even with high mass resolving power and mass accuracy. To this end, many supplementary methods have been used to create experimental databases for accurate mass matching, including bulk or spatially resolved bottom-up and/or top-down proteomics. Herein, we describe the application of 193 nm ultraviolet photodissociation (UVPD) for fragmentation of quadrupole isolated singly charged ubiquitin (m/z 8565) by MALDI-UVPD on a UHMR HF Orbitrap. This platform permitted the high-resolution accurate mass measurement of not just terminal fragments but also large internal fragments. The outlined workflow demonstrates the feasibility of top-down analyses of isolated MALDI protein ions and the potential toward more comprehensive characterization of proteoforms in MALDI imaging applications.
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Affiliation(s)
- Kevin J Zemaitis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - William Kew
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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7
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Gonzalez LE, Szalwinski LJ, Sams TC, Dziekonski ET, Cooks RG. Metabolomic and Lipidomic Profiling of Bacillus Using Two-Dimensional Tandem Mass Spectrometry. Anal Chem 2022; 94:16838-16846. [DOI: 10.1021/acs.analchem.2c03961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- L. Edwin Gonzalez
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lucas J. Szalwinski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Thomas C. Sams
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Eric T. Dziekonski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - R. Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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8
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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9
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Morgan TE, Wootton CA, Marzullo B, Paris J, Kerr A, Ellacott SH, van Agthoven MA, Barrow MP, Bristow AWT, Perrier S, O'Connor PB. Characterization Across a Dispersity: Polymer Mass Spectrometry in the Second Dimension. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2153-2161. [PMID: 34264672 DOI: 10.1021/jasms.1c00106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Due to the natural dispersity that is present in synthetic polymers, an added complexity is always present in the analysis of polymeric species. Tandem mass spectrometry analysis requires the isolation of individual precursors before a fragmentation event to allow the unambiguous characterization of these species and is not viable at certain levels of complexity due to achievable isolation widths. Two-dimensional mass spectrometry (2DMS) fragments ions and correlates fragments with their corresponding precursors without the need for isolation. In this study, 2DMS electron capture dissociation (ECD) fragmentation of a polyoxazoline and polyacrylamide species was carried out, resulting in the analysis of byproducts and individual polymer species without the use of chromatographic techniques. This study shows that 2DMS ECD is a powerful tool for the analysis of polyacrylamide and polyoxazoline species and offers a new dimension in the characterization of polymers.
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Affiliation(s)
- Tomos E Morgan
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Christopher A Wootton
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Bryan Marzullo
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Johanna Paris
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Andrew Kerr
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Sean H Ellacott
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Maria A van Agthoven
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Anthony W T Bristow
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, United Kingdom
| | - Sebastien Perrier
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
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10
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Driver T, Averbukh V, Frasiński LJ, Marangos JP, Edelson-Averbukh M. Two-Dimensional Partial Covariance Mass Spectrometry for the Top-Down Analysis of Intact Proteins. Anal Chem 2021; 93:10779-10788. [PMID: 34309360 DOI: 10.1021/acs.analchem.1c00332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same fragmentation pathway of the same parent (e.g., peptide) ion. Here, we apply 2D-PC-MS to the analysis of intact protein ions in a standard linear ion trap mass analyzer, using the fact that the fragment-fragment correlation signals are much more specific to the biomolecular sequence than one-dimensional (1D) tandem mass spectrometry (MS/MS) signals at the same mass accuracy and resolution. We show that from the distribution of signals on a 2D-PC-MS map it is possible to extract the charge state of both parent and fragment ions without resolving the isotopic envelope. Furthermore, the 2D map of fragment-fragment correlations naturally separates the products of the primary decomposition pathways of the molecular ions from those of the secondary ones. We access this spectral information using an adapted version of the Hough transform. We demonstrate the successful identification of highly charged, intact protein molecules bypassing the need for high mass resolution. Using this technique, we also perform the in silico deconvolution of the overlapping fragment ion signals from two co-isolated and co-fragmented intact proteins, demonstrating a viable new method for the concurrent mass spectrometric identification of a mixture of intact protein ions from the same fragment ion spectrum.
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Affiliation(s)
- Taran Driver
- The Blackett Laboratory, Imperial College London, London SW7 2AZ, U.K
| | - Vitali Averbukh
- The Blackett Laboratory, Imperial College London, London SW7 2AZ, U.K
| | | | - Jon P Marangos
- The Blackett Laboratory, Imperial College London, London SW7 2AZ, U.K
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11
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Paris J, Morgan TE, Marzullo BP, Wootton CA, Barrow MP, O'Hara J, O'Connor PB. Two-Dimensional Mass Spectrometry Analysis of IgG1 Antibodies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1716-1724. [PMID: 34152763 DOI: 10.1021/jasms.1c00096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Two-dimensional mass spectrometry (2DMS) is a new, and theoretically ideal, data-independent analysis tool, which allows the characterization of a complex mixture and was used in the bottom-up analysis of IgG1 for the identification of post-translational modifications. The new peak picking algorithm allows the distinction between chimeric peaks in proteomics. In this application, the processing of 2DMS data correlates fragments to their corresponding precursors, with fragments from precursors which are <0.1 m/z at m/z 840 easily resolved, without the need for quadrupole or chromatographic separation.
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Affiliation(s)
- Johanna Paris
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Tomos E Morgan
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Bryan P Marzullo
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - John O'Hara
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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12
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Phase Correction for Absorption Mode Two-Dimensional Mass Spectrometry. Molecules 2021; 26:molecules26113388. [PMID: 34205070 PMCID: PMC8199897 DOI: 10.3390/molecules26113388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/03/2022] Open
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.
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13
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Clowers BH, Cabrera E, Anderson G, Deng L, Moser K, Van Aken G, DeBord JD. Masked Multiplexed Separations to Enhance Duty Cycle for Structures for Lossless Ion Manipulations. Anal Chem 2021; 93:5727-5734. [PMID: 33797223 DOI: 10.1021/acs.analchem.0c04799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The experimental paradigm of one ion packet release per spectrum severely hinders throughput in broadband ion mobility spectrometry (IMS) systems (e.g., drift tube and traveling wave systems). Ion trapping marginally mitigates this problem, but the duty cycle deficit is amplified when moving to high resolution, long pathlength systems. As a consequence, new multiplexing strategies that maximize throughput while preserving peak fidelity are essential for high-resolution IMS separations [e.g., structures for lossless ion manipulations (SLIMs) and multi-pass technologies]. Currently, broadly applicable deconvolution strategies for Hadamard-based ion multiplexing are limited to a narrow range of modulation sequences and do not fully maximize the ion signal generated during separation across an extended path length. Compared to prior Hadamard deconvolution errors that rely upon peak picking or discrete error classification, the masked deconvolution matrix technique exploits the knowledge that Hadamard transform artifacts are reflected about the central, primary signal [i.e., the true arrival time distribution (ATD)]. By randomly inducing mathematical artifacts, it is possible to identify spectral artifacts simply by their high degree of variability relative to the core ATD. It is important to note that the deweighting approach using the masked deconvolution matrix does not make any assumptions about the underlying transform and is applicable to any multiplexing strategy employing binary sequences. In addition to demonstrating a 100-fold increase in the total number of ions detected, the effective deconvolution of data from 5, 6, 7, and 8-bit pseudo-random sequences expands the utility and efficiency of the SLIM platform.
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Affiliation(s)
- Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Elvin Cabrera
- Department of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Gordon Anderson
- GAA Custom Engineering, Kennewick, Washington 99338, United States
| | - Liulin Deng
- MOBILion Systems Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Kelly Moser
- MOBILion Systems Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Gregory Van Aken
- MOBILion Systems Inc., Chadds Ford, Pennsylvania 19317, United States
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14
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Halper M, Delsuc MA, Breuker K, van Agthoven MA. Narrowband Modulation Two-Dimensional Mass Spectrometry and Label-Free Relative Quantification of Histone Peptides. Anal Chem 2020; 92:13945-13952. [PMID: 32960586 PMCID: PMC7581016 DOI: 10.1021/acs.analchem.0c02843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Two-dimensional mass
spectrometry (2D MS) on a Fourier transform
ion cyclotron resonance (FT-ICR) mass analyzer allows for tandem mass
spectrometry without requiring ion isolation. In the ICR cell, the
precursor ion radii are modulated before fragmentation, which results
in modulation of the abundance of their fragments. The resulting 2D
mass spectrum enables a correlation between the precursor and fragment
ions. In a standard broadband 2D MS, the range of precursor ion cyclotron
frequencies is determined by the lowest mass-to-charge (m/z) ratio to be fragmented in the 2D MS experiment,
which leads to precursor ion m/z ranges that are much wider than necessary, thereby limiting the
resolving power for precursor ions and the accuracy of the correlation
between the precursor and fragment ions. We present narrowband modulation
2D MS, which increases the precursor ion resolving power by reducing
the precursor ion m/z range, with
the aim of resolving the fragment ion patterns of overlapping isotopic
distributions. In this proof-of-concept study, we compare broadband
and narrowband modulation 2D mass spectra of an equimolar mixture
of histone peptide isoforms. In narrowband modulation 2D MS, we were
able to separate the fragment ion patterns of all 13C isotopes
of the different histone peptide forms. We further demonstrate the
potential of narrowband 2D MS for label-free quantification of peptides.
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Affiliation(s)
- Matthias Halper
- Institute for Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Marc-André Delsuc
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, UMR 7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France.,CASC4DE, Pôle API, 300 Bd. Sébastien Grant, 67400 Illkirch-Graffenstaden, France
| | - Kathrin Breuker
- Institute for Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Maria A van Agthoven
- Institute for Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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15
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Paris J, Morgan TE, Wootton CA, Barrow MP, O'Hara J, O'Connor PB. Facile Determination of Phosphorylation Sites in Peptides Using Two-Dimensional Mass Spectrometry. Anal Chem 2020; 92:6817-6821. [PMID: 32286050 DOI: 10.1021/acs.analchem.0c00884] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Detection and characterization of phosphopeptides by infrared multiphoton dissociation two-dimensional mass spectrometry (IRMPD 2DMS) is shown to be particularly effective. A mixture of phosphopeptides was analyzed by 2DMS without any prior separation. 2DMS enables the data independent analysis of the mixture and the correlation of the fragments to their precursor ions. The extraction of neutral loss lines corresponding to the loss of phosphate under IRMPD fragmentation allows the selective identification of phosphopeptides. Resonance of the 10.6 μm infrared radiation with the vibrational modes of the phosphate functional group produced efficient absorption and high cleavage coverage of the phosphopeptides at much lower irradiation fluence than for nonphosphorylated peptides improving discrimination. Additionally, the localization of the phosphate group was determined.
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Affiliation(s)
- Johanna Paris
- University of Warwick, Department of Chemistry, Coventry CV4 7AL, United Kingdom
| | - Tomos E Morgan
- University of Warwick, Department of Chemistry, Coventry CV4 7AL, United Kingdom
| | | | - Mark P Barrow
- University of Warwick, Department of Chemistry, Coventry CV4 7AL, United Kingdom
| | - John O'Hara
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | - Peter B O'Connor
- University of Warwick, Department of Chemistry, Coventry CV4 7AL, United Kingdom
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16
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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17
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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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18
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Snyder DT, Szalwinski LJ, St John Z, Cooks RG. Two-Dimensional Tandem Mass Spectrometry in a Single Scan on a Linear Quadrupole Ion Trap. Anal Chem 2019; 91:13752-13762. [PMID: 31592640 DOI: 10.1021/acs.analchem.9b03123] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A two-dimensional tandem mass spectrometry (2D MS/MS) scan has been developed for the linear quadrupole ion trap. Precursor ions are mass-selectively excited using a nonlinear ac frequency sweep at constant rf voltage, while simultaneously, all product ions of the excited precursor ions are ejected from the ion trap using a broad-band waveform. The fragmentation time of the precursor ions correlates with the precursor m/z value (the first mass dimension) and also with the ejection time of the product ions, allowing the correlation between precursor and product ions. Additionally, the second mass dimension (product ions' m/z values) is recovered through fast Fourier transform of each mass spectral peak, revealing either intentionally introduced "frequency tags" or the product ion micropacket frequencies, both of which can be converted to product ion m/z through the classical Mathieu parameters, thereby revealing a product ion mass spectrum for every precursor ion without prior isolation. We demonstrate the utility of this method for analyzing a broad range of structurally related precursor ions, including chemical warfare agent simulants, fentanyls and other opioids, amphetamines, cathinones, antihistamines, and tetracyclic antidepressants.
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Affiliation(s)
- Dalton T Snyder
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Lucas J Szalwinski
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Zachary St John
- Department of Chemistry , The College of New Jersey , Ewing Township , New Jersey 08618 , United States
| | - R Graham Cooks
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
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19
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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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20
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Snyder DT, Szalwinski LJ, Wells JM, Cooks RG. Logical MS/MS scans: a new set of operations for tandem mass spectrometry. Analyst 2018; 143:5438-5452. [PMID: 30311922 DOI: 10.1039/c8an01661e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new set of operations for tandem mass spectrometry in a linear ion trap is described. Logical MS/MS operations categorize compounds in mixtures based on characteristic structural features as revealed by MS/MS behavior recorded in multiple fragmentation pathways. This approach is a conceptual extension of tandem mass spectrometry in which interrogation of the full data domain is performed by simultaneous implementation of precursor and neutral loss scans. This process can be thought of as moving through the 2D MS/MS data domain along multiple scan lines simultaneously, which allows experiments that explore the 2D data domain of MS/MS to be couched in terms of logical operations, AND, NAND (not and), OR (inclusive or), XOR (exclusive or), NOT, etc. Examples of particular logical conditions include all precursor ions that fragment to both of two selected product ions (logical AND), or all precursor ions that do not produce a specified fragment ion (logical NOT). These and other operational modes (TRUE/FALSE, XOR, OR, etc.) complement and extend the existing set of conventional MS/MS scans, namely product scans, precursor scans, and neutral loss scans. We describe the implementation of logical MS/MS scans on a commercial linear ion trap mass spectrometer using simple mixtures of amphetamines and fentanyl analogues and argue their utility for complex mixture analysis.
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Affiliation(s)
- Dalton T Snyder
- Purdue University Department of Chemistry, West Lafayette, IN 47907, USA.
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21
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Floris F, Chiron L, Lynch AM, Barrow MP, Delsuc MA, O'Connor PB. Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1700-1705. [PMID: 29869327 PMCID: PMC6060996 DOI: 10.1007/s13361-018-1978-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/13/2018] [Accepted: 04/21/2018] [Indexed: 05/05/2023]
Abstract
Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about ~23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from ~23% to ~42%. Graphical Abstract Two-dimensional mass spectrometry, when applied to primary fragment ions from the source, allows deep-sequencing of the protein calmodulin.
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Affiliation(s)
- Federico Floris
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Lionel Chiron
- CASC4DE, 20 Avenue du Neuhof, 67100, Strasbourg, France
| | - Alice M Lynch
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Marc-André Delsuc
- CASC4DE, 20 Avenue du Neuhof, 67100, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche, U596; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, Université de Strasbourg, 67404, Illkirch-Graffenstaden, France
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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22
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Floris F, Chiron L, Lynch AM, Barrow MP, Delsuc MA, O’Connor PB. Top-Down Deep Sequencing of Ubiquitin Using Two-Dimensional Mass Spectrometry. Anal Chem 2018; 90:7302-7309. [DOI: 10.1021/acs.analchem.8b00500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Federico Floris
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Lionel Chiron
- CASC4DE, 20 Avenue du Neuhof, 67100, Strasbourg, France
| | - Alice M. Lynch
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Mark P. Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Marc-André Delsuc
- CASC4DE, 20 Avenue du Neuhof, 67100, Strasbourg, France
- Institut de Génétique
et de Biologie Moléculaire et Cellulaire, Institut National
de la Santé et de la Recherche, U596; Centre National de la
Recherche Scientifique, Unité Mixte de Recherche 7104; Université
de Strasbourg, 67404, Illkirch-Graffenstaden, France
| | - Peter B. O’Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
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23
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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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24
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Floris F, van Agthoven MA, Chiron L, Wootton CA, Lam PYY, Barrow MP, Delsuc MA, O'Connor PB. Bottom-Up Two-Dimensional Electron-Capture Dissociation Mass Spectrometry of Calmodulin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:207-210. [PMID: 28975559 DOI: 10.1007/s13361-017-1812-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 08/26/2017] [Accepted: 09/08/2017] [Indexed: 06/07/2023]
Abstract
Two-dimensional mass spectrometry (2D MS) is a tandem mass spectrometry technique that allows data-independent fragmentation of all precursors in a mixture without previous isolation, through modulation of the ion cyclotron frequency in the ICR-cell prior to fragmentation. Its power as an analytical technique has been proven particularly for proteomics. Recently, a comparison study between 1D and 2D MS has been performed using infrared multiphoton dissociation (IRMPD) on calmodulin (CaM), highlighting the capabilities of the technique in both top-down (TDP) and bottom-up proteomics (BUP). The goal of this work is to expand this study on CaM using electron-capture dissociation (ECD) 2D MS as a single complementary BUP experiment in order to enhance the cleavage coverage of the protein under analysis. By adding the results of the BUP 2D ECD MS to the 2D IRMPD MS analysis of CaM, the total cleavage coverage increased from ~40% to ~68%. Graphical abstract ᅟ.
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Affiliation(s)
| | | | | | | | | | | | - Marc-André Delsuc
- CASC4DE, Illkirch-Graffenstaden, France
- IGBMC, Illkirch-Graffenstaden, France
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25
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Floris F, Vallotto C, Chiron L, Lynch AM, Barrow MP, Delsuc MA, O’Connor PB. Polymer Analysis in the Second Dimension: Preliminary Studies for the Characterization of Polymers with 2D MS. Anal Chem 2017; 89:9892-9899. [DOI: 10.1021/acs.analchem.7b02086] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Federico Floris
- University of Warwick, Department of Chemistry, Coventry, CV4 7AL, United Kingdom
| | - Claudio Vallotto
- University of Warwick, Department of Chemistry, Coventry, CV4 7AL, United Kingdom
| | - Lionel Chiron
- CASC4DE, 20 Avenue du Neuhof, 67100, Strasbourg, France
| | - Alice M. Lynch
- University of Warwick, Department of Chemistry, Coventry, CV4 7AL, United Kingdom
| | - Mark P. Barrow
- University of Warwick, Department of Chemistry, Coventry, CV4 7AL, United Kingdom
| | - Marc-André Delsuc
- CASC4DE, 20 Avenue du Neuhof, 67100, Strasbourg, France
- Institut
de Génétique et de Biologie Moléculaire et Cellulaire,
Institut National de la Santé et de la Recherche, U596, Centre
National de la Recherche Scientifique, Unité Mixte de Recherche
7104, Université de Strasbourg, 67404 Illkirch-Graffenstaden, France
| | - Peter B. O’Connor
- University of Warwick, Department of Chemistry, Coventry, CV4 7AL, United Kingdom
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26
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Bray F, Bouclon J, Chiron L, Witt M, Delsuc MA, Rolando C. Nonuniform Sampling Acquisition of Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Increased Mass Resolution of Tandem Mass Spectrometry Precursor Ions. Anal Chem 2017; 89:8589-8593. [PMID: 28787122 DOI: 10.1021/acs.analchem.7b01850] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Obtaining the full MS/MS map for fragments and precursors of complex mixtures without hyphenation with chromatographic separation by a data-independent acquisition is a challenge in mass spectrometry which is solved by two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). Until now 2D FTICR MS afforded only a moderate resolution for precursor ion since this resolution is limited by the number of evolution interval steps to which the number of scans, the acquisition time, and the sample consumption are proportional. An overnight acquisition is already required to reach a quadrupole mass filter-like unit mass resolution. Here, we report that 2D FTICR MS using nonuniform sampling (NUS) obtained by randomly skipping points in the first dimension corresponding to the precursor selection gives access, after data processing, to the same structural information contained in a complex mixture. The resolution increases roughly as the inverse of the NUS ratio, up to 26 times at NUS 1/32, leading to an acquisition time reduced in the same ratio compared to a classical acquisition at the same resolution. As an example, the analysis of a natural oil is presented.
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Affiliation(s)
- Fabrice Bray
- Univ. Lille , CNRS, MSAP USR 3290, FR 3688 FRABIO, FR 2638 Institut Eugène-Michel Chevreul, F-59000 Lille, France
| | - Julien Bouclon
- Univ. Lille , CNRS, MSAP USR 3290, FR 3688 FRABIO, FR 2638 Institut Eugène-Michel Chevreul, F-59000 Lille, France.,École Normale Supérieure, PSL Research University , Département de Chimie, 24, Rue Lhomond, F-75005 Paris, France
| | - Lionel Chiron
- CASC4DE , Le Lodge, 20, Avenue du Neuhof, F-67100 Strasbourg, France
| | - Matthias Witt
- Bruker Daltonik , FTMS Applications, Fahrenheitstrasse 4, D-28359 Bremen, Germany
| | - Marc-André Delsuc
- Univ. Strasbourg , INSERM U596, CNRS UMR 7104, F-67404 Illkirch-Graffenstaden, France
| | - Christian Rolando
- Univ. Lille , CNRS, MSAP USR 3290, FR 3688 FRABIO, FR 2638 Institut Eugène-Michel Chevreul, F-59000 Lille, France
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27
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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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