1
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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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2
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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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3
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Zhang W, Yang C, Liu J, Liang Z, Shan Y, Zhang L, Zhang Y. Accurate discrimination of leucine and isoleucine residues by combining continuous digestion with multiple MS 3 spectra integration in protein sequence. Talanta 2022; 249:123666. [PMID: 35717752 DOI: 10.1016/j.talanta.2022.123666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 12/26/2022]
Abstract
Protein de novo sequencing based on tandem mass spectrometry is a crucial technology that enables the identification of peptides without searching databases and assembling unknown sequence proteins, especially for monoclonal antibodies (mAbs). However, the discrimination of leucine (Leu) and isoleucine (Ile) residues in the target protein sequence is still challenging. Herein, we developed an accurate method by continuous digestion with MS3-based fragmentation and multiple spectra integration (evaluated by combined verification score, CVS) to distinguish Leu and Ile residues. Continuous digestion promotes the diversity of peptides in order to expose more Leu and Ile at the N-terminal. CVS integrates multiple MS3 spectra to reduce the interference from noise and co-fragmented ions and improve accuracy. This method successfully resolved all 75 Leu/Ile in bovine serum albumin, especially 3 consecutive Leu/Ile. We further applied the method to analyze trastuzumab and 67 out of the 68 Leu/Ile from the light chain and heavy chain were accurately discriminated, demonstrating the great potential in mAbs sequencing.
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Affiliation(s)
- Weijie Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chao Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Yichu Shan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
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4
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Edwards HM, Wu HT, Julian RR, Jackson GP. Differentiation of leucine and isoleucine residues in peptides using charge transfer dissociation mass spectrometry (CTD-MS). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9246. [PMID: 34927767 DOI: 10.1002/rcm.9246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
RATIONALE The function of a protein or the binding affinity of an antibody can be substantially altered by the replacement of leucine (Leu) with isoleucine (Ile), and vice versa, so the ability to identify the correct isomer using mass spectrometry can help resolve important biological questions. Tandem mass spectrometry approaches for Leu/Ile (Xle) discrimination have been developed, but they all have certain limitations. METHODS Four model peptides and two wild-type peptide sequences containing either Leu or Ile residues were subjected to charge transfer dissociation (CTD) mass spectrometry on a modified three-dimensional ion trap. The peptides were analyzed in both the 1+ and 2+ charge states, and the results were compared to conventional collision-induced dissociation spectra of the same peptides obtained using the same instrument. RESULTS CTD resulted in 100% sequence coverage for each of the studied peptides and provided a variety of side-chain cleavages, including d, w and v ions. Using CTD, reliable d and w ions of Xle residues were observed more than 80% of the time. When present, d ions are typically greater than 10% of the abundance of the corresponding a ions from which they derive, and w ions are typically more abundant than the z ions from which they derive. CONCLUSIONS CTD has the benefit of being applicable to both 1+ and 2+ precursor ions, and the overall performance is comparable to that of other high-energy activation techniques like hot electron capture dissociation and UV photodissociation. CTD does not require chemical modifications of the precursor peptides, nor does it require additional levels of isolation and fragmentation.
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Affiliation(s)
- Halle M Edwards
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, USA
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5
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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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6
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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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7
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Marzullo BP, Morgan TE, Theisen A, Haris A, Wootton CA, Perry SJ, Saeed M, Barrow MP, O'Connor PB. Combining Ultraviolet Photodissociation and Two-Dimensional Mass Spectrometry: A Contemporary Approach for Characterizing Singly Charged Agrochemicals. Anal Chem 2021; 93:9462-9470. [PMID: 34192872 DOI: 10.1021/acs.analchem.1c01185] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet photodissociation (UVPD) has been shown to produce extensive structurally informative data for a variety of chemically diverse compounds. Herein, we demonstrate the performance of the 193 nm UVPD fragmentation technique on structural/moiety characterization of 14 singly charged agrochemicals. Two-dimensional mass spectrometry (2DMS) using infrared multiphoton dissociation (IRMPD) and electron-induced dissociation (EID) have previously been applied to a select range of singly charged pesticides. The ≥80% moiety coverage achieved for the majority of the species by the UVPD and 2D-UVPD methods was on par with and, in some cases, superior to the data obtained by other fragmentation techniques in previous studies, demonstrating that UVPD is viable for these types of species. A three-dimensional (3D) peak picking method was implemented to extract the data from the 2DMS spectrum, overcoming the limitations of the line extraction method used in previous studies, successfully separating precursor specific fragments with milli-Dalton accuracy. Whole spectrum internal calibration combined with 3D peak picking obtained sub-part-per-million (ppm) to part-per-billion (ppb) mass accuracies across the entire 2DMS spectrum.
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Affiliation(s)
- Bryan P Marzullo
- 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
| | - Alina Theisen
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Anisha Haris
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - Simon J Perry
- Product Metabolism & Analytical Sciences, Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Mansoor Saeed
- Product Metabolism & Analytical Sciences, Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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8
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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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9
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Tian C, Sun M, Quan J. Molecular chirality of Macrolide antibiotics. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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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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11
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Marzullo BP, Morgan TE, Wootton CA, Perry SJ, Saeed M, Barrow MP, O'Connor PB. Advantages of Two-Dimensional Electron-Induced Dissociation and Infrared Multiphoton Dissociation Mass Spectrometry for the Analysis of Agrochemicals. Anal Chem 2020; 92:11687-11695. [PMID: 32700900 DOI: 10.1021/acs.analchem.0c01585] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Analysis of agrochemicals in an environmental matrix is challenging because these samples contain multiple agrochemicals, their metabolites, degradation products, and endogenous compounds. The analysis of such complex samples is achieved using chromatographic separation techniques coupled to mass spectrometry. Herein, we demonstrate a two-dimensional mass spectrometry (2DMS) technique on a 12 T Fourier transform ion cyclotron resonance mass spectrometer that can analyze a mixture of agrochemicals without using chromatography or quadrupole isolation in a single experiment. The resulting 2DMS contour plot contains abundant tandem MS information for each component in the sample and correlates product ions to their corresponding precursor ions. Two different fragmentation methods are employed, infrared multiphoton dissociation (IRMPD) and electron-induced dissociation (EID), with 2DMS to analyze the mixture of singly charged agrochemicals. The product ions of one of the agrochemicals, pirimiphos-methyl, present in the sample was used to internally calibrate the entire 2DMS spectrum, achieving sub part per million (ppm) to part per billion (ppb) mass accuracies for all species analyzed. The work described in this study will show the advantages of the 2DMS approach, by grouping species with common fragments/core structure and mutual functional groups, using precursor lines and neutral loss lines. In addition, the rich spectral information obtained from IRMPD and EID 2DMS contour plots can accurately identify and characterize agrochemicals.
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Affiliation(s)
- Bryan P Marzullo
- 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
| | | | - Simon J Perry
- Product Metabolism & Analytical Sciences, Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Mansoor Saeed
- Product Metabolism & Analytical Sciences, Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, 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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Chiu CKC, Lam YPY, Wootton CA, Barrow MP, Sadler PJ, O'Connor PB. Metallocomplex-Peptide Interactions Studied by Ultrahigh Resolution Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:594-601. [PMID: 31967804 DOI: 10.1021/jasms.9b00054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The OsII arene anticancer complex [(η6-bip)Os(en)Cl]+ (Os1-Cl; where bip = biphenyl and en = ethylenediamine) binds strongly to DNA1 and biomolecules. Here we investigate the interaction between Os1-Cl and the model protein, BSA, using ultrahigh resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The specific binding location of Os1 on BSA was investigated with the use of collisionally activated dissociation (CAD) and electron capture dissociation (ECD). CAD MS/MS was found to dissociate the osmium complex from the metallo-peptide complex readily producing unmodified fragments and losing location information. ECD MS/MS, however, successfully retains the osmium modification on the peptides upon fragmentation allowing localization of metallocomplex binding. This study reveals that lysine is a possible binding location for Os1-Cl, apart from the expected binding sites at methionine, histidine, and cysteine. Using a nano liquid chromatography (nLC)-FT-ICR ECD MS/MS study, multiple binding locations, including the N-terminus and C-terminus of digested peptides, glutamic acid, and lysine were also revealed. These results show the multitargeting binding ability of the organo-osmium compound and can be used as a standard workflow for more complex systems, e.g., metallocomplex-cell MS analysis, to evaluate their behavior toward commonly encountered biomolecules.
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Affiliation(s)
- Cookson K C Chiu
- 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
| | - Christopher A Wootton
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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13
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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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14
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Zhang J, Jia S, Lu W, Li W, Jiang R, Liu Y, Yang X, Zou S, Zou X, Zhong H. Real-time laser induced chemical derivatizations of peptide N-Terminus for in-situ mass spectrometric sequencing at sub-picomole and nanosecond scale. Anal Chim Acta 2019; 1100:1-11. [PMID: 31987129 DOI: 10.1016/j.aca.2019.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 11/30/2022]
Abstract
Distinguishing b- and y-ions is essential to compute amino acid sequences from either N- or C-terminus in mass spectrometry. We described herein a solvent free and real time on-plate derivatization approach that can tag N-terminus of peptides at microliter level with p-chlorobenzaldehyde or 2-hydroxy-5-methylisophthalaldehyde for matrix assisted laser desorption ionization mass spectrometry (MALDI MS). Less than 1 μL of sample solutions can be directly mixed with equal volumes of p-chlorobenzaldehyde or 2-hydroxy-5-methylisophthalaldehyde and α-cyano-4-hydroxycinnamic acid (CHCA), a matrix compound to co-crystalize with analytes for efficient absorption of laser energy and peptide ionization. When the mixture spotted on the sample plate is irradiated with the 3rd harmonic (355 nm) of Nd3+:YAG laser pulses (3 ns width), N-terminal amine groups of peptides instantly react with carbonyl groups of chlorobenzaldehyde or 2-hydroxy-5-methylisophthalaldehyde. Resultant peptides carrying with on-plate formed azomethine group (-CN-) are simultaneously protonated and isolated as precursor ions for subsequent collision-activated dissociation. The mass shift with unique Cl isotopic signature unambiguously distinguishes b ions from y ions and other ions. This method does not need extensive sample preparation and is useful for those samples with limited quantities down to sub-picomole level in sub-microliter volumes. The efficiency was demonstrated with synthetic peptides and tryptic peptides of model proteins. It was found that 2-hydroxy-5-methylisophthalaldehyde provides improved yield for peptides containing lysine residues. Unknown proteins of human saliva and bovine milk as well as phosphopeptides have been identified.
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Affiliation(s)
- Juan Zhang
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Shanshan Jia
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Wenting Lu
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Weidan Li
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Ruowei Jiang
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Yanping Liu
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Xiaojie Yang
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Si Zou
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Xuekun Zou
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China
| | - Hongying Zhong
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Wuhan, Hubei, 430079, PR China; Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, PR China.
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15
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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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16
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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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17
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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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18
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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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