1
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Rahman M, Marzullo BP, Lam PY, Barrow MP, Holman SW, Ray AD, O'Connor PB. Unveiling the intricacy of gapmer oligonucleotides through advanced tandem mass spectrometry approaches and scan accumulation for 2DMS. Analyst 2024; 149:4687-4701. [PMID: 39101388 PMCID: PMC11382339 DOI: 10.1039/d4an00484a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Antisense oligonucleotides (ASOs) are crucial for biological applications as they bind to complementary RNA sequences, modulating protein expression. ASOs undergo synthetic modifications like phosphorothioate (PS) backbone and locked nucleic acid (LNA) to enhance stability and specificity. Tandem mass spectrometry (MS) techniques were employed to study gapmer ASOs, which feature a DNA chain within RNA segments at both termini, revealing enhanced cleavages with ultraviolet photodissociation (UVPD) and complementary fragment ions from collision-induced dissociation (CID) and electron detachment dissociation (EDD). 2DMS, a data-independent analysis technique, allowed for comprehensive coverage and identification of shared fragments across multiple precursor ions. EDD fragmentation efficiency correlated with precursor ion charge states, with higher charges facilitating dissociation due to intramolecular repulsions. An electron energy of 22.8 eV enabled electron capture and radical-based cleavage. Accumulating multiple scans and generating average spectra improved signal intensity, aided by denoising algorithms. Data analysis utilised a custom Python script capable of handling modifications and generating unique mass lists.
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Affiliation(s)
- Mohammed Rahman
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Bryan P Marzullo
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Pui Yiu Lam
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Stephen W Holman
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, AstraZeneca, SK10 2NA, UK
| | - Andrew D Ray
- New Modalities & Parental Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 2NA, UK
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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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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Abou-Dib A, Aubriet F, Hertzog J, Vernex-Loset L, Schramm S, Carré V. Next Challenges for the Comprehensive Molecular Characterization of Complex Organic Mixtures in the Field of Sustainable Energy. Molecules 2022; 27:8889. [PMID: 36558021 PMCID: PMC9786309 DOI: 10.3390/molecules27248889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
The conversion of lignocellulosic biomass by pyrolysis or hydrothermal liquefaction gives access to a wide variety of molecules that can be used as fuel or as building blocks in the chemical industry. For such purposes, it is necessary to obtain their detailed chemical composition to adapt the conversion process, including the upgrading steps. Petroleomics has emerged as an integral approach to cover a missing link in the investigation bio-oils and linked products. It relies on ultra-high-resolution mass spectrometry to attempt to unravel the contribution of many compounds in complex samples by a non-targeted approach. The most recent developments in petroleomics partially alter the discriminating nature of the non-targeted analyses. However, a peak referring to one chemical formula possibly hides a forest of isomeric compounds, which may present a large chemical diversity concerning the nature of the chemical functions. This identification of chemical functions is essential in the context of the upgrading of bio-oils. The latest developments dedicated to this analytical challenge will be reviewed and discussed, particularly by integrating ion source features and incorporating new steps in the analytical workflow. The representativeness of the data obtained by the petroleomic approach is still an important issue.
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Affiliation(s)
| | | | | | | | | | - Vincent Carré
- LCP A2MC, Université de Lorraine, F-57000 Metz, France
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4
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Theisen A, Wootton CA, Haris A, Morgan TE, Lam YPY, Barrow MP, O’Connor PB. Enhancing Biomolecule Analysis and 2DMS Experiments by Implementation of (Activated Ion) 193 nm UVPD on a FT-ICR Mass Spectrometer. Anal Chem 2022; 94:15631-15638. [DOI: 10.1021/acs.analchem.2c02354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Alina Theisen
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Anisha Haris
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Tomos E. Morgan
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Yuko P. Y. Lam
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Mark P. Barrow
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Peter B. O’Connor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
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5
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Paris J, Theisen A, Marzullo BP, Haris A, Morgan TE, Barrow MP, O’Hara J, O’Connor PB. Multimodal Tandem Mass Spectrometry Techniques for the Analysis of Phosphopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1126-1133. [PMID: 35604791 PMCID: PMC9264387 DOI: 10.1021/jasms.1c00353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Collisionally activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), ultraviolet photodissociation (UVPD), electron capture dissociation and electron detachment dissociation (EDD) experiments were conducted on a set of phosphopeptides, in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation patterns were compared and varied according to the fragmentation mechanisms and the composition of the peptides. CAD and IRMPD produced similar fragmentation profiles of the phosphopeptides, while UVPD produced a large number of complementary fragments. Electron-based dissociation techniques displayed lower fragmentation efficiencies, despite retaining the labile phosphate group, and drastically different fragmentation profiles. EDD produced complex spectra whose interpretation proved challenging.
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Affiliation(s)
- Johanna Paris
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alina Theisen
- 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
| | - Anisha Haris
- 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
| | - 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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6
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Identification, production and bioactivity of casein phosphopeptides – A review. Food Res Int 2022; 157:111360. [DOI: 10.1016/j.foodres.2022.111360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 01/23/2023]
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7
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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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8
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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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9
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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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10
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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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11
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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
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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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