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Article ; Online: Developments in Trapped Ion Mobility Mass Spectrometry to Probe the Early Stages of Peptide Aggregation.

Depraz Depland, Agathe / Stroganova, Iuliia / Wootton, Christopher A / Rijs, Anouk M

Journal of the American Society for Mass Spectrometry

2023 Volume 34, Issue 2, Page(s) 193–204

Abstract: Ion mobility mass spectrometry (IM-MS) has proven to be an excellent method to characterize the structure of amyloidogenic protein and peptide aggregates, which are formed in coincidence with the development of neurodegenerative diseases. However, it ... ...

Abstract	Ion mobility mass spectrometry (IM-MS) has proven to be an excellent method to characterize the structure of amyloidogenic protein and peptide aggregates, which are formed in coincidence with the development of neurodegenerative diseases. However, it remains a challenge to obtain detailed structural information on all conformational intermediates, originating from the early onset of those pathologies, due to their complex and heterogeneous environment. One way to enhance the insights and the identification of these early stage oligomers is by employing high resolution ion mobility mass spectrometry experiments. This would allow us to enhance the mobility separation and MS characterization. Trapped ion mobility spectrometry (TIMS) is an ion mobility technique known for its inherently high resolution and has successfully been applied to the analysis of protein conformations among others. To obtain conformational information on fragile peptide aggregates, the instrumental parameters of the TIMS-Quadrupole-Time-of-Flight mass spectrometer (TIMS-qToF-MS) have to be optimized to allow the study of intact aggregates and ensure their transmission toward the detector. Here, we investigate the suitability and application of TIMS to probe the aggregation process, targeting the well-characterized M307-N319 peptide segment of the TDP-43 protein, which is involved in the development of amyotrophic lateral sclerosis. By studying the influence of key parameters over the full mass spectrometer, such as source temperature, applied voltages or RFs among others, we demonstrate that by using an optimized instrumental method TIMS can be used to probe peptide aggregation.
MeSH term(s)	Humans ; Ion Mobility Spectrometry/methods ; Peptides/analysis ; Mass Spectrometry/methods ; Protein Conformation ; Amyotrophic Lateral Sclerosis
Chemical Substances	Peptides
Language	English
Publishing date	2023-01-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.2c00253
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Article ; Online: Top-Down Protein Analysis by Tandem-Trapped Ion Mobility Spectrometry/Mass Spectrometry (Tandem-TIMS/MS) Coupled with Ultraviolet Photodissociation (UVPD) and Parallel Accumulation/Serial Fragmentation (PASEF) MS/MS Analysis.

Liu, Fanny C / Ridgeway, Mark E / Wootton, Christopher A / Theisen, Alina / Panczyk, Erin M / Meier, Florian / Park, Melvin A / Bleiholder, Christian

Journal of the American Society for Mass Spectrometry

2023 Volume 34, Issue 10, Page(s) 2232–2246

Abstract: Top-down" proteomics analyzes intact proteins and identifies proteoforms by their intact mass as well as the observed fragmentation pattern in tandem mass spectrometry (MS/MS) experiments. Recently, hybrid ion mobility spectrometry-mass spectrometry (IM/ ...

Abstract	"Top-down" proteomics analyzes intact proteins and identifies proteoforms by their intact mass as well as the observed fragmentation pattern in tandem mass spectrometry (MS/MS) experiments. Recently, hybrid ion mobility spectrometry-mass spectrometry (IM/MS) methods have gained traction for top-down experiments, either by allowing top-down analysis of individual isomers or alternatively by improving signal/noise and dynamic range for fragment ion assignment. We recently described the construction of a tandem-trapped ion mobility spectrometer/mass spectrometer (tandem-TIMS/MS) coupled with an ultraviolet (UV) laser and demonstrated a proof-of-principle for top-down analysis by UV photodissociation (UVPD) at 2-3 mbar. The present work builds on this with an exploration of a top-down method that couples tandem-TIMS/MS with UVPD and parallel-accumulation serial fragmentation (PASEF) MS/MS analysis. We first survey types and structures of UVPD-specific fragment ions generated in the 2-3 mbar pressure regime of our instrument. Notably, we observe UVPD-induced fragment ions with multiple conformations that differ from those produced in the absence of UV irradiation. Subsequently, we discuss how MS/MS spectra of top-down fragment ions lend themselves ideally for probability-based scoring methods developed in the bottom-up proteomics field and how the ability to record automated PASEF-MS/MS spectra resolves ambiguities in the assignment of top-down fragment ions. Finally, we describe the coupling of tandem-TIMS/MS workflows with UVPD and PASEF-MS/MS analysis for native top-down protein analysis.
MeSH term(s)	Tandem Mass Spectrometry/methods ; Ion Mobility Spectrometry ; Proteins/analysis ; Ions ; Ultraviolet Rays
Chemical Substances	Proteins ; Ions
Language	English
Publishing date	2023-08-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.3c00187
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Article ; Online: Top-Down Proteoform Analysis by 2D MS with Quadrupolar Detection

Polák, Marek / Palasser, Michael / Kádek, Alan / Kavan, Daniel / Wootton, Christopher A. / Delsuc, Marc-André / Breuker, Kathrin / Novák, Petr / van Agthoven, Maria A.

Analytical Chemistry. 2023 Oct. 25, v. 95, no. 44 p.16123-16130

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 ... ...

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.
Keywords	analytical chemistry ; chemical species ; spectrometers ; tandem mass spectrometry
Language	English
Dates of publication	2023-1025
Size	p. 16123-16130.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c02225
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Article ; Online: Fine Structure in Isotopic Peak Distributions Measured Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: A Comparison between an Infinity ICR Cell and a Dynamically Harmonized ICR Cell.

Xu, Jingsha / Li, Meng / Marzullo, Bryan / Wootton, Christopher A / Barrow, Mark P / O'Connor, Peter B

Journal of the American Society for Mass Spectrometry

2022 Volume 33, Issue 8, Page(s) 1499–1509

Abstract: The fine structure of isotopic peak distributions of glutathione in mass spectra is measured using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) at 12 and 15 T magnetic field, with an infinity cell and a dynamically harmonized ... ...

Abstract	The fine structure of isotopic peak distributions of glutathione in mass spectra is measured using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) at 12 and 15 T magnetic field, with an infinity cell and a dynamically harmonized cell (DHC) respectively. The resolved peaks in the fine structure of glutathione consist of
MeSH term(s)	Calibration ; Cyclotrons ; Fourier Analysis ; Glutathione ; Mass Spectrometry/methods
Chemical Substances	Glutathione (GAN16C9B8O)
Language	English
Publishing date	2022-06-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.2c00093
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Article ; Online: Enhancing Biomolecule Analysis and 2DMS Experiments by Implementation of (Activated Ion) 193 nm UVPD on a FT-ICR Mass Spectrometer.

Theisen, Alina / Wootton, Christopher A / Haris, Anisha / Morgan, Tomos E / Lam, Yuko P Y / Barrow, Mark P / O'Connor, Peter B

Analytical chemistry

2022 Volume 94, Issue 45, Page(s) 15631–15638

Abstract: Ultraviolet photodissociation is a fast, photon-mediated fragmentation method that yields high sequence coverage and informative cleavages of biomolecules. In this work, 193 nm UVPD was coupled with a 12 Tesla FT-ICR mass spectrometer and 10.6 μm ... ...

Abstract	Ultraviolet photodissociation is a fast, photon-mediated fragmentation method that yields high sequence coverage and informative cleavages of biomolecules. In this work, 193 nm UVPD was coupled with a 12 Tesla FT-ICR mass spectrometer and 10.6 μm infrared multi-photon dissociation to provide gentle slow-heating of UV-irradiated ions. No internal instrument hardware modifications were required. Adjusting the timing of laser pulses to the ion motion within the ICR cell provided consistent fragmentation yield shot-to-shot and may also be used to monitor ion positions within the ICR cell. Single-pulse UVPD of the native-like 5+ charge state of ubiquitin resulted in 86.6% cleavage coverage. Additionally, IR activation post UVPD doubled the overall fragmentation yield and boosted the intensity of UVPD-specific x-type fragments up to 4-fold. This increased yield effect was also observed for the 6+ charge state of ubiquitin, albeit less pronounced. This indicates that gentle slow-heating serves to sever tethered fragments originating from non-covalently linked compact structures and makes activation post UVPD an attractive option to boost fragmentation efficiency for top-down studies. Lastly, UVPD was implemented and optimized as a fragmentation method for 2DMS, a data-independent acquisition method. UVPD-2DMS was demonstrated to be a viable method using BSA digest peptides as a model system.
MeSH term(s)	Tandem Mass Spectrometry/methods ; Ultraviolet Rays ; Ions ; Peptides ; Ubiquitin
Chemical Substances	Ions ; Peptides ; Ubiquitin
Language	English
Publishing date	2022-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c02354
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Article ; Online: Differentiation of Dihydroxylated Vitamin D

Haris, Anisha / Lam, Yuko P Y / Wootton, Christopher A / Theisen, Alina / Marzullo, Bryan P / Schorr, Pascal / Volmer, Dietrich A / O'Connor, Peter B

Journal of the American Society for Mass Spectrometry

2022 Volume 33, Issue 6, Page(s) 1022–1030

Abstract: Vitamin D compounds are a group of secosteroids derived from cholesterol that are vital for maintaining bone health in humans. Recent studies have shown extraskeletal effects of vitamin D, involving vitamin D metabolites such as the dihydroxylated ... ...

Abstract	Vitamin D compounds are a group of secosteroids derived from cholesterol that are vital for maintaining bone health in humans. Recent studies have shown extraskeletal effects of vitamin D, involving vitamin D metabolites such as the dihydroxylated vitamin D
MeSH term(s)	Cholecalciferol ; Chromatography, Liquid/methods ; Cyclotrons ; Humans ; Tandem Mass Spectrometry/methods ; Vitamin D ; Vitamins
Chemical Substances	Vitamins ; Vitamin D (1406-16-2) ; Cholecalciferol (1C6V77QF41)
Language	English
Publishing date	2022-05-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.2c00085
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Article ; Online: Top-Down Proteoform Analysis by 2D MS with Quadrupolar Detection.

Polák, Marek / Palasser, Michael / Kádek, Alan / Kavan, Daniel / Wootton, Christopher A / Delsuc, Marc-André / Breuker, Kathrin / Novák, Petr / van Agthoven, Maria A

Analytical chemistry

2023 Volume 95, Issue 44, Page(s) 16123–16130

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.
MeSH term(s)	Proteomics/methods ; Tandem Mass Spectrometry/methods ; Ubiquitin ; Cyclotrons ; Fourier Analysis
Chemical Substances	Ubiquitin
Language	English
Publishing date	2023-10-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c02225
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Article: Facile Determination of Phosphorylation Sites in Peptides Using Two-Dimensional Mass Spectrometry

Paris, Johanna / Morgan, Tomos E / Wootton, Christopher A / Barrow, Mark P / O’Hara, John / O’Connor, Peter B

Analytical chemistry. 2020 Apr. 14, v. 92, no. 10

2020

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. ... ...

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.
Keywords	absorption ; analytical chemistry ; dissociation ; infrared radiation ; irradiation ; mass spectrometry ; phosphates ; phosphopeptides ; phosphorylation
Language	English
Dates of publication	2020-0414
Size	p. 6817-6821.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.0c00884
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Article ; Online: Two-Dimensional Mass Spectrometry Analysis of IgG1 Antibodies.

Paris, Johanna / Morgan, Tomos E / Marzullo, Bryan P / Wootton, Christopher A / Barrow, Mark P / O'Hara, John / O'Connor, Peter B

Journal of the American Society for Mass Spectrometry

2021 Volume 32, Issue 7, Page(s) 1716–1724

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 ...

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
MeSH term(s)	Humans ; Immunoglobulin G/analysis ; Immunoglobulin G/chemistry ; Protein Processing, Post-Translational ; Proteomics/methods ; Tandem Mass Spectrometry/methods
Chemical Substances	Immunoglobulin G
Language	English
Publishing date	2021-06-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.1c00096
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Article: Combining Ultraviolet Photodissociation and Two-Dimensional Mass Spectrometry: A Contemporary Approach for Characterizing Singly Charged Agrochemicals

Marzullo, Bryan P. / Morgan, Tomos E. / Theisen, Alina / Haris, Anisha / Wootton, Christopher A. / Perry, Simon J. / Saeed, Mansoor / Barrow, Mark P. / O’Connor, Peter B.

Analytical chemistry. 2021 July 01, v. 93, no. 27

2021

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 ... ...

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.
Keywords	agrochemicals ; analytical chemistry ; calibration ; dissociation ; mass spectrometry ; moieties ; photolysis
Language	English
Dates of publication	2021-0701
Size	p. 9462-9470.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c01185
Database	NAL-Catalogue (AGRICOLA)

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