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Article ; Online: Native and Ion Mobility Mass Spectrometry Characterization of Alpha 1 Antitrypsin Variants and Oligomers.

Vickers, Sarah / Irving, James / Lomas, David A / Thalassinos, Konstantinos

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2750, Page(s) 41–55

Abstract: In this chapter, we describe a method for analyzing both recombinant and plasma-derived alpha 1 antitrypsin and its oligomers by means of native ion mobility mass spectrometry. Our experimental workflow can be applied to other variants of alpha 1 ... ...

Abstract	In this chapter, we describe a method for analyzing both recombinant and plasma-derived alpha 1 antitrypsin and its oligomers by means of native ion mobility mass spectrometry. Our experimental workflow can be applied to other variants of alpha 1 antitrypsin and its oligomers as well as being used to probe their interactions with small molecules in the gas phase.
MeSH term(s)	alpha 1-Antitrypsin/genetics ; Ion Mobility Spectrometry ; Plasma ; Workflow ; Mass Spectrometry
Chemical Substances	alpha 1-Antitrypsin
Language	English
Publishing date	2023-12-18
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3605-3_5
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Article ; Online: Developments in tandem ion mobility mass spectrometry.

Eldrid, Charles / Thalassinos, Konstantinos

Biochemical Society transactions

2020 Volume 48, Issue 6, Page(s) 2457–2466

Abstract: Ion Mobility (IM) coupled to mass spectrometry (MS) is a useful tool for separating species of interest out of small quantities of heterogenous mixtures via a combination of m/z and molecular shape. While tandem MS instruments are common, instruments ... ...

Abstract	Ion Mobility (IM) coupled to mass spectrometry (MS) is a useful tool for separating species of interest out of small quantities of heterogenous mixtures via a combination of m/z and molecular shape. While tandem MS instruments are common, instruments which employ tandem IM are less so with the first commercial IM-MS instrument capable of multiple IM selection rounds being released in 2019. Here we explore the history of tandem IM instruments, recent developments, the applications to biological systems and expected future directions.
MeSH term(s)	Biophysics/history ; Biophysics/trends ; Chemistry Techniques, Analytical/history ; Chemistry Techniques, Analytical/trends ; Equipment Design ; History, 20th Century ; History, 21st Century ; Ion Mobility Spectrometry/instrumentation ; Ion Mobility Spectrometry/methods ; Ion Mobility Spectrometry/trends ; Ions ; Tandem Mass Spectrometry/instrumentation ; Tandem Mass Spectrometry/methods ; Tandem Mass Spectrometry/trends
Chemical Substances	Ions
Language	English
Publishing date	2020-10-29
Publishing country	England
Document type	Historical Article ; Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20190788
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Article ; Online: Integration of Mass Spectrometry Data for Structural Biology.

Britt, Hannah M / Cragnolini, Tristan / Thalassinos, Konstantinos

Chemical reviews

2021 Volume 122, Issue 8, Page(s) 7952–7986

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, ... ...

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.
MeSH term(s)	Biology ; Intrinsically Disordered Proteins ; Macromolecular Substances ; Mass Spectrometry/methods ; Protein Conformation
Chemical Substances	Intrinsically Disordered Proteins ; Macromolecular Substances
Language	English
Publishing date	2021-09-10
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/acs.chemrev.1c00356
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Article ; Online: Modeling Flexible Protein Structure With AlphaFold2 and Crosslinking Mass Spectrometry.

Manalastas-Cantos, Karen / Adoni, Kish R / Pfeifer, Matthias / Märtens, Birgit / Grünewald, Kay / Thalassinos, Konstantinos / Topf, Maya

Molecular & cellular proteomics : MCP

2024 Volume 23, Issue 3, Page(s) 100724

Abstract: We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2 and conformer selection ...

Abstract	We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2 and conformer selection using XL-MS data. For conformer selection, we developed two scores-the monolink probability score (MP) and the crosslink probability score (XLP)-both of which are based on residue depth from the protein surface. We benchmarked MP and XLP on a large dataset of decoy protein structures and showed that our scores outperform previously developed scores. We then tested our methodology on three proteins having an open and closed conformation in the Protein Data Bank: Complement component 3 (C3), luciferase, and glutamine-binding periplasmic protein, first generating ensembles using AF2, which were then screened for the open and closed conformations using experimental XL-MS data. In five out of six cases, the most accurate model within the AF2 ensembles-or a conformation within 1 Å of this model-was identified using crosslinks, as assessed through the XLP score. In the remaining case, only the monolinks (assessed through the MP score) successfully identified the open conformation of glutamine-binding periplasmic protein, and these results were further improved by including the "occupancy" of the monolinks. This serves as a compelling proof-of-concept for the effectiveness of monolinks. In contrast, the AF2 assessment score was only able to identify the most accurate conformation in two out of six cases. Our results highlight the complementarity of AF2 with experimental methods like XL-MS, with the MP and XLP scores providing reliable metrics to assess the quality of the predicted models. The MP and XLP scoring functions mentioned above are available at https://gitlab.com/topf-lab/xlms-tools.
MeSH term(s)	Glutamine ; Furylfuramide ; Periplasmic Proteins ; Mass Spectrometry ; Protein Conformation ; Membrane Proteins
Chemical Substances	Glutamine (0RH81L854J) ; Furylfuramide (054NR2135Y) ; Periplasmic Proteins ; Membrane Proteins
Language	English
Publishing date	2024-01-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2024.100724
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Article ; Online: Structural basis of substrate progression through the bacterial chaperonin cycle.

Gardner, Scott / Darrow, Michele C / Lukoyanova, Natalya / Thalassinos, Konstantinos / Saibil, Helen R

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 50, Page(s) e2308933120

Abstract: The bacterial chaperonin GroEL-GroES promotes protein folding through ATP-regulated cycles of substrate protein binding, encapsulation, and release. Here, we have used cryoEM to determine structures of GroEL, GroEL-ADP· ... ...

Abstract	The bacterial chaperonin GroEL-GroES promotes protein folding through ATP-regulated cycles of substrate protein binding, encapsulation, and release. Here, we have used cryoEM to determine structures of GroEL, GroEL-ADP·BeF
MeSH term(s)	Ribulose-Bisphosphate Carboxylase/metabolism ; Adenosine Triphosphate/metabolism ; Chaperonin 60/metabolism ; Chaperonin 10/chemistry ; Protein Folding ; Protein Binding
Chemical Substances	Ribulose-Bisphosphate Carboxylase (EC 4.1.1.39) ; Adenosine Triphosphate (8L70Q75FXE) ; Chaperonin 60 ; Chaperonin 10
Language	English
Publishing date	2023-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2308933120
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Article: Integration of Mass Spectrometry Data for Structural Biology

Britt, Hannah M. / Cragnolini, Tristan / Thalassinos, Konstantinos

Chemical reviews. 2021 Sept. 10, v. 122, no. 8

2021

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.
Keywords	computer software ; crosslinking ; data collection ; glycosylation ; hydroxyl radicals ; mass spectrometry ; nuclear pore ; proteasome endopeptidase complex ; solvents ; stoichiometry ; structural biology
Language	English
Dates of publication	2021-0910
Size	p. 7952-7986.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/acs.chemrev.1c00356
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Article ; Online: Concentration-dependent coulombic effects in travelling wave ion mobility spectrometry collision cross section calibration.

Eldrid, Charles / O'Connor, Eloise / Thalassinos, Konstantinos

Rapid communications in mass spectrometry : RCM

2020 Volume 34 Suppl 4, Page(s) e8613

Abstract: Rationale: Travelling wave ion mobility spectrometry (TWIMS) is increasingly being used as a method for calculating the collision cross sections (CCSs) of protein ions. To calculate the CCS values of unknown ions, however, the TWIMS device needs to be ... ...

Abstract	Rationale: Travelling wave ion mobility spectrometry (TWIMS) is increasingly being used as a method for calculating the collision cross sections (CCSs) of protein ions. To calculate the CCS values of unknown ions, however, the TWIMS device needs to be calibrated using calibrant proteins of known CCS values. The effect of calibrant protein concentration on the accuracy of the resulting calibration curve has not been explicitly studied so far. We hypothesised that at high protein concentrations the ion density within the TWIMS device will be such that ions will experience space charge effects resulting in deviations, as well as broadening, of ion arrival time distributions (ATDs). Calibration curves using these altered ATDs would therefore result in incorrect CCS values being calculated for the protein ions of interest. Methods: Three protein CCS calibrants, avidin, bovine serum albumin and β-lactgobulin, were prepared at different concentrations and used to calculate the CCS of a non-calibrant protein. Data were collected on a Synapt G1 ion mobility mass spectrometer with a nano-electrospray ionisation (nESI) source using capillaries prepared in house. Results: Increasing the concentration of CCS calibrants caused ATD broadening and shifted the ATD peak tops, leading to a significant increase in calculated CCS values. Conclusions: The concentration of protein calibrants can directly affect the quality of the CCS calibration in TWIMS experiments.
Language	English
Publishing date	2020-02-19
Publishing country	England
Document type	Journal Article
ZDB-ID	58731-x
ISSN	1097-0231 ; 0951-4198
ISSN (online)	1097-0231
ISSN	0951-4198
DOI	10.1002/rcm.8613
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Article ; Online: Linking Gas-Phase and Solution-Phase Protein Unfolding via Mobile Proton Simulations.

Eldrid, Charles / Cragnolini, Tristan / Ben-Younis, Aisha / Zou, Junjie / Raleigh, Daniel P / Thalassinos, Konstantinos

Analytical chemistry

2022 Volume 94, Issue 46, Page(s) 16113–16121

Abstract: Native mass spectrometry coupled to ion mobility (IM-MS) combined with collisional activation (CA) of ions in the gas phase ( ...

Abstract	Native mass spectrometry coupled to ion mobility (IM-MS) combined with collisional activation (CA) of ions in the gas phase (
MeSH term(s)	Protons ; Protein Unfolding ; Molecular Dynamics Simulation ; Proteins/chemistry ; Ions/chemistry ; Protein Conformation
Chemical Substances	Protons ; Proteins ; Ions
Language	English
Publishing date	2022-11-09
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.2c03352
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Article ; Online: Optimization Workflow for the Analysis of Cross-Linked Peptides Using a Quadrupole Time-of-Flight Mass Spectrometer.

James, Juliette M B / Cryar, Adam / Thalassinos, Konstantinos

Analytical chemistry

2019 Volume 91, Issue 3, Page(s) 1808–1814

Abstract: Cross-linking mass spectrometry is an emerging structural biology technique. Almost exclusively, the analyzer of choice for such an experiment has been the Orbitrap. We present an optimized protocol for the use of a Synapt G2-Si for the analysis of cross- ...

Abstract	Cross-linking mass spectrometry is an emerging structural biology technique. Almost exclusively, the analyzer of choice for such an experiment has been the Orbitrap. We present an optimized protocol for the use of a Synapt G2-Si for the analysis of cross-linked peptides. We first tested six different energy ramps and analyzed the fragmentation behavior of cross-linked peptides identified by xQuest. By combining the most successful energy ramps, cross-link yield can be increased by up to 40%. When compared to previously published Orbitrap data, the Synapt G2-Si also offers improved fragmentation of the β peptide. In order to improve cross-link quality control we have also developed ValidateXL, a programmatic solution that works with existing cross-linking software to improve cross-link quality control.
MeSH term(s)	Amino Acid Sequence ; Animals ; Cattle ; Cross-Linking Reagents ; Peptide Fragments/analysis ; Peptide Fragments/chemistry ; Serum Albumin, Bovine/analysis ; Serum Albumin, Bovine/chemistry ; Software ; Succinimides/chemistry ; Tandem Mass Spectrometry/methods ; Tandem Mass Spectrometry/statistics & numerical data
Chemical Substances	Cross-Linking Reagents ; Peptide Fragments ; Succinimides ; Serum Albumin, Bovine (27432CM55Q) ; bis(sulfosuccinimidyl)suberate (E647932J7Z)
Language	English
Publishing date	2019-01-23
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.8b02319
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Article: Optimization Workflow for the Analysis of Cross-Linked Peptides Using a Quadrupole Time-of-Flight Mass Spectrometer

James, Juliette M. B / Cryar, Adam / Thalassinos, Konstantinos

Analytical chemistry. 2019 Jan. 08, v. 91, no. 3

2019

Abstract	Cross-linking mass spectrometry is an emerging structural biology technique. Almost exclusively, the analyzer of choice for such an experiment has been the Orbitrap. We present an optimized protocol for the use of a Synapt G2-Si for the analysis of cross-linked peptides. We first tested six different energy ramps and analyzed the fragmentation behavior of cross-linked peptides identified by xQuest. By combining the most successful energy ramps, cross-link yield can be increased by up to 40%. When compared to previously published Orbitrap data, the Synapt G2-Si also offers improved fragmentation of the β peptide. In order to improve cross-link quality control we have also developed ValidateXL, a programmatic solution that works with existing cross-linking software to improve cross-link quality control.
Keywords	computer software ; crosslinking ; energy ; mass spectrometry ; peptides ; quality control ; spectrometers ; structural biology
Language	English
Dates of publication	2019-0108
Size	p. 1808-1814.
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.8b02319
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