1
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Benoit F, Wang X, Dai J, Geue N, England RM, Bristow AWT, Barran PE. Exploring the Conformational Landscape of Poly(l-lysine) Dendrimers Using Ion Mobility Mass Spectrometry. Anal Chem 2024; 96:9390-9398. [PMID: 38812282 PMCID: PMC11170554 DOI: 10.1021/acs.analchem.4c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
Ion mobility mass spectrometry (IM-MS) measures the mass, size, and shape of ions in the same experiment, and structural information is provided via collision cross-section (CCS) values. The majority of commercially available IM-MS instrumentation relies on the use of CCS calibrants, and here, we present data from a family of poly(l-lysine) dendrimers and explore their suitability for this purpose. In order to test these compounds, we employed three different IM-MS platforms (Agilent 6560 IM-QToF, Waters Synapt G2, and a home-built variable temperature drift tube IM-MS) and used them to investigate six different generations of dendrimers in two buffer gases (helium and nitrogen). Each molecule gives a highly discrete CCS distribution suggestive of single conformers for each m/z value. The DTCCSN2 values of this series of molecules (molecular weight: 330-16,214 Da) range from 182 to 2941 Å2, which spans the CCS range that would be found by many synthetic molecules including supramolecular compounds and many biopolymers. The CCS values for each charge state were highly reproducible in day-to-day analysis on each instrument, although we found small variations in the absolute CCS values between instruments. The rigidity of each dendrimer was probed using collisionally activated and high-temperature IM-MS experiments, where no evidence for a significant CCS change ensued. Taken together, this data indicates that these polymers are candidates for CCS calibration and could also help to reconcile differences found in CCS measurements on different instrument geometries.
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Affiliation(s)
- Florian Benoit
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Xudong Wang
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Junxiao Dai
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Niklas Geue
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Richard M. England
- Advanced
Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Anthony W. T. Bristow
- Chemical
Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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2
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Ito R, Ohshimo K, Misaizu F. Intra-host π-π interactions in crown ether complexes revealed by cryogenic ion mobility-mass spectrometry. Phys Chem Chem Phys 2024; 26:12537-12544. [PMID: 38619106 DOI: 10.1039/d4cp00835a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Cryogenic ion mobility-mass spectrometry was performed to investigate the relative abundance of conformers of dinaphtho-24-crown-8 (DN24C8) complexes with alkali metal cations M+ (M = Li, Na, K, Rb, and Cs). The "closed" conformers of M+(DN24C8) with short distances between two naphthalene rings in the crown ethers were predominantly observed for all complexes at 86 K. The two noncovalent interactions, host-guest and intra-host interactions, were analyzed separately by density functional theory calculations to reveal the origin of the stability of the closed conformers. As a result, it was revealed that the intra-host π-π interactions have a more critical role in determining the stability of the conformers than the host-guest interactions. The closed conformers of M+(DN24C8) also have wider regions of the π-π interactions than those of the M+(dibenzo-24-crown-8) complexes.
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Affiliation(s)
- Ryosuke Ito
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Keijiro Ohshimo
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Fuminori Misaizu
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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3
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Griffiths D, Anderson M, Richardson K, Inaba-Inoue S, Allen WJ, Collinson I, Beis K, Morris M, Giles K, Politis A. Cyclic Ion Mobility for Hydrogen/Deuterium Exchange-Mass Spectrometry Applications. Anal Chem 2024; 96:5869-5877. [PMID: 38561318 PMCID: PMC11024883 DOI: 10.1021/acs.analchem.3c05753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful tool to probe protein dynamics. As a bottom-up technique, HDX-MS provides information at peptide-level resolution, allowing structural localization of dynamic changes. Consequently, the HDX-MS data quality is largely determined by the number of peptides that are identified and monitored after deuteration. Integration of ion mobility (IM) into HDX-MS workflows has been shown to increase the data quality by providing an orthogonal mode of peptide ion separation in the gas phase. This is of critical importance for challenging targets such as integral membrane proteins (IMPs), which often suffer from low sequence coverage or redundancy in HDX-MS analyses. The increasing complexity of samples being investigated by HDX-MS, such as membrane mimetic reconstituted and in vivo IMPs, has generated need for instrumentation with greater resolving power. Recently, Giles et al. developed cyclic ion mobility (cIM), an IM device with racetrack geometry that enables scalable, multipass IM separations. Using one-pass and multipass cIM routines, we use the recently commercialized SELECT SERIES Cyclic IM spectrometer for HDX-MS analyses of four detergent solubilized IMP samples and report its enhanced performance. Furthermore, we develop a novel processing strategy capable of better handling multipass cIM data. Interestingly, use of one-pass and multipass cIM routines produced unique peptide populations, with their combined peptide output being 31 to 222% higher than previous generation SYNAPT G2-Si instrumentation. Thus, we propose a novel HDX-MS workflow with integrated cIM that has the potential to enable the analysis of more complex systems with greater accuracy and speed.
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Affiliation(s)
- Damon Griffiths
- Faculty
of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, Princess
Street, Manchester M1 7DN, United Kingdom
| | - Malcolm Anderson
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Keith Richardson
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Satomi Inaba-Inoue
- Department
of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford
Appleton Laboratory, Research Complex at Harwell, Oxfordshire, Didcot OX11 0FA, United Kingdom
- Diffraction
and Scattering Division, Japan Synchrotron
Radiation Research Institute, SPring-8, 1-1-1, Kouto, Sayo, Hyogo 679-5198, Japan
| | - William J. Allen
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Ian Collinson
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Konstantinos Beis
- Department
of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford
Appleton Laboratory, Research Complex at Harwell, Oxfordshire, Didcot OX11 0FA, United Kingdom
| | - Michael Morris
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Kevin Giles
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Argyris Politis
- Faculty
of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, Princess
Street, Manchester M1 7DN, United Kingdom
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4
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Geue N, Winpenny REP, Barran PE. Ion Mobility Mass Spectrometry for Large Synthetic Molecules: Expanding the Analytical Toolbox. J Am Chem Soc 2024; 146:8800-8819. [PMID: 38498971 PMCID: PMC10996010 DOI: 10.1021/jacs.4c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/20/2024]
Abstract
Understanding the composition, structure and stability of larger synthetic molecules is crucial for their design, yet currently the analytical tools commonly used do not always provide this information. In this perspective, we show how ion mobility mass spectrometry (IM-MS), in combination with tandem mass spectrometry, complementary techniques and computational methods, can be used to structurally characterize synthetic molecules, make and predict new complexes, monitor disassembly processes and determine stability. Using IM-MS, we present an experimental and computational framework for the analysis and design of complex molecular architectures such as (metallo)supramolecular cages, nanoclusters, interlocked molecules, rotaxanes, dendrimers, polymers and host-guest complexes.
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Affiliation(s)
- Niklas Geue
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Richard E. P. Winpenny
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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5
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Villacob RA, Feizi N, Beno SC, Solouki T. Collision-Induced Unfolding, Tandem MS, Bottom-up Proteomics, and Interactomics for Identification of Protein Complexes in Native Surface Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:13-30. [PMID: 38095581 DOI: 10.1021/jasms.3c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Endogenously occurring salts and nonvolatile matrix components in untreated biological surfaces can suppress protein ionization and promote adduct formation, challenging protein identification. Characterization of labile proteins within biological specimens is particularly demanding because additional purification or sample treatment steps can be time-intensive and can disrupt noncovalent interactions. It is demonstrated that the combined use of collision-induced unfolding, tandem mass spectrometry, and bottom-up proteomics improves protein characterization in native surface mass spectrometry (NSMS). This multiprong analysis is achieved by acquiring NSMS, MS/MS, ion mobility (IM), and bottom-up proteomics data from a single surface extracted sample. The validity of this multiprong approach was confirmed by the successful characterization of nine surface-deposited proteins, with molecular weights ranging from 8 to 147 kDa, in two separate mixtures. Bottom-up proteomics provided a list of proteins to match against observed proteins in NSMS and their detected subunits in tandem MS. The method was applied to characterize endogenous proteins from untreated chicken liver samples. The subcapsular liver sampling for NSMS analysis allowed for the detection of endogenous proteins with molecular weights of up to ∼220 kDa. Moreover, using IM-MS, collision cross sections and collision-induced unfolding pathways of enzymatic proteins and protein complexes of up to 145 kDa were obtained.
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Affiliation(s)
- Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Neda Feizi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sarah C Beno
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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6
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Zercher BP, Feng Y, Bush MF. Towards IM n with Electrostatic Drift Fields: Resetting the Potential of Trapped Ions Between Dimensions of Ion Mobility. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 495:117163. [PMID: 37928050 PMCID: PMC10621600 DOI: 10.1016/j.ijms.2023.117163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Increasing the dimensionality of ion mobility (IM) presents an enticing opportunity to increase the information content and selectivity of many analyses. However, for implementations of IM that use constant electrostatic gradients to separate ions in a buffer gas, technical challenges have limited the adoption of the technique and number of dimensions within individual experiments. Here, we introduce a strategy to "reset" the potentials of ions between IM dimensions. To achieve this, mobility-selected ions are trapped between dimensions of IM, using a combination of RF and electrostatic fields, while the subsequent dimension of IM is devoid of any drift field. By applying an incremental voltage ramp, the potential of the trapping region is elevated, simultaneously establishing the drift field in the subsequent dimension of IM. The trapped ions are then released and separated. We measured similar arrival-time distributions of protein ions using this strategy and a method without potential resetting, suggesting that potential resetting can be performed without additional losses or activation of ions. The findings of those experiments were corroborated by ion trajectory simulations, which exhibited a very small changes in ion position and no significant changes in effective temperatures during potential resetting. Finally, we demonstrate that IM information can be preserved during potential resetting by selecting subpopulations of 9+ cytochrome c ions, resetting their potential, subjecting them to a second-dimension IM separation, and observing the retention of conformers within each subpopulation. We anticipate that this strategy will be useful for advancing flexible, multidimensional experiments on electrostatic IM instruments.
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Affiliation(s)
- Benjamin P. Zercher
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Yuan Feng
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
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7
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Naylor CN, Nagy G. Permethylation and Metal Adduction: A Toolbox for the Improved Characterization of Glycolipids with Cyclic Ion Mobility Separations Coupled to Mass Spectrometry. Anal Chem 2023; 95:13725-13732. [PMID: 37650842 DOI: 10.1021/acs.analchem.3c03448] [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: 09/01/2023]
Abstract
Lipids are an important class of molecules involved in various biological functions but remain difficult to characterize through mass-spectrometry-based methods because of their many possible isomers. Glycolipids, specifically, play important roles in cell signaling but display an even greater level of isomeric heterogeneity as compared to other lipid classes stemming from the introduction of a carbohydrate and its corresponding linkage position and α/β anomericity at the headgroup. While liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) remains the gold standard technique in lipidomics, it is still unable to characterize all isomeric species, thus presenting the need for new, orthogonal, methodologies. Ion mobility spectrometry-mass spectrometry (IMS-MS) can provide an additional dimension of information that supplements LC-MS/MS workflows, but has seen little use for glycolipid analyses. Herein, we present an analytical toolbox that enables the characterization of various glycolipid isomer sets using high-resolution cyclic ion mobility separations coupled with mass spectrometry (cIMS-MS). Specifically, we utilized a combination of both permethylation and metal adduction to fully resolve isomeric sphingolipids and ceramides with our cIMS-MS platform. We also introduce a new metric that can enable comparing peak-to-peak resolution across varying cIMS-MS pathlengths. Overall, we envision that our presented methodologies are highly amenable to existing LC-MS/MS-based workflows and can also have broad utility toward other omics-based analyses.
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Affiliation(s)
- Cameron N Naylor
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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8
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Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
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Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
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9
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Ujma J, Jhingree J, Norgate E, Upton R, Wang X, Benoit F, Bellina B, Barran P. Protein Unfolding in Freeze Frames: Intermediate States are Revealed by Variable-Temperature Ion Mobility-Mass Spectrometry. Anal Chem 2022; 94:12248-12255. [PMID: 36001095 PMCID: PMC9453741 DOI: 10.1021/acs.analchem.2c03066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas phase is an idealized laboratory for the study of protein structure, from which it is possible to examine stable and transient forms of mass-selected ions in the absence of bulk solvent. With ion mobility-mass spectrometry (IM-MS) apparatus built to operate at both cryogenic and elevated temperatures, we have examined conformational transitions that occur to the monomeric proteins: ubiquitin, lysozyme, and α-synuclein as a function of temperature and in source activation. We rationalize the experimental observations with a temperature-dependent framework model and comparison to known conformers. Data from ubiquitin show unfolding transitions that proceed through diverse and highly elongated intermediate states, which converge to more compact structures. These findings contrast with data obtained from lysozyme─a protein where (un)-folding plasticity is restricted by four disulfide linkages, although this is alleviated in its reduced form. For structured proteins, collision activation of the protein ions in-source enables subsequent "freezing" or thermal annealing of unfolding intermediates, whereas disordered proteins restructure substantially at 250 K even without activation, indicating that cold denaturation can occur without solvent. These data are presented in the context of a toy model framework that describes the relative occupancy of the available conformational space.
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Affiliation(s)
- Jakub Ujma
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jacquelyn Jhingree
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Emma Norgate
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rosie Upton
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Xudong Wang
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Florian Benoit
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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10
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Ito R, He X, Ohshimo K, Misaizu F. Large Conformational Change in the Isomerization of Flexible Crown Ether Observed at Low Temperature. J Phys Chem A 2022; 126:4359-4366. [PMID: 35786937 DOI: 10.1021/acs.jpca.2c02271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamic processes of conformational changes of supramolecules are important to understand the motion in synthetic supramolecules. Although a host-guest complex is the most basic supramolecule, a detailed mechanism of its conformational changes has rarely been studied. Here, we observed the large conformational change of a dibenzo-24-crown-8 complex with four guest ions (Ag+, Na+, K+, and NH4+) at low temperature in the gas phase. The isomerization between the two types of conformers, which have different distances between the two benzene rings, proceeds even at 86 K. Using variable-temperature ion mobility-mass spectrometry (IM-MS) at 100-210 K, the activation energy for the isomerization is determined to be rather small (4.8-9.0 kJ mol-1). Reaction pathway calculations revealed that the isomerization is caused by the sequential rotation of two single bonds in the crown ether ring. The present cryogenic IM-MS study of the host-guest complexes at the molecular level opens an approach to detailed understanding of the motion in supramolecules.
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Affiliation(s)
- Ryosuke Ito
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Xi He
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Keijiro Ohshimo
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Fuminori Misaizu
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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11
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Norgate EL, Upton R, Hansen K, Bellina B, Brookes C, Politis A, Barran PE. Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage. Angew Chem Int Ed Engl 2022; 61:e202115047. [PMID: 35313047 PMCID: PMC9325448 DOI: 10.1002/anie.202115047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 12/12/2022]
Abstract
The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.
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Affiliation(s)
- Emma L Norgate
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - Rosie Upton
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - Kjetil Hansen
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Bruno Bellina
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - C Brookes
- Bristol-Myers Squibb, Moreton, Wirral, CH46 1QW, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Perdita E Barran
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
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12
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Norgate EL, Upton R, Hansen K, Bellina B, Brookes C, Politis A, Barran PE. Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202115047. [PMID: 38505418 PMCID: PMC10947158 DOI: 10.1002/ange.202115047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/07/2022]
Abstract
The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.
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Affiliation(s)
- Emma L. Norgate
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Rosie Upton
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Kjetil Hansen
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Bruno Bellina
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - C. Brookes
- Bristol-Myers SquibbMoretonWirralCH46 1QWUK
| | - Argyris Politis
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Perdita E. Barran
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
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13
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Liu FC, Ridgeway ME, Park MA, Bleiholder C. Tandem-trapped ion mobility spectrometry/mass spectrometry ( tTIMS/MS): a promising analytical method for investigating heterogenous samples. Analyst 2022; 147:2317-2337. [PMID: 35521797 PMCID: PMC9914546 DOI: 10.1039/d2an00335j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ion mobility spectrometry/mass spectrometry (IMS/MS) is widely used to study various levels of protein structure. Here, we review the current state of affairs in tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS). Two different tTIMS/MS instruments are discussed in detail: the first tTIMS/MS instrument, constructed from coaxially aligning two TIMS devices; and an orthogonal tTIMS/MS configuration that comprises an ion trap for irradiation of ions with UV photons. We discuss the various workflows the two tTIMS/MS setups offer and how these can be used to study primary, tertiary, and quaternary structures of protein systems. We also discuss, from a more fundamental perspective, the processes that lead to denaturation of protein systems in tTIMS/MS and how to soften the measurement so that biologically meaningful structures can be characterised with tTIMS/MS. We emphasize the concepts underlying tTIMS/MS to underscore the opportunities tandem-ion mobility spectrometry methods offer for investigating heterogeneous samples.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | | | | | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA. .,Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390, USA
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14
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Ito R, Ohshimo K, Misaizu F. Structures of dibenzo-24-crown-8 complex with an NH4+ ion studied by cryogenic ion mobility-mass spectrometry. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Ion Mobility Mass Spectrometry for Structural Elucidation of Petroleum Compounds. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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McCullagh M, Goscinny S, Palmer M, Ujma J. Investigations into pesticide charge site isomers using conventional IM and cIM systems. Talanta 2021; 234:122604. [PMID: 34364418 DOI: 10.1016/j.talanta.2021.122604] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/05/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022]
Abstract
A growing number of pesticides are being used around the world necessitating strict regulatory policies to guarantee consumer safety. Liquid Chromatography - Mass Spectrometry (LC-MS) is a highly sensitive method for pesticide screening, which provides retention time, mass/charge ratios and the relative abundances of characteristic product ions. Variability in the latter necessitates relatively large tolerances (±30%, SANCO/12682/2019, current EU regulation). One cause of this variability may stem from the presence of different charge-site isomers (charge carrier being a proton, sodium cation, potassium cation and alike); each yielding a set of different product ions, of which the relative ratios are influenced by solution and ion source conditions. Consequently, varying relative abundances may be observed for analyte ions produced from calibration standards, chemical residues in food matrices and across different instruments. Ion Mobility Spectrometry (IMS) is a fast, gas phase separation technique which can resolve charge-site isomers based on differences in their collisional cross sections (CCSs). We previously used the IM device embedded in LC-IM-MS geometry to generate a pesticide CCS database and subsequently focussed upon identification of pesticides which form charge-site isomers. Latterly, we applied this approach to screen food commodities for pesticide residues. In some instances, isomer separation was clear, however sometimes broad, unresolved distributions were observed. Using a high-resolution cyclic IM device (cIM) we resolved and determined CCS values of species of indoxacarb, spinosad, fenpyroximate, epoxiconazole, metaflumizone and avermectin. Furthermore, utilising novel cIM functionalities (tandem-IM) we discovered that two spinosyn sodimers can interconvert in the gas phase.
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Affiliation(s)
| | - Séverine Goscinny
- Scientific Institute of Public Health, 14, Rue Juliette Wytsman, 1050, Brussels, Belgium
| | - Martin Palmer
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, UK
| | - Jakub Ujma
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, UK
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17
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Ohshimo K, He X, Ito R, Misaizu F. Conformer Separation of Dibenzo-Crown-Ether Complexes with Na + and K + Ions Studied by Cryogenic Ion Mobility-Mass Spectrometry. J Phys Chem A 2021; 125:3718-3725. [PMID: 33904306 DOI: 10.1021/acs.jpca.1c02300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We performed cryogenic ion mobility-mass spectrometry (IM-MS) to study conformations of dibenzo-crown-ether complexes with Na+ and K+ ions at 86 K in the gas phase. Four dibenzo-crown-ethers (dibenzo-18-crown-6, dibenzo-21-crown-7, dibenzo-24-crown-8, and dibenzo-30-crown-10) with different cavity ring sizes were investigated. For dibenzo-18-crown-6 complexes with Na+ and K+, only one type of conformer was assigned by comparing the experimental collision cross sections with those predicted theoretically for candidate structures. In this conformer, the distance between two benzene rings in the complexes was long due to the open form of the dibenzo-18-crown-6. This open conformer was consistent with the previous laser spectroscopic studies of the cold complex ions in the gas phase. For dibenzo-21-crown-7 and dibenzo-24-crown-8 complexes with Na+ and K+, two types of conformers were clearly separated by IM-MS. These two conformer types were assigned to "open" and "closed" forms in which benzene-benzene distances were long and short, respectively. Observed relative abundances of the open and closed conformers qualitatively agreed with the Boltzmann distribution using Gibbs energies of the conformers calculated by quantum chemical calculations. For the Na+(dibenzo-30-crown-10) complex, open and closed conformers were also observed in IM-MS. On the other hand, only the closed conformer was observed for the K+(dibenzo-30-crown-10) complex. This closed conformer was similar to the "wraparound" structure, which was proposed in the previous studies in the solution. In conclusion, the closed conformers were formed by the deformation of flexible crown ethers with large cavity ring sizes. In addition, the diameter of the K+ ion was suitable to form the closed conformer by deformation of the molecular structure of dibenzo-30-crown-10.
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Affiliation(s)
- Keijiro Ohshimo
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Xi He
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Ryosuke Ito
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Fuminori Misaizu
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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18
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Panczyk EM, Snyder DT, Ridgeway ME, Somogyi Á, Park MA, Wysocki VH. Surface-Induced Dissociation of Protein Complexes Selected by Trapped Ion Mobility Spectrometry. Anal Chem 2021; 93:5513-5520. [PMID: 33751887 DOI: 10.1021/acs.analchem.0c05373] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Native mass spectrometry (nMS), particularly in conjunction with gas-phase ion mobility spectrometry measurements, has proven useful as a structural biology tool for evaluating the stoichiometry, conformation, and topology of protein complexes. Here, we demonstrate the combination of trapped ion mobility spectrometry (TIMS) and surface-induced dissociation (SID) on a Bruker SolariX XR 15 T FT-ICR mass spectrometer for the structural analysis of protein complexes. We successfully performed SID on mobility-selected protein complexes, including the streptavidin tetramer and cholera toxin B with bound ligands. Additionally, TIMS-SID was employed on a mixture of the peptides desArg1 and desArg9 bradykinin to mobility-separate and identify the individual peptides. Importantly, results show that native-like conformations can be maintained throughout the TIMS analysis. The TIMS-SID spectra are analogous to SID spectra acquired using quadrupole mass selection, indicating little measurable, if any, structural rearrangement during mobility selection. Mobility parking was used on the ion or mobility of interest and 50-200 SID mass spectra were averaged. High-quality TIMS-SID spectra were acquired over a period of 2-10 min, comparable to or slightly longer than SID coupled with ion mobility on various instrument platforms in our laboratory. The ultrahigh resolving power of the 15 T FT-ICR allowed for the identification and relative quantification of overlapping SID fragments with the same nominal m/z based on isotope patterns, and it shows promise as a platform to probe small mass differences, such as protein/ligand binding or post-translational modifications. These results represent the potential of TIMS-SID-MS for the analysis of both protein complexes and peptides.
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Affiliation(s)
- Erin M Panczyk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dalton T Snyder
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark E Ridgeway
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Árpád Somogyi
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States.,Campus Chemical Instrument Center, Mass Spectrometry and Proteomics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States.,Campus Chemical Instrument Center, Mass Spectrometry and Proteomics, The Ohio State University, Columbus, Ohio 43210, United States
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19
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Masike K, Stander MA, de Villiers A. Recent applications of ion mobility spectrometry in natural product research. J Pharm Biomed Anal 2021; 195:113846. [PMID: 33422832 DOI: 10.1016/j.jpba.2020.113846] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
Ion mobility spectrometry (IMS) is a rapid separation technique capable of extracting complementary structural information to chromatography and mass spectrometry (MS). IMS, especially in combination with MS, has experienced inordinate growth in recent years as an analytical technique, and elicited intense interest in many research fields. In natural product analysis, IMS shows promise as an additional tool to enhance the performance of analytical methods used to identify promising drug candidates. Potential benefits of the incorporation of IMS into analytical workflows currently used in natural product analysis include the discrimination of structurally similar secondary metabolites, improving the quality of mass spectral data, and the use of mobility-derived collision cross-section (CCS) values as an additional identification criterion in targeted and untargeted analyses. This review aims to provide an overview of the application of IMS to natural product analysis over the last six years. Instrumental aspects and the fundamental background of IMS will be briefly covered, and recent applications of the technique for natural product analysis will be discussed to demonstrate the utility of the technique in this field.
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Affiliation(s)
- Keabetswe Masike
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Maria A Stander
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa; Central Analytical Facility, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - André de Villiers
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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20
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Rivera ES, Djambazova KV, Neumann EK, Caprioli RM, Spraggins JM. Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4614. [PMID: 32955134 PMCID: PMC8211109 DOI: 10.1002/jms.4614] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 05/02/2023]
Abstract
Imaging mass spectrometry (IMS) technologies are capable of mapping a wide array of biomolecules in diverse cellular and tissue environments. IMS has emerged as an essential tool for providing spatially targeted molecular information due to its high sensitivity, wide molecular coverage, and chemical specificity. One of the major challenges for mapping the complex cellular milieu is the presence of many isomers and isobars in these samples. This challenge is traditionally addressed using orthogonal liquid chromatography (LC)-based analysis, though, common approaches such as chromatography and electrophoresis are not able to be performed at timescales that are compatible with most imaging applications. Ion mobility offers rapid, gas-phase separations that are readily integrated with IMS workflows in order to provide additional data dimensionality that can improve signal-to-noise, dynamic range, and specificity. Here, we highlight recent examples of ion mobility coupled to IMS and highlight their importance to the field.
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Key Words
- IMS
- desorption electrospray ionization, DESI
- drift tube ion mobility spectrometry, DTIMS
- high-field asymmetric waveform ion mobility, FAIMS
- imaging mass spectrometry
- infrared matrix-assisted laser desorption electrospray ionization, IR-MALDESI
- ion mobility
- laser ablation electrospray ionization, LAESI
- lipids
- liquid extraction surface analysis, LESA
- liquid microjunction, (LMJ)
- matrix-assisted laser desorption electrospray ionization, MALDI
- metabolites
- proteins
- tissue analysis
- trapped ion mobility spectrometry, TIMS
- travelling wave ion mobility spectrometry, TWIMS
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Affiliation(s)
- Emilio S. Rivera
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Katerina V. Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
| | - Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
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21
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Tainaka S, Ujihira T, Kubo M, Kida M, Shimoyama D, Muramatsu S, Abe M, Haino T, Ebata T, Misaizu F, Ohshimo K, Inokuchi Y. Conformation of K+(Crown Ether) Complexes Revealed by Ion Mobility–Mass Spectrometry and Ultraviolet Spectroscopy. J Phys Chem A 2020; 124:9980-9990. [DOI: 10.1021/acs.jpca.0c09068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sota Tainaka
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Tomoyuki Ujihira
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Mayuko Kubo
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Motoki Kida
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Daisuke Shimoyama
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Satoru Muramatsu
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Manabu Abe
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Takeharu Haino
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Takayuki Ebata
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Fuminori Misaizu
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Keijiro Ohshimo
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Yoshiya Inokuchi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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22
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Ohshimo K, Sato R, Misaizu F. Intramolecular Dispersion Attraction in Tetraalkylammonium Cations Revealed by Cryogenic Ion Mobility Mass Spectrometry. J Phys Chem A 2020; 124:7999-8004. [DOI: 10.1021/acs.jpca.0c04817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Keijiro Ohshimo
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki,
Aoba-ku, Sendai 980-8578, Japan
| | - Ryosuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki,
Aoba-ku, Sendai 980-8578, Japan
| | - Fuminori Misaizu
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki,
Aoba-ku, Sendai 980-8578, Japan
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23
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Jeanne Dit Fouque K, Fernandez-Lima F. Following Structural Changes by Thermal Denaturation Using Trapped Ion Mobility Spectrometry-Mass Spectrometry. J Phys Chem B 2020; 124:6257-6265. [PMID: 32560586 PMCID: PMC8341290 DOI: 10.1021/acs.jpcb.0c04276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The behavior of biomolecules as a function of the solution temperature is often crucial to assessing their biological activity and function. While heat-induced changes of biomolecules are traditionally monitored using optical spectroscopy methods, their conformational changes and unfolding transitions remain challenging to interpret. In the present work, the structural transitions of bovine serum albumin (BSA) in native conditions (100 mM aqueous ammonium acetate) were investigated as a function of the starting solution temperature (T ∼ 23-70 °C) using a temperature-controlled nanoelectrospray ionization source (nESI) coupled to a trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) instrument. The charge state distribution of the monomeric BSA changed from a native-like, narrow charge state ([M + 12H]12+ to [M + 16H]16+ at ∼23 °C) and narrow mobility distribution toward an unfolded-like, broad charge state (up to [M + 46H]46+ at ∼70 °C) and broad mobility distribution. Inspection of the average charge state and collision cross section (CCS) distribution suggested a two-state unfolding transition with a melting temperature Tm ∼ 56 ± 1 °C; however, the inspection of the CCS profiles at the charge state level as a function of the solution temperature showcases at least six structural transitions (T1-T7). If the starting solution concentration is slightly increased (from 2 to 25 μM), this method can detect nonspecific BSA dimers and trimers which dissociate early (Td ∼ 34 ± 1 °C) and may disturb the melting curve of the BSA monomer. In a single experiment, this technology provides a detailed view of the solution, protein structural landscape (mobility vs solution temperature vs relative intensity for each charge state).
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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24
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Link BA, Sindt AJ, Shimizu LS, Do TD. Selective host-guest chemistry, self-assembly and conformational preferences of m-xylene macrocycles probed by ion-mobility spectrometry mass spectrometry. Phys Chem Chem Phys 2020; 22:9290-9300. [PMID: 32309846 DOI: 10.1039/c9cp06938k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We demonstrated ion-mobility spectrometry mass spectrometry (IMS-MS) as a powerful tool for interrogating and preserving selective chemistry including non-covalent and host-guest complexes of m-xylene macrocycles formed in solution. The technique readily revealed the unique favorability of a thiourea-containing macrocycle MXT to Zn2+ to form a dimer complex with the cation in an off-axis sandwich structure having the Zn-S bonds in a tetrahedral coordination environment. Replacing thiourea with urea generates MXU which formed high-order oligomerization with weak binding interactions to neutral DMSO guests detected at every oligomer size. The self-assembly pathway observed for this macrocycle is consistent with the crystalline assembly. Further transformation of urea into squaramide produces MXS, a rare receptor for probing sulfate in solution. Tight complexes were observed for both monomeric and dimeric of MXS in which HSO4- bound stronger than SO42- to the host. The position of HSO4- at the binding cavity is a 180° inversion of the reported crystallographic SO42-. The MXS dimer formed a prism-like shape with HSO4- exhibiting strong contacts with the 8 amine protons of two MXS macrocycles. By eliminating intermolecular interferences, we detected the low energy structures of MXS with collisional cross section (CCS) matching cis-trans and cis-cis squaramides-amines, both were not observed in crystallization trials. The experiments collectively unravel multiple facets of macrocycle chemistry including conformational flexibility, self-assembly and ligand binding; all in one analysis. Our findings illustrate an inexpensive and widely applicable approach to investigate weak but important interactions that define the shape and binding of macrocycles.
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Affiliation(s)
- Benjamin A Link
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA.
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25
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Hebert MJ, Russell DH. Tracking the Structural Evolution of 4-Aminobenzoic Acid in the Transition from Solution to the Gas Phase. J Phys Chem B 2020; 124:2081-2087. [DOI: 10.1021/acs.jpcb.9b10576] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Michael J. Hebert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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26
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France AP, Migas LG, Sinclair E, Bellina B, Barran PE. Using Collision Cross Section Distributions to Assess the Distribution of Collision Cross Section Values. Anal Chem 2020; 92:4340-4348. [DOI: 10.1021/acs.analchem.9b05130] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Aidan P. France
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Lukasz G. Migas
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Eleanor Sinclair
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
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27
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Grabarics M, Lettow M, Kirk AT, von Helden G, Causon TJ, Pagel K. Plate-height model of ion mobility-mass spectrometry. Analyst 2020; 145:6313-6333. [DOI: 10.1039/d0an00433b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In analogy to chromatography, a plate-height model of drift tube ion mobility-mass spectrometry is presented that describes zone broadening and resolving power in ion mobility separations.
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Affiliation(s)
- Márkó Grabarics
- Department of Biology
- Chemistry and Pharmacy
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
| | - Maike Lettow
- Department of Biology
- Chemistry and Pharmacy
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
| | - Ansgar T. Kirk
- Institute of Electrical Engineering and Measurement Technology
- Department of Sensors and Measurement Technology
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society
- Department of Molecular Physics
- 14195 Berlin
- Germany
| | - Tim J. Causon
- Department of Chemistry
- Institute of Analytical Chemistry
- University of Natural Resources and Life Sciences
- Vienna
- 1190 Vienna
| | - Kevin Pagel
- Department of Biology
- Chemistry and Pharmacy
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
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28
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Haynes IW, Wu G, Haque MA, Li H, Do TD. Conformational Preference of Macrocycles Investigated by Ion-Mobility Mass Spectrometry and Distance Geometry Modeling. Anal Chem 2019; 91:13439-13447. [DOI: 10.1021/acs.analchem.9b02100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Isaac W. Haynes
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Guangcheng Wu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Md. Ashraful Haque
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Hao Li
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Thanh D. Do
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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29
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Giles K, Ujma J, Wildgoose J, Pringle S, Richardson K, Langridge D, Green M. A Cyclic Ion Mobility-Mass Spectrometry System. Anal Chem 2019; 91:8564-8573. [PMID: 31141659 DOI: 10.1021/acs.analchem.9b01838] [Citation(s) in RCA: 265] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Improvements in the performance and availability of commercial instrumentation have made ion mobility-mass spectrometry (IM-MS) an increasingly popular approach for the structural analysis of ionic species as well as for separation of complex mixtures. Here, a new research instrument is presented which enables complex experiments, extending the current scope of IM technology. The instrument is based on a Waters SYNAPT G2-S i IM-MS platform, with the IM separation region modified to accept a cyclic ion mobility (cIM) device. The cIM region consists of a 98 cm path length, closed-loop traveling wave (TW)-enabled IM separator positioned orthogonally to the main ion optical axis. A key part of this geometry and its flexibility is the interface between the ion optical axis and the cIM, where a planar array of electrodes provides control over the TW direction and subsequent ion motion. On either side of the array, there are ion guides used for injection, ejection, storage, and activation of ions. In addition to single and multipass separations around the cIM, providing selectable mobility resolution, the instrument design and control software enable a range of "multifunction" experiments such as mobility selection, activation, storage, IMS n, and importantly custom combinations of these functions. Here, the design and performance of the cIM-MS instrument is highlighted, with a mobility resolving power of approximately 750 demonstrated for 100 passes around the cIM device using a reverse sequence peptide pair. The multifunction capabilities are demonstrated through analysis of three isomeric pentasaccharide species and the small protein ubiquitin.
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Affiliation(s)
- Kevin Giles
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Jakub Ujma
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Jason Wildgoose
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Steven Pringle
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Keith Richardson
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - David Langridge
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Martin Green
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
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30
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Eldrid C, Ujma J, Kalfas S, Tomczyk N, Giles K, Morris M, Thalassinos K. Gas Phase Stability of Protein Ions in a Cyclic Ion Mobility Spectrometry Traveling Wave Device. Anal Chem 2019; 91:7554-7561. [PMID: 31117399 PMCID: PMC7006968 DOI: 10.1021/acs.analchem.8b05641] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Ion
mobility mass spectrometry (IM-MS) allows separation of native
protein ions into “conformational families”. Increasing
the IM resolving power should allow finer structural information to
be obtained and can be achieved by increasing the length of the IM
separator. This, however, increases the time that protein ions spend
in the gas phase and previous experiments have shown that the initial
conformations of small proteins can be lost within tens of milliseconds.
Here, we report on investigations of protein ion stability using a
multipass traveling wave (TW) cyclic IM (cIM) device. Using this device,
minimal structural changes were observed for Cytochrome C after hundreds
of milliseconds, while no changes were observed for a larger multimeric
complex (Concanavalin A). The geometry of the instrument (Q-cIM-ToF)
also enables complex tandem IM experiments to be performed, which
were used to obtain more detailed collision-induced unfolding pathways
for Cytochrome C. The instrument geometry provides unique capabilities
with the potential to expand the field of protein analysis via IM-MS.
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Affiliation(s)
- Charles Eldrid
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom
| | - Jakub Ujma
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Symeon Kalfas
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom
| | - Nick Tomczyk
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Kevin Giles
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Mike Morris
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College , University of London , London , WC1E 7HX , United Kingdom
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31
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Gabelica V, Shvartsburg AA, Afonso C, Barran P, Benesch JL, Bleiholder C, Bowers MT, Bilbao A, Bush MF, Campbell JL, Campuzano ID, Causon T, Clowers BH, Creaser CS, De Pauw E, Far J, Fernandez‐Lima F, Fjeldsted JC, Giles K, Groessl M, Hogan CJ, Hann S, Kim HI, Kurulugama RT, May JC, McLean JA, Pagel K, Richardson K, Ridgeway ME, Rosu F, Sobott F, Thalassinos K, Valentine SJ, Wyttenbach T. Recommendations for reporting ion mobility Mass Spectrometry measurements. MASS SPECTROMETRY REVIEWS 2019; 38:291-320. [PMID: 30707468 PMCID: PMC6618043 DOI: 10.1002/mas.21585] [Citation(s) in RCA: 274] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 05/02/2023]
Abstract
Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0 ) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site2 rue Robert Escarpit, 33600PessacFrance
| | | | | | - Perdita Barran
- Michael Barber Centre for Collaborative Mass SpectrometryManchester Institute for Biotechnology, University of ManchesterManchesterUK
| | - Justin L.P. Benesch
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford, Mansfield Road, OX1 3TAOxfordUK
| | - Christian Bleiholder
- Department of Chemistry and BiochemistryFlorida State UniversityTallahasseeFlorida32311
| | | | - Aivett Bilbao
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWashington
| | - Matthew F. Bush
- Department of ChemistryUniversity of WashingtonSeattleWashington
| | | | | | - Tim Causon
- University of Natural Resources and Life Sciences (BOKU)Department of Chemistry, Division of Analytical ChemistryViennaAustria
| | - Brian H. Clowers
- Department of ChemistryWashington State UniversityPullmanWashington
| | - Colin S. Creaser
- Centre for Analytical ScienceDepartment of Chemistry, Loughborough UniversityLoughboroughUK
| | - Edwin De Pauw
- Laboratoire de spectrométrie de masse (L.S.M.) − Molecular SystemsUniversité de LiègeLiègeBelgium
| | - Johann Far
- Laboratoire de spectrométrie de masse (L.S.M.) − Molecular SystemsUniversité de LiègeLiègeBelgium
| | | | | | | | - Michael Groessl
- Department of Nephrology and Hypertension and Department of BioMedical ResearchInselspital, Bern University Hospital, University of Bern, Switzerland and TofwerkThunSwitzerland
| | | | - Stephan Hann
- University of Natural Resources and Life Sciences (BOKU)Department of Chemistry, Division of Analytical ChemistryViennaAustria
| | - Hugh I. Kim
- Department of ChemistryKorea UniversitySeoulKorea
| | | | - Jody C. May
- Department of ChemistryCenter for Innovative Technology, Vanderbilt UniversityNashvilleTennessee
| | - John A. McLean
- Department of ChemistryCenter for Innovative Technology, Vanderbilt UniversityNashvilleTennessee
| | - Kevin Pagel
- Freie Universitaet BerlinInstitute for Chemistry and BiochemistryBerlinGermany
| | | | | | - Frédéric Rosu
- CNRS, INSERM and University of BordeauxInstitut Européen de Chimie et BiologiePessacFrance
| | - Frank Sobott
- Antwerp UniversityBiomolecular & Analytical Mass SpectrometryAntwerpBelgium
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
- School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonWC1E 6BTUK
- United Kingdom and Institute of Structural and Molecular BiologyDepartment of Biological Sciences, Birkbeck College, University of LondonLondonWC1E 7HXUK
| | - Stephen J. Valentine
- C. Eugene Bennett Department of ChemistryWest Virginia UniversityMorgantownWest Virginia
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32
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Sinclair E, Hollywood KA, Yan C, Blankley R, Breitling R, Barran P. Mobilising ion mobility mass spectrometry for metabolomics. Analyst 2019; 143:4783-4788. [PMID: 30209461 DOI: 10.1039/c8an00902c] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chromatography-based mass spectrometry approaches (xC-MS) are commonly used in untargeted metabolomics, providing retention time, m/z values and metabolite-specific fragments, all of which are used to identify and validate an unknown analyte. Ion mobility-mass spectrometry (IM-MS) is emerging as an enhancement to classic xC-MS strategies, by offering additional ion separation as well as collision cross section (CCS) determination. In order to apply such an approach to a metabolomics workflow, verified data from metabolite standards is necessary. In this work we present experimental DTCCSN2 values for a range of metabolites in positive and negative ionisation modes using drift tube-ion mobility-mass spectrometry (DT-IM-MS) with nitrogen as the buffer gas. The value of DTCCSN2 measurements for application in metabolite identification relies on a robust technique that acquires measurements of high reproducibility. We report that the CCS values found for 86% of metabolites measured in replicate have a relative standard deviation lower than 0.2%. Examples of metabolites with near identical mass are demonstrated to be separated by ion mobility with over 4% difference in DTCCSN2 values. We conclude that the integration of ion mobility into current LC-MS workflows can aid in small molecule identification for both targeted and untargeted metabolite screening.
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Affiliation(s)
- Eleanor Sinclair
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Princess Street, Manchester, M1 7DN, UK.
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33
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Haler JRN, Massonnet P, Far J, de la Rosa VR, Lecomte P, Hoogenboom R, Jérôme C, De Pauw E. Gas-Phase Dynamics of Collision Induced Unfolding, Collision Induced Dissociation, and Electron Transfer Dissociation-Activated Polymer Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:563-572. [PMID: 30523570 DOI: 10.1007/s13361-018-2115-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/24/2018] [Accepted: 11/24/2018] [Indexed: 06/09/2023]
Abstract
Polymer characterizations are often performed using mass spectrometry (MS). Aside from MS and different tandem MS (MS/MS) techniques, ion mobility-mass spectrometry (IM-MS) has been recently added to the inventory of characterization technique. However, only few studies have focused on the reproducibility and robustness of polymer IM-MS analyses. Here, we perform collisional and electron-mediated activation of polymer ions before measuring IM drift times, collision cross-sections (CCS), or reduced ion mobilities (K0). The resulting IM behavior of different activated product ions is then compared to non-activated native intact polymer ions. First, we analyzed collision induced unfolding (CIU) of precursor ions to test the robustness of polymer ion shapes. Then, we focused on fragmentation product ions to test for shape retentions from the precursor ions: cation ejection species (CES) and product ions with m/z and charge state values identical to native intact polymer ions. The CES species are formed using both collision induced dissociation (CID) and electron transfer dissociation (ETD, formally ETnoD) experiments. Only small drift time, CCS, or K0 deviations between the activated/formed ions are observed compared to the native intact polymer ions. The polymer ion shapes seem to depend solely on their mass and charge state. The experiments were performed on three synthetic homopolymers: poly(ethoxy phosphate) (PEtP), poly(2-n-propyl-2-oxazoline) (Pn-PrOx), and poly(ethylene oxide) (PEO). These results confirm the robustness of polymer ion CCSs for IM calibration, especially singly charged polymer ions. The results are also discussed in the context of polymer analyses, CCS predictions, and probing ion-drift gas interaction potentials. Graphical Abstract.
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Affiliation(s)
- Jean R N Haler
- Mass Spectrometry Laboratory, MolSys Research unit, Quartier Agora, University of Liège, Allée du Six Aout 11, B-4000, Liège, Belgium.
| | - Philippe Massonnet
- Mass Spectrometry Laboratory, MolSys Research unit, Quartier Agora, University of Liège, Allée du Six Aout 11, B-4000, Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research unit, Quartier Agora, University of Liège, Allée du Six Aout 11, B-4000, Liège, Belgium
| | - Victor R de la Rosa
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, B-9000, Ghent, Belgium
| | - Philippe Lecomte
- Center for Education and Research on Macromolecules, CESAM Research Unit, Quartier Agora, University of Liège, Allée du Six Aout 13, B-4000, Liège, Belgium
| | - Richard Hoogenboom
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, B-9000, Ghent, Belgium
| | - Christine Jérôme
- Center for Education and Research on Macromolecules, CESAM Research Unit, Quartier Agora, University of Liège, Allée du Six Aout 13, B-4000, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research unit, Quartier Agora, University of Liège, Allée du Six Aout 11, B-4000, Liège, Belgium
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34
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Ion Mobility in Structural Biology. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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35
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Abstract
A sizeable proportion of active protein sequences lack structural motifs making them irresolvable by NMR and crystallography. Such intrinsically disordered proteins (IDPs) or regions (IDRs) play a major role in biological mechanisms. They are often involved in cell regulation processes, and by extension can be the perpetrator or signifier of disease. In light of their importance and the shortcomings of conventional methods of biophysical analysis to identify them and to describe their conformational variance, IDPs and IDRs have been termed "the dark proteome." In this chapter we describe the use of ion mobility-mass spectrometry (IM-MS) coupled with electrospray ionization to analyze the conformational diversity of IDPs. Using the LEA protein COR15A as an exemplar system and contrasting it with the behavior of myoglobin, we outline the methods for analyzing an IDP using nanoelectrospray ionization coupled with IM-MS, covering sample preparation, purification; optimization of mass spectrometry conditions and tuning parameters; data collection and analysis. Following this, we detail the use of a "toy" model that provides a predictive framework for the study of all proteins with ESI-IM-MS.
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36
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Do TD, Checco JW, Tro M, Shea JE, Bowers MT, Sweedler JV. Conformational investigation of the structure-activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of Aplysia californica involved in the feeding circuit. Phys Chem Chem Phys 2018; 20:22047-22057. [PMID: 30112548 DOI: 10.1039/c8cp03661f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins and peptides in nature are almost exclusively made from l-amino acids, and this is even more absolute in the metazoan. With the advent of modern bioanalytical techniques, however, previously unappreciated roles for d-amino acids in biological processes have been revealed. Over 30 d-amino acid containing peptides (DAACPs) have been discovered in animals where at least one l-residue has been isomerized to the d-form via an enzyme-catalyzed process. In Aplysia californica, GdFFD and GdYFD (the lower-case letter "d" indicates a d-amino acid residue) modulate the feeding behavior by activating the Aplysia achatin-like neuropeptide receptor (apALNR). However, little is known about how the three-dimensional conformation of DAACPs influences activity at the receptor, and the role that d-residues play in these peptide conformations. Here, we use a combination of computational modeling, drift-tube ion-mobility mass spectrometry, and receptor activation assays to create a simple model that predicts bioactivities for a series of GdFFD analogs. Our results suggest that the active conformations of GdFFD and GdYFD are similar to their lowest energy conformations in solution. Our model helps connect the predicted structures of GdFFD analogs to their activities, and highlights a steric effect on peptide activity at position 1 on the GdFFD receptor apALNR. Overall, these methods allow us to understand ligand-receptor interactions in the absence of high-resolution structural data.
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Affiliation(s)
- Thanh D Do
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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37
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Chai M, Young MN, Liu FC, Bleiholder C. A Transferable, Sample-Independent Calibration Procedure for Trapped Ion Mobility Spectrometry (TIMS). Anal Chem 2018; 90:9040-9047. [DOI: 10.1021/acs.analchem.8b01326] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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38
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Eyers CE, Vonderach M, Ferries S, Jeacock K, Eyers PA. Understanding protein–drug interactions using ion mobility–mass spectrometry. Curr Opin Chem Biol 2018; 42:167-176. [DOI: 10.1016/j.cbpa.2017.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/22/2017] [Indexed: 01/23/2023]
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39
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Fundamentals of ion mobility spectrometry. Curr Opin Chem Biol 2018; 42:51-59. [DOI: 10.1016/j.cbpa.2017.10.022] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 12/13/2022]
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40
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Ben-Nissan G, Sharon M. The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes. Curr Opin Chem Biol 2018; 42:25-33. [PMID: 29128665 PMCID: PMC5796646 DOI: 10.1016/j.cbpa.2017.10.026] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/19/2017] [Accepted: 10/24/2017] [Indexed: 12/16/2022]
Abstract
Ion-mobility mass spectrometry (IM-MS) is an approach that can provide information on the stoichiometry, composition, protein contacts and topology of protein complexes. The power of this approach lies not only in its sensitivity and speed of analysis, but also in the fact that it is a technique that can capture the repertoire of conformational states adopted by protein assemblies. Here, we describe the array of available IM-MS based tools, and demonstrate their application to the structural characterization of various protein complexes, including challenging systems as amyloid aggregates and membrane proteins. We also discuss recent studies in which IM-MS was applied towards investigations of conformational transitions and stabilization effects induced by protein interactions.
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Affiliation(s)
- Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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41
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Jiang LX, Liu QY, Li XN, He SG. Design and Application of a High-Temperature Linear Ion Trap Reactor. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:78-84. [PMID: 29080205 DOI: 10.1007/s13361-017-1828-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/30/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
A high-temperature linear ion trap reactor with hexapole design was homemade to study ion-molecule reactions at variable temperatures. The highest temperature for the trapped ions is up to 773 K, which is much higher than those in available reports. The reaction between V2O6- cluster anions and CO at different temperatures was investigated to evaluate the performance of this reactor. The apparent activation energy was determined to be 0.10 ± 0.02 eV, which is consistent with the barrier of 0.12 eV calculated by density functional theory. This indicates that the current experimental apparatus is prospective to study ion-molecule reactions at variable temperatures, and more kinetic details can be obtained to have a better understanding of chemical reactions that have overall barriers. Graphical Abstract.
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Affiliation(s)
- Li-Xue Jiang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qing-Yu Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiao-Na Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.
| | - Sheng-Gui He
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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42
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Improving the discovery of secondary metabolite natural products using ion mobility-mass spectrometry. Curr Opin Chem Biol 2017; 42:160-166. [PMID: 29287234 DOI: 10.1016/j.cbpa.2017.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/30/2017] [Accepted: 12/11/2017] [Indexed: 02/07/2023]
Abstract
Secondary metabolite discovery requires an unbiased, comprehensive workflow to detect unknown unknowns for which little to no molecular knowledge exists. Untargeted mass spectrometry-based metabolomics is a powerful platform, particularly when coupled with ion mobility for high-throughput gas-phase separations to increase peak capacity and obtain gas-phase structural information. Ion mobility data are described by the amount of time an ion spends in the drift cell, which is directly related to an ion's collision cross section (CCS). The CCS parameter describes the size, shape, and charge of a molecule and can be used to characterize unknown metabolomic species. Here, we describe current and emerging applications of ion mobility-mass spectrometry for prioritization, discovery and structure elucidation, and spatial/temporal characterization.
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43
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Zietek BM, Mengerink Y, Jordens J, Somsen GW, Kool J, Honing M. Adduct-ion formation in trapped ion mobility spectrometry as a potential tool for studying molecular structures and conformations. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s12127-017-0227-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Haler JRN, Kune C, Massonnet P, Comby-Zerbino C, Jordens J, Honing M, Mengerink Y, Far J, De Pauw E. Comprehensive Ion Mobility Calibration: Poly(ethylene oxide) Polymer Calibrants and General Strategies. Anal Chem 2017; 89:12076-12086. [DOI: 10.1021/acs.analchem.7b02564] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jean R. N. Haler
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Christopher Kune
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Philippe Massonnet
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Clothilde Comby-Zerbino
- Institut
Lumière Matière, Université de Lyon, Université Lyon 1, CNRS, 69100 Villeurbanne, France
| | | | | | | | - Johann Far
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
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45
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Identification and characterization of pesticide metabolites in Brassica species by liquid chromatography travelling wave ion mobility quadrupole time-of-flight mass spectrometry (UPLC-TWIMS-QTOF-MS). Food Chem 2017; 244:292-303. [PMID: 29120785 DOI: 10.1016/j.foodchem.2017.09.131] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 01/24/2023]
Abstract
A new mass spectrometric method for evaluating metabolite formation of the pesticides thiacloprid, azoxystrobin, and difenoconazole was developed for the Brassica species pak choi and broccoli. Both, distribution and transformation kinetics of the active compounds and their metabolites were analyzed by UPLC-TWIMS-QTOF-MS. Additionally, HR-MS analysis and structure elucidation tools such as diagnostic ions, isotopic matches, and collision cross sections were applied for metabolites identification. Following the application of two plant protection products (containing the above-mentioned active compounds) in a greenhouse study plant material was cryo-milled and extracted with water/methanol. The residual levels of active compounds were identified at certain timepoints during pre-harvest intervals and in the final products. Different phase I and phase II metabolites of the pesticides were identified in different plant organs such as leaves, stems, (broccoli) heads, and roots. Three individual degradation pathways and distribution profiles are suggested including eight thiacloprid, eleven azoxystrobin and three difenoconazole metabolites.
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Davidson KL, Bush MF. Effects of Drift Gas Selection on the Ambient-Temperature, Ion Mobility Mass Spectrometry Analysis of Amino Acids. Anal Chem 2017; 89:2017-2023. [DOI: 10.1021/acs.analchem.6b04605] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kimberly L. Davidson
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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