1
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Gozzo TA, Bush MF. Effects of charge on protein ion structure: Lessons from cation-to-anion, proton-transfer reactions. MASS SPECTROMETRY REVIEWS 2024; 43:500-525. [PMID: 37129026 DOI: 10.1002/mas.21847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Collision cross-section values, which can be determined using ion mobility experiments, are sensitive to the structures of protein ions and useful for applications to structural biology and biophysics. Protein ions with different charge states can exhibit very different collision cross-section values, but a comprehensive understanding of this relationship remains elusive. Here, we review cation-to-anion, proton-transfer reactions (CAPTR), a method for generating a series of charge-reduced protein cations by reacting quadrupole-selected cations with even-electron monoanions. The resulting CAPTR products are analyzed using a combination of ion mobility, mass spectrometry, and collisional activation. We compare CAPTR to other charge-manipulation strategies and review the results of various CAPTR-based experiments, exploring their contribution to a deeper understanding of the relationship between protein ion structure and charge state.
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Affiliation(s)
- Theresa A Gozzo
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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2
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Gozzo TA, Bush MF. Quantitatively Differentiating Antibodies Using Charge-State Manipulation, Collisional Activation, and Ion Mobility-Mass Spectrometry. Anal Chem 2024; 96:505-513. [PMID: 38146701 DOI: 10.1021/acs.analchem.3c04638] [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: 12/27/2023]
Abstract
Antibody-based therapeutics continue to expand both in the number of products and in their use in patients. These heterogeneous proteins challenge traditional drug characterization strategies, but ion mobility (IM) and mass spectrometry (MS) approaches have eased the challenge of higher-order structural characterization. Energy-dependent IM-MS, e.g., collision-induced unfolding (CIU), has been demonstrated to be sensitive to subtle differences in structure. In this study, we combine a charge-reduction method, cation-to-anion proton-transfer reactions (CAPTR), with energy-dependent IM-MS and varied solution conditions to probe their combined effects on the gas-phase structures of IgG1κ and IgG4κ from human myeloma. CAPTR paired with MS-only analysis improves the confidence of charge-state assignments and the resolution of the interfering protein species. Collision cross-section distributions were determined for each of the charge-reduced products. Similarity scoring was used to quantitatively compare distributions determined from matched experiments analyzing samples of the two antibodies. Relative to workflows using energy-dependent IM-MS without charge-state manipulation, combining CAPTR and energy-dependent IM-MS enhanced the differentiation of these antibodies. Combined, these results indicate that CAPTR can benefit many aspects of antibody characterization and differentiation.
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Affiliation(s)
- Theresa A Gozzo
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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3
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Lantz C, Lopez J, Goring AK, Zenaidee MA, Biggs K, Whitelegge JP, Ogorzalek Loo RR, Klärner FG, Schrader T, Bitan G, Loo JA. Characterization of Molecular Tweezer Binding on α-Synuclein with Native Top-Down Mass Spectrometry and Ion Mobility-Mass Spectrometry Reveals a Mechanism for Aggregation Inhibition. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2739-2747. [PMID: 37936057 PMCID: PMC10959575 DOI: 10.1021/jasms.3c00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Parkinson's disease, a neurodegenerative disease that affects 15 million people worldwide, is characterized by deposition of α-synuclein into Lewy Bodies in brain neurons. Although this disease is prevalent worldwide, a therapy or cure has yet to be found. Several small compounds have been reported to disrupt fibril formation. Among these compounds is a molecular tweezer known as CLR01 that targets lysine and arginine residues. This study aims to characterize how CLR01 interacts with various proteoforms of α-synuclein and how the structure of α-synuclein is subsequently altered. Native mass spectrometry (nMS) measurements of α-synuclein/CLR01 complexes reveal that multiple CLR01 molecules can bind to α-synuclein proteoforms such as α-synuclein phosphorylated at Ser-129 and α-synuclein bound with copper and manganese ions. The binding of one CLR01 molecule shifts the ability for α-synuclein to bind other ligands. Electron capture dissociation (ECD) with Fourier transform-ion cyclotron resonance (FT-ICR) top-down (TD) mass spectrometry of α-synuclein/CLR01 complexes pinpoints the locations of the modifications on each proteoform and reveals that CLR01 binds to the N-terminal region of α-synuclein. CLR01 binding compacts the gas-phase structure of α-synuclein, as shown by ion mobility-mass spectrometry (IM-MS). These data suggest that when multiple CLR01 molecules bind, the N-terminus of α-synuclein shifts toward a more compact state. This compaction suggests a mechanism for CLR01 halting the formation of oligomers and fibrils involved in many neurodegenerative diseases.
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Affiliation(s)
- Carter Lantz
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Jaybree Lopez
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Andrew K. Goring
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Muhammad A. Zenaidee
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW, Australia
| | - Karl Biggs
- Department of Neurology and Brain Research Institute, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Julian P. Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Rachel R. Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | | | - Thomas Schrader
- Institute of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW, Australia
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA 90095 USA
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4
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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5
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Tao J, Jia S, Wang M, Huang Z, Wang B, Zhang W, Wei Y, Li W, Jiang H, Du Z. Systematic Identification of Proteins Binding with Cisplatin in Blood by Affinity Chromatography and a Four-Dimensional Proteomic Method. J Proteome Res 2021; 20:4553-4565. [PMID: 34427088 DOI: 10.1021/acs.jproteome.1c00535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cisplatin is widely used for the treatment of various solid tumors. It is mainly administered by intravenous injection, and a substantial amount of the drug will bind to plasma proteins, a feature that is closely related to its pharmacokinetics, activity, toxicity, and side effects. However, due to the unique properties of platinum complexes and the complexity of the blood proteome, existing methods cannot systematically identify the binding proteome of cisplatin in blood. In this study, high-abundance protein separation and an ion mobility mass spectrometry-based 4D proteomic method were combined to systematically and comprehensively identify the binding proteins of cisplatin in blood. The characteristic isotope patterns of platinated peptides and a similarity algorithm were utilized to eliminate false-positive identification. Finally, 39 proteins were found to be platinated. Bioinformatics analysis showed that the identified proteins were mainly involved in the complement and coagulation cascade pathways. The binding ratio of some peptides with cisplatin was measured based on the area ratio of the free peptide using the parallel reaction monitoring method. This study provides a new method for systematically identifying binding proteins of metal drugs in blood, and the identified proteins might be helpful for understanding the toxicity of platinum anticancer drugs.
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Affiliation(s)
- Jianmei Tao
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Shuailong Jia
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430030, Hubei Province, PR China
| | - Meiqin Wang
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Zhuobin Huang
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Bo Wang
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Wenwen Zhang
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Yinyu Wei
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Wenzhuo Li
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Hongliang Jiang
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Zhifeng Du
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
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6
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Weisbrod CR, Anderson LC, Hendrickson CL, Schaffer LV, Shortreed MR, Smith LM, Shabanowitz J, Hunt DF. Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis. Anal Chem 2021; 93:9119-9128. [PMID: 34165955 DOI: 10.1021/acs.analchem.1c00847] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-transfer reactions (PTRs) have emerged as a powerful tool for the study of intact proteins. When coupled with m/z-selective kinetic excitation, such as parallel ion parking (PIP), one can exert exquisite control over rates of reaction with a high degree of specificity. This allows one to "concentrate", in the gas phase, nearly all the signals from an intact protein charge state envelope into a single charge state, improving the signal-to-noise ratio (S/N) by 10× or more. While this approach has been previously reported, here we show that implementing these technologies on a 21 T FT-ICR MS provides a tremendous advantage for intact protein analysis. Advanced strategies for performing PTR with PIP were developed to complement this unique instrument, including subjecting all analyte ions entering the mass spectrometer to PTR and PIP. This experiment, which we call "PTR-MS1-PIP", generates a pseudo-MS1 spectrum derived from ions that are exposed to the PTR reagent and PIP waveforms but have not undergone any prior true mass filtering or ion isolation. The result is an extremely rapid and significant improvement in the spectral S/N of intact proteins. This permits the observation of many more proteoforms and reduces ion injection periods for subsequent tandem mass spectrometry characterization. Additionally, the product ion parking waveform has been optimized to enhance the PTR rate without compromise to the parking efficiency. We demonstrate that this process, called "rapid park", can improve reaction rates by 5-10× and explore critical factors discovered to influence this process. Finally, we demonstrate how coupling PTR-MS1 and rapid park provides a 10-fold reduction in ion injection time, improving the rate of tandem MS sequencing.
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Affiliation(s)
- Chad R Weisbrod
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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7
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Zhou M, Lantz C, Brown KA, Ge Y, Paša-Tolić L, Loo JA, Lermyte F. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem Sci 2020; 11:12918-12936. [PMID: 34094482 PMCID: PMC8163214 DOI: 10.1039/d0sc04392c] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
In biology, it can be argued that if the genome contains the script for a cell's life cycle, then the proteome constitutes an ensemble cast of actors that brings these instructions to life. Their interactions with each other, co-factors, ligands, substrates, and so on, are key to understanding nearly any biological process. Mass spectrometry is well established as the method of choice to determine protein primary structure and location of post-translational modifications. In recent years, top-down fragmentation of intact proteins has been increasingly combined with ionisation of noncovalent assemblies under non-denaturing conditions, i.e., native mass spectrometry. Sequence, post-translational modifications, ligand/metal binding, protein folding, and complex stoichiometry can thus all be probed directly. Here, we review recent developments in this new and exciting field of research. While this work is written primarily from a mass spectrometry perspective, it is targeted to all bioanalytical scientists who are interested in applying these methods to their own biochemistry and chemical biology research.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Frederik Lermyte
- Department of Chemistry, Institute of Chemistry and Biochemistry, Technical University of Darmstadt 64287 Darmstadt Germany
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège 4000 Liège Belgium
- School of Engineering, University of Warwick Coventry CV4 7AL UK
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8
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Cziferszky M, Gust R. Top-down mass spectrometry reveals multiple interactions of an acetylsalicylic acid bearing Zeise's salt derivative with peptides. J Biol Inorg Chem 2020; 25:285-293. [PMID: 32060649 PMCID: PMC7082381 DOI: 10.1007/s00775-020-01760-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/24/2020] [Indexed: 11/30/2022]
Abstract
Synergistic effects and promising anticancer activities encourage the combination of non-steroidal anti-inflammatory drugs with metallodrugs. Here, we discuss the interactions of an organometallic complex consisting of an acetylsalicylic acid (ASA) moiety attached to a PtII center via an alkenol linker in a Zeise's salt-type coordination (ASA-buten-PtCl3) with model peptides angiotensin 1 (AT), substance P (Sub P), and ubiquitin (UQ). Top-down mass spectrometry experiments show that the amino acid involved in the initial binding to the metal complex controls the coordination sphere of PtII in the adducts. The strong trans labilizing effect of the coordinating sulfur atom in Met causes fast release of the organic moiety and leads to the formation of dimers and oligomers in the case of Sub P. In contrast, interactions with nitrogen donors in AT result in stable adducts containing the intact ASA-buten-PtII complex. UQ forms two sets of PtII adducts, only one of them retains the ASA moiety, which is presumably the result of an unexpected binding geometry. Importantly, UQ is additionally acetylated at various Ser and Lys residues by the ASA-buten-PtCl3 complex. Control experiments with ASA are negative. This is the first example of concomitant platination and acetylation of a peptide with an ASA metal complex.
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Affiliation(s)
- Monika Cziferszky
- Department of Pharmaceutical Chemistry, CMBI-Center for Molecular Biosciences, CCB-Centrum for Chemistry and Biomedicine, Innsbruck, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Gust
- Department of Pharmaceutical Chemistry, CMBI-Center for Molecular Biosciences, CCB-Centrum for Chemistry and Biomedicine, Innsbruck, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria.
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9
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Foreman DJ, McLuckey SA. Recent Developments in Gas-Phase Ion/Ion Reactions for Analytical Mass Spectrometry. Anal Chem 2020; 92:252-266. [PMID: 31693342 PMCID: PMC6949396 DOI: 10.1021/acs.analchem.9b05014] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- David J Foreman
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907-2084 , United States
| | - Scott A McLuckey
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907-2084 , United States
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10
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Historical, current and future developments of travelling wave ion mobility mass spectrometry: A personal perspective. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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11
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Paul D, Marchand A, Verga D, Teulade-Fichou MP, Bombard S, Rosu F, Gabelica V. Probing ligand and cation binding sites in G-quadruplex nucleic acids by mass spectrometry and electron photodetachment dissociation sequencing. Analyst 2019; 144:3518-3524. [PMID: 31020955 DOI: 10.1039/c9an00398c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry provides exquisite details on ligand and cation binding stoichiometries with a DNA target. The next important step is to develop reliable methods to determine the cation and ligand binding sites in each complex separated by using a mass spectrometer. To circumvent the caveat of ligand derivatization for cross-linking, which may alter the ligand binding mode, we explored a tandem mass spectrometry (MS/MS) method that does not require ligand derivatization, and is therefore also applicable to localize metal cations. By putting more negative charge states on the complexes using supercharging agents, and by creating radical ions by electron photodetachment, oligonucleotide bonds become weaker than the DNA-cation or DNA-ligand noncovalent bonds upon collision-induced dissociation of the radicals. This electron photodetachment (EPD) method allows one to locate the binding regions of cations and ligands by top-down sequencing of the oligonucleotide target. The very potent G-quadruplex ligands 360A and PhenDC3 were found to replace a potassium cation and bind close to the central loop of 4-repeat human telomeric sequences.
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Affiliation(s)
- Dababrata Paul
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site, 2 rue Robert Escarpit, 33600 Pessac, France.
| | - Adrien Marchand
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site, 2 rue Robert Escarpit, 33600 Pessac, France.
| | - Daniela Verga
- Institut Curie, PSL Research University, CNRS-UMR 9187, INSERM U1196, F-91405 Orsay, France and Université Paris Sud, Université Paris-Saclay, CNRS-UMR 9187, INSERM U1196, F-91405 Orsay, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, CNRS-UMR 9187, INSERM U1196, F-91405 Orsay, France and Université Paris Sud, Université Paris-Saclay, CNRS-UMR 9187, INSERM U1196, F-91405 Orsay, France
| | - Sophie Bombard
- Institut Curie, PSL Research University, CNRS-UMR 9187, INSERM U1196, F-91405 Orsay, France and Université Paris Sud, Université Paris-Saclay, CNRS-UMR 9187, INSERM U1196, F-91405 Orsay, France
| | - Frédéric Rosu
- CNRS UMS3033, Inserm US001, IECB, 2 rue Robert Escarpit, 33607 Pessac, France.
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site, 2 rue Robert Escarpit, 33600 Pessac, France.
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12
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Chouinard CD, Nagy G, Smith RD, Baker ES. Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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13
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Lermyte F, Valkenborg D, Loo JA, Sobott F. Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. MASS SPECTROMETRY REVIEWS 2018; 37:750-771. [PMID: 29425406 PMCID: PMC6131092 DOI: 10.1002/mas.21560] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 05/11/2023]
Abstract
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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14
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Gadzuk-Shea MM, Bush MF. Effects of Charge State on the Structures of Serum Albumin Ions in the Gas Phase: Insights from Cation-to-Anion Proton-Transfer Reactions, Ion Mobility, and Mass Spectrometry. J Phys Chem B 2018; 122:9947-9955. [DOI: 10.1021/acs.jpcb.8b08427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Meagan M. Gadzuk-Shea
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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15
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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16
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Mass spectrometry as a powerful tool to study therapeutic metallodrugs speciation mechanisms: Current frontiers and perspectives. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.02.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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Hanozin E, Mignolet B, Morsa D, Sluysmans D, Duwez AS, Stoddart JF, Remacle F, De Pauw E. Where Ion Mobility and Molecular Dynamics Meet To Unravel the (Un)Folding Mechanisms of an Oligorotaxane Molecular Switch. ACS NANO 2017; 11:10253-10263. [PMID: 28881131 DOI: 10.1021/acsnano.7b04833] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
At the interface between foldamers and mechanically interlocked molecules, oligorotaxanes exhibit a spring-like folded secondary structure with remarkable mechanical and physicochemical properties. Among these properties, the ability of oligorotaxanes to act as molecular switches through controlled modulations of their spatial extension over (un)folding dynamics is of particular interest. The present study aims to assess and further characterize this remarkable feature in the gas phase using mass spectrometry tools. In this context, we focused on the [4]5NPR+12 oligorotaxane molecule complexed with PF6- counterion and probed its co-conformational states as a function of the in-source-generated charge states. Data were interpreted in light of electronic secondary structure computations at the PM6 and DFT levels. Our results highlight two major co-conformational groups associated either with folded compact structures, notably stabilized by intramolecular π-π interactions and predominant for low charge states or with fully stretched structures resulting from significant Coulombic repulsions at high charge states. Between, the oligorotaxane adopts intermediate folded co-conformations, suggesting a stepwise unfolding pathway under increasing repulsive Coulombic constraints. The reversibility of this superstructural transition was next interrogated under electron-driven (nondissociative electron transfer) and heat-driven (collision-induced unfolding) activation stimuli. The outcomes support the feasibility to either unfold or (partially) refold the oligorotaxane foldamer on purpose in the gas phase. Our results show that the balance between the stabilizing π-π interactions and the versatile Coulomb interactions dictates the elongation state of the foldamer in the gas phase and emphasizes the adequacy of mass spectrometry tools for the superstructural characterization of desolvated prototypical artificial molecular machines.
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Affiliation(s)
| | | | | | | | | | - J Fraser Stoddart
- Mechanostereochemistry Group, Northwestern University , Evanston, Illinois 60208, United States
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18
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Laszlo KJ, Bush MF. Interpreting the Collision Cross Sections of Native-like Protein Ions: Insights from Cation-to-Anion Proton-Transfer Reactions. Anal Chem 2017. [PMID: 28636334 DOI: 10.1021/acs.analchem.7b01474] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of charge state on structures of native-like cations of serum albumin, streptavidin, avidin, and alcohol dehydrogenase were probed using cation-to-anion proton-transfer reactions (CAPTR), ion mobility, mass spectrometry, and complementary energy-dependent experiments. The CAPTR products all have collision cross-section (Ω) values that are within 5.5% of the original precursor cations. The first CAPTR event for each precursor yields products that have smaller Ω values and frequently exhibit the greatest magnitude of change in Ω resulting from a single CAPTR event. To investigate how the structures of the precursors affect the structures of the products, ions were activated as a function of energy prior to CAPTR. In each case, the Ω values of the activated precursors increase with increasing energy, but the Ω values of the CAPTR products are smaller than the activated precursors. To investigate the stabilities of the CAPTR products, the products were activated immediately prior to ion mobility. These results show that additional structures with smaller or larger Ω values can be populated and that the structures and stabilities of these ions depend most strongly on the identity of the protein and the charge state of the product, rather than the charge state of the precursor or the number of CAPTR events. Together, these results indicate that the excess charges initially present on native-like ions have a modest, but sometimes statistically significant, effect on their Ω values. Therefore, potential contributions from charge state should be considered when using experimental Ω values to elucidate structures in solution.
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Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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19
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Jhingree JR, Bellina B, Pacholarz KJ, Barran PE. Charge Mediated Compaction and Rearrangement of Gas-Phase Proteins: A Case Study Considering Two Proteins at Opposing Ends of the Structure-Disorder Continuum. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1450-1461. [PMID: 28585116 PMCID: PMC5486678 DOI: 10.1007/s13361-017-1692-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 05/22/2023]
Abstract
Charge reduction in the gas phase provides a direct means of manipulating protein charge state, and when coupled to ion mobility mass spectrometry (IM-MS), it is possible to monitor the effect of charge on protein conformation in the absence of solution. Use of the electron transfer reagent 1,3-dicyanobenzene, coupled with IM-MS, allows us to monitor the effect of charge reduction on the conformation of two proteins deliberately chosen from opposite sides of the order to disorder continuum: bovine pancreatic trypsin inhibitor (BPTI) and beta casein. The ordered BPTI presents compact conformers for each of three charge states accompanied by narrow collision cross-section distributions (TWCCSDN2→He). Upon reduction of BPTI, irrespective of precursor charge state, the TWCCSN2→He decreases to a similar distribution as found for the nESI generated ion of identical charge. The behavior of beta casein upon charge reduction is more complex. It presents over a wide charge state range (9-28), and intermediate charge states (13-18) have broad TWCCSDN2→He with multiple conformations, where both compaction and rearrangement are seen. Further, we see that the TWCCSDN2→He of the latter charge states are even affected by the presence of radical anions. Overall, we conclude that the flexible nature of some proteins result in broad conformational distributions comprised of many families, even for single charge states, and the barrier between different states can be easily overcome by an alteration of the net charge. Graphical Abstract ᅟ.
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Affiliation(s)
- Jacquelyn R Jhingree
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Bruno Bellina
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Kamila J Pacholarz
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Perdita E Barran
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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20
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Laszlo KJ, Buckner JH, Munger EB, Bush MF. Native-Like and Denatured Cytochrome c Ions Yield Cation-to-Anion Proton Transfer Reaction Products with Similar Collision Cross-Sections. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1382-1391. [PMID: 28224394 PMCID: PMC5555649 DOI: 10.1007/s13361-017-1620-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 05/04/2023]
Abstract
The relationship between structures of protein ions, their charge states, and their original structures prior to ionization remains challenging to decouple. Here, we use cation-to-anion proton transfer reactions (CAPTR) to reduce the charge states of cytochrome c ions in the gas phase, and ion mobility to probe their structures. Ions were formed using a new temperature-controlled nanoelectrospray ionization source at 25 °C. Characterization of this source demonstrates that the temperature of the liquid sample is decoupled from that of the atmospheric pressure interface, which is heated during CAPTR experiments. Ionization from denaturing conditions yields 18+ to 8+ ions, which were each isolated and reacted with monoanions to generate all CAPTR products with charge states of at least 3+. The highest, intermediate, and lowest charge-state products exhibit collision cross-section distributions that are unimodal, multimodal, and unimodal, respectively. These distributions depend strongly on the charge state of the product, although those for the intermediate charge-state products also depend on that of the precursor. The distributions of the 3+ products are all similar, with averages that are less than half that of the 18+ precursor ions. Ionization of cytochrome c from native-like conditions yields 7+ and 6+ ions. The 3+ CAPTR products from these precursors have slightly more compact collision cross-section distributions that are indistinguishable from those for the 3+ CAPTR products from denaturing conditions. More broadly, these results indicate that the collision cross-sections of ions of this single domain protein depend strongly on charge state for charge states greater than ~4. Graphical Abstract ᅟ.
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Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - John H Buckner
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
- Department of Chemistry, Carleton College, One North College Street, Northfield, MN, 55057, USA
| | - Eleanor B Munger
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.
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21
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Garimella SVB, Webb IK, Prabhakaran A, Attah IK, Ibrahim YM, Smith RD. Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1442-1449. [PMID: 28560562 PMCID: PMC5551421 DOI: 10.1007/s13361-017-1680-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/29/2017] [Accepted: 04/03/2017] [Indexed: 05/06/2023]
Abstract
Here we describe instrumental approaches for performing dual polarity ion confinement, transport, ion mobility separations, and reactions in structures for lossless ion manipulations (SLIM). Previous means of ion confinement in SLIM, based upon rf-generated pseudopotentials and DC fields for lateral confinement, cannot trap ions of opposite polarity simultaneously. Here we explore alternative approaches to provide simultaneous lateral confinement of both ion polarities. Traveling wave ion mobility (IM) separations experienced in such SLIM cause ions of both polarities to migrate in the same directions and exhibit similar separations. The ion motion (and relative motion of the two polarities) under both surfing and IM separation conditions are discussed. In surfing conditions the two polarities are transported losslessly and non-reactively in their respective potential minima (higher absolute voltage regions confine negative polarities, and lower absolute potential regions are populated by positive polarities). In separation mode, where ions roll over an overtaking traveling wave, the two polarities can interact during the rollovers. Strategies to minimize overlap of the two ion populations to prevent reactive losses during separations are presented. A theoretical treatment of the time scales over which two populations (injected into a DC field-free region of the dual polarity SLIM device) interact is considered, and SLIM designs for allowing ion/ion interactions and other manipulations with dual polarities at 4 Torr are presented. Graphical Abstract ᅟ.
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Affiliation(s)
- Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ian K Webb
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Aneesh Prabhakaran
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Isaac K Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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22
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Laszlo KJ, Munger EB, Bush MF. Effects of Solution Structure on the Folding of Lysozyme Ions in the Gas Phase. J Phys Chem B 2017; 121:2759-2766. [PMID: 28301724 PMCID: PMC5486214 DOI: 10.1021/acs.jpcb.7b00783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The fidelity between the structures of proteins in solution and protein ions in the gas phase is critical to experiments that use gas-phase measurements to infer structures in solution. Here we generate ions of lysozyme, a 129-residue protein whose native tertiary structure contains four internal disulfide bonds, from three solutions that preserve varying extents of the original native structure. We then use cation-to-anion proton-transfer reactions (CAPTR) to reduce the charge states of those ions in the gas phase and ion mobility to probe their structures. The collision cross section (Ω) distributions of each CAPTR product depends to varying extents on the original solution, the charge state of the product, and the charge state of the precursor. For example, the Ω distributions of the 6+ ions depend strongly on the original solutions conditions and to a lesser extent on the charge state of the precursor. Energy-dependent experiments suggest that very different structures are accessible to disulfide-reduced and disulfide-intact ions, but similar Ω distributions are formed at high energy for disulfide-intact ions from denaturing and from aqueous conditions. The Ω distributions of the 3+ ions are all similar but exhibit subtle differences that depend more strongly on the original solutions conditions than other factors. More generally, these results suggest that specific CAPTR products may be especially sensitive to specific elements of structure in solution.
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Affiliation(s)
- Kenneth J. Laszlo
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Eleanor B. Munger
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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23
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Diversity in Gold Finger Structure Elucidated by Traveling‐Wave Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612494] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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24
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Du Z, de Paiva REF, Nelson K, Farrell NP. Diversity in Gold Finger Structure Elucidated by Traveling‐Wave Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2017; 56:4464-4467. [DOI: 10.1002/anie.201612494] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/13/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Zhifeng Du
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | | | - Kristina Nelson
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | - Nicholas P. Farrell
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
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25
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Boschmans J, Lemière F, Sobott F. Analyzing complex mixtures of drug-like molecules: Ion mobility as an adjunct to existing liquid chromatography-(tandem) mass spectrometry methods. J Chromatogr A 2017; 1490:80-88. [DOI: 10.1016/j.chroma.2017.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/24/2017] [Accepted: 02/09/2017] [Indexed: 12/17/2022]
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26
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Lermyte F, Łącki MK, Valkenborg D, Gambin A, Sobott F. Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:69-76. [PMID: 27495285 DOI: 10.1007/s13361-016-1444-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/11/2016] [Accepted: 06/26/2016] [Indexed: 06/06/2023]
Abstract
Owing to its versatility, electron transfer dissociation (ETD) has become one of the most commonly utilized fragmentation techniques in both native and non-native top-down mass spectrometry. However, several competing reactions-primarily different forms of charge reduction-occur under ETD conditions, as evidenced by the distorted isotope patterns usually observed. In this work, we analyze these isotope patterns to compare the stability of nondissociative electron transfer (ETnoD) products, specifically noncovalent c/z fragment complexes, across a range of ubiquitin conformational states. Using ion mobility, we find that more extended states are more prone to fragment release. We obtain evidence that for a given charge state, populations of ubiquitin ions formed either directly by electrospray ionization or through collapse of more extended states upon charge reduction, span a similar range of collision cross-sections. Products of gas-phase collapse are, however, less stabilized towards unfolding than the native conformation, indicating that the ions retain a memory of previous conformational states. Furthermore, this collapse of charge-reduced ions is promoted if the ions are 'preheated' using collisional activation, with possible implications for the kinetics of gas-phase compaction. Graphical Abstract ᅟ.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium
- Center for Proteomics, University of Antwerp, Antwerpen, Belgium
| | | | - Dirk Valkenborg
- Center for Proteomics, University of Antwerp, Antwerpen, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Antwerp, Belgium
| | - Anna Gambin
- Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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27
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Lermyte F, Sobott F. A broader view on ion heating in traveling-wave devices using fragmentation of CsI clusters and extent of H˙ migration as molecular thermometers. Analyst 2017; 142:3388-3399. [DOI: 10.1039/c7an00161d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Traveling-wave-dependent ion ‘heating’ is observed during mass spectrometry experiments under both ion mobility and electron transfer dissociation conditions and investigated using novel molecular ‘thermometers’.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular & Analytical Mass Spectrometry Group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
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28
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Souza GHMF, Guest PC, Martins-de-Souza D. LC-MS E, Multiplex MS/MS, Ion Mobility, and Label-Free Quantitation in Clinical Proteomics. Methods Mol Biol 2017; 1546:57-73. [PMID: 27896757 DOI: 10.1007/978-1-4939-6730-8_4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteomic tools can only be implemented in clinical settings if high-throughput, automated, sensitive, and accurate methods are developed. This has driven researchers to the edge of mass spectrometry (MS)-based proteomics capacity. Here we provide an overview of recent achievements in mass spectrometric technologies and instruments. This includes development of high and ultra definition-MSE (HDMSE and UDMSE) through implementation of ion mobility (IM) MS towards sensitive and accurate label-free proteomics using ultra performance liquid chromatography (UPLC). Label free UPLC-HDMSE is less expensive than labeled-based quantitative proteomics and has no limits regarding the number of samples that can be analyzed and compared, which is an important requirement for supporting clinical applications.
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Affiliation(s)
- Gustavo Henrique Martins Ferreira Souza
- Mass Spectrometry Applications & Development Laboratory, Waters Corporation, 125, Alphaville Industrial, Barueri, 06455-020, Campinas, São Paulo, SP, Brazil.
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
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29
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Laszlo KJ, Munger EB, Bush MF. Folding of Protein Ions in the Gas Phase after Cation-to-Anion Proton-Transfer Reactions. J Am Chem Soc 2016; 138:9581-8. [PMID: 27399988 PMCID: PMC4999245 DOI: 10.1021/jacs.6b04282] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The structure and folding of a protein in solution depends on noncovalent interactions within the protein and those with surrounding ions and molecules. Decoupling these interactions in solution is challenging, which has hindered the development of accurate physics-based models for structure prediction. Investigations of proteins in the gas phase can be used to selectively decouple factors affecting the structures of proteins. Here, we use cation-to-anion proton-transfer reactions (CAPTR) to reduce the charge states of denatured ubiquitin ions in the gas phase, and ion mobility to probe their structures. In CAPTR, a precursor charge state is selected (P) and reacted with monoanions to generate charge-reduced product ions (C). Following each CAPTR event, denatured ubiquitin ions (13+ to 6+) yield products that rapidly isomerize to structures that have smaller collision cross sections (Ω). The Ω values of CAPTR product ions depend strongly on C and very weakly on P. Pre- and post-CAPTR activation was then used to probe the potential-energy surfaces of the precursor and product ions, respectively. Post-CAPTR activation showed that ions of different P fold differently and populate different regions of the potential-energy surface of that ion. Finally, pre-CAPTR activation showed that the structures of protein ions can be indirectly investigated using ion mobility of their CAPTR product ions, even for subtle structural differences that are not apparent from ion mobility characterization of the activated precursor ions. More generally, these results show that CAPTR strongly complements existing techniques for characterizing the structures and dynamics of biological molecules in the gas phase.
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Affiliation(s)
- Kenneth J. Laszlo
- University of Washington, Department of Chemistry, Box 351700 Seattle, WA 98195-1700
| | - Eleanor B. Munger
- 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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30
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Bu J, Fisher CM, Gilbert JD, Prentice BM, McLuckey SA. Selective Covalent Chemistry via Gas-Phase Ion/ion Reactions: An Exploration of the Energy Surfaces Associated with N-Hydroxysuccinimide Ester Reagents and Primary Amines and Guanidine Groups. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1089-1098. [PMID: 27020926 DOI: 10.1007/s13361-016-1359-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 01/28/2016] [Accepted: 01/30/2016] [Indexed: 06/05/2023]
Abstract
Selective covalent bond forming reactions (referred to as covalent reactions) can occur in gas-phase ion/ion reactions and take place via the formation of a long-lived chemical complex. The gas-phase ion/ion reactivity between sulfo-N-hydroxysuccinimide (sulfo-NHS) ester reagent anions and peptide cations containing a primary amine or guanidine group has been examined via DFT calculations and complex dissociation rate measurements. The results reveal insights regarding the roles of the barriers of competing processes within the complex. When the covalent reaction is exothermic, two prototypical cases, determined by the nature of the energy surface, are apparent. The product partitioning between covalent reaction and simple proton transfer upon dissociation of the long-lived complex is sensitive to activation conditions when the transition state barrier for covalent reaction is relatively high (case 1) but is insensitive to activation conditions when the transition state barrier is relatively low (case 2). Covalent reaction efficiencies are very high in case 2 scenarios, such as when the reactive site is a guanidine and the anion attachment site is a guanidinium ion. Covalent reaction efficiencies are variable, and generally low, in case 1 scenarios, such as when an amine is the reactive site and an ammonium ion is the site of anion attachment. A relatively long slow-heating step prior to the complex dissociation step, however, can dramatically increase covalent reaction yield in case 1 scenarios. Graphical Abstract ᅟ.
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Affiliation(s)
- Jiexun Bu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Christine M Fisher
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Joshua D Gilbert
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Boone M Prentice
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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31
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Rathore D, Aboufazeli F, Dodds ED. Obtaining complementary polypeptide sequence information from a single precursor ion packet via sequential ion mobility-resolved electron transfer and vibrational activation. Analyst 2016; 140:7175-83. [PMID: 26357706 DOI: 10.1039/c5an01225b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tandem mass spectrometry (MS/MS) is now well-known as a powerful tool for characterizing the primary structures of peptides and proteins; however, in many cases the use of but a single dissociation method provides only a partial view of the amino acid sequences and post-translational modification patterns of polypeptides. While the application of multiple fragmentation methods can be more informative, this introduces the burden of acquiring multiple MS/MS spectra per analyte, thus reducing the effective duty cycle of such methods. In this work, initial proof-of-concept is provided for a method designed to overcome these barriers. This method relies on the complementary fragmentation information that can be provided by performing collision-induced dissociation (CID) and electron transfer dissociation (ETD) in concert, while also taking advantage of an ion mobility (IM) dimension to temporally resolve the occurrence of CID and ETD when applied to a single accumulated packet of precursor ions. In this way, the significant proportion of the precursor ion population that remains unreacted in ETD experiments is subjected to CID rather than being fruitlessly discarded. In addition, the two distinct fragmentation spectra can be extracted from their corresponding IM domains to render readily interpretable individual fragmentation spectra. This scheme was demonstrated for several polypeptides ranging from 1.3 to 8.6 kDa in molecular weight. In each case, IM-resolved CID and ETD events resulted in b/y and c/z ions, respectively, which each covered both unique and overlapping sequence information. These findings demonstrate that the combination of CID and ETD can be achieved with greater utilization of the available ion population and little or no loss of duty cycle.
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Affiliation(s)
- Deepali Rathore
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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32
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Boschmans J, Jacobs S, Williams JP, Palmer M, Richardson K, Giles K, Lapthorn C, Herrebout WA, Lemière F, Sobott F. Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers. Analyst 2016; 141:4044-54. [DOI: 10.1039/c5an02456k] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Computational methods are employed to study the protomers in ESI-IM-MS.
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Affiliation(s)
- Jasper Boschmans
- Biomolecular & Analytical Mass Spectrometry group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | - Sam Jacobs
- Molecular Spectroscopy group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | | | | | | | | | - Cris Lapthorn
- Faculty of Engineering & Science
- University of Greenwich
- Chatham
- UK
| | - Wouter A. Herrebout
- Molecular Spectroscopy group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | - Filip Lemière
- Biomolecular & Analytical Mass Spectrometry group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
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33
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Laszlo KJ, Bush MF. Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2152-61. [PMID: 26323617 PMCID: PMC4655144 DOI: 10.1007/s13361-015-1245-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/23/2015] [Accepted: 08/01/2015] [Indexed: 05/08/2023]
Abstract
Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures. Graphical Abstract ᅟ.
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Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA.
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34
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Characterization of top-down ETD in a travelling-wave ion guide. Methods 2015; 89:22-9. [DOI: 10.1016/j.ymeth.2015.05.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/30/2015] [Accepted: 05/19/2015] [Indexed: 11/20/2022] Open
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35
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Lermyte F, Sobott F. Electron transfer dissociation provides higher-order structural information of native and partially unfolded protein complexes. Proteomics 2015; 15:2813-22. [DOI: 10.1002/pmic.201400516] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 03/13/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Frederik Lermyte
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
| | - Frank Sobott
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
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36
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Lermyte F, Williams JP, Brown JM, Martin EM, Sobott F. Extensive Charge Reduction and Dissociation of Intact Protein Complexes Following Electron Transfer on a Quadrupole-Ion Mobility-Time-of-Flight MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1068-76. [PMID: 25862188 DOI: 10.1007/s13361-015-1124-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/25/2015] [Accepted: 03/01/2015] [Indexed: 05/23/2023]
Abstract
Non-dissociative charge reduction, typically considered to be an unwanted side reaction in electron transfer dissociation (ETD) experiments, can be enhanced significantly in order to reduce the charge state of intact protein complexes to as low as 1+ on a commercially available Q-IM-TOF instrument. This allows for the detection of large complexes beyond 100,000 m/z, while at the same time generating top-down ETD fragments, which provide sequence information from surface-exposed parts of the folded structure. Optimization of the supplemental activation has proven to be crucial in these experiments and the charge-reduced species are most likely the product of both proton transfer (PTR) and non-dissociative electron transfer (ETnoD) reactions that occur prior to the ion mobility cell. Applications of this approach range from deconvolution of complex spectra to the manipulation of charge states of gas-phase ions.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
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37
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Hanozin E, Morsa D, De Pauw E. Energetics and structural characterization of isomers using ion mobility and gas-phase H/D exchange: Learning from lasso peptides. Proteomics 2015; 15:2823-34. [DOI: 10.1002/pmic.201400534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/03/2015] [Accepted: 03/17/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Emeline Hanozin
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
| | - Denis Morsa
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
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38
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Ma Q, Ma W, Chen X, Wang Z, Bai H, Zhang L, Li W, Wang C, Li X. Comprehensive analysis of fatty alcohol ethoxylates by ultra high pressure hydrophilic interaction chromatography coupled with ion mobility spectrometry mass spectrometry using a custom-designed sub-2 μm column. J Sep Sci 2015; 38:2182-91. [PMID: 25847530 DOI: 10.1002/jssc.201500185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Qiang Ma
- Chinese Academy of Inspection and Quarantine; Beijing China
- Weldon School of Biomedical Engineering; Purdue University; West Lafayette IN USA
| | - Wei Ma
- Post-Doctoral Mobile Station of Chemical Engineering and Technology; Harbin Institute of Technology; Harbin China
| | - Xi Chen
- Waters Corporation; Shanghai China
| | - Ziming Wang
- College of Chemistry; Jilin University; Changchun China
| | - Hua Bai
- Chinese Academy of Inspection and Quarantine; Beijing China
| | - Lanwei Zhang
- Post-Doctoral Mobile Station of Chemical Engineering and Technology; Harbin Institute of Technology; Harbin China
| | - Wentao Li
- Chinese Academy of Inspection and Quarantine; Beijing China
| | - Chao Wang
- Chinese Academy of Inspection and Quarantine; Beijing China
| | - Xinshi Li
- Chinese Academy of Inspection and Quarantine; Beijing China
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39
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Donohoe GC, Arndt JR, Valentine SJ. Online deuterium hydrogen exchange and protein digestion coupled with ion mobility spectrometry and tandem mass spectrometry. Anal Chem 2015; 87:5247-54. [PMID: 25893550 DOI: 10.1021/acs.analchem.5b00277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Online deuterium hydrogen exchange (DHX) and pepsin digestion (PD) is demonstrated using drift tube ion mobility spectrometry (DTIMS) coupled with linear ion trap (LTQ) mass spectrometry (MS) with electron transfer dissociation (ETD) capabilities. DHX of deuterated ubiquitin, followed by subsequent quenching and digestion, is performed within ∼60 s, yielding 100% peptide sequence coverage. The high reproducibility of the IMS separation allows spectral feature matching between two-dimensional IMS-MS datasets (undeuterated and deuterated) without the need for dataset alignment. Extracted ion drift time distributions (XIDTDs) of deuterated peptic peptides are mobility-matched to corresponding XIDTDs of undeuterated peptic peptides that were identified using collision-induced dissociation (CID). Matching XIDTDs allows a straightforward identification and deuterium retention evaluation for labeled peptides. Aside from the mobility separation, the ion trapping capabilities of the LTQ, combined with ETD, are demonstrated to provide single-residue resolution. Deuterium retention for the c- series ions across residues M(1)-L(15) and N(25)-R(42) are in good agreement with the known secondary structural elements within ubiquitin.
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Affiliation(s)
- Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - James R Arndt
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
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40
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Affiliation(s)
- Jody C. May
- Department
of Chemistry,
Center for Innovative Technology, Vanderbilt Institute for Chemical
Biology, Vanderbilt Institute for Integrative Biosystems Research
and Education , Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A. McLean
- Department
of Chemistry,
Center for Innovative Technology, Vanderbilt Institute for Chemical
Biology, Vanderbilt Institute for Integrative Biosystems Research
and Education , Vanderbilt University, Nashville, Tennessee 37235, United States
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41
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Zhu F, Glover MS, Shi H, Trinidad JC, Clemmer DE. Populations of metal-glycan structures influence MS fragmentation patterns. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:25-35. [PMID: 25315458 PMCID: PMC4276451 DOI: 10.1007/s13361-014-1000-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 09/04/2014] [Accepted: 09/07/2014] [Indexed: 05/19/2023]
Abstract
The structures and collision-induced dissociation (CID) fragmentation patterns of the permethylated glycan Man5GlcNAc2 are investigated by a combination of hybrid ion mobility spectrometry (IMS), mass spectrometry (MS), and MS/MS techniques. IMS analysis of eight metal-adducted glycans ([Man5GlcNAc2 + M](2+), where M = Mn, Fe, Co, Ni, Cu, Mg, Ca, and Ba) shows distinct conformer patterns. These conformers appear to arise from individual metals binding at different sites on the glycan. Fragmentation studies suggest that these different binding sites influence the CID fragmentation patterns. This paper describes a series of separation, activation, and fragmentation studies that assess which fragments arise from each of the different gas-phase conformer states. Comparison of the glycan distributions formed under gentle ionization conditions with those obtained after activation of the gas-phase ions suggests that these conformer binding states also appear to exist in solution.
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Affiliation(s)
- Feifei Zhu
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Matthew S. Glover
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Huilin Shi
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Jonathan C. Trinidad
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
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42
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Baba T, Campbell JL, Le Blanc JCY, Hager JW, Thomson BA. Electron Capture Dissociation in a Branched Radio-Frequency Ion Trap. Anal Chem 2014; 87:785-92. [DOI: 10.1021/ac503773y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Takashi Baba
- AB Sciex, 71 Four Valley Drive, Concord, Ontario, L4K 4V8, Canada
| | | | | | - James W. Hager
- AB Sciex, 71 Four Valley Drive, Concord, Ontario, L4K 4V8, Canada
| | - Bruce A. Thomson
- AB Sciex, 71 Four Valley Drive, Concord, Ontario, L4K 4V8, Canada
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43
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Wills RH, Habtemariam A, Lopez-Clavijo AF, Barrow MP, Sadler PJ, O'Connor PB. Insights into the binding sites of organometallic ruthenium anticancer compounds on peptides using ultra-high resolution mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:662-672. [PMID: 24488754 DOI: 10.1007/s13361-013-0819-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 12/12/2013] [Accepted: 12/14/2013] [Indexed: 06/03/2023]
Abstract
The binding sites of two ruthenium(II) organometallic complexes of the form [(η(6)-arene)Ru(N,N)Cl](+), where arene/N,N = biphenyl (bip)/bipyridine (bipy) for complex AH076, and biphenyl (bip)/o-phenylenediamine (o-pda) for complex AH078, on the peptides angiotensin and bombesin have been investigated using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. Fragmentation was performed using collisionally activated dissociation (CAD), with, in some cases, additional data being provided by electron capture dissociation (ECD). The primary binding sites were identified as methionine and histidine, with further coordination to phenylalanine, potentially through a π-stacking interaction, which has been observed here for the first time. This initial peptide study was expanded to investigate protein binding through reaction with insulin, on which the binding sites proposed are histidine, glutamic acid, and tyrosine. Further reaction of the ruthenium complexes with the oxidized B chain of insulin, in which two cysteine residues are oxidized to cysteine sulfonic acid (Cys-SO3H), and glutathione, which had been oxidized with hydrogen peroxide to convert the cysteine to cysteine sulfonic acid, provided further support for histidine and glutamic acid binding, respectively.
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Affiliation(s)
- Rebecca H Wills
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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44
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Lermyte F, Konijnenberg A, Williams JP, Brown JM, Valkenborg D, Sobott F. ETD allows for native surface mapping of a 150 kDa noncovalent complex on a commercial Q-TWIMS-TOF instrument. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:343-50. [PMID: 24408179 DOI: 10.1007/s13361-013-0798-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 10/29/2013] [Accepted: 11/04/2013] [Indexed: 05/11/2023]
Abstract
Top-down approaches for the characterization of intact proteins and macromolecular complexes are becoming increasingly popular, since they potentially simplify and speed up the assignment process. Here we demonstrate how, on a commercially available Q-TWIMS-TOF instrument, we performed top-down ETD of the native form of tetrameric alcohol dehydrogenase. We achieved good sequence coverage throughout the first 81 N-terminal amino acids of ADH, with the exception of a loop located on the inside of the protein. This is in agreement with the exposed parts of the natively folded protein according to the crystal structure. Choosing the right precursor charge state and applying supplemental activation were found to be key to obtaining a high ETD fragmentation efficiency. Finally, we briefly discuss opportunities to further increase the performance of ETD based on our results.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
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45
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Murray BS, Menin L, Scopelliti R, Dyson PJ. Conformational control of anticancer activity: the application of arene-linked dinuclear ruthenium(ii) organometallics. Chem Sci 2014. [DOI: 10.1039/c4sc00116h] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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46
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Houel S, Hilliard M, Yu YQ, McLoughlin N, Martin SM, Rudd PM, Williams JP, Chen W. N- and O-Glycosylation Analysis of Etanercept Using Liquid Chromatography and Quadrupole Time-of-Flight Mass Spectrometry Equipped with Electron-Transfer Dissociation Functionality. Anal Chem 2013; 86:576-84. [DOI: 10.1021/ac402726h] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Stephane Houel
- Late Stage Development,
Pharmaceutical Life Sciences, Waters Corporation, Milford, Massachusetts 01757, United States
| | - Mark Hilliard
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion,
Blackrock, County Dublin, Ireland
| | - Ying Qing Yu
- Late Stage Development,
Pharmaceutical Life Sciences, Waters Corporation, Milford, Massachusetts 01757, United States
| | - Niaobh McLoughlin
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion,
Blackrock, County Dublin, Ireland
| | - Silvia Millan Martin
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion,
Blackrock, County Dublin, Ireland
| | - Pauline M. Rudd
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion,
Blackrock, County Dublin, Ireland
| | | | - Weibin Chen
- Late Stage Development,
Pharmaceutical Life Sciences, Waters Corporation, Milford, Massachusetts 01757, United States
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47
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Pepin R, Laszlo KJ, Peng B, Marek A, Bush MF, Tureček F. Comprehensive Analysis of Gly-Leu-Gly-Gly-Lys Peptide Dication Structures and Cation-Radical Dissociations Following Electron Transfer: From Electron Attachment to Backbone Cleavage, Ion–Molecule Complexes, and Fragment Separation. J Phys Chem A 2013; 118:308-24. [DOI: 10.1021/jp411100c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Robert Pepin
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Kenneth J. Laszlo
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Bo Peng
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Aleš Marek
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
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48
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Williams JP, Pringle S, Richardson K, Gethings L, Vissers JPC, De Cecco M, Houel S, Chakraborty AB, Yu YQ, Chen W, Brown JM. Characterisation of glycoproteins using a quadrupole time-of-flight mass spectrometer configured for electron transfer dissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2383-2390. [PMID: 24097394 DOI: 10.1002/rcm.6684] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 07/08/2013] [Accepted: 07/08/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Electron transfer dissociation (ETD) within ion trapping mass spectrometers has proven to be a useful tool for the characterisation of post-translational modifications. In this study, we describe the implementation of ETD upon a modified quadrupole time-of-flight (Q-ToF) system and methods for the analysis of glycoproteins. METHODS Liquid chromatography electrospray ionisation mass spectrometry (LC/ESI-MS) was performed using a hybrid quadrupole/ion mobility/oa-ToF mass spectrometer equipped with ETD functionality. 1,4-Dicyanobenzene reagent anions necessary for the ETD reaction were generated from a glow discharge region located within the ESI source block. ETD reactions occurred in the stacked ring travelling wave ion guide (located after the quadrupole mass filter and prior to the oa-ToF mass analyser). LC/ETD was performed upon 'super-charged' tryptic glycopeptide ions produced from the recombinant monoclonal antibody trastuzumab. LC/ETD was also performed on ions from the smaller glycopeptides obtained from erythropoietin. RESULTS ETD performed upon the quadruply 'super-charged' N-linked glycopeptide ions of trastuzumab and the triply charged O-linked glycopeptide ions of erythropoietin provided both glycosylation site assignments and full sequence information, respectively. Tandem mass (MS/MS) spectra employing collision-induced dissociation (CID) were dominated by oxonium product ions hampering full peptide sequence characterisation. CONCLUSIONS LC/ETD on the Q-ToF system proved effective at characterising a number of different N-linked glyco-forms of the tryptic peptide, EEQYNSTYR, from trastuzumab as well as glyco-forms from the O-linked tryptic peptide, EASIPPDAASAAPLR, from erythropoietin. The data demonstrates that the glycopeptide site heterogeneity of trastuzumab and erythropoietin can be accurately characterised. In addition, the post-column mixing of the super-charging reagent, m-NBA, is an effective method to increase the precursor ion charge state and to improve ETD reaction efficiency.
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49
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Meier SM, Novak M, Kandioller W, Jakupec MA, Arion VB, Metzler-Nolte N, Keppler BK, Hartinger CG. Identification of the structural determinants for anticancer activity of a ruthenium arene peptide conjugate. Chemistry 2013; 19:9297-307. [PMID: 23712572 DOI: 10.1002/chem.201300889] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Indexed: 11/07/2022]
Abstract
Organometallic Ru(arene)-peptide bioconjugates with potent in vitro anticancer activity are rare. We have prepared a conjugate of a Ru(arene) complex with the neuropeptide [Leu(5)]-enkephalin. [Chlorido(η(6)-p-cymene)(5-oxo-κO-2-{(4-[(N-tyrosinyl-glycinyl-glycinyl-phenylalanyl-leucinyl-NH2)propanamido]-1H-1,2,3-triazol-1-yl)methyl}-4H-pyronato-κO)ruthenium(II)] (8) shows antiproliferative activity in human ovarian carcinoma cells with an IC50 value as low as 13 μM, whereas the peptide or the Ru moiety alone are hardly cytotoxic. The conjugation strategy for linking the Ru(cym) (cym=η(6)-p-cymene) moiety to the peptide involved N-terminal modification of an alkyne-[Leu(5)]-enkephalin with a 2-(azidomethyl)-5-hydroxy-4H-pyran-4-one linker, using Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC), and subsequent metallation with the Ru(cym) moiety. The ruthenium-bioconjugate was characterized by high resolution top-down electrospray ionization mass spectrometry (ESI-MS) with regard to peptide sequence, linker modification and metallation site. Notably, complete sequence coverage was obtained and the Ru(cym) moiety was confirmed to be coordinated to the pyronato linker. The ruthenium-bioconjugate was analyzed with respect to cytotoxicity-determining constituents, and through the bioconjugate models [{2-(azidomethyl)-5-oxo-κO-4H-pyronato-κO}chloride (η(6)-p-cymene)ruthenium(II)] (5) and [chlorido(η(6)-p-cymene){5-oxo-κO-2-([(4-(phenoxymethyl)-1H-1,2,3-triazol-1-yl]methyl)-4H-pyronato-κO}ruthenium(II)] (6) the Ru(cym) fragment with a triazole-carrying pyronato ligand was identified as the minimal unit required to achieve in vitro anticancer activity.
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Affiliation(s)
- Samuel M Meier
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Strasse 42, 1090 Vienna, Austria
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50
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Prentice BM, McLuckey SA. Gas-phase ion/ion reactions of peptides and proteins: acid/base, redox, and covalent chemistries. Chem Commun (Camb) 2013; 49:947-65. [PMID: 23257901 PMCID: PMC3557538 DOI: 10.1039/c2cc36577d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gas-phase ion/ion reactions are emerging as useful and flexible means for the manipulation and characterization of peptide and protein biopolymers. Acid/base-like chemical reactions (i.e., proton transfer reactions) and reduction/oxidation (redox) reactions (i.e., electron transfer reactions) represent relatively mature classes of gas-phase chemical reactions. Even so, especially in regards to redox chemistry, the widespread utility of these two types of chemistries is undergoing rapid growth and development. Additionally, a relatively new class of gas-phase ion/ion transformations is emerging which involves the selective formation of functional-group-specific covalent bonds. This feature details our current work and perspective on the developments and current capabilities of these three areas of ion/ion chemistry with an eye towards possible future directions of the field.
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Affiliation(s)
- Boone M. Prentice
- Purdue University – Department of Chemistry, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Scott A. McLuckey
- Purdue University – Department of Chemistry, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
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