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Heissel S, He Y, Jankevics A, Shi Y, Molina H, Viner R, Scheltema RA. Fast and Accurate Disulfide Bridge Detection. Mol Cell Proteomics 2024; 23:100759. [PMID: 38574859 PMCID: PMC11067345 DOI: 10.1016/j.mcpro.2024.100759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/08/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
Recombinant expression of proteins, propelled by therapeutic antibodies, has evolved into a multibillion dollar industry. Essential here is the quality control assessment of critical attributes, such as sequence fidelity, proper folding, and posttranslational modifications. Errors can lead to diminished bioactivity and, in the context of therapeutic proteins, an elevated risk for immunogenicity. Over the years, many techniques were developed and applied to validate proteins in a standardized and high-throughput fashion. One parameter has, however, so far been challenging to assess. Disulfide bridges, covalent bonds linking two cysteine residues, assist in the correct folding and stability of proteins and thus have a major influence on their efficacy. Mass spectrometry promises to be an optimal technique to uncover them in a fast and accurate fashion. In this work, we present a unique combination of sample preparation, data acquisition, and analysis facilitating the rapid and accurate assessment of disulfide bridges in purified proteins. Through microwave-assisted acid hydrolysis, the proteins are digested rapidly and artifact-free into peptides, with a substantial degree of overlap over the sequence. The nonspecific nature of this procedure, however, introduces chemical background, which is efficiently removed by integrating ion mobility preceding the mass spectrometric measurement. The nonspecific nature of the digestion step additionally necessitates new developments in data analysis, for which we extended the XlinkX node in Proteome Discoverer to efficiently process the data and ensure correctness through effective false discovery rate correction. The entire workflow can be completed within 1 h, allowing for high-throughput, high-accuracy disulfide mapping.
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Affiliation(s)
- Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA.
| | - Yi He
- Thermo Fisher Scientific, San Jose, California, USA
| | - Andris Jankevics
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Structural Proteomics Group, Department of Biochemistry and Systems Biology, University of Liverpool, Liverpool, UK
| | - Yuqi Shi
- Thermo Fisher Scientific, San Jose, California, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, California, USA.
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Structural Proteomics Group, Department of Biochemistry and Systems Biology, University of Liverpool, Liverpool, UK.
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2
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Chaturvedi S, Bawake S, Sharma N. Recent advancements in disulfide bridge characterization: Insights from mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9713. [PMID: 38361473 DOI: 10.1002/rcm.9713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 02/17/2024]
Abstract
RATIONALE Disulfide bridges (DSB) play an important role in stabilizing three-dimensional structures of biopharmaceuticals, single purified proteins, and various cyclic peptide drugs that contain disulfide in their structures. Incorrect cross-linking known as DSB scrambling results in misfolded structures that can be inactive, immunogenic, and susceptible to aggregation. Very few articles have been published on the experimental annotation of DSBs in proteins and cyclic peptide drugs. Accurate characterization of the disulfide bond is essential for understanding protein confirmation. METHODS Characterizing DSBs using mass spectrometry (MS) involves the chemical and enzymatic digestion of samples to obtain smaller peptide fragments, in both reduced and nonreduced forms. Subsequently, these samples are analyzed using MS to locate the DSB, either through interpretation or by employing various software tools. RESULTS The main challenge in DSB analysis methods using sample preparation is to obtain a sample solution in which nonnative DSBs are not formed due to high pH, temperature, and presence of free sulfhydryl groups. Formation of nonnative DSBs can lead to erroneous annotation of disulfide bond. Sample preparation techniques, fragmentation methods for DSB analysis, and contemporary approaches for DSB mapping using this fragmentation were discussed. CONCLUSIONS This review presents the latest advancement in MS-based characterization; also a critical perspective is presented for further annotation of DSBs using MS, primarily for single purified proteins or peptides that are densely connected and rich in cysteine. Despite significant breakthroughs resulting from advancements in MS, the analysis of disulfide bonds is not straightforward; it necessitates expertise in sample preparation and interpretation.
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Affiliation(s)
- Sachin Chaturvedi
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (Ministry of Chemicals and Fertilizers, Government of India), NIPER Ahmedabad Opposite Air force Station Palaj, Gandhinagar, Gujarat, India
| | - Sanket Bawake
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (Ministry of Chemicals and Fertilizers, Government of India), NIPER Ahmedabad Opposite Air force Station Palaj, Gandhinagar, Gujarat, India
| | - Nitish Sharma
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (Ministry of Chemicals and Fertilizers, Government of India), NIPER Ahmedabad Opposite Air force Station Palaj, Gandhinagar, Gujarat, India
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3
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Habeck T, Maciel EVS, Kretschmer K, Lermyte F. Charge site manipulation to enhance top-down fragmentation efficiency. Proteomics 2024; 24:e2300082. [PMID: 37043727 DOI: 10.1002/pmic.202300082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
In recent years, top-down mass spectrometry has become a widely used approach to study proteoforms; however, improving sequence coverage remains an important goal. Here, two different proteins, α-synuclein and bovine carbonic anhydrase, were subjected to top-down collision-induced dissociation (CID) after electrospray ionisation. Two high-boiling solvents, DMSO and propylene carbonate, were added to the protein solution in low concentration (2%) and the effects on the top-down fragmentation patterns of the proteins were systematically investigated. Each sample was measured in triplicate, which revealed highly reproducible differences in the top-down CID fragmentation patterns in the presence of a solution additive, even if the same precursor charge state was isolated in the quadrupole of the instrument. Further investigation supports the solution condition-dependent selective formation of different protonation site isomers as the underlying cause of these differences. Higher sequence coverage was often observed in the presence of additives, and the benefits of this approach became even more evident when datasets from different solution conditions were combined, as increases up to 35% in cleavage coverage were obtained. Overall, this approach therefore represents a promising opportunity to increase top-down fragmentation efficiency.
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Affiliation(s)
- Tanja Habeck
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Edvaldo Vasconcelos Soares Maciel
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Kevin Kretschmer
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Frederik Lermyte
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
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4
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Po A, Eyers CE. Top-Down Proteomics and the Challenges of True Proteoform Characterization. J Proteome Res 2023; 22:3663-3675. [PMID: 37937372 PMCID: PMC10696603 DOI: 10.1021/acs.jproteome.3c00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Top-down proteomics (TDP) aims to identify and profile intact protein forms (proteoforms) extracted from biological samples. True proteoform characterization requires that both the base protein sequence be defined and any mass shifts identified, ideally localizing their positions within the protein sequence. Being able to fully elucidate proteoform profiles lends insight into characterizing proteoform-unique roles, and is a crucial aspect of defining protein structure-function relationships and the specific roles of different (combinations of) protein modifications. However, defining and pinpointing protein post-translational modifications (PTMs) on intact proteins remains a challenge. Characterization of (heavily) modified proteins (>∼30 kDa) remains problematic, especially when they exist in a population of similarly modified, or kindred, proteoforms. This issue is compounded as the number of modifications increases, and thus the number of theoretical combinations. Here, we present our perspective on the challenges of analyzing kindred proteoform populations, focusing on annotation of protein modifications on an "average" protein. Furthermore, we discuss the technical requirements to obtain high quality fragmentation spectral data to robustly define site-specific PTMs, and the fact that this is tempered by the time requirements necessary to separate proteoforms in advance of mass spectrometry analysis.
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Affiliation(s)
- Allen Po
- Centre
for Proteome Research, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, Faculty of Health & Life
Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
| | - Claire E. Eyers
- Centre
for Proteome Research, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, Faculty of Health & Life
Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
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5
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Javanshad R, Taylor CJ, Delavari N, Barkman TJ, Stull F, Venter AR. Analysis of histidine-tagged recombinant proteins from nickel and copper coated surfaces by direct electrospray ionization and desorption electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37 Suppl 1:e9516. [PMID: 37013403 DOI: 10.1002/rcm.9516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/28/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
RATIONALE Purification of recombinant proteins is a necessary step for functional or structural studies and other applications. Immobilized metal affinity chromatography is a common recombinant protein purification method. Mass spectrometry (MS) allows for confirmation of identity of expressed proteins and unambiguous detection of enzymatic substrates and reaction products. We demonstrate the detection of enzymes purified on immobilized metal affinity surfaces by direct or ambient ionization MS, and follow their enzymatic reactions by direct electrospray ionization (ESI) or desorption electrospray ionization (DESI). METHODS A protein standard, His-Ubq, and two recombinant proteins, His-SHAN and His-CS, expressed in Escherichia coli were immobilized on two immobilized metal affinity systems, Cu-nitriloacetic acid (Cu-NTA) and Ni-NTA. The proteins were purified on surface, and released in the ESI spray solvent for direct infusion, when using the 96-well plate form factor, or analyzed directly from immobilized metal affinity-coated microscope slides by DESI-MS. Enzyme activity was followed by incubating the substrates in wells or by depositing substrate on immobilized protein on coated slides for analysis. RESULTS Small proteins (His-Ubq) and medium proteins (His-SAHN) could readily be detected from 96-well plates by direct infusion ESI, or from microscope slides by DESI-MS after purification on surface from clarified E. coli cell lysate. Protein oxidation was observed for immobilized proteins on both Cu-NTA and Ni-NTA; however, this did not hamper the enzymatic reactions of these proteins. Both the nucleosidase reaction products for His-SAHN and the methylation product of His-CS (theobromine to caffeine) were detected. CONCLUSIONS The immobilization, purification, release and detection of His-tagged recombinant proteins using immobilized metal affinity surfaces for direct infusion ESI-MS or ambient DESI-MS analyses were successfully demonstrated. Recombinant proteins were purified to allow identification directly out of clarified cell lysate. Biological activities of the recombinant proteins were preserved allowing the investigation of enzymatic activity via MS.
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Affiliation(s)
- Roshan Javanshad
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | | | - Niusha Delavari
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
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Wei B, Zenaidee MA, Lantz C, Williams BJ, Totten S, Ogorzalek Loo RR, Loo JA. Top-down mass spectrometry and assigning internal fragments for determining disulfide bond positions in proteins. Analyst 2022; 148:26-37. [PMID: 36399030 PMCID: PMC9772244 DOI: 10.1039/d2an01517j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Disulfide bonds in proteins have a substantial impact on protein structure, stability, and biological activity. Localizing disulfide bonds is critical for understanding protein folding and higher-order structure. Conventional top-down mass spectrometry (TD-MS), where only terminal fragments are assigned for disulfide-intact proteins, can access disulfide information, but suffers from low fragmentation efficiency, thereby limiting sequence coverage. Here, we show that assigning internal fragments generated from TD-MS enhances the sequence coverage of disulfide-intact proteins by 20-60% by returning information from the interior of the protein sequence, which cannot be obtained by terminal fragments alone. The inclusion of internal fragments can extend the sequence information of disulfide-intact proteins to near complete sequence coverage. Importantly, the enhanced sequence information that arise from the assignment of internal fragments can be used to determine the relative position of disulfide bonds and the exact disulfide connectivity between cysteines. The data presented here demonstrates the benefits of incorporating internal fragment analysis into the TD-MS workflow for analyzing disulfide-intact proteins, which would be valuable for characterizing biotherapeutic proteins such as monoclonal antibodies and antibody-drug conjugates.
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Affiliation(s)
- Benqian Wei
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA.
| | - Muhammad A Zenaidee
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA.
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW, Australia
| | - Carter Lantz
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA.
| | | | | | - Rachel R Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA.
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
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7
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Watts E, Thyer R, Ellington AD, Brodbelt JS. Integrated Top-Down and Bottom-Up Mass Spectrometry for Characterization of Diselenide Bridging Patterns of Synthetic Selenoproteins. Anal Chem 2022; 94:11175-11184. [PMID: 35930618 DOI: 10.1021/acs.analchem.2c01433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
With the rapid acceleration in the design and development of new biotherapeutics, ensuring consistent quality and understanding degradation pathways remain paramount, requiring an array of analytical methods including mass spectrometry. The incorporation of non-canonical amino acids, such as for synthetic selenoproteins, creates additional challenges. A comprehensive strategy to characterize selenoproteins should serve dual purposes of providing sequence confirmation and mapping of selenocysteine bridge locations and the identification of unanticipated side products. In the present study, a combined approach exploiting the benefits of both top-down and bottom-up mass spectrometry was developed. Both electron-transfer/higher-energy collision dissociation and 213 nm ultraviolet photodissociation were utilized to provide complementary information, allowing high quality characterization, localization of diselenide bridges for complex proteins, and the identification of previously unreported selenoprotein dimers.
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Affiliation(s)
- Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ross Thyer
- Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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8
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Macias LA, Brodbelt JS. Investigation of Product Ions Generated by 193 nm Ultraviolet Photodissociation of Peptides and Proteins Containing Disulfide Bonds. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1315-1324. [PMID: 35736955 DOI: 10.1021/jasms.2c00124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Disulfide bridges are unique post-translational modifications (PTM) that contribute to protein architecture and modulate function. This PTM, however, challenges top-down mass spectrometry by cyclizing stretches of the protein sequence. In order to produce and release detectable product ions that contribute to the assignment of proteoforms, regions of a protein encapsulated by disulfide bonds require two fragmentation events: cleavage of the protein backbone and cleavage of the disulfide bond. Traditional collisional activation methods do not cleave disulfide bonds efficiently, often leading to low sequence coverage of proteins that incorporate this feature. To address this challenge, we have evaluated the fragmentation pathways enabled by 193 nm ultraviolet photodissociation (UVPD) and UVPD coupled to electron transfer dissociation for the characterization of protein structures incorporating disulfide bonds. Cleavage of disulfide bonds by either approach results in S-S and C-S dissociation products that result from a combination of homolytic cleavage and hydrogen-transfer processes. Characterization of these product ions elevates interpretation of complex top-down spectra of proteins that incorporate disulfide bonds.
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Affiliation(s)
- Luis A Macias
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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9
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Challen B, Cramer R. Advances in ionisation techniques for mass spectrometry-based omics research. Proteomics 2022; 22:e2100394. [PMID: 35709387 DOI: 10.1002/pmic.202100394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022]
Abstract
Omics analysis by mass spectrometry (MS) is a vast field, with proteomics, metabolomics and lipidomics dominating recent research by exploiting biological MS ionisation techniques. Traditional MS ionisation techniques such as electrospray ionisation have limitations in analyte-specific sensitivity, modes of sampling and throughput, leading to many researchers investigating new ionisation methods for omics research. In this review, we examine the current landscape of these new ionisation techniques, divided into the three groups of (electro)spray-based, laser-based and other miscellaneous ionisation techniques. Due to the wide range of new developments, this review can only provide a starting point for further reading on each ionisation technique, as each have unique benefits, often for specialised applications, which promise beneficial results for different areas in the omics world.
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Affiliation(s)
- Bob Challen
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
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10
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Tucholski T, Ge Y. Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms. MASS SPECTROMETRY REVIEWS 2022; 41:158-177. [PMID: 32894796 PMCID: PMC7936991 DOI: 10.1002/mas.21653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with its ultrahigh mass-resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top-down, middle-down, and native MS-based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT-ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in-depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post-translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT-ICR MS and emerging applications, such as native top-down FT-ICR MS and high-throughput top-down FT-ICR MS-based proteomics at 21 T, are also covered. Historically, the information gleaned from FT-ICR MS analyses have helped provide biological insights. We predict FT-ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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12
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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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13
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Adhikari S, Xia Y, McLuckey SA. Top-Down Analysis of Disulfide-Linked Proteins Using Photoinduced Radical Reactions and ET-DDC. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 444:116173. [PMID: 31372092 PMCID: PMC6675022 DOI: 10.1016/j.ijms.2019.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Top-down characterization of proteins via tandem mass spectrometry (MS/MS) can be challenging due to the presence of multiple disulfide bond linkages; which significantly inhibit the backbone cleavage efficiency for the formation of structurally informative fragment ions. In this study, we present a strategy of pairing a solution-phase photoinitiating system with dipolar direct current induced collisional activation of electron transfer products (ET-DDC) of proteins for a top-down MS/MS approach. The photoinitiating system allows for a rapid scission of all the disulfide linkages in the protein (on the time scale of seconds) with high efficiency (near to complete reduction); while ET-DDC collisional activation improves the fragmentation efficiency for the protein via broadband activation of all the first-generation charge reduced precursor ions (e.g., electron transfer no-dissociation or ETnoD products) from electron transfer reactions over a wide mass-to-charge range. As a result, this approach enabled the generation of extensive sequence informative fragment ion yields for a rapid and enhanced structural characterization of disulfide-linked proteins.
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Affiliation(s)
- Sarju Adhikari
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yu Xia
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Address reprint requests to: Dr. Scott A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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14
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Li X, Yang X, Hoang V, Liu YH. Characterization of Protein Disulfide Linkages by MS In-Source Dissociation Comparing to CID and ETD Tandem MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:519-528. [PMID: 30478816 DOI: 10.1007/s13361-018-2103-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/18/2018] [Accepted: 11/01/2018] [Indexed: 05/19/2023]
Abstract
Direct characterization of disulfide linkages in proteins by mass spectrometry has been challenging. Here, we report analysis of disulfide linkages in insulin variant, endothelin 3, and relaxin 2 by in-source dissociation (ISD) during LC-MS. A duplet insulin peptide from Glu-C digestion that contains peptides p1 and p2 (from chains A and B, respectively) was selected as a model peptide. This duplet peptide has an inter-chain disulfide bond between p1 and p2, and an intra-chain disulfide bond in p1. To compare the gas-phase fragmentation, it was subjected to ISD MS and MS/MS methods, including collision-induced dissociation (CID) and electron transfer dissociation (ETD). The pattern and efficiency of peptide backbone and disulfide cleavage varied with these dissociation methods. ETD, CID, and ISD were able to generate single backbone, double backbone, and triple (double backbone and single disulfide bond) cleavages in this model peptide, respectively. Specifically, CID did not cleave disulfide bonds and ETD was able to only cleave the inter-chain disulfide bond at low efficiency, limiting their usage in this disulfide analysis. In contrast, ISD was able to cleave the intra-chain disulfide bond in addition to peptide backbone, creating multiple fragment ions that allow accurate assignment of both intra- and inter-chain disulfide linkages. ISD was also successfully applied to determine double disulfide linkages in endothelin 3 and relaxin 2 peptides. This study contributes to the fundamental understanding of disulfide bond cleavages in different gas-phase fragmentations and provides an efficient cleavage strategy for identification of disulfide bonds in proteins by ISD ESI-MS. Graphical Abstract.
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Affiliation(s)
- Xiaojuan Li
- Bioprocess Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA.
| | - Xiaoyu Yang
- Bioprocess Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Van Hoang
- Bioprocess Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Yan-Hui Liu
- Bioprocess Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
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15
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Ke M, Zhang H, Ding J, Xiong X, Li F, Chingin K, Kou W, Liu A, Zhu T, Fang X, Chen H. Generating Supercharged Protein Ions for Breath Analysis by Extractive Electrospray Ionization Mass Spectrometry. Anal Chem 2019; 91:3215-3220. [DOI: 10.1021/acs.analchem.8b03114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mufang Ke
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, People’s Republic of China
| | - Hua Zhang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, People’s Republic of China
| | - Jianhua Ding
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, People’s Republic of China
| | - Xingchuang Xiong
- National Institute of Metrology, Beijing 100029, People’s Republic of China
| | - Fenglei Li
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, People’s Republic of China
| | - Konstantin Chingin
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, People’s Republic of China
| | - Wei Kou
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, People’s Republic of China
| | - Aiying Liu
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, People’s Republic of China
| | - Tenggao Zhu
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, People’s Republic of China
| | - Xiang Fang
- National Institute of Metrology, Beijing 100029, People’s Republic of China
| | - Huanwen Chen
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, People’s Republic of China
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16
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Zhao X, Shen Y, Tong W, Wang G, Chen DDY. Deducing disulfide patterns of cysteine-rich proteins using signature fragments produced by top-down mass spectrometry. Analyst 2019; 143:817-823. [PMID: 29362732 DOI: 10.1039/c7an01625e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Direct mapping of protein disulfide patterns using top-down mass spectrometry (MS) is often hampered by inadequate fragmentation at the disulfide-enclosing region, and insufficient structural information provided by the fragments. Here we used electron-transfer/high energy collision dissociation (EThcD) to improve the fragmentation efficiency, and developed strategies that minimize the false positive identification of fragments and deconvolute the signals representing specific modifications made to the disulfide-cleavage-induced fragments. We observed clear correlations between unique modification (attachment or removal of H or SH) patterns and the number of disulfide bonds that enclose the corresponding region. Using the characteristic signature fragments, we in part localized the Cys-bridging sites in disulfide-scrambled lysozymes, and reduced the number of putative disulfide patterns from 104 to 6. The results demonstrated the feasibility of direct analysis of complex disulfide patterns using top-down MS.
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Affiliation(s)
- Xiuxiu Zhao
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, and School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
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17
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Xiao Y, Li M, Larocque R, Zhang F, Malhotra A, Chen J, Linhardt RJ, Konermann L, Xu D. Dimerization interface of osteoprotegerin revealed by hydrogen-deuterium exchange mass spectrometry. J Biol Chem 2018; 293:17523-17535. [PMID: 30254073 DOI: 10.1074/jbc.ra118.004489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/20/2018] [Indexed: 01/13/2023] Open
Abstract
Previous structural studies of osteoprotegerin (OPG), a crucial negative regulator of bone remodeling and osteoclastogenesis, were mostly limited to the N-terminal ligand-binding domains. It is now known that the three C-terminal domains of OPG also play essential roles in its function by mediating OPG dimerization, OPG-heparan sulfate (HS) interactions, and formation of the OPG-HS-receptor activator of nuclear factor κB ligand (RANKL) ternary complex. Employing hydrogen-deuterium exchange MS methods, here we investigated the structure of full-length OPG in complex with HS or RANKL in solution. Our data revealed two noteworthy aspects of the OPG structure. First, we found that the interconnection between the N- and C-terminal domains is much more rigid than previously thought, possibly because of hydrophobic interactions between the fourth cysteine-rich domain and the first death domain. Second, we observed that two hydrophobic clusters located in two separate C-terminal domains directly contribute to OPG dimerization, likely by forming a hydrophobic dimerization interface. Aided by site-directed mutagenesis, we further demonstrated that an intact dimerization interface is essential for the biological activity of OPG. Our study represents an important step toward deciphering the structure-function relationship of the full-length OPG protein.
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Affiliation(s)
- Yiming Xiao
- From the Department of Chemistry, University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Miaomiao Li
- the Department of Oral Biology, University of Buffalo, Buffalo, New York 14214, and
| | - Rinzhi Larocque
- the Department of Oral Biology, University of Buffalo, Buffalo, New York 14214, and
| | - Fuming Zhang
- the Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Anju Malhotra
- the Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jianle Chen
- the Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Robert J Linhardt
- the Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Lars Konermann
- From the Department of Chemistry, University of Western Ontario, London, Ontario N6A 5B7, Canada,
| | - Ding Xu
- the Department of Oral Biology, University of Buffalo, Buffalo, New York 14214, and
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18
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Strategy for peptide quantification using LC–MS in regulated bioanalysis: case study with a glucose-responsive insulin. Bioanalysis 2018; 10:1207-1220. [PMID: 30062907 DOI: 10.4155/bio-2018-0089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: Advances in technology have led to a shift for peptide quantification from traditional ligand-binding assays to LC–MS/MS-based analysis, which presents challenges, in other assay sensitivity, specificity and ruggedness, in addition to lacking of regulatory guidance, especially for the hybrid assay format. Methodology & results: This report communicates a strategy that has been employed in our laboratories for method development and assay validation, and exemplified in a case study of MK-2640, a glucose-responsive insulin, in multiple matrices. Intact MK-2640 was monitored, while immunoaffinity purification and SPE were used to support the rat/dog GLP and clinical studies, respectively. The rationale and considerations behind our approach, as well as the acceptance criteria applied to the assay validation are discussed.
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19
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Chen B, Lin Z, Alpert AJ, Fu C, Zhang Q, Pritts WA, Ge Y. Online Hydrophobic Interaction Chromatography-Mass Spectrometry for the Analysis of Intact Monoclonal Antibodies. Anal Chem 2018; 90:7135-7138. [PMID: 29846060 DOI: 10.1021/acs.analchem.8b01865] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Therapeutic monoclonal antibodies (mAbs) are an important class of drugs for a wide spectrum of human diseases. Liquid chromatography (LC) coupled to mass spectrometry (MS) is one of the techniques in the forefront for comprehensive characterization of analytical attributes of mAbs. Among various protein chromatography modes, hydrophobic interaction chromatography (HIC) is a popular offline nondenaturing separation technique utilized to purify and analyze mAbs, typically with the use of non-MS-compatible mobile phases. Herein we demonstrate for the first time, the application of direct HIC-MS and HIC-tandem MS (MS/MS) with electron capture dissociation (ECD) for analyzing intact mAbs on quadrupole-time-of-flight (Q-TOF) and Fourier transform ion cyclotron resonance (FTICR) mass spectrometers, respectively. Our method allows for rapid determination of relative hydrophobicity, intact masses, and glycosylation profiles of mAbs as well as sequence and structural characterization of the complementarity-determining regions in an online configuration.
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Affiliation(s)
- Bifan Chen
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,Human Proteomics Program, School of Medicine and Public Health , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | | | - Cexiong Fu
- Process Analytical , AbbVie Inc , North Chicago , Illinois 60064 , United States
| | - Qunying Zhang
- Process Analytical , AbbVie Inc , North Chicago , Illinois 60064 , United States
| | - Wayne A Pritts
- Process Analytical , AbbVie Inc , North Chicago , Illinois 60064 , United States
| | - Ying Ge
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,Human Proteomics Program, School of Medicine and Public Health , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
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20
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How can native mass spectrometry contribute to characterization of biomacromolecular higher-order structure and interactions? Methods 2018; 144:3-13. [PMID: 29704661 DOI: 10.1016/j.ymeth.2018.04.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/03/2018] [Accepted: 04/21/2018] [Indexed: 01/16/2023] Open
Abstract
Native mass spectrometry (MS) is an emerging approach for characterizing biomacromolecular structure and interactions under physiologically relevant conditions. In native MS measurement, intact macromolecules or macromolecular complexes are directly ionized from a non-denaturing solvent, and key noncovalent interactions that hold the complexes together can be preserved for MS analysis in the gas phase. This technique provides unique multi-level structural information such as conformational changes, stoichiometry, topology and dynamics, complementing conventional biophysical techniques. Despite the maturation of native MS and greatly expanded range of applications in recent decades, further dissemination is needed to make the community aware of such a technique. In this review, we attempt to provide an overview of the current body of knowledge regarding major aspects of native MS and explain how such technique contributes to the characterization of biomacromolecular higher-order structure and interactions.
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21
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Nshanian M, Lakshmanan R, Chen H, Ogorzalek Loo RR, Loo JA. Enhancing Sensitivity of Liquid Chromatography-Mass Spectrometry of Peptides and Proteins Using Supercharging Agents. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 427:157-164. [PMID: 29750076 PMCID: PMC5937529 DOI: 10.1016/j.ijms.2017.12.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Trifluoroacetic acid (TFA) is often used as a mobile phase modifier to enhance reversed phase chromatographic performance. TFA adjusts solution pH and is an ion-pairing agent, but it is not typically suitable for electrospray ionization-mass spectrometry (ESI-MS) and liquid chromatography/MS (LC/MS) because of its significant signal suppression. Supercharging agents elevate peptide and protein charge states in ESI, increasing tandem MS (MS/MS) efficiency. Here, LC/MS protein supercharging was effected by adding agents to LC mobile phase solvents. Significantly, the ionization suppression generally observed with TFA was, for the most part, rescued by supercharging agents, with improved separation efficiency (higher number of theoretical plates) and lowered detection limits.
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Affiliation(s)
- Michael Nshanian
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095
| | - Rajeswari Lakshmanan
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH 45701
| | - Rachel R. Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Molecular Biology Institute, and UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, CA 90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Molecular Biology Institute, and UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, CA 90095
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22
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Metwally H, Konermann L. Crown Ether Effects on the Location of Charge Carriers in Electrospray Droplets: Implications for the Mechanism of Protein Charging and Supercharging. Anal Chem 2018; 90:4126-4134. [DOI: 10.1021/acs.analchem.8b00099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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23
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Li P, Kreft I, Jackson GP. Top-Down Charge Transfer Dissociation (CTD) of Gas-Phase Insulin: Evidence of a One-Step, Two-Electron Oxidation Mechanism. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:284-296. [PMID: 28786096 PMCID: PMC5803485 DOI: 10.1007/s13361-017-1700-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/24/2017] [Accepted: 04/27/2017] [Indexed: 05/03/2023]
Abstract
Top-down analyses of protonated insulin cations of charge states of 4+, 5+, or 6+ were performed by exposing the isolated precursor ions to a beam of helium cations with kinetic energy of more than 6 keV, in a technique termed charge transfer dissociation (CTD). The ~100 ms charge transfer reaction resulted in approximately 20% conversion efficiency to other intact charge exchange products (CTnoD), and a range of low abundance fragment ions. To increase backbone and sulfide cleavages, and to provide better structural information than straightforward MS2 CTD, the CTnoD oxidized products were isolated and subjected to collisional activation at the MS3 level. The MS3 CTD/CID reaction effectively broke the disulfide linkages, separated the two chains, and yielded more structurally informative fragment ions within the inter-chain cyclic region. CTD also provided doubly oxidized intact product ions at the MS2 level, and resonance ejection of the singly oxidized product ion revealed that the doubly oxidized product originates directly from the isolated precursor ion and not from consecutive CTD reactions of a singly oxidized intermediate. MS4 experiments were employed to help identify potential radical cations and diradical cations, but the results were negative or inconclusive. Nonetheless, the two-electron oxidation process is a demonstration of the very large potential energy (>20 eV) available through CTD, and is a notable capability for a 3D ion trap platform. Graphical Abstract ᅟ.
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Affiliation(s)
- Pengfei Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Iris Kreft
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506-6121, USA
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506-6121, USA.
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24
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Metwally H, McAllister RG, Popa V, Konermann L. Mechanism of Protein Supercharging by Sulfolane and m-Nitrobenzyl Alcohol: Molecular Dynamics Simulations of the Electrospray Process. Anal Chem 2016; 88:5345-54. [DOI: 10.1021/acs.analchem.6b00650] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Haidy Metwally
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Robert G. McAllister
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Vlad Popa
- Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Lars Konermann
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
- Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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25
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Wongkongkathep P, Li H, Zhang X, Loo RRO, Julian RR, Loo JA. Enhancing Protein Disulfide Bond Cleavage by UV Excitation and Electron Capture Dissociation for Top-Down Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 390:137-145. [PMID: 26644781 PMCID: PMC4669582 DOI: 10.1016/j.ijms.2015.07.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The application of ion pre-activation with 266 nm ultraviolet (UV) laser irradiation combined with electron capture dissociation (ECD) is demonstrated to enhance top-down mass spectrometry sequence coverage of disulfide bond containing proteins. UV-based activation can homolytically cleave a disulfide bond to yield two separated thiol radicals. Activated ECD experiments of insulin and ribonuclease A containing three and four disulfide bonds, respectively, were performed. UV-activation in combination with ECD allowed the three disulfide bonds of insulin to be cleaved and the overall sequence coverage to be increased. For the larger sized ribonuclease A with four disulfide bonds, irradiation from an infrared laser (10.6 µm) to disrupt non-covalent interactions was combined with UV-activation to facilitate the cleavage of up to three disulfide bonds. Preferences for disulfide bond cleavage are dependent on protein structure and sequence. Disulfide bonds can reform if the generated radicals remain in close proximity. By varying the time delay between the UV-activation and the ECD events, it was determined that disulfide bonds reform within 10-100 msec after their UV-homolytic cleavage.
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Affiliation(s)
- Piriya Wongkongkathep
- Department of Chemistry and Biochemistry, University of California-Los Angeles Los Angeles, CA 90095
| | - Huilin Li
- Department of Biological Chemistry, University of California-Los Angeles Los Angeles, CA 90095
| | - Xing Zhang
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521
| | - Rachel R. Ogorzalek Loo
- Department of Biological Chemistry, University of California-Los Angeles Los Angeles, CA 90095
| | - Ryan R. Julian
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles Los Angeles, CA 90095
- Department of Biological Chemistry, University of California-Los Angeles Los Angeles, CA 90095
- UCLA/DOE Institute of Genomics and Proteomics, University of California-Los Angeles Los Angeles, CA 90095
- Corresponding author at: University of California-Los Angeles, Department of Chemistry and Biochemistry, 402 Boyer Hall, Molecular Biology Institute, Los Angeles, CA, United States, Tel.: +1 310 794 7023; fax: +1 310 206 4038, (J.A. Loo)
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26
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Sohn CH, Gao J, Thomas DA, Kim TY, Goddard WA, Beauchamp JL. Mechanisms and energetics of free radical initiated disulfide bond cleavage in model peptides and insulin by mass spectrometry. Chem Sci 2015; 6:4550-4560. [PMID: 29142703 PMCID: PMC5666513 DOI: 10.1039/c5sc01305d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/20/2015] [Indexed: 11/21/2022] Open
Abstract
Direct radical substitution at sulfur initiates disulfide bond cleavage by hydrogen-deficient radicals in peptides and proteins.
We investigate the mechanism of disulfide bond cleavage in gaseous peptide and protein ions initiated by a covalently-attached regiospecific acetyl radical using mass spectrometry (MS). Highly selective S–S bond cleavages with some minor C–S bond cleavages are observed by a single step of collisional activation. We show that even multiple disulfide bonds in intact bovine insulin are fragmented in the MS2 stage, releasing the A- and B-chains with a high yield, which has been challenging to achieve by other ion activation methods. Yet, regardless of the previous reaction mechanism studies, it has remained unclear why (1) disulfide bond cleavage is preferred to peptide backbone fragmentation, and why (2) the S–S bond that requires the higher activation energy conjectured in previously suggested mechanisms is more prone to be cleaved than the C–S bond by hydrogen-deficient radicals. To probe the mechanism of these processes, model peptides possessing deuterated β-carbon(s) at the disulfide bond are employed. It is suggested that the favored pathway of S–S bond cleavage is triggered by direct acetyl radical attack at sulfur with concomitant cleavage of the S–S bond (SH2). The activation energy for this process is substantially lower by ∼9–10 kcal mol–1 than those of peptide backbone cleavage processes determined by density functional quantum chemical calculations. Minor reaction pathways are initiated by hydrogen abstraction from the α-carbon or the β-carbon of a disulfide, followed by β-cleavages yielding C–S or S–S bond scissions. The current mechanistic findings should be generally applicable to other radical-driven disulfide bond cleavages with different radical species such as the benzyl and methyl pyridyl radicals.
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Affiliation(s)
- Chang Ho Sohn
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - Jinshan Gao
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - Daniel A Thomas
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - Tae-Young Kim
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - William A Goddard
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA . .,Materials and Process Simulation Center , Beckman Institute , California Institute of Technology , Pasadena , CA 91125 , USA
| | - J L Beauchamp
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
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27
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Cai Y, Zheng Q, Liu Y, Helmy R, Loo JA, Chen H. Integration of electrochemistry with ultra-performance liquid chromatography/mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:341-51. [PMID: 26307715 PMCID: PMC4552337 DOI: 10.1255/ejms.1318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
This study presents the development of ultra-performance liquid chromatography (UPLC) mass spectrometry (MS) combined with electrochemistry (EC) for the first time and its application for the structural analysis of proteins/peptides that contain disulfide bonds. In our approach, a protein/peptide mixture sample undergoes a fast UPLC separation and subsequent electrochemical reduction in an electrochemical flow cell followed by online MS and tandem mass spectrometry (MS/MS) analyses. The electrochemical cell is coupled to the mass spectrometer using our recently developed desorption electrospray ionization (DESI) interface. Using this UPLC/EC/DESI-MS method, peptides that contain disulfide bonds can be differentiated from those without disulfide bonds, as the former are electroactive and reducible. MS/MS analysis of the disulfide-reduced peptide ions provides increased information on the sequence and disulfide-linkage pattern. In a reactive DESI- MS detection experiment in which a supercharging reagent was used to dope the DESI spray solvent, increased charging was obtained for the UPLC-separated proteins. Strikingly, upon online electrolytic reduction, supercharged proteins (e.g., α-lactalbumin) showed even higher charging, which will be useful in top- down protein structure MS analysis as increased charges are known to promote protein ion dissociation. Also, the separation speed and sensitivity are enhanced by approximately 1(~)2 orders of magnitude by using UPLC for the liquid chromatography (LC)/EC/MS platform, in comparison to the previously used high- performance liquid chromatography (HPLC). This UPLC/EC/DESI-MS method combines the power of fast UPLC separation, fast electrochemical conversion, and online MS structural analysis for a potentially valuable tool for proteomics research and bioanalysis.
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Affiliation(s)
- Yi Cai
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701 USA.
| | - Qiuling Zheng
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701 USA.
| | - Yong Liu
- Department of Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., Rahway, NJ 07065, USA.
| | - Roy Helmy
- Department of Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., Rahway, NJ 07065, USA.
| | - Joseph A Loo
- Dep artment of Chemistry and Biochemistry, Department of Biological Chemistry, David Geffen School of Medicine at UCLA, and UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, CA 90095, USA.
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701 USA.
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