1
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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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Ladouce R, MacAleese L, Wittine K, Merćep M, Girod M. Specific detection of protein carbonylation sites by 473 nm photodissociation mass spectrometry. Anal Bioanal Chem 2023; 415:6619-6632. [PMID: 37755489 DOI: 10.1007/s00216-023-04956-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023]
Abstract
The study of protein oxidation remains a challenge despite the biomedical interest in reliable biomarkers of oxidative stress. This is particularly true for carbonylations although, recently, liquid chromatography-mass spectrometry techniques (LC-MS) have been proposed to detect this non-enzymatic and poorly distributed oxidative modification of proteins using untargeted or carbonyl-reactive probe methods. These methods proved to be feasible but could not preserve the dynamic range of the protein sample, making it impossible to quantify oxidatively modified proteoforms compared with native proteoforms. Here, we propose an innovative method based on the implementation of a reactive carbonyl probe conjugated with a laser-sensitive chromophore, dabcyl-aminooxy, which confers optical specificity to the LC-MS approach. In addition, our protein carbonyl detection method allows us to localize individual carbonylation sites by observing fragments of derivatized oxidized peptides. Two model proteins, alpha-synuclein and beta-lactoglobulin, were oxidized and carbonylation sites were detected, resulting in the identification of respectively 34 and 77 different carbonylated amino acids. Thus, we demonstrated the application of a direct and sensitive method for studying protein carbonylation sites in complex protein extracts.
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Affiliation(s)
- Romain Ladouce
- Zora Fundation, Ruđera Boškovića 21, 21000, Split, Croatia
- Mediterranean Institute for Life Sciences (MedILS), Meštrovićevo šetalište 45, 21000, Split, Croatia
| | - Luke MacAleese
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1 - Institut Lumière Matière (iLM), Lyon, France
| | - Karlo Wittine
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia
- Selvita Ltd, Prilaz baruna Filipovića 29, 10000, Zagreb, Croatia
| | - Mladen Merćep
- Zora Fundation, Ruđera Boškovića 21, 21000, Split, Croatia
- Mediterranean Institute for Life Sciences (MedILS), Meštrovićevo šetalište 45, 21000, Split, Croatia
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia
| | - Marion Girod
- Universite Claude Bernard Lyon 1, ISA UMR 5280, CNRS, 69100, Villeurbanne, France.
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3
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Strizzi S, Bernardo L, D'Ursi P, Urbinati C, Bianco A, Limanaqi F, Manconi A, Milanesi M, Macchi A, Di Silvestre D, Cavalleri A, Pareschi G, Rusnati M, Clerici M, Mauri P, Biasin M. An innovative strategy to investigate microbial protein modifications in a reliable fast and sensitive way: A therapy oriented proof of concept based on UV-C irradiation of SARS-CoV-2 spike protein. Pharmacol Res 2023; 194:106862. [PMID: 37479104 DOI: 10.1016/j.phrs.2023.106862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
The characterization of modifications of microbial proteins is of primary importance to dissect pathogen lifecycle mechanisms and could be useful in identifying therapeutic targets. Attempts to solve this issue yielded only partial and non-exhaustive results. We developed a multidisciplinary approach by coupling in vitro infection assay, mass spectrometry (MS), protein 3D modelling, and surface plasma resonance (SPR). As a proof of concept, the effect of low UV-C (273 nm) irradiation on SARS-CoV-2 spike (S) protein was investigated. Following UV-C exposure, MS analysis identified, among other modifications, the disruption of a disulphide bond within the conserved S2 subunit of S protein. Computational analyses revealed that this bond breakage associates with an allosteric effect resulting in the generation of a closed conformation with a reduced ability to bind the ACE2 receptor. The UV-C-induced reduced affinity of S protein for ACE2 was further confirmed by SPR analyses and in vitro infection assays. This comprehensive approach pinpoints the S2 domain of S protein as a potential therapeutic target to prevent SARS-CoV-2 infection. Notably, this workflow could be used to screen a wide variety of microbial protein domains, resulting in a precise molecular fingerprint and providing new insights to adequately address future epidemics.
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Affiliation(s)
- Sergio Strizzi
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Letizia Bernardo
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Pasqualina D'Ursi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Chiara Urbinati
- Unit of Macromolecular Interaction Analysis, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Andrea Bianco
- Italian National Institute for Astrophysics (INAF) - Brera Astronomical Observatory, Via E. Bianchi, 46, Merate, 23807 Lecco, Italy
| | - Fiona Limanaqi
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
| | - Andrea Manconi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Maria Milanesi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy; Unit of Macromolecular Interaction Analysis, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Alberto Macchi
- Italian National Institute for Astrophysics (INAF) - Brera Astronomical Observatory, Via E. Bianchi, 46, Merate, 23807 Lecco, Italy
| | - Dario Di Silvestre
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Adalberto Cavalleri
- Epidemiology and Prevention Unit, IRCCS Foundation, Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133 Milan, Italy
| | - Giovanni Pareschi
- Italian National Institute for Astrophysics (INAF) - Brera Astronomical Observatory, Via E. Bianchi, 46, Merate, 23807 Lecco, Italy
| | - Marco Rusnati
- Unit of Macromolecular Interaction Analysis, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy; Don C. Gnocchi Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Foundation, Via A. Capecelatro 66, 20148 Milan, íItaly
| | - PierLuigi Mauri
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy; Interdisciplinary Research Center "Health Science", Sant'Anna School of Advanced Studies, 56127 Pisa, Italy.
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
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4
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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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5
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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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6
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Guillaubez JV, Pitrat D, Bretonnière Y, Lemoine J, Girod M. Relative quantification of sulfenic acids in plasma proteins using differential labelling and mass spectrometry coupled with 473 nm photo-dissociation analysis: A multiplexed approach applied to an Alzheimer's disease cohort. Talanta 2022; 250:123745. [PMID: 35870285 DOI: 10.1016/j.talanta.2022.123745] [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: 05/19/2022] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 10/17/2022]
Abstract
Cysteine (Cys) is subject to a variety of reversible post-translational modifications such as formation of sulfenic acid (Cys-SOH). If this modification is often involved in normal biological activities, it can also be the result of oxidative damage. Indeed, oxidative stress yields abnormal cysteine oxidations that affect protein function and structure and can lead to neurodegenerative diseases. In a context of population ageing, validation of novel biomarkers for detection of neurodegenerative diseases is important. However, Cys-SOH proteins investigation in large human cohorts is challenging due to their low abundance and lability under endogenous conditions. To improve the detection specificity towards the oxidized protein subpopulation, we developed a method that makes use of a mass spectrometer coupled with visible laser induced dissociation (LID) to add a stringent optical specificity to the mass selectivity. Since peptides do not naturally absorb in the visible range, this approach relies on the proper chemical derivatization of Cys-SOH with a chromophore functionalized with a cyclohexanedione. To compensate for the significant variability in total protein expression within the samples and any experimental bias, a normalizing strategy using free thiol (Cys-SH) cysteine peptides derivatized with a maleimide chromophore as internal references was used. Thanks to the differential tagging, oxidative ratios were then obtained for 69 Cys-containing peptides from 19 proteins tracked by parallel reaction monitoring (PRM) LID, in a cohort of 49 human plasma samples from Alzheimer disease (AD) patients. A statistical analysis indicated that, for the proteins monitored, the Cys oxidative ratio does not correlate with the diagnosis of AD. Nevertheless, the PRM-LID method allows the unbiased, sensitive and robust relative quantification of Cys oxidation within cohorts of samples.
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Affiliation(s)
- Jean-Valery Guillaubez
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France
| | - Delphine Pitrat
- Laboratoire de Chimie ENS Lyon, UMR, 5582, ENS Lyon CNRS et Université Lyon 1, France
| | - Yann Bretonnière
- Laboratoire de Chimie ENS Lyon, UMR, 5582, ENS Lyon CNRS et Université Lyon 1, France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France
| | - Marion Girod
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France.
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7
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Miller SA, Fouque KJD, Ridgeway ME, Park MA, Fernandez-Lima F. Trapped Ion Mobility Spectrometry, Ultraviolet Photodissociation, and Time-of-Flight Mass Spectrometry for Gas-Phase Peptide Isobars/Isomers/Conformers Discrimination. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1267-1275. [PMID: 35658468 PMCID: PMC9262853 DOI: 10.1021/jasms.2c00091] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Trapped ion mobility spectrometry (TIMS) when coupled with mass spectrometry (MS) offers great advantages for the separation of isobaric, isomeric, and/or conformeric species. In the present work, we report the advantages of coupling TIMS with a low-cost, ultraviolet photodissociation (UVPD) linear ion trap operated at few mbars prior to time-of-flight (ToF) MS analysis for the effective characterization of isobaric, isomeric, and/or conformeric species based on mobility-selected fragmentation patterns. These three traditional challenges to MS-based separations are illustrated for the case of biologically relevant model systems: H3.1 histone tail PTM isobars (K4Me3/K18Ac), lanthipeptide regioisomers (overlapping/nonoverlapping ring patterns), and a model peptide conformer (angiotensin I). The sequential nature of the TIMS operation allows for effective synchronization with the ToF MS scans, in addition to parallel operation between the TIMS and the UVPD trap. Inspection of the mobility-selected UVPD MS spectra showed that for all three cases considered, unique fragmentation patterns (fingerprints) were observed per mobility band. Different from other IMS-UVPD implementations, the higher resolution of the TIMS device allowed for high mobility resolving power (R > 100) and effective mobility separation. The mobility selected UVPD MS provided high sequence coverage (>85%) with a fragmentation efficiency up to ∼40%.
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Affiliation(s)
- Samuel A. Miller
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
| | | | - Melvin A. Park
- Bruker Daltonics Inc., Billerica, MA 01821, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
- Corresponding Author: Francisco Fernandez-Lima,
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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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Bakshi T, Pham D, Kaur R, Sun B. Hidden Relationships between N-Glycosylation and Disulfide Bonds in Individual Proteins. Int J Mol Sci 2022; 23:ijms23073742. [PMID: 35409101 PMCID: PMC8998389 DOI: 10.3390/ijms23073742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/04/2023] Open
Abstract
N-Glycosylation (NG) and disulfide bonds (DBs) are two prevalent co/post-translational modifications (PTMs) that are often conserved and coexist in membrane and secreted proteins involved in a large number of diseases. Both in the past and in recent times, the enzymes and chaperones regulating these PTMs have been constantly discovered to directly interact with each other or colocalize in the ER. However, beyond a few model proteins, how such cooperation affects N-glycan modification and disulfide bonding at selective sites in individual proteins is largely unknown. Here, we reviewed the literature to discover the current status in understanding the relationships between NG and DBs in individual proteins. Our results showed that more than 2700 human proteins carry both PTMs, and fewer than 2% of them have been investigated in the associations between NG and DBs. We summarized both these proteins with the reported relationships in the two PTMs and the tools used to discover the relationships. We hope that, by exposing this largely understudied field, more investigations can be encouraged to unveil the hidden relationships of NG and DBs in the majority of membranes and secreted proteins for pathophysiological understanding and biotherapeutic development.
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Affiliation(s)
- Tania Bakshi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - David Pham
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Raminderjeet Kaur
- Faculty of Health Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Bingyun Sun
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Correspondence:
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10
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Zhao X, Zhang S, Ma Q, Zhang X, Ma X. Rapid Disulfide Mapping in Peptides and Proteins by meta-Chloroperoxybenzoic Acid ( mCPBA) Oxidation and Tandem Mass Spectrometry. Anal Chem 2021; 93:14618-14625. [PMID: 34704736 DOI: 10.1021/acs.analchem.1c02379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Disulfide bonds are a class of important post-translational modifications that play important roles in modulating the structures and functions of proteins. Therefore, the mapping of disulfide linkages in peptides and proteins is indispensable for complete structure characterization and functional studies. As disulfide bonds in protonated ions do not dissociate readily under low-energy collision-induced dissociation (CID), they are usually chemically cleaved or activated prior to mass spectrometry (MS) or tandem MS (MS/MS) analysis. In this study, we report a new method that allows the mapping of disulfide linkages in peptides and proteins through meta-chloroperoxybenzoic acid (mCPBA)-based disulfide oxidation and MS/MS. Upon oxidation, the disulfide bond is converted to a thiosulfinate group, i.e., S(═O)-S, in a rapid (>60% yield in 1 min) and highly specific approach in an aqueous phase. The thiosulfinate group is then preferentially cleaved by MS/MS. For interchain disulfide linkages, this leads to a facile peptide chain separation and the identification of disulfide-linked peptides. For intrachain disulfide linkages, collisional activation of the thiosulfinate leads to disulfide cleavage and fragmentation of the peptide backbone constrained by the disulfide loop, enabling a near-complete peptide sequencing. The mCPBA oxidation-based disulfide mapping strategy can be readily integrated with bottom-up or top-down protein analysis for comprehensive protein structure elucidation, e.g., digested lysozyme and intact human insulin.
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Affiliation(s)
- Xu Zhao
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qiang Ma
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaoxiao Ma
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
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11
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Hou X, Shi Y, Yang M, Yu S, Fan X, Liang J, Pan X, Wang X. Fabrication of poly( t-butyl betaine carboxylate)-based nanoparticles and study on their in vivo biosecurity. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2021; 32:2387-2401. [PMID: 34428381 DOI: 10.1080/09205063.2021.1971822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The purpose of this article was to fabricate the novel poly(t-butyl betaine carboxylate)-S-S-poly (1, 3-dioxan-2-one) nanoparticles (PCB-tBU-S-S-PDI NPs) and study their in vivo biosecurity. The poly(t-butyl betaine carboxylate) (PCB-tBU) segment was conjugated to the poly(1, 3-dioxan-2-one)(PDI) moity with a disulfide bond to obtain the copolymer PCB-tBU-S-S-PDI. Hydrogen nuclear magnetic resonance (1H NMR) and Fourier transform infrared spectroscopy (FTIR) spectra were applied to study the structure of PCB-tBU-S-S-PDI. The cargo-free NPs were administrated to Sprague-Dawley (SD) rats by intraperitoneal injection every 3 days for 30 days. Then, the blood routine examination, blood biochemistry, and histologic slides of rat's organs were carried out to monitor the in vivo biosecurity of cargo-free PCB-tBU-S-S-PDI NPs. 1H NMR and FTIR spectra confirmed the successfully synthesis of PCB-tBU-S-S-PDI. The cargo-free NPs showed spherical morphology with an average of 139.8 ± 0.26 nm. The results of blood biochemistry and blood routine examination suggested that the cargo-free PCB-tBU-S-S-PDI NPs did not show any influence on the liver and renal functions of treated rats. Significantly, the physiological slides of treated rat's organs did not show any physiological and pathological changes. These phenomena suggested that the PCB-tBU-S-S-PDI NPs had good biosecurity, and it could be used as a vehicle for antineoplastic drug delivery.
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Affiliation(s)
- Xueyan Hou
- College of pharmacy, Xinxiang Medical University, Xinxiang, P.R. China
| | - Yongli Shi
- College of pharmacy, Xinxiang Medical University, Xinxiang, P.R. China
| | - Mingbo Yang
- College of pharmacy, Xinxiang Medical University, Xinxiang, P.R. China
| | - Shasha Yu
- College of pharmacy, Xinxiang Medical University, Xinxiang, P.R. China
| | - Xue Fan
- College of pharmacy, Xinxiang Medical University, Xinxiang, P.R. China
| | - Jinna Liang
- College of pharmacy, Xinxiang Medical University, Xinxiang, P.R. China
| | - Xiaofei Pan
- College of pharmacy, Xinxiang Medical University, Xinxiang, P.R. China
| | - Xiao Wang
- College of pharmacy, Xinxiang Medical University, Xinxiang, P.R. China
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12
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Gammelgaard SK, Petersen SB, Haselmann KF, Nielsen PK. Characterization of Insulin Dimers by Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1910-1918. [PMID: 33084334 DOI: 10.1021/jasms.0c00257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
High-molecular weight products (HMWP) are an important critical quality attribute in research and development of insulin biopharmaceuticals. We here demonstrate on two case studies of covalent insulin dimers, induced by Fe2+ incubation or ultraviolet (UV) light stress, that de novo characterization in top-down mass spectrometry (MS) workflows can identify cross-link types and sites. On the MS2 level, electron-transfer/higher-energy collision dissociation (EThcD) efficiently cleaved the interchain disulfide bonds in the dimers to reveal cross-link connectivities between chains. The combined utilization of EThcD and 213 nm ultraviolet photodissociation (UVPD) facilitated identification of the chemical composition of the cross-links. Identification of cross-link sites between chains at residue level was achievable for both dimers with MS3 analysis of MS2 fragments cleaved at the cross-link or additionally the interchain disulfide bonds. UVPD provided identification of cross-link sites in the Fe2+-induced dimer without MS3, while cross-link site identification with MS2 was not possible for the UV light-induced dimer. Thus, using varied multistage approaches, it was discovered that in the UV light-induced dimer, Tyr14 of the A-chain participated in an -O-S- cross-link in which the sulfur was derived either from Cys7 or Cys19 of the B-chain. In the Fe2+-induced dimer, Phe1 from both B-chains were cross-linked through a -CH2-. The UV chromophoric side chain of Phe1 was indicated in the cross-link, explaining why UVPD-MS2 was effective in fragmenting the cross-link and nearby backbone bonds. Our results demonstrated that higher-energy collisional dissociation (HCD), EThcD, and UVPD combined with MS3 were powerful tools for direct de novo characterization of cross-linked insulin dimers.
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Affiliation(s)
- Simon K Gammelgaard
- Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
- Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 7, 9220 Aalborg, Denmark
| | - Steffen B Petersen
- Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 7, 9220 Aalborg, Denmark
| | - Kim F Haselmann
- Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Peter Kresten Nielsen
- Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
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13
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Guillaubez JV, Pitrat D, Bretonnière Y, Lemoine J, Girod M. Unbiased Detection of Cysteine Sulfenic Acid by 473 nm Photodissociation Mass Spectrometry: Toward Facile In Vivo Oxidative Status of Plasma Proteins. Anal Chem 2021; 93:2907-2915. [PMID: 33522244 DOI: 10.1021/acs.analchem.0c04484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cysteine (Cys) is prone to diverse post-translational modifications in proteins, including oxidation into sulfenic acid (Cys-SOH) by reactive oxygen species generated under oxidative stress. Detection of low-concentration and metastable Cys-SOH within complex biological matrices is challenging due to the dynamic concentration range of proteins in the samples. Herein, visible laser-induced dissociation (LID) implemented in a mass spectrometer was used for streamlining the detection of Cys oxidized proteins owing to proper derivatization of Cys-SOH with a chromophore tag functionalized with a cyclohexanedione group. Once grafted, peptides undergo a high fragmentation yield under LID, leading concomitantly to informative backbone ions and to a chromophore reporter ion. Seventy-nine percent of the Cys-containing tryptic peptides derived from human serum albumin and serotransferrin tracked by parallel reaction monitoring (PRM) were detected as targets subjected to oxidation. These candidates as well as Cys-containing peptides predicted by in silico trypsin digestion of five other human plasma proteins were then tracked in real plasma samples to pinpoint the endogenous Cys-SOH subpopulation. Most of the targeted peptides were detected in all plasma samples by LID-PRM, with significant differences in their relative amounts. By eliminating the signal of interfering co-eluted compounds, LID-PRM surpasses conventional HCD (higher-energy collisional dissociation)-PRM in detecting grafted Cys-SOH-containing peptides and allows now to foresee clinical applications in large human cohorts.
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Affiliation(s)
- Jean-Valery Guillaubez
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Delphine Pitrat
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon I, Laboratoire de Chimie, F-69342 Lyon, France
| | - Yann Bretonnière
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon I, Laboratoire de Chimie, F-69342 Lyon, France
| | - Jérôme Lemoine
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Marion Girod
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
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14
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Yang X, Xia Y. Mapping Complex Disulfide Bonds via Implementing Photochemical Reduction Online with Liquid Chromatography-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:307-314. [PMID: 33136395 DOI: 10.1021/jasms.0c00324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Assigning disulfide linkage is a crucial task for protein identification. The current bottom-up proteomics workflow has limitations in characterizing peptide digests containing multiple disulfide bonds due to the difficulty of controlling partial reduction via conventional chemical reduction methods. Previously, our lab reported the development of an acetone/2-propanol (IPA) photoinitiating system for rapid (on second time scale) and tunable disulfide bond reduction. Herein, we incorporated this reaction system onto a liquid chromatography-mass spectrometry (LC-MS) system for bottom-up protein analysis applications. The photochemical reduction reaction was implemented in a flow microreactor which allowed for up to 15 s 254 nm UV irradiation. The microreactor was installed post LC separation and right before electrospray ionization, while a T-junction was used to introduce the photoinitiating solution to the LC eluent before entering the microreactor. The degree of disulfide reduction was tunable from partial reduction to complete reduction for peptides containing one or multiple disulfide bonds. Significantly improved sequence coverage was obtained from complete disulfide reduction, while assignment of the disulfide connectivity was facilitated from partial disulfide reduction when coupled with tandem mass spectrometry via collision-induced dissociation. As a proof-of-concept test, trypsin digests of lysozyme (four disulfide bonds) and bovine serum albumin (BSA, 17 disulfide bonds) were analyzed by the LC-MS system coupled with online reduction. Sequence coverage was improved from 35% to 100% and 13% to 87% for lysozyme and BSA, respectively. All four disulfide bonds of lysozyme were determined. For BSA, nine disulfide bonds were characterized and eight adjacent disulfide bonds were narrowed down.
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Affiliation(s)
- Xiaoyue Yang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
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15
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Kuo CM, Wei SY, Du SH, Lin JL, Chu CH, Chen CH, Tai JH, Chen SH. Comprehensive Workflow for Mapping Disulfide Linkages Including Free Thiols and Error Checking by On-Line UV-Induced Precolumn Reduction and Spiked Control. Anal Chem 2020; 93:1544-1552. [PMID: 33378175 DOI: 10.1021/acs.analchem.0c03866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mapping highly complicated disulfide linkages and free thiols via liquid chromatography-tandem mass spectrometry (LC-MS2) is challenging because of the difficulties in optimizing sample preparation to acquire critical MS data and detecting mispairings. Herein, we report a highly efficient and comprehensive workflow using an on-line UV-induced precolumn reduction tandem mass spectrometry (UV-LC-MS2) coupled with two-stage data analysis and spiked control. UV-LC-MS2 features a gradient run of acetonitrile containing a tunable percentage of photoinitiators (acetone/alcohol) that drives the sample to the MS through a UV-flow cell and reverse phase column to separate UV-induced products for subsequent fragmentation via low energy collision-induced dissociation. This allowed the alkylated thiol-containing and UV-reduced cysteine-containing peptides to be identified by a nontargeted database search. Expected or unexpected disulfide/thiol mapping was then carried out based on the search results, and data were derived from partially reduced species by photochemical reaction. Complete assignments of native and scrambled disulfide linkages of insulin, α-lactalbumin, and bovine serum albumin (BSA) as well as the free C34-BSA were demonstrated using none or single enzyme digestion. This workflow was applied to characterize unknown disulfide/thiol patterns of the recombinant cyclophilin 1 monomer (rTvCyP1 mono) from the human pathogen Trichomonas vaginalis. α-Lactalbumin was judiciously chosen as a spiked control to minimize mispairings due to sample preparation. rTvCyP1 was determined to contain a high percentage of thiol (>80%). The rest of rTvCyP1 mono were identified to contain two disulfide/thiol patterns, of which C41-C169 linkage was confirmed to exist as C53-C181 in rTvCyP2, a homologue of rTvCyP1. This platform identifies heterogeneous protein disulfide/thiol patterns in a de-novo fashion with artifact control, opening up an opportunity to characterize crude proteins for many applications.
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Affiliation(s)
- Chin-Ming Kuo
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Shih-Yao Wei
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Shu-Han Du
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Jung-Lee Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chien-Hsin Chu
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | | - Jung-Hsiang Tai
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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16
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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17
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Gammelgaard S, Petersen SB, Haselmann KF, Nielsen PK. Direct Ultraviolet Laser-Induced Reduction of Disulfide Bonds in Insulin and Vasopressin. ACS OMEGA 2020; 5:7962-7968. [PMID: 32309706 PMCID: PMC7161042 DOI: 10.1021/acsomega.9b04375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/24/2020] [Indexed: 05/05/2023]
Abstract
Ultraviolet (UV) light has been shown to induce reduction of disulfide bonds in proteins in solution. The photoreduction is proposed to be a result of electron donation from excited Tyr or Trp residues. In this work, a powerful UV femtosecond laser was used to generate photoreduced products, while the hypothesis of Tyr/Trp mediation was studied with spectroscopy and mass spectrometry. With limited irradiation times of 3 min or less at 280 nm, the laser-induced reduction in arginine vasopressin and human insulin led to significant yields of ∼3% stable reduced product. The photogenerated thiols required acidic pH for stabilization, while neutral pH primarily caused scrambling and trisulfide formation. Interestingly, there was no direct evidence that Tyr/Trp mediation was a required criterion for the photoreduction of disulfide bonds. Intermolecular electron transfer remained a possibility for insulin but was ruled out for vasopressin. We propose that an additional mechanism should be increasingly considered in UV light-induced reduction of disulfide bonds in solution, in which a single UV photon is directly absorbed by the disulfide bond.
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Affiliation(s)
- Simon
K. Gammelgaard
- Global
Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
- Department
of Health Science and Technology, Aalborg
University, Fredrik Bajers Vej 7, 9220 Aalborg, Denmark
| | - Steffen B. Petersen
- Department
of Health Science and Technology, Aalborg
University, Fredrik Bajers Vej 7, 9220 Aalborg, Denmark
| | - Kim F. Haselmann
- Global
Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Peter Kresten Nielsen
- Global
Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
- . Tel: (+45) 3079 0375
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18
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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19
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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20
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Shaw JB, Liu W, Vasil′ev YV, Bracken CC, Malhan N, Guthals A, Beckman JS, Voinov VG. Direct Determination of Antibody Chain Pairing by Top-down and Middle-down Mass Spectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation. Anal Chem 2020; 92:766-773. [PMID: 31769659 PMCID: PMC7819135 DOI: 10.1021/acs.analchem.9b03129] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
One challenge associated with the discovery and development of monoclonal antibody (mAb) therapeutics is the determination of heavy chain and light chain pairing. Advances in MS instrumentation and MS/MS methods have greatly enhanced capabilities for the analysis of large intact proteins yielding much more detailed and accurate proteoform characterization. Consequently, direct interrogation of intact antibodies or F(ab')2 and Fab fragments has the potential to significantly streamline therapeutic mAb discovery processes. Here, we demonstrate for the first time the ability to efficiently cleave disulfide bonds linking heavy and light chains of mAbs using electron capture dissociation (ECD) and 157 nm ultraviolet photodissociation (UVPD). The combination of intact mAb, Fab, or F(ab')2 mass, intact LC and Fd masses, and CDR3 sequence coverage enabled determination of heavy chain and light chain pairing from a single experiment and experimental condition. These results demonstrate the potential of top-down and middle-down proteomics to significantly streamline therapeutic antibody discovery.
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Affiliation(s)
- Jared B. Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Weijing Liu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Yury V. Vasil′ev
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Carter C. Bracken
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Neha Malhan
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Adrian Guthals
- Mapp Biopharmaceutical Inc., 6160 Lusk Boulevard #105, San Diego, California 92121, United States
| | - Joseph S. Beckman
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Valery G. Voinov
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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21
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Mao F, Yu K, He J, Zhou Q, Zhang G, Wang W, Li N, Zhang H, Jiang J. Real-time monitoring of electroreduction and labelling of disulfide-bonded peptides and proteins by mass spectrometry. Analyst 2019; 144:6898-6904. [PMID: 31638109 DOI: 10.1039/c9an01420a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The accurate determination of disulfide bonds for protein identification is in high demand. In this study, a simple electrochemical-mass spectrometry (EC-MS) method that possesses advantages of real-time information, simultaneous disulfide bond electroreduction and tagging was developed. In this EC-MS, an ITO glass corner functions as a counter electrode and spray system, and allows the direct sampling of the droplet-scale reacting solution in real-time. The application of this method was successfully demonstrated by electrochemical reduction of oxidized glutathione (GSSG) with one disulfide bond as well as insulin with multiple disulfide bonds. The preferred electroreduction of intermolecular-bonded disulfides for insulin has been observed and the intramolecular bond was not favored. Moreover, simultaneously tagging the formed thiol residues from electroreduction of GSSG using electrogenerated intermediates such as dopamine orthoquinone (DQ) and benzoquinone (Q) was performed. A proof-of-concept was also demonstrated with a large molecule, β-lactoglobulin A. The relationship between signal strength and operating parameters was also studied. This method successfully detected the reduction reaction of the disulfide bond in the polypeptide and protein. The detection limit (S/N ≥ 3) is 0.398 μg mL-1. These results suggest that this EC-MS platform can count cysteine moieties in proteins using a single drop of sample and in real-time and is promising for protein identification experiments.
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Affiliation(s)
- Fengjiao Mao
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, P.R. China.
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22
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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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23
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Mukherjee S, Fang M, Kok WM, Kapp EA, Thombare VJ, Huguet R, Hutton CA, Reid GE, Roberts BR. Establishing Signature Fragments for Identification and Sequencing of Dityrosine Cross-Linked Peptides Using Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2019; 91:12129-12133. [DOI: 10.1021/acs.analchem.9b02986] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Soumya Mukherjee
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Mengxuan Fang
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - W. Mei Kok
- University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
| | - Eugene A. Kapp
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Varsha J. Thombare
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Craig A. Hutton
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Gavin E. Reid
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Blaine R. Roberts
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
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24
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Ben Nasr F, Alata I, Scuderi D, Lepère V, Brenner V, Jaïdane NE, Zehnacker A. Effects of complexation with sulfuric acid on the photodissociation of protonated Cinchona alkaloids in the gas phase. Phys Chem Chem Phys 2019; 21:15439-15451. [PMID: 31257399 DOI: 10.1039/c9cp01518c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of complexation with sulfuric acid on the photo-dissociation of protonated Cinchona alkaloids, namely cinchonidine (Cd), quinine (Qn) and quinidine (Qd), is studied by combining laser spectroscopy with quantum chemical calculations. The protonated complexes are structurally characterized in a room-temperature ion trap by means of infra-red multiple photon dissociation (IRMPD) spectroscopy in the fingerprint and the ν(XH) (X = C, N, O) stretch regions. Comparison with density functional theory calculations including dispersion (DFT-D) unambiguously shows that the complex consists of a doubly protonated Cinchona alkaloid strongly bound to a bisulfate HSO4- anion, which bridges the two protonated sites of the Cinchona alkaloid. UV excitation of the complex does not induce loss of specific photo fragments, in contrast to the protonated monomer or dimer, for which photo-specific fragments were observed. Indeed the UV-induced fragmentation pattern is identical to that observed in collision-induced dissociation experiments. Analysis of the nature of the first electronic transitions at the second order approximate coupled-cluster level (CC2) explains the difference in the behavior of the complex relative to the monomer or dimer towards UV excitation.
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Affiliation(s)
- Feriel Ben Nasr
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France. and Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA) Université de Tunis El Manar, LSAMA, Tunis 1060, Tunisia
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Debora Scuderi
- Univ. Paris-Sud, Laboratoire de Chimie Physique, UMR 8000, and CNRS, Orsay, F-91405, France
| | - Valeria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | | | - Nejm-Eddine Jaïdane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA) Université de Tunis El Manar, LSAMA, Tunis 1060, Tunisia
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
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25
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Girod M. Increasing specificity of tandem mass spectrometry by laser-induced dissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 3:64-71. [PMID: 29689642 DOI: 10.1002/rcm.8148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
Mass spectrometry offers an arsenal of tools for diverse proteomic investigations. This perspective article reviews some of the recent developments in the field of coupling laser-induced dissociation with mass spectrometry (LID-MS). Strategies involving labelling with a chromophore to induce specific photo-absorption properties are considered, with a focus on specific amino acid derivatization. Some of the opportunities and challenges of LID-MS after targeted labelling for increasing specificity in complex sample analysis are discussed.
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Affiliation(s)
- Marion Girod
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
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26
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Talbert LE, Zhang X, Hendricks N, Alizadeh A, Julian RR. Synthesis of New S-S and C-C Bonds by Photoinitiated Radical Recombination Reactions in the Gas Phase. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 441:25-31. [PMID: 31607789 PMCID: PMC6788626 DOI: 10.1016/j.ijms.2019.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Photoinitiated radical chemistry has proven to be useful for breaking covalent bonds within many biomolecules in the gas phase. Herein, we demonstrate that radical chemistry is useful for bond synthesis in the gas phase. Single peptides containing two cysteine residues capped with propylmercaptan (PM) often form disulfide bonds following ultraviolet excitation at 266 nm and loss of both PM groups. Similarly, noncovalently bound peptide pairs where each peptide contains a single cysteine residue can be induced to form disulfide bonds. Comparison with disulfide bound species sampled directly from solution yields identical collisional activation spectra, suggesting that native disulfide bonds have been recapitulated in the gas phase syntheses. Another approach utilizing radical chemistry for covalent bond synthesis involves creation of a reactive diradical that can first abstract hydrogen from a target peptide, creating a new radical site, and then recombine the second radical with the new radical to form a covalent bond. This chemistry is illustrated with 2-(hydroxymethyl-3,5-diiodobenzoate)-18-crown-6 ether, which attaches noncovalently to protonated primary amines in peptides and proteins. Following photoactivation and crosslinking, the site of noncovalent adduct attachment can frequently be determined. The ramifications of these observations on peptide structure and noncovalent attachment of 18-crown-6-based molecules is discussed.
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27
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Cui L, Ma Y, Li M, Wei Z, Fei Q, Huan Y, Li H, Zheng L. Disulfide linkage assignment based on reducing electrochemistry and mass spectrometry using a lead electrode. Talanta 2019; 199:643-651. [PMID: 30952309 DOI: 10.1016/j.talanta.2019.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 11/29/2022]
Abstract
The study of disulfide linkage is a crucial part of the quality assessment of biopharmaceutical products because disulfide bonds stabilize the tertiary structure of proteins and maintain protein functions. Therefore, a suitable method is highly required for disulfide linkage assignment when nested disulfide bonds formed with closely spaced cysteine residues. A novel approach for disulfide linkage assignment of disulfide-rich peptides and proteins via electrochemical reduction on a lead electrode with mass spectrometry is presented in this paper. The method features partial electrochemical reduction and alkylation of peptides followed by alkylated peptide sequencing based on tandem mass spectrometry. Lead was chosen for the first time as an electrode material for disulfide bond reduction, because it has the advantages of maintenance free (only infrequent polishing needed), easy operation in DC mode, and reusability. Without any special sample preparation and any chemical reduction agents, disulfide bond in peptides can be cleaved rapidly. The new method was successfully tested with two peptides and one protein containing nested disulfide bonds.
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Affiliation(s)
- Lili Cui
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Yongge Ma
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Ming Li
- Department of Chemistry, National Institute of Metrology, Beijing 100029, China.
| | - Zhonglin Wei
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Qiang Fei
- College of Chemistry, Jilin University, Changchun 130012, China.
| | - Yanfu Huan
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Hongmei Li
- Department of Chemistry, National Institute of Metrology, Beijing 100029, China
| | - Lianyou Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
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28
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Ye S, Li M, Jiang Y, Gong X, Xiong X, Liu D, Zhao B, Fang X. Ion manipulation and enrichment mass spectrometer for cleavage of disulfide bond via ion/ion reaction. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:311-315. [PMID: 30672057 DOI: 10.1002/jms.4333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/27/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
A novel mass spectrometer with the capability of ion manipulation and enrichment was developed to perform gas-phase ion/ion reactions followed by product ions accumulation. The development of this apparatus opens opportunities for more complex sequences of ion manipulations, thus offers the potential on extensive application involving ion/ion reaction. Here, cleavage of disulfide bond in peptide was demonstrated based upon this ion manipulation and enrichment mass spectrometer. Two typical peptides including S-glutathionylated ARACAKA with an intermolecular disulfide bond, and oxytocin with an intramolecular disulfide bond were chosen as typical samples to demonstrate the ability of the apparatus. After ion/ion reaction between selected peptide cations and periodate ions (IO4 - ), two kinds of product ions (eg, [M + O + H]+ and [M + H + Na + IO4 ]+ ) were enriched with a number of accumulation events. Afterwards, the enriched ions were subjected to activation, and the disulfide bond cleavage was clearly observed from the tandem mass spectra. These results illustrate the potential of this apparatus for ion manipulation performing ion/ion reaction, and low abundance product ion enrichment.
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Affiliation(s)
- Sijian Ye
- Department of Chemistry & Environmental Engineering, Changchun University of Science and Technology, Changchun, 130022, PR China
- College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Ming Li
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, PR China
| | - You Jiang
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, PR China
| | - Xiaoyun Gong
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, PR China
| | - Xingchuang Xiong
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, PR China
| | - Dajun Liu
- Department of Chemistry & Environmental Engineering, Changchun University of Science and Technology, Changchun, 130022, PR China
| | - Bo Zhao
- Department of Chemistry & Environmental Engineering, Changchun University of Science and Technology, Changchun, 130022, PR China
| | - Xiang Fang
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, PR China
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29
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van Agthoven MA, Lam YPY, O'Connor PB, Rolando C, Delsuc MA. Two-dimensional mass spectrometry: new perspectives for tandem mass spectrometry. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2019; 48:213-229. [PMID: 30863873 PMCID: PMC6449292 DOI: 10.1007/s00249-019-01348-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/24/2019] [Accepted: 02/06/2019] [Indexed: 12/11/2022]
Abstract
Fourier transform ion cyclotron resonance mass analysers (FT-ICR MS) can offer the highest resolutions and mass accuracies in mass spectrometry. Mass spectra acquired in an FT-ICR MS can yield accurate elemental compositions of all compounds in a complex sample. Fragmentation caused by ion-neutral, ion-electron, or ion-photon interactions leads to more detailed structural information on compounds. The most often used method to correlate compounds and their fragment ions is to isolate the precursor ions from the sample before fragmentation. Two-dimensional mass spectrometry (2D MS) offers a method to correlate precursor and fragment ions without requiring precursor isolation. 2D MS therefore enables easy access to the fragmentation patterns of all compounds from complex samples. In this article, the principles of FT-ICR MS are reviewed and the 2D MS experiment is explained. Data processing for 2D MS is detailed, and the interpretation of 2D mass spectra is described.
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Affiliation(s)
- Maria A van Agthoven
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV47AL, UK
| | - Yuko P Y Lam
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV47AL, UK
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV47AL, UK
| | - Christian Rolando
- MSAP USR 3290, Université Lille, Sciences et Technologies, 59655, Villeneuve d'Ascq Cedex, France
| | - Marc-André Delsuc
- Institut de Génétique, Biologie Moléculaire et Cellulaire, INSERM, U596, CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France.
- CASC4DE, 20 avenue du Neuhof, 67100, Strasbourg, France.
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30
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Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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31
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Adhikari S, Yang X, Xia Y. Acetone/Isopropanol Photoinitiating System Enables Tunable Disulfide Reduction and Disulfide Mapping via Tandem Mass Spectrometry. Anal Chem 2018; 90:13036-13043. [PMID: 30350608 PMCID: PMC6310128 DOI: 10.1021/acs.analchem.8b04019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Herein, we report the development of a new photochemical system which enables rapid and tunable disulfide bond reduction and its application in disulfide mapping via online coupling with mass spectrometry (MS). Acetone, a clean and electrospray ionization (ESI) compatible solvent, is used as the photoinitiator (1% volume) in the solvent system consisting of 1:1 alkyl alcohol and water. Under ultraviolet (UV) irradiation (∼254 nm), the acetone/alcohol system produces hydroxyalkyl radicals, which are responsible for disulfide bond cleavage in peptides. Acetone/isopropanol is most suitable for optimizing the disulfide reduction products, leading to almost complete conversion in less than 5 s when the reaction is conducted in a flow microreactor. The flow microreactor device not only facilitates direct coupling with ESI-MS but also allows fine-tuning of the extent of disulfide reduction by varying the UV exposure time. Near full sequence coverage for peptides consisting of intra- or interchain disulfide bonds has been achieved from complete disulfide reduction and online tandem mass spectrometry (MS/MS) via low energy collision-induced dissociation. Coupling different degrees of partial disulfide reduction with ESI-MS/MS allows disulfide mapping as demonstrated for characterizing the three disulfide bonds in insulin.
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Affiliation(s)
- Sarju Adhikari
- Department of Chemistry, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Xiaoyue Yang
- Department of Chemistry, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yu Xia
- Department of Chemistry, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
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32
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Bonner J, Talbert LE, Akkawi N, Julian RR. Simplified identification of disulfide, trisulfide, and thioether pairs with 213 nm UVPD. Analyst 2018; 143:5176-5184. [PMID: 30264084 PMCID: PMC6197924 DOI: 10.1039/c8an01582a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Disulfide heterogeneity and other non-native crosslinks introduced during therapeutic antibody production and storage could have considerable negative effects on clinical efficacy, but tracking these modifications remains challenging. Analysis must also be carried out cautiously to avoid introduction of disulfide scrambling or reduction, necessitating the use of low pH digestion with less specific proteases. Herein we demonstrate that 213 nm ultraviolet photodissociation streamlines disulfide elucidation through bond-selective dissociation of sulfur-sulfur and carbon-sulfur bonds in combination with less specific backbone dissociation. Importantly, both types of fragmentation can be initiated in a single MS/MS activation stage. In addition to disulfide mapping, it is also shown that thioethers and trisulfides can be identified by characteristic fragmentation patterns. The photochemistry resulting from 213 nm excitation facilitates a simplified, two-tiered data processing approach that allows observation of all native disulfide bonds, scrambled disulfide bonds, and non-native sulfur-based linkages in a pepsin digest of Rituximab. Native disulfides represented the majority of bonds according to ion count, but the highly solvent-exposed heavy/light interchain disulfides were found to be most prone to modification. Production and storage methods that facilitate non-native links are discussed. Due to the importance of heavy and light chain connectivity for antibody structure and function, this region likely requires particular attention in terms of its influence on maintaining structural fidelity.
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Affiliation(s)
- James Bonner
- Department of Chemistry, University of California, Riverside, California 92521, USA.
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33
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MacAleese L, Girod M, Nahon L, Giuliani A, Antoine R, Dugourd P. Radical Anions of Oxidized vs. Reduced Oxytocin: Influence of Disulfide Bridges on CID and Vacuum UV Photo-Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1826-1834. [PMID: 29949057 DOI: 10.1007/s13361-018-1989-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/27/2018] [Accepted: 05/05/2018] [Indexed: 06/08/2023]
Abstract
The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage induced by vacuum UV (VUV) radiations. In particular, the effect of the presence (or absence in reduced OT) of oxytocin's internal disulfide bridge is evaluated in terms of photo-fragmentation yield and nature of the photo-fragments. Intact, as well as reduced, OT is studied as dianions and radical anions. Radical anions are prepared and photo-fragmented in two-color experiments (UV + VUV) in a linear ion trap. VUV photo-fragmentation patterns are analyzed and compared, and radical-induced mechanisms are proposed. The effect of VUV is principally to ionize but secondary fragmentation is also observed. This secondary fragmentation seems to be considerably enabled by the initial position of the radical on the molecule. In particular, the possibility to form a radical on free cysteines seems to increase the susceptibility to VUV fragmentation. Interestingly, disulfide bridges, which are fundamental for protein structure, could also be responsible for an increased resistance to ionizing radiations. Graphical Abstract.
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Affiliation(s)
- Luke MacAleese
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut Lumière Matière UMR 5306, 69622, Villeurbanne, France.
| | - Marion Girod
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques UMR 5280, 69100, Villeurbanne, France
| | - Laurent Nahon
- Synchrotron SOLEIL, BP 48 St Aubin, 91192, Gif Sur Yvette, France
| | - Alexandre Giuliani
- Synchrotron SOLEIL, BP 48 St Aubin, 91192, Gif Sur Yvette, France
- UAR1008 CEPIA, INRA, BP 71627, 44316, Nantes, France
| | - Rodolphe Antoine
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut Lumière Matière UMR 5306, 69622, Villeurbanne, France
| | - Philippe Dugourd
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut Lumière Matière UMR 5306, 69622, Villeurbanne, France
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34
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Talbert LE, Julian RR. Directed-Backbone Dissociation Following Bond-Specific Carbon-Sulfur UVPD at 213 nm. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1760-1767. [PMID: 29623659 PMCID: PMC6087500 DOI: 10.1007/s13361-018-1934-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/16/2018] [Accepted: 02/23/2018] [Indexed: 05/22/2023]
Abstract
Ultraviolet photodissociation or UVPD is an increasingly popular option for tandem-mass spectrometry experiments. UVPD can be carried out at many wavelengths, and it is important to understand how the results will be impacted by this choice. Here, we explore the utility of 213 nm photons for initiating bond-selective fragmentation. It is found that bonds previously determined to be labile at 266 nm, including carbon-iodine and sulfur-sulfur bonds, can also be cleaved with high selectivity at 213 nm. In addition, many carbon-sulfur bonds that are not subject to direct dissociation at 266 nm can be selectively fragmented at 213 nm. This capability can be used to site-specifically create alaninyl radicals that direct backbone dissociation at the radical site, creating diagnostic d-ions. Furthermore, the additional carbon-sulfur bond fragmentation capability leads to signature triplets for fragmentation of disulfide bonds. Absorption of amide bonds can enhance dissociation of nearby labile carbon-sulfur bonds and can be used for stochastic backbone fragmentation typical of UVPD experiments at shorter wavelengths. Several potential applications of the bond-selective fragmentation chemistry observed at 213 nm are discussed. Graphical Abstract ᅟ.
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Affiliation(s)
- Lance E Talbert
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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35
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Soleiman-Beigi M, Ghiasbeigi E. A study to identify S-S and S-S-S bonds in organic compounds by mass spectrometry and ultraviolet and Raman spectroscopy techniques. J Sulphur Chem 2018. [DOI: 10.1080/17415993.2018.1511791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
| | - Elahe Ghiasbeigi
- Department of Chemistry, Basic of Sciences Faculty, Ilam University, Ilam, Iran
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36
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Rush MJ, Riley NM, Westphall MS, Coon JJ. Top-Down Characterization of Proteins with Intact Disulfide Bonds Using Activated-Ion Electron Transfer Dissociation. Anal Chem 2018; 90:8946-8953. [PMID: 29949341 PMCID: PMC6434944 DOI: 10.1021/acs.analchem.8b01113] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Here we report the fragmentation of disulfide linked intact proteins using activated-ion electron transfer dissociation (AI-ETD) for top-down protein characterization. This fragmentation method is then compared to the alternative methods of beam-type collisional activation (HCD), electron transfer dissociation (ETD), and electron transfer and higher-energy collision dissociation (EThcD). We analyzed multiple precursor charge states of the protein standards bovine insulin, α-lactalbumin, lysozyme, β-lactoglobulin, and trypsin inhibitor. In all cases, we found that AI-ETD provides a boost in protein sequence coverage information and the generation of fragment ions from within regions enclosed by disulfide bonds. AI-ETD shows the largest improvement over the other techniques when analyzing highly disulfide linked and low charge density precursor ions. This substantial improvement is attributed to the concurrent irradiation of the gas phase ions while the electron-transfer reaction is taking place, mitigating nondissociative electron transfer, helping unfold the gas phase protein during the electron transfer event, and preventing disulfide bond reformation. We also show that AI-ETD is able to yield comparable sequence coverage information when disulfide bonds are left intact relative to proteins that have been reduced and alkylated. This work demonstrates that AI-ETD is an effective fragmentation method for the analysis of proteins with intact disulfide bonds, dramatically enhancing sequence ion generation and total sequence coverage compared to HCD and ETD.
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Affiliation(s)
- Matthew J.P. Rush
- Genome Center of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Nicholas M. Riley
- Genome Center of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | | | - Joshua J. Coon
- Genome Center of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
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37
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Quick MM, Crittenden CM, Rosenberg JA, Brodbelt JS. Characterization of Disulfide Linkages in Proteins by 193 nm Ultraviolet Photodissociation (UVPD) Mass Spectrometry. Anal Chem 2018; 90:8523-8530. [PMID: 29902373 PMCID: PMC6050148 DOI: 10.1021/acs.analchem.8b01556] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Deciphering disulfide bond patterns in proteins remains a significant challenge. In the present study, interlinked disulfide bonds connecting peptide chains are homolytically cleaved with 193 nm ultraviolet photodissociation (UVPD). Analysis of insulin showcased the ability of UVPD to cleave multiple disulfide bonds and provide sequence coverage of the peptide chains in the same MS/MS event. For proteins containing more complex disulfide bonding patterns, an approach combining partial reduction and alkylation mitigated disulfide scrambling and allowed assignment of the array of disulfide bonds. The 4 disulfide bonds of lysozyme and the 19 disulfide bonds of serotransferrin were characterized through LC/UVPD-MS analysis of nonreduced and partially reduced protein digests.
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38
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Cramer CN, Kelstrup CD, Olsen JV, Haselmann KF, Nielsen PK. Generic Workflow for Mapping of Complex Disulfide Bonds Using In-Source Reduction and Extracted Ion Chromatograms from Data-Dependent Mass Spectrometry. Anal Chem 2018; 90:8202-8210. [DOI: 10.1021/acs.analchem.8b01603] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Christian N. Cramer
- Protein Engineering, Global Research, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
- Proteomics Program, Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Christian D. Kelstrup
- Proteomics Program, Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jesper V. Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kim F. Haselmann
- Protein Engineering, Global Research, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Peter Kresten Nielsen
- Protein Engineering, Global Research, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
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39
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Guo W, Tan W, Zhao M, Zheng L, Tao K, Chen D, Fan X. Direct Photocatalytic S–H Bond Cyanation with Green “CN” Source. J Org Chem 2018; 83:6580-6588. [DOI: 10.1021/acs.joc.8b00887] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Wei Guo
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
| | - Wen Tan
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
| | - Mingming Zhao
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
| | - Lvyin Zheng
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
| | - Kailiang Tao
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
| | - Deliang Chen
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
| | - Xiaolin Fan
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
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40
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Sekowski S, Terebka M, Veiko A, Lapshina E, Sulkowska U, Zavodnik IB, Abdulladjanova N, Mavlyanov S, Roszkowska A, Zamaraeva M. Epigallocatechin gallate (EGCG) activity against UV light-induced photo damages in erythrocytes and serum albumin—theoretical and experimental studies. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Garcia L, Girod M, Rompais M, Dugourd P, Carapito C, Lemoine J. Data-Independent Acquisition Coupled to Visible Laser-Induced Dissociation at 473 nm (DIA-LID) for Peptide-Centric Specific Analysis of Cysteine-Containing Peptide Subset. Anal Chem 2018; 90:3928-3935. [PMID: 29465226 DOI: 10.1021/acs.analchem.7b04821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Thanks to comprehensive and unbiased sampling of all precursor ions, the interest to move toward bottom-up proteomic with data-independent acquisition (DIA) is continuously growing. DIA offers precision and reproducibility performances comparable to true targeted methods but has the advantage of enabling retrospective data testing with the hypothetical presence of new proteins of interest. Nonetheless, the chimeric nature of DIA MS/MS spectra inherent to concomitant transmission of a multiplicity of precursor ions makes the confident identification of peptides often challenging, even with spectral library-based extraction strategy. The introduction of specificity at the fragmentation step upon ultraviolet or visible laser-induced dissociation (LID) range targeting only the subset of cysteine-containing peptides (Cys-peptide) has been proposed as an option to streamline and reduce the search space. Here, we describe the first coupling between DIA and visible LID at 473 nm to test for the presence of Cys-peptides with a peptide-centric approach. As a test run, a spectral library was built for a pool of Cys-synthetic peptides used as surrogates of human kinases (1 peptide per protein). By extracting ion chromatograms of query standard and kinase peptides spiked at different concentration levels in an Escherichia coli proteome lysate, DIA-LID demonstrates a dynamic range of detection of at least 3 decades and coefficients of precision better than 20%. Finally, the spectral library was used to search for endogenous kinases in human cellular extract.
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Affiliation(s)
- Lény Garcia
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , UMR 5280, 5 rue de la Doua , F-69100 Villeurbanne , France
| | - Marion Girod
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , UMR 5280, 5 rue de la Doua , F-69100 Villeurbanne , France
| | - Magali Rompais
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC , Université de Strasbourg, CNRS , UMR 7178, 25 rue Becquerel , 67087 Strasbourg , France
| | - Philippe Dugourd
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC , Université de Strasbourg, CNRS , UMR 7178, 25 rue Becquerel , 67087 Strasbourg , France
| | - Jérôme Lemoine
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques , UMR 5280, 5 rue de la Doua , F-69100 Villeurbanne , France
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42
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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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43
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Lakbub JC, Shipman JT, Desaire H. Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins. Anal Bioanal Chem 2017; 410:2467-2484. [PMID: 29256076 DOI: 10.1007/s00216-017-0772-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/09/2017] [Accepted: 11/17/2017] [Indexed: 12/21/2022]
Abstract
Disulfide bonds are important structural moieties of proteins: they ensure proper folding, provide stability, and ensure proper function. With the increasing use of proteins for biotherapeutics, particularly monoclonal antibodies, which are highly disulfide bonded, it is now important to confirm the correct disulfide bond connectivity and to verify the presence, or absence, of disulfide bond variants in the protein therapeutics. These studies help to ensure safety and efficacy. Hence, disulfide bonds are among the critical quality attributes of proteins that have to be monitored closely during the development of biotherapeutics. However, disulfide bond analysis is challenging because of the complexity of the biomolecules. Mass spectrometry (MS) has been the go-to analytical tool for the characterization of such complex biomolecules, and several methods have been reported to meet the challenging task of mapping disulfide bonds in proteins. In this review, we describe the relevant, recent MS-based techniques and provide important considerations needed for efficient disulfide bond analysis in proteins. The review focuses on methods for proper sample preparation, fragmentation techniques for disulfide bond analysis, recent disulfide bond mapping methods based on the fragmentation techniques, and automated algorithms designed for rapid analysis of disulfide bonds from liquid chromatography-MS/MS data. Researchers involved in method development for protein characterization can use the information herein to facilitate development of new MS-based methods for protein disulfide bond analysis. In addition, individuals characterizing biotherapeutics, especially by disulfide bond mapping in antibodies, can use this review to choose the best strategies for disulfide bond assignment of their biologic products. Graphical Abstract This review, describing characterization methods for disulfide bonds in proteins, focuses on three critical components: sample preparation, mass spectrometry data, and software tools.
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Affiliation(s)
- Jude C Lakbub
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS, 66045, USA
| | - Joshua T Shipman
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS, 66045, USA
| | - Heather Desaire
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS, 66045, USA.
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Garcia L, Lemoine J, Dugourd P, Girod M. Fragmentation patterns of chromophore-tagged peptides in visible laser induced dissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1985-1992. [PMID: 28884878 DOI: 10.1002/rcm.7984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/21/2017] [Accepted: 09/02/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Tandem mass spectrometry (MS/MS) is the pivotal tool for protein structural characterization and quantification. Identification relies on the fragmentation step of tryptic peptides in bottom-up strategy. Specificity of fragmentation can be obtained using laser-induced dissociation (LID) in the visible range, after tagging of the targeted peptides with an adequate chromophore. Backbone fragmentation is required to obtain specific fragments and confident identification. We present herein a study of fragmentation patterns of chromophore-tagged peptides in LID, showing the potential of LID methodology to provide the maximum number of fragments for further identification and quantification. METHODS A total of 401 cysteine-containing tryptic peptides originating from the human proteome were derivatizated on the thiol group of cysteine with a Dabcyl maleimide chromophore, which has a high photo-absorption cross section at 473 nm. The derivatized peptides were then analyzed by LID at 473 nm on a Q Exactive instrument. RESULTS LID spectra present a characteristic fragment at m/z 252.112 for all precursors. This product ion arises from the internal dissociation of the Dabcyl chromophore. Several peptide-backbone fragment ions are also detected. Results show the quasi absence of fragmentation at the cysteine site. This indicates that part of the energy must be redistributed across the entire system despite excitation initially localized at the chromophore. Indeed, the fragmentation mainly occurs at 3 to 5 amino acids from the derivatized cysteine residue. CONCLUSIONS LID of derivatized cysteine-containing peptides displays the initial fragmentation of the chromophore. As energy is redistributed all along the peptide sequence, fragmentation of the peptide backbone is also observed. Thus, LID of chromophore-tagged peptides produces adequate fragment ions, allowing both good sequence coverage for a greater confidence of identification, and a large choice of transitions for specific quantification.
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Affiliation(s)
- Lény Garcia
- Univ de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Jérôme Lemoine
- Univ de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Philippe Dugourd
- Univ de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, VILLEURBANNE, France
| | - Marion Girod
- Univ de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
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45
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R Julian R. The Mechanism Behind Top-Down UVPD Experiments: Making Sense of Apparent Contradictions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1823-1826. [PMID: 28702929 PMCID: PMC5711567 DOI: 10.1007/s13361-017-1721-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 05/21/2023]
Abstract
Top-down ultraviolet photodissociation (UVPD) allows greater sequence coverage than any other currently available method, often fracturing the vast majority of peptide bonds in whole proteins. At the same time, UVPD can be used to dissociate noncovalent complexes assembled from multiple proteins without breaking any covalent bonds. Although the utility of these experiments is unquestioned, the mechanism underlying these seemingly contradictory results has been the subject of many discussions. Herein, some fundamental considerations of photochemistry are briefly summarized within the context of a proposed mechanism that rationalizes the experimental results obtained by UVPD. Considerations for future instrument design, in terms of wavelength choice and power, are briefly discussed. Graphical Abstract ᅟ.
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Affiliation(s)
- Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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46
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Quick MM, Mehaffey MR, Johns RW, Parker WR, Brodbelt JS. SITS Derivatization of Peptides to Enhance 266 nm Ultraviolet Photodissociation (UVPD). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1462-1472. [PMID: 28315237 DOI: 10.1007/s13361-017-1650-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 06/06/2023]
Abstract
N-terminal derivatization of peptides with the chromogenic reagent 4-acetamido-4-isothiocyanatostilbene-2,2-disulfonic acid (SITS) is demonstrated to enhance the efficiency of 266 nm ultraviolet photodissociation (UVPD). Attachment of the chromophore results in a mass shift of 454 Da and provides significant gains in the number and abundances of diagnostic fragment ions upon UVPD. Activation of SITS-tagged peptides with 266 nm UVPD leads to many fragment ions akin to the a/b/y ions commonly produced by CID, along with other sequence ions (c, x, and z) typically accessed through higher energy pathways. Extreme bias towards C-terminal fragment ions is observed upon activation of SITS-tagged peptides using multiple 266 nm laser pulses. Due to the high reaction efficiency of the isothiocyanate coupling to the N-terminus of peptides, we demonstrate the ability to adapt this strategy to a high-throughput LC-MS/MS workflow with 266 nm UVPD. Graphical Abstract ᅟ.
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Affiliation(s)
- M Montana Quick
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - Robert W Johns
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, 78712, USA
| | - W Ryan Parker
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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47
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Lyon YA, Beran G, Julian RR. Leveraging Electron Transfer Dissociation for Site Selective Radical Generation: Applications for Peptide Epimer Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1365-1373. [PMID: 28374314 PMCID: PMC5497491 DOI: 10.1007/s13361-017-1627-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 06/07/2023]
Abstract
Traditional electron-transfer dissociation (ETD) experiments operate through a complex combination of hydrogen abundant and hydrogen deficient fragmentation pathways, yielding c and z ions, side-chain losses, and disulfide bond scission. Herein, a novel dissociation pathway is reported, yielding homolytic cleavage of carbon-iodine bonds via electronic excitation. This observation is very similar to photodissociation experiments where homolytic cleavage of carbon-iodine bonds has been utilized previously, but ETD activation can be performed without addition of a laser to the mass spectrometer. Both loss of iodine and loss of hydrogen iodide are observed, with the abundance of the latter product being greatly enhanced for some peptides after additional collisional activation. These observations suggest a novel ETD fragmentation pathway involving temporary storage of the electron in a charge-reduced arginine side chain. Subsequent collisional activation of the peptide radical produced by loss of HI yields spectra dominated by radical-directed dissociation, which can be usefully employed for identification of peptide isomers, including epimers. Graphical Abstract ᅟ.
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Affiliation(s)
- Yana A Lyon
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Gregory Beran
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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48
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Mu X, Song T, Siu CK, Chu IK. Tautomerization and Dissociation of Molecular Peptide Radical Cations. CHEM REC 2017. [DOI: 10.1002/tcr.201700013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiaoyan Mu
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
| | - Tao Song
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
| | - Chi-Kit Siu
- Department of Biology and Chemistry; City University of Hong Kong; 83 Tat Chee Avenue Kowloon Tong, Hong Kong SAR P. R. China
| | - Ivan K. Chu
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
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49
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Durand KL, Tan L, Stinson CA, Love-Nkansah CB, Ma X, Xia Y. Assigning Peptide Disulfide Linkage Pattern Among Regio-Isomers via Methoxy Addition to Disulfide and Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1099-1108. [PMID: 28194735 DOI: 10.1007/s13361-017-1595-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/02/2017] [Accepted: 01/03/2017] [Indexed: 06/06/2023]
Abstract
Pinpointing disulfide linkage pattern is critical in the characterization of proteins and peptides consisting of multiple disulfide bonds. Herein, we report a method based on coupling online disulfide modification and tandem mass spectrometry (MS/MS) to distinguish peptide disulfide regio-isomers. Such a method relies on a new disulfide bond cleavage reaction in solution, involving methanol as a reactant and 254 nm ultraviolet (UV) irradiation. This reaction leads to selective cleavage of a disulfide bond and formation of sulfenic methyl ester (-SOCH3) at one cysteine residue and a thiol (-SH) at the other. Under low energy collision-induced dissociation (CID), cysteine sulfenic methyl ester motif produces a signature methanol loss (-32 Da), allowing its identification from other possible isomeric structures such as S-hydroxylmethyl (-SCH2OH) and methyl sulfoxide (-S(O)-CH3). Since disulfide bond can be selectively cleaved and modified upon methoxy addition, subsequent MS2 CID of the methoxy addition product provides enhanced sequence coverage as demonstrated by the analysis of bovine insulin. More importantly, this reaction does not induce disulfide scrambling, likely due to the fact that radical intermediates are not involved in the process. An approach based on methoxy addition followed by MS3 CID has been developed for assigning disulfide linkage patterns in peptide disulfide regio-isomers. This methodology was successfully applied to characterizing peptide systems having two disulfide bonds and three disulfide linkage isomers: side-by-side, overlapped, and looped-within-a-loop configurations. Graphical Abstract ᅟ.
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Affiliation(s)
- Kirt L Durand
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Lei Tan
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Craig A Stinson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | | | - Xiaoxiao Ma
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Yu Xia
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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50
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Pilo AL, Zhao F, McLuckey SA. Gas-Phase Oxidation via Ion/Ion Reactions: Pathways and Applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:991-1004. [PMID: 28050870 PMCID: PMC5438755 DOI: 10.1007/s13361-016-1554-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/31/2016] [Accepted: 11/05/2016] [Indexed: 06/06/2023]
Abstract
Here, we provide an overview of pathways available upon the gas-phase oxidation of peptides and DNA via ion/ion reactions and explore potential applications of these chemistries. The oxidation of thioethers (i.e., methionine residues and S-alkyl cysteine residues), disulfide bonds, S-nitrosylated cysteine residues, and DNA to the [M+H+O]+ derivative via ion/ion reactions with periodate and peroxymono-sulfate anions is demonstrated. The oxidation of neutral basic sites to various oxidized structures, including the [M+H+O]+, [M-H]+, and [M-H-NH3]+ species, via ion/ion reactions is illustrated and the oxidation characteristics of two different oxidizing reagents, periodate and persulfate anions, are compared. Lastly, the highly efficient generation of molecular radical cations via ion/ion reactions with sulfate radical anion is summarized. Activation of the newly generated molecular radical peptide cations results in losses of various neutral side chains, several of which generate dehydroalanine residues that can be used to localize the amino acid from which the dehydroalanine was generated. The chemistries presented herein result in a diverse range of structures that can be used for a variety of applications, including the identification and localization of S-alkyl cysteine residues, the oxidative cleavage of disulfide bonds, and the generation of molecular radical cations from even-electron doubly protonated peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Feifei Zhao
- 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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