1
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Kuo CM, Jen HH, Chen FY, Akbarian M, Ou TH, Liu KY, Lin JL, Chen SH. High-performance peptide and disulfide mapping by direct injection of intact proteins using on-line coupled UV-liquid chromatography microdroplet mass spectrometry (UVLC-MMS). Anal Chim Acta 2023; 1279:341790. [PMID: 37827684 DOI: 10.1016/j.aca.2023.341790] [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: 05/20/2023] [Revised: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
Microdroplet mass spectrometry (MMS), achieving ultra-fast enzyme digestion in the ionization source, holds great promises for innovating protein analysis. Here, in-depth protein characterization is demonstrated by direct injection of intact protein mixtures via on-line coupling MMS with capillary C4 liquid chromatography (LC) containing UV windows (UVLC-MMS) through an enzyme introduction tee. We showed complete sets of peptides of individual proteins (hemoglobin, bovine serum albumin, and ribonuclease A) in a mixture could be obtained in one injection. Such full (100%) sequence coverage, however, could not be achieved by conventional nanoLC-MS method using bottom-up approach with single enzyme. Moreover, direct injection of a chaperone α-crystalline (α-Cry) complex yielded identification of post-translational modifications including novel sites and semi-quantitative characterization including 3:1 stoichiometry ratio of αA- and αB-Cry sub-units and ∼1.4 phosphorylation/subunit on S45 (novel site) and S122 (main site) of αA-Cry, ∼0.7 phosphorylation/subunit on S19 (main site) and S45 of αB-Cry, as well as 100% acetylation on both N-termini of each subunits by matching the mass and retention time of the intact and its digested peptides. Furthermore, trifluoroacetic acid was able to be used in the mobile phase with UVLC-MMS to improve the separation of differentially reduced intact species and detectability of the droplet-digested products. This allowed us to completely map four disulfide linkages of ribonuclease A based on collision-induced dissociation of disulfide clusters, some of which would otherwise not be detected, preventing scrambling or shuffling errors arising from lengthy bulk solution digestion by the bottom-up approach. Integration of UVLC and MMS greatly improves droplet digestion efficiency and MS detection, enabling highly efficient workflow for in-depth and accurate protein characterization.
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Affiliation(s)
- Chin-Ming Kuo
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
| | - Hung-Hsiang Jen
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
| | - Fung-Yu Chen
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
| | - Mohsen Akbarian
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
| | - Tai-Hong Ou
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
| | - Kang-Yu Liu
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
| | - Jung-Lee Lin
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan.
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2
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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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3
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Olsen C, Wiborg E, Lundanes E, Abadpour S, Scholz H, Wilson SR. On‐line reduction of insulin disulfide bonds with photoinduced radical reactions, upstream to nano liquid chromatography‐mass spectrometry. SEPARATION SCIENCE PLUS 2022. [DOI: 10.1002/sscp.202200022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christine Olsen
- Department of Chemistry University of Oslo Blindern Oslo Norway
| | - Elisa Wiborg
- Department of Chemistry University of Oslo Blindern Oslo Norway
| | - Elsa Lundanes
- Department of Chemistry University of Oslo Blindern Oslo Norway
| | - Shadab Abadpour
- Hybrid Technology Hub‐Centre of Excellence Faculty of Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
- Department of Transplant Medicine and Institute for Surgical Research Oslo University Hospital, Oslo, Norway
| | - Hanne Scholz
- Hybrid Technology Hub‐Centre of Excellence Faculty of Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
- Department of Transplant Medicine and Institute for Surgical Research Oslo University Hospital, Oslo, Norway
| | - Steven Ray Wilson
- Department of Chemistry University of Oslo Blindern Oslo Norway
- Hybrid Technology Hub‐Centre of Excellence Faculty of Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
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4
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Yang X, Zhang L, Xia Y. Photochemical Disulfide-Ene Modification Enhances Protein Sequencing and Disulfide Mapping by Mass Spectrometry. Anal Chem 2021; 93:15231-15235. [PMID: 34751558 DOI: 10.1021/acs.analchem.1c04214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A new photochemical disulfide-ene reaction system capable of alkylating protein disulfide bonds in seconds has been established. The system is simple, containing acetone and isopropanol for disulfide reduction under 254 nm UV irradiation and norbornene as a highly efficient alkylation reagent. Enhanced characterization of disulfide-rich proteins with significantly shortened analysis time is demonstrated by coupling the reaction online with mass spectrometry.
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Affiliation(s)
- Xiaoyue Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Longfei Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yu Xia
- Department of Chemistry, Tsinghua University, Beijing 100084, China
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5
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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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6
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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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7
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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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8
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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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9
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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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10
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Zeng N, Long Z, Wang Y, Sun J, Ouyang J, Na N. An Acetone Sensor Based on Plasma-Assisted Cataluminescence and Mechanism Studies by Online Ionizations. Anal Chem 2019; 91:15763-15768. [DOI: 10.1021/acs.analchem.9b04023] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ni Zeng
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zi Long
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jianghui Sun
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Na Na
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
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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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