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Chaturvedi S, Bawake S, Sharma N. Recent advancements in disulfide bridge characterization: Insights from mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9713. [PMID: 38361473 DOI: 10.1002/rcm.9713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 02/17/2024]
Abstract
RATIONALE Disulfide bridges (DSB) play an important role in stabilizing three-dimensional structures of biopharmaceuticals, single purified proteins, and various cyclic peptide drugs that contain disulfide in their structures. Incorrect cross-linking known as DSB scrambling results in misfolded structures that can be inactive, immunogenic, and susceptible to aggregation. Very few articles have been published on the experimental annotation of DSBs in proteins and cyclic peptide drugs. Accurate characterization of the disulfide bond is essential for understanding protein confirmation. METHODS Characterizing DSBs using mass spectrometry (MS) involves the chemical and enzymatic digestion of samples to obtain smaller peptide fragments, in both reduced and nonreduced forms. Subsequently, these samples are analyzed using MS to locate the DSB, either through interpretation or by employing various software tools. RESULTS The main challenge in DSB analysis methods using sample preparation is to obtain a sample solution in which nonnative DSBs are not formed due to high pH, temperature, and presence of free sulfhydryl groups. Formation of nonnative DSBs can lead to erroneous annotation of disulfide bond. Sample preparation techniques, fragmentation methods for DSB analysis, and contemporary approaches for DSB mapping using this fragmentation were discussed. CONCLUSIONS This review presents the latest advancement in MS-based characterization; also a critical perspective is presented for further annotation of DSBs using MS, primarily for single purified proteins or peptides that are densely connected and rich in cysteine. Despite significant breakthroughs resulting from advancements in MS, the analysis of disulfide bonds is not straightforward; it necessitates expertise in sample preparation and interpretation.
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Affiliation(s)
- Sachin Chaturvedi
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (Ministry of Chemicals and Fertilizers, Government of India), NIPER Ahmedabad Opposite Air force Station Palaj, Gandhinagar, Gujarat, India
| | - Sanket Bawake
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (Ministry of Chemicals and Fertilizers, Government of India), NIPER Ahmedabad Opposite Air force Station Palaj, Gandhinagar, Gujarat, India
| | - Nitish Sharma
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (Ministry of Chemicals and Fertilizers, Government of India), NIPER Ahmedabad Opposite Air force Station Palaj, Gandhinagar, Gujarat, India
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2
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Elsayed YY, Kühl T, Imhof D. Edman Degradation Reveals Unequivocal Analysis of the Disulfide Connectivity in Peptides and Proteins. Anal Chem 2024; 96:4057-4066. [PMID: 38407829 DOI: 10.1021/acs.analchem.3c04229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Disulfide bridges in peptides and proteins play an essential role in maintaining their conformation, structural integrity, and consequently function. Despite ongoing efforts, it is still not possible to detect disulfide bonds and the connectivity of multiply bridged peptides directly through a simple and sufficiently validated protein sequencing or peptide mapping method. Partial or complete reduction and chemical cysteine modification are required as initial steps, followed by the application of a proper detection method. Edman degradation (ED) has been used for primary sequence determination but is largely neglected since the establishment of mass spectrometry (MS)-based protein sequencing. Here, we evaluated and thoroughly characterized the phenyl thiohydantoin (PTH) cysteine derivatives PTH-S-methyl cysteine and PTH-S-carbamidomethyl cysteine as bioanalytical standards for cysteine detection and quantification as well as for the elucidation of the disulfide connectivity in peptides by ED. Validation of the established derivatives was performed according to the guidelines of the International Committee of Harmonization on bioanalytical method validation, and their analytical properties were confirmed as reference standards. A series of model peptides was sequenced to test the usability of the PTH-Cys-derivatives as standards, whereas the native disulfide-bonded peptides CCAP-vil, μ-conotoxin KIIIA, and human insulin were used as case studies to determine their disulfide bond connectivity completely independent of MS analysis.
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Affiliation(s)
- Yomnah Y Elsayed
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn 53121, Germany
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St, Cairo 11566, Egypt
| | - Toni Kühl
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn 53121, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn 53121, Germany
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3
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Jeanne Dit Fouque K, Wellmann M, Leyva Bombuse D, Santos-Fernandez M, Cintron-Diaz YL, Gomez-Hernandez ME, Kaplan D, Voinov VG, Fernandez-Lima F. Effective discrimination of gas-phase peptide conformers using TIMS-ECD-ToF MS/MS. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5216-5223. [PMID: 34698320 PMCID: PMC8596503 DOI: 10.1039/d1ay01461g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In the present work, four, well-studied, model peptides (e.g., substance P, bradykinin, angiotensin I and AT-Hook 3) were used to correlate structural information provided by ion mobility and ECD/CID fragmentation in a TIMS-q-EMS-ToF MS/MS platform, incorporporating an electromagnetostatic cell (EMS). The structural heterogeneity of the model peptides was observed by (i) multi-component ion mobility profiles (high ion mobility resolving power, R ∼115-145), and (ii) fast online characteristic ECD fragmentation patterns per ion mobility band (∼0.2 min). Particularly, it was demonstrated that all investigated species were probably conformers, involving cis/trans-isomerizations at X-Pro peptide bond, following the same protonation schemes, in good agreement with previous ion mobility and single point mutation experiments. The comparison between ion mobility selected ECD spectra and traditional FT-ICR ECD MS/MS spectra showed comparable ECD fragmentation efficiencies but differences in the ratio of radical (˙)/prime (') fragment species (H˙ transfer), which were associated with the differences in detection time after the electron capture event. The analysis of model peptides using online TIMS-q-EMSToF MS/MS provided complementary structural information on the intramolecular interactions that stabilize the different gas-phase conformations to those obtained by ion mobility or ECD alone.
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Affiliation(s)
- K Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
| | - M Wellmann
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Kiel 24098, Germany
| | - D Leyva Bombuse
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - M Santos-Fernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Y L Cintron-Diaz
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - M E Gomez-Hernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - D Kaplan
- KapScience LLC, Tewksbury, MA 01876, USA
| | - V G Voinov
- e-MSion Inc., Corvallis, OR 97330, USA
- Linus Pauling Institute and Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - F Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
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4
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Deslignière E, Botzanowski T, Diemer H, Cooper-Shepherd DA, Wagner-Rousset E, Colas O, Béchade G, Giles K, Hernandez-Alba O, Beck A, Cianférani S. High-Resolution IMS-MS to Assign Additional Disulfide Bridge Pairing in Complementarity-Determining Regions of an IgG4 Monoclonal Antibody. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2505-2512. [PMID: 34437803 DOI: 10.1021/jasms.1c00151] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Monoclonal antibodies (mAbs) have taken on an increasing importance for the treatment of various diseases, including cancers and immunological disorders. Disulfide bonds play a pivotal role in therapeutic antibody structure and activity relationships. Disulfide connectivity and cysteine-related variants are considered as critical quality attributes that must be monitored during mAb manufacturing and storage, as non-native disulfide bridges and aggregates might be responsible for loss of biological function and immunogenicity. The presence of cysteine residues in the complementarity-determining regions (CDRs) is rare in human antibodies but may be critical for the antigen-binding or deleterious for therapeutic antibody development. Consequently, in-depth characterization of their disulfide network is a prerequisite for mAb developability assessment. Mass spectrometry (MS) techniques represent powerful tools for accurate identification of disulfide connectivity. We report here on the MS-based characterization of an IgG4 comprising two additional cysteine residues in the CDR of its light chain. Classical bottom-up approaches after trypsin digestion first allowed identification of a dipeptide containing two disulfide bridges. To further investigate the conformational heterogeneity of the disulfide-bridged dipeptide, we performed ion mobility spectrometry-mass spectrometry (IMS-MS) experiments. Our results highlight benefits of high resolution IMS-MS to tackle the conformational landscape of disulfide peptides generated after trypsin digestion of a humanized IgG4 mAb under development. By comparing arrival time distributions of the mAb-collected and synthetic peptides, cyclic IMS afforded unambiguous assessment of disulfide bonds. In addition to classical peptide mapping, qualitative high-resolution IMS-MS can be of great interest to identify disulfide bonds within therapeutic mAbs.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | | | - Elsa Wagner-Rousset
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Olivier Colas
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Guillaume Béchade
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, Cheshire SK9 4AX, U.K
| | - Kevin Giles
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, Cheshire SK9 4AX, U.K
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Alain Beck
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
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5
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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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6
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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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7
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Delvaux C, Massonnet P, Kune C, Haler JRN, Upert G, Mourier G, Gilles N, Quinton L, De Pauw E, Far J. Combination of Capillary Zone Electrophoresis-Mass Spectrometry, Ion Mobility-Mass Spectrometry, and Theoretical Calculations for Cysteine Connectivity Identification in Peptides Bearing Two Intramolecular Disulfide Bonds. Anal Chem 2020; 92:2425-2434. [PMID: 31885261 DOI: 10.1021/acs.analchem.9b03206] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Disulfide bonds between cysteine residues are commonly involved in the stability of numerous peptides and proteins and are crucial for providing biological activities. In such peptides, the appropriate cysteine connectivity ensures the proper conformation allowing an efficient binding to their molecular targets. Disulfide bond connectivity characterization is still challenging and is a critical issue in the analysis of structured peptides/proteins targeting pharmaceutical or pharmacological utilizations. This study describes the development of new and fast gas-phase and in-solution electrophoretic methods coupled to mass spectrometry to characterize the cysteine connectivity of disulfide bonds. For this purpose, disulfide isomers of three peptides bearing two intramolecular disulfide bonds but different cysteine connectivity have been investigated. Capillary zone electrophoresis and ion mobility both coupled to mass spectrometry were used to perform the separation in both aqueous and gas phases, respectively. The separation efficiency of each technique has been critically evaluated and compared. Finally, theoretical calculations were performed to support and explain the experimental data based on the predicted physicochemical properties of the different peptides.
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Affiliation(s)
- Cédric Delvaux
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora , University of Liège , Allée du Six Août 11 , B-4000 Liège , Belgium
| | - Philippe Massonnet
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora , University of Liège , Allée du Six Août 11 , B-4000 Liège , Belgium.,Maastricht Multimodal Molecular Imaging (M4I) Institute , Division of Imaging Mass Spectrometry , Maastricht , Limburg , Netherlands
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora , University of Liège , Allée du Six Août 11 , B-4000 Liège , Belgium
| | - Jean R N Haler
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora , University of Liège , Allée du Six Août 11 , B-4000 Liège , Belgium.,Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Gregory Upert
- Commissariat à l'Energie Atomique , DRF/Institut Joliot/SIMOPRO, Université Paris Sud , 91191 Gif-sur-Yvette , France
| | - Gilles Mourier
- Commissariat à l'Energie Atomique , DRF/Institut Joliot/SIMOPRO, Université Paris Sud , 91191 Gif-sur-Yvette , France
| | - Nicolas Gilles
- Commissariat à l'Energie Atomique , DRF/Institut Joliot/SIMOPRO, Université Paris Sud , 91191 Gif-sur-Yvette , France
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora , University of Liège , Allée du Six Août 11 , B-4000 Liège , Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora , University of Liège , Allée du Six Août 11 , B-4000 Liège , Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora , University of Liège , Allée du Six Août 11 , B-4000 Liège , Belgium
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8
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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: 8] [Impact Index Per Article: 1.6] [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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9
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Denisov SS, Ippel JH, Mans BJ, Dijkgraaf I, Hackeng TM. SecScan: a general approach for mapping disulfide bonds in synthetic and recombinant peptides and proteins. Chem Commun (Camb) 2019; 55:1374-1377. [PMID: 30520894 DOI: 10.1039/c8cc08777f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Selenocysteine scanning (SecScan) is a novel technique to map disulfide networks in proteins independent of structure-based distance information and mass spectrometry. SecScan applies systematic substitution of single Cys by Sec in combination with NMR spectroscopy for reliable and unambiguous determination of disulfide bond networks.
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Affiliation(s)
- Stepan S Denisov
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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10
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Kolli V, Schumacher KN, Dodds ED. Ion mobility-resolved collision-induced dissociation and electron transfer dissociation of N-glycopeptides: gathering orthogonal connectivity information from a single mass-selected precursor ion population. Analyst 2018; 142:4691-4702. [PMID: 29119999 DOI: 10.1039/c7an01196b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glycopeptide-level mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses are commonly performed to establish site-specific protein glycosylation profiles that are of central importance to gaining structure-function insights on glycoproteins. Confoundingly, the complete characterization of glycopeptide connectivity usually requires the acquisition of multiple MS/MS fragmentation spectra. Complementary ion fragmentation techniques such as collision-induced dissociation (CID) and electron transfer dissociation (ETD) are often applied in concert to address this need. While structurally informative, the requirement for acquisition of two MS/MS spectra per analyte places considerable limitations upon the breadth and depth of large-scale glycoproteomic inquiry. Here, a previously developed method of multiplexing CID and ETD is applied to the study of glycopeptides for the first time. Integration of the two dissociation methods was accomplished through addition of an ion mobility (IM) dimension that disperses the two stages of MS/MS in time. This allows the two MS/MS spectra to be acquired within a few milliseconds of one another, and to be deconvoluted in post-processing. Furthermore, the method allows both fragmentation readouts to be obtained from the same precursor ion packet, thus reducing the inefficiencies imposed by separate CID and ETD acquisitions and the relatively poor precursor ion to fragment ion conversion typical of ETD. N-Linked glycopeptide ions ranging in molecular weight from 1.8 to 6.5 kDa were generated from four model glycoproteins that collectively encompassed paucimannosidic, high mannose, and complex types of N-glycosylation. In each case, IM-resolved CID and ETD events provided complete coverage of the glycan topology and peptide sequence coverages ranging from 48.4% (over 32 amino acid residues) to 85.7% (over eight amino acid residues). The potential of this method for large-scale glycoproteomic analysis is discussed.
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Affiliation(s)
- Venkata Kolli
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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11
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Massonnet P, Haler JRN, Upert G, Smargiasso N, Mourier G, Gilles N, Quinton L, De Pauw E. Disulfide Connectivity Analysis of Peptides Bearing Two Intramolecular Disulfide Bonds Using MALDI In-Source Decay. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1995-2002. [PMID: 29987664 DOI: 10.1007/s13361-018-2022-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/07/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Disulfide connectivity in peptides bearing at least two intramolecular disulfide bonds is highly important for the structure and the biological activity of the peptides. In that context, analytical strategies allowing a characterization of the cysteine pairing are of prime interest for chemists, biochemists, and biologists. For that purpose, this study evaluates the potential of MALDI in-source decay (ISD) for characterizing cysteine pairs through the systematic analysis of identical peptides bearing two disulfide bonds, but not the same cysteine connectivity. Three different matrices have been tested in positive and/or in negative mode (1,5-DAN, 2-AB and 2-AA). As MALDI-ISD is known to partially reduce disulfide bonds, the data analysis of this study rests firstly on the deconvolution of the isotope pattern of the parent ions. Moreover, data analysis is also based on the formed fragment ions and their signal intensities. Results from MS/MS-experiments (MALDI-ISD-MS/MS) constitute the last reference for data interpretation. Owing to the combined use of different ISD-promoting matrices, cysteine connectivity identification could be performed on the considered peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Philippe Massonnet
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium.
| | - Jean R N Haler
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Gregory Upert
- Commissariat à l'Energie Atomique, DRF/SIMOPRO, 91191, Gif sur Yvette, France
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Gilles Mourier
- Commissariat à l'Energie Atomique, DRF/SIMOPRO, 91191, Gif sur Yvette, France
| | - Nicolas Gilles
- Commissariat à l'Energie Atomique, DRF/SIMOPRO, 91191, Gif sur Yvette, France
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
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12
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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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13
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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14
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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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15
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Haler JRN, Kune C, Massonnet P, Comby-Zerbino C, Jordens J, Honing M, Mengerink Y, Far J, De Pauw E. Comprehensive Ion Mobility Calibration: Poly(ethylene oxide) Polymer Calibrants and General Strategies. Anal Chem 2017; 89:12076-12086. [DOI: 10.1021/acs.analchem.7b02564] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jean R. N. Haler
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Christopher Kune
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Philippe Massonnet
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Clothilde Comby-Zerbino
- Institut
Lumière Matière, Université de Lyon, Université Lyon 1, CNRS, 69100 Villeurbanne, France
| | | | | | | | - Johann Far
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
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16
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Jhingree JR, Bellina B, Pacholarz KJ, Barran PE. Charge Mediated Compaction and Rearrangement of Gas-Phase Proteins: A Case Study Considering Two Proteins at Opposing Ends of the Structure-Disorder Continuum. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1450-1461. [PMID: 28585116 PMCID: PMC5486678 DOI: 10.1007/s13361-017-1692-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 05/22/2023]
Abstract
Charge reduction in the gas phase provides a direct means of manipulating protein charge state, and when coupled to ion mobility mass spectrometry (IM-MS), it is possible to monitor the effect of charge on protein conformation in the absence of solution. Use of the electron transfer reagent 1,3-dicyanobenzene, coupled with IM-MS, allows us to monitor the effect of charge reduction on the conformation of two proteins deliberately chosen from opposite sides of the order to disorder continuum: bovine pancreatic trypsin inhibitor (BPTI) and beta casein. The ordered BPTI presents compact conformers for each of three charge states accompanied by narrow collision cross-section distributions (TWCCSDN2→He). Upon reduction of BPTI, irrespective of precursor charge state, the TWCCSN2→He decreases to a similar distribution as found for the nESI generated ion of identical charge. The behavior of beta casein upon charge reduction is more complex. It presents over a wide charge state range (9-28), and intermediate charge states (13-18) have broad TWCCSDN2→He with multiple conformations, where both compaction and rearrangement are seen. Further, we see that the TWCCSDN2→He of the latter charge states are even affected by the presence of radical anions. Overall, we conclude that the flexible nature of some proteins result in broad conformational distributions comprised of many families, even for single charge states, and the barrier between different states can be easily overcome by an alteration of the net charge. Graphical Abstract ᅟ.
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Affiliation(s)
- Jacquelyn R Jhingree
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Bruno Bellina
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Kamila J Pacholarz
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Perdita E Barran
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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17
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Cramer CN, Kelstrup CD, Olsen JV, Haselmann KF, Nielsen PK. Complete Mapping of Complex Disulfide Patterns with Closely-Spaced Cysteines by In-Source Reduction and Data-Dependent Mass Spectrometry. Anal Chem 2017; 89:5949-5957. [DOI: 10.1021/acs.analchem.7b00424] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Christian N. Cramer
- Protein
Engineering, Global Research, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
- Proteomics
Program, The Novo Nordisk Foundation Center for Protein Research,
Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Christian D. Kelstrup
- Proteomics
Program, The Novo Nordisk Foundation Center for Protein Research,
Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jesper V. Olsen
- Proteomics
Program, The Novo Nordisk Foundation Center for Protein Research,
Faculty of Health and Medical Sciences, 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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18
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Sarbu M, Zhu F, Peter-Katalinić J, Clemmer DE, Zamfir AD. Application of ion mobility tandem mass spectrometry to compositional and structural analysis of glycopeptides extracted from the urine of a patient diagnosed with Schindler disease. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1929-1937. [PMID: 26443390 DOI: 10.1002/rcm.7288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/17/2015] [Accepted: 07/23/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Schindler disease is caused by the deficient activity of α-N-acetylgalactosaminidase, which leads to an abnormal accumulation of O-glycopeptides in tissues and body fluids. In this work the Schindler condition is for the first time approached by ion mobility (IMS) tandem mass spectrometry (MS/MS), for determining urine glycopeptide fingerprints and discriminate isomeric structures. METHODS IMS-MS experiments were conducted on a Synapt G2s mass spectrometer operating in negative ion mode. A glycopeptide mixture extracted from the urine of a patient suffering from Schindler disease was dissolved in methanol and infused into the mass spectrometer by electrospray ionization using a syringe-pump system. MS/MS was performed by collision-induced dissociation (CID) at low energies, after mobility separation in the transfer cell. Data acquisition and processing were performed using MassLynx and Waters Driftscope software. RESULTS IMS-MS data indicated that the attachment of one or two amino acids to the carbohydrate backbone has a minimal influence on the molecule conformation, which limits the discrimination of the free oligosaccharides from the glycosylated amino acids and dipeptides. The structural analysis by CID MS/MS in combination with IMS-MS of species exhibiting the same m/z but different configurations demonstrated for the first time the presence of positional isomers for some of the Schindler disease biomarker candidates. CONCLUSIONS The IMS-MS and CID MS/MS platform was for the first time optimized and applied to Schindler disease glycourinome. By this approach the separation and characterization of Neu5Ac positional isomers was possible. IMS CID MS/MS showed the ability to determine the type of the glycopeptide isomers from a series of possible candidates.
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Affiliation(s)
- Mirela Sarbu
- West University of Timisoara, Romania
- Aurel Vlaicu University of Arad, Romania
| | - Feifei Zhu
- Department of Chemistry, Indiana University, Bloomington, USA
| | - Jasna Peter-Katalinić
- Institute for Medical Physics and Biophysics, University of Muenster, Germany
- Department of Biotechnology, University of Rijeka, Croatia
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, USA
| | - Alina D Zamfir
- Aurel Vlaicu University of Arad, Romania
- National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Romania
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19
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Wang Y, Han Y, Fan E, Zhang K. Analytical strategies used to identify the readers of histone modifications: A review. Anal Chim Acta 2015; 891:32-42. [PMID: 26388362 DOI: 10.1016/j.aca.2015.06.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 10/23/2022]
Abstract
The so-called "readers" of histone post-translational modifications (HPTMs) refer to proteins or complexes that are recruited to HPTMs thus eventually regulate gene transcription. To identify these "readers", mass spectrometry plays an essential role following various enriching strategies. These enriching methods include the use of modified histone peptides/proteins or chemically synthesized histones/nucleosomes containing desired HPTMs to enrich the readers of HPTMs. Despite the peptide- or protein-based assay is straightforward and easy to perform for most labs, this strategy has limited applications for those weak or combinational interactions among various HPTMs and false-positive results are a potential big problem. While the results derived from synthesized histone proteins/nucleosomes is more reliable as it mimics the real chromatic conditions thus is able to analyze the binders of those cross-talked HPTMs, usually the synthesis is so difficult that their applications are impeded for high throughput analysis. In this review, an overview of these analytical techniques is provided and their advantages and disadvantages are discussed.
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Affiliation(s)
- Ye Wang
- Department of Chemistry, Nankai University, 300071 Tianjin, China
| | - Yanpu Han
- Department of Chemistry, Nankai University, 300071 Tianjin, China
| | - Enguo Fan
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Stefan-Meier-Straße 17, 79104 Freiburg, Germany; School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Jungong Road No. 516, 200093 Shanghai, China.
| | - Kai Zhang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Medical University, 300070 Tianjin, China; Department of Chemistry, Nankai University, 300071 Tianjin, China.
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20
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Maurer MM, Donohoe GC, Valentine SJ. Advances in ion mobility-mass spectrometry instrumentation and techniques for characterizing structural heterogeneity. Analyst 2015; 140:6782-98. [PMID: 26114255 DOI: 10.1039/c5an00922g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Enabling IM-MS instrumentation and techniques for characterizing sample structural heterogeneity have developed rapidly over the last five years.
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Affiliation(s)
- Megan M. Maurer
- C. Eugene Bennett Department of Chemistry
- West Virginia University
- Morgantown
- USA
| | - Gregory C. Donohoe
- C. Eugene Bennett Department of Chemistry
- West Virginia University
- Morgantown
- USA
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