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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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2
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Juvonen M, Bakx E, Schols H, Tenkanen M. Separation of isomeric cereal-derived arabinoxylan-oligosaccharides by collision induced dissociation-travelling wave ion mobility spectrometry-tandem mass spectrometry (CID-TWIMS-MS/MS). Food Chem 2021; 366:130544. [PMID: 34314932 DOI: 10.1016/j.foodchem.2021.130544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 06/12/2021] [Accepted: 07/04/2021] [Indexed: 01/08/2023]
Abstract
The potential of travelling wave ion mobility spectroscopy in combination with collision induced dissociation tandem mass spectrometry (CID-TWIMS-MS/MS) to separate cereal-derived isomeric arabinoxylan-oligosaccharides (A)XOS was investigated. Three trisaccharide, four tetrasaccharide, and four pentasaccharide (A)XOS isomers were analyzed by positive and negative ionization TWIMS-MS and CID-TWIMS-MS/MS. The tri- and pentasaccharide isomers were distinguishable by the ATDs of the precursor ions. The CID-TWIMS-MS/MS could separate most of the isomeric fragment ions produced from tetra- and pentasaccharide (A)XOS. Finally, the base peak mobility spectrum is introduced as a practical tool for (A)XOS fingerprinting.
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Affiliation(s)
- Minna Juvonen
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, 00014 University of Helsinki, Finland.
| | - Edwin Bakx
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
| | - Henk Schols
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
| | - Maija Tenkanen
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, 00014 University of Helsinki, Finland
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3
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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4
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Leiva-Carrasco MJ, Jiménez-Chávez S, Harvey DJ, Parra NC, Tavares KC, Camacho F, González A, Sánchez O, Montesino R, Toledo JR. In vivo modification of the goat mammary gland glycosylation pathway. N Biotechnol 2020; 61:11-21. [PMID: 33157282 DOI: 10.1016/j.nbt.2020.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/25/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
Complex recombinant glycoproteins produced as potential biopharmaceuticals in goat's milk have an aberrant pattern of N-glycosylation due to the lack of multi-antennary structures. Overexpression of glycosyltransferases may increase oligosaccharide branching of the desired glycoproteins. Here, human erythropoietin fused to human IgG Fc (EPO-Fc) was co-expressed with N-acetyl-glucosaminyltransferase-IVa (GnT-IVa) by adenoviral transduction in goat mammary gland to evaluate the in vivo modification of N-glycosylation pattern in this tissue. Adenoviral vectors, containing the EPO-Fc and GnT-IVa sequences were assembled for in vitro and in vivo expression in mammalian cell culture or in goat mammary gland. Protein detection was assessed by gel electrophoresis and western blot, and N-glycans were identified by HPLC and mass spectrometry. GnT-IVa overexpression and its colocalization with EPO-Fc in the Golgi apparatus of SiHa cells were demonstrated. N-glycan analysis of in vitro and in vivo expression of EPO-Fc modified by GnT-IVa (EPO-Fc/GnT-IVa) showed an increase in high molecular weight structures, which corresponded to tri- and tetra-antennary N-glycans in SiHa cells and mostly tri-antennary N-glycans in goat's milk from transformed mammary tissue. The results confirmed that successful modification of the goat mammary gland secretion pathway could be achieved by co-expressing glycoenzymes together with the glycoprotein of interest. This is the first report of modification of the N-glycosylation pattern in the goat mammary gland in vivo, and constitutes a step forward for improving the use of the mammary gland as a bioreactor for the production of complex recombinant proteins.
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Affiliation(s)
- María J Leiva-Carrasco
- Biotechnology and Biopharmaceuticals Laboratory, Pathophysiology Department, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile; Biotechnology and Biomedicine Center SpA, Granada 168, Villumanque, Concepcion, Chile
| | - Silvana Jiménez-Chávez
- Biotechnology and Biopharmaceuticals Laboratory, Pathophysiology Department, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile; Biotechnology and Biomedicine Center SpA, Granada 168, Villumanque, Concepcion, Chile
| | - David J Harvey
- Oxford Glycobiology Institute, Biochemistry Department, South Parks Road, Oxford, OX1 3QU, UK
| | - Natalie C Parra
- Department of Pharmacology, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile
| | - Kaio C Tavares
- Molecular and Developmental Biology Laboratory, Experimental Biology Center (NUBEX), University of Fortaleza (UNIFOR), Fortaleza, CE, Brazil
| | - Frank Camacho
- Department of Pharmacology, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile
| | - Alain González
- Biotechnology and Biopharmaceuticals Laboratory, Pathophysiology Department, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile
| | - Oliberto Sánchez
- Department of Pharmacology, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile
| | - Raquel Montesino
- Biotechnology and Biopharmaceuticals Laboratory, Pathophysiology Department, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile; Biotechnology and Biomedicine Center SpA, Granada 168, Villumanque, Concepcion, Chile.
| | - Jorge R Toledo
- Biotechnology and Biopharmaceuticals Laboratory, Pathophysiology Department, School of Biological Sciences, University of Concepcion, Victor Lamas 1290, P.O. Box 160C, Concepcion, Chile; Biotechnology and Biomedicine Center SpA, Granada 168, Villumanque, Concepcion, Chile.
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5
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Wei J, Tang Y, Ridgeway ME, Park MA, Costello CE, Lin C. Accurate Identification of Isomeric Glycans by Trapped Ion Mobility Spectrometry-Electronic Excitation Dissociation Tandem Mass Spectrometry. Anal Chem 2020; 92:13211-13220. [PMID: 32865981 DOI: 10.1021/acs.analchem.0c02374] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) has become a powerful tool for glycan structural characterization due to its ability to separate isomers and provide collision cross section (CCS) values that facilitate structural assignment. However, IM-based isomer analysis may be complicated by the presence of multiple gas-phase conformations of a single structure that not only increases difficulty in isomer separation but can also introduce the possibility for misinterpretation of conformers as isomers. Here, the ion mobility behavior of several sets of isomeric glycans, analyzed as their permethylated derivatives, in both nonreduced and reduced forms, was investigated by gated-trapped ion mobility spectrometry (G-TIMS). Notably, reducing-end reduction, commonly performed to remove anomerism-induced chromatographic peak splitting, did not eliminate the conformational heterogeneity of permethylated glycans in the gas phase. At a mobility resolving power of ∼100, 14 out of 22 structures showed more than one conformation. These results highlight the need to use IMS devices with high mobility resolving power for better separation of isomers and to acquire additional structural information that can differentiate isomers from conformers. Online electronic excitation dissociation (EED) MS/MS analysis of isomeric glycan mixtures following G-TIMS separation showed that EED can generate isomer-specific fragments while producing nearly identical tandem mass spectra for conformers, thus allowing confident identification of isomers with minimal evidence of any ambiguity resulting from the presence of conformers. G-TIMS EED MS/MS analysis of N-linked glycans released from ovalbumin revealed that several mobility features previously thought to arise from isomeric structures were conformers of a single structure. Finally, analysis of ovalbumin N-glycans from different sources showed that the G-TIMS EED MS/MS approach can accurately determine the batch-to-batch variations in glycosylation profiles at the isomer level, with confident assignment of each isomeric structure.
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Affiliation(s)
- Juan Wei
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States
| | - Yang Tang
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Mark E Ridgeway
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | - Melvin A Park
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States
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6
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Harvey DJ. NEGATIVE ION MASS SPECTROMETRY FOR THE ANALYSIS OF N-LINKED GLYCANS. MASS SPECTROMETRY REVIEWS 2020; 39:586-679. [PMID: 32329121 DOI: 10.1002/mas.21622] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/13/2019] [Accepted: 12/22/2019] [Indexed: 05/03/2023]
Abstract
N-glycans from glycoproteins are complex, branched structures whose structural determination presents many analytical problems. Mass spectrometry, usually conducted in positive ion mode, often requires extensive sample manipulation, usually by derivatization such as permethylation, to provide the necessary structure-revealing fragment ions. The newer but, so far, lesser used negative ion techniques, on the contrary, provide a wealth of structural information not present in positive ion spectra that greatly simplify the analysis of these compounds and can usually be conducted without the need for derivatization. This review describes the use of negative ion mass spectrometry for the structural analysis of N-linked glycans and emphasises the many advantages that can be gained by this mode of operation. Biosynthesis and structures of the compounds are described followed by methods for release of the glycans from the protein. Methods for ionization are discussed with emphasis on matrix-assisted laser desorption/ionization (MALDI) and methods for producing negative ions from neutral compounds. Acidic glycans naturally give deprotonated species under most ionization conditions. Fragmentation of negative ions is discussed next with particular reference to those ions that are diagnostic for specific features such as the branching topology of the glycans and substitution positions of moieties such as fucose and sulfate, features that are often difficult to identify easily by conventional techniques such as positive ion fragmentation and exoglycosidase digestions. The advantages of negative over positive ions for this structural work are emphasised with an example of a series of glycans where all other methods failed to produce a structure. Fragmentation of derivatized glycans is discussed next, both with respect to derivatives at the reducing terminus of the molecules, and to methods for neutralization of the acidic groups on sialic acids to both stabilize them for MALDI analysis and to produce the diagnostic fragments seen with the neutral glycans. The use of ion mobility, combined with conventional mass spectrometry is described with emphasis on its use to extract clean glycan spectra both before and after fragmentation, to separate isomers and its use to extract additional information from separated fragment ions. A section on applications follows with examples of the identification of novel structures from lower organisms and tables listing the use of negative ions for structural identification of specific glycoproteins, glycans from viruses and uses in the biopharmaceutical industry and in medicine. The review concludes with a summary of the advantages and disadvantages of the technique. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
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7
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Bansal P, Yatsyna V, AbiKhodr AH, Warnke S, Ben Faleh A, Yalovenko N, Wysocki VH, Rizzo TR. Using SLIM-Based IMS-IMS Together with Cryogenic Infrared Spectroscopy for Glycan Analysis. Anal Chem 2020; 92:9079-9085. [PMID: 32456419 PMCID: PMC7349563 DOI: 10.1021/acs.analchem.0c01265] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
Abstract
The isomeric heterogeneity of glycans poses a great challenge for their analysis. While combining ion mobility spectrometry (IMS) with tandem mass spectrometry is a powerful means for identifying and characterizing glycans, it has difficulty distinguishing the subtlest differences between isomers. Cryogenic infrared spectroscopy provides an additional dimension for glycan identification that is extremely sensitive to their structure. Our approach to glycan analysis combines ultrahigh-resolution IMS-IMS using structures for lossless ion manipulation (SLIM) with cryogenic infrared spectroscopy. We present here the design of a SLIM board containing a series of on-board traps in which we perform collision-induced dissociation (CID) at pressures in the millibar range. We characterize the on-board CID process by comparing the fragments generated from a pentapeptide to those obtained on a commercial tandem mass spectrometer. We then apply our new technique to study the mobility and vibrational spectra of CID fragments from two human milk oligosaccharides. Comparison of both the fragment drift times and IR spectra with those of suitable reference compounds allows us to identify their specific isomeric form, including the anomericity of the glycosidic linkage, demonstrating the power of this tool for glycan analysis.
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Affiliation(s)
- Priyanka Bansal
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Vasyl Yatsyna
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
- Department
of Physics, University of Gothenburg, 412 96 Gotheburg, Sweden
| | - Ali H. AbiKhodr
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Stephan Warnke
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Ahmed Ben Faleh
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Natalia Yalovenko
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Thomas R. Rizzo
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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8
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Quaranta A, Spasova M, Passarini E, Karlsson I, Ndreu L, Thorsén G, Ilag LL. N-Glycosylation profiling of intact target proteins by high-resolution mass spectrometry (MS) and glycan analysis using ion mobility-MS/MS. Analyst 2020; 145:1737-1748. [DOI: 10.1039/c9an02081k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycosylation characterization could lead to the discovery of biomarkers and is crucial in quality control of biopharmaceuticals. Here we present a method to quantify glycoforms on intact proteins, with parallel glycan identification by IMS-MS/MS.
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Affiliation(s)
- Alessandro Quaranta
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Maya Spasova
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Elena Passarini
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Isabella Karlsson
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Lorena Ndreu
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Gunnar Thorsén
- IVL Swedish Environmental Research Institute
- 11428 Stockholm
- Sweden
| | - Leopold L. Ilag
- Department of Environmental Science and Analytical Chemistry
- Stockholm University
- 10691 Stockholm
- Sweden
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9
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Struwe WB, Harvey DJ. Ion Mobility-Mass Spectrometry of Glycoconjugates. Methods Mol Biol 2019; 2084:203-219. [PMID: 31729663 DOI: 10.1007/978-1-0716-0030-6_13] [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] [Indexed: 02/25/2023]
Abstract
Glycoconjugates are diverse biomolecules that are dynamically assembled to regulate and fine-tune numerous cellular processes. Their biosynthesis is nontemplate-driven, achieved stepwise in discrete locations within the cell, giving rise to a range of complex branched structures that pose a significant challenge in structural biology. Mass spectrometry is the leading method for analysis of glycoconjugates, and the addition of ion mobility has proven valuable for improving structural assignments of individual glycans in complex biological mixtures. In this chapter, we briefly discuss recent applications of IM for glycomics and describe how to acquire, interpret, and analyze IM-MS data for the analysis of glycans.
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Affiliation(s)
- Weston B Struwe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, UK.
| | - David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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10
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Lane CS, McManus K, Widdowson P, Flowers SA, Powell G, Anderson I, Campbell JL. Separation of Sialylated Glycan Isomers by Differential Mobility Spectrometry. Anal Chem 2019; 91:9916-9924. [PMID: 31283185 PMCID: PMC6686149 DOI: 10.1021/acs.analchem.9b01595] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/18/2019] [Indexed: 12/28/2022]
Abstract
Mass spectrometry has proven itself to be an important technology for characterizing intact glycoproteins, glycopeptides, and released glycans. However, these molecules often present significant challenges during analysis. For example, glycans of identical molecular weights can be present in many isomeric forms, with one form having dramatically more biological activity than the others. Discriminating among these isomeric forms using mass spectrometry alone can be daunting, which is why orthogonal techniques, such as ion mobility spectrometry, have been explored. Here, we demonstrate the use of differential mobility spectrometry (DMS) to separate isomeric glycans differing only in the linkages of sialic acid groups (e.g., α 2,3 versus α 2,6). This ability extends from a small trisaccharide species to larger biantennary systems and is driven, in part, by the role of intramolecular solvation of the charge site(s) on these ions within the DMS environment.
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Affiliation(s)
- Catherine S. Lane
- SCIEX, Phoenix House, Centre Park, Warrington WA1 1RX, United Kingdom
| | - Kirsty McManus
- Allergan
Biologics Limited, 12 Estuary Banks, Speke, Liverpool L24 8RB, United Kingdom
| | - Philip Widdowson
- Allergan
Biologics Limited, 12 Estuary Banks, Speke, Liverpool L24 8RB, United Kingdom
| | | | - Gerard Powell
- Allergan
Biologics Limited, 12 Estuary Banks, Speke, Liverpool L24 8RB, United Kingdom
| | - Ian Anderson
- Allergan
Biologics Limited, 12 Estuary Banks, Speke, Liverpool L24 8RB, United Kingdom
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11
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Jin C, Harvey DJ, Struwe WB, Karlsson NG. Separation of Isomeric O-Glycans by Ion Mobility and Liquid Chromatography–Mass Spectrometry. Anal Chem 2019; 91:10604-10613. [DOI: 10.1021/acs.analchem.9b01772] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - David J. Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Weston B. Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Chemistry Research laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Niclas G. Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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12
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Munro JB, Lee KK. Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Glycoprotein. Curr HIV Res 2019; 16:5-12. [PMID: 29268688 DOI: 10.2174/1570162x16666171222110025] [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: 05/05/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in structural characterization of the HIV envelope glycoprotein (Env) have provided a high-resolution glimpse of the architecture of this target for neutralizing antibodies and the machinery responsible for mediating receptor binding and membrane fusion. These structures primarily capture the detailed organization of the receptor-naive, prefusion conformation of Env, but under native solution conditions Env is highly dynamic, sampling multiple conformational states as well as exhibiting local protein flexibility. METHODS Special emphasis is placed on the use of biophysical methods, including single-molecule fluorescence microscopy and hydrogen/deuterium-exchange mass spectrometry. RESULTS Using novel biophysical approaches, striking isolate-specific differences in Env's dynamic profile have been revealed that appear to underlie phenotypic differences of the viral isolates such as neutralization sensitivity and CD4 receptor reactivity. CONCLUSION Structural studies are complemented by novel biophysical investigations that enable visualization of the dynamics of HIV-1 Env under native conditions. These approaches will also enable us to gain new insights into the mechanisms of action of antibodies and drugs.
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Affiliation(s)
- James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States
| | - Kelly K Lee
- Department of Medicinal Chemistry and Biological Physics Structure and Design Program, University of Washington, Seattle, WA, United States
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13
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 PMCID: PMC7757723 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California, Davis, Davis, California 95616, United States
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14
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Harvey DJ, Struwe WB. Structural Studies of Fucosylated N-Glycans by Ion Mobility Mass Spectrometry and Collision-Induced Fragmentation of Negative Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1179-1193. [PMID: 29790113 PMCID: PMC6003995 DOI: 10.1007/s13361-018-1950-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 05/03/2023]
Abstract
There is considerable potential for the use of ion mobility mass spectrometry in structural glycobiology due in large part to the gas-phase separation attributes not typically observed by orthogonal methods. Here, we evaluate the capability of traveling wave ion mobility combined with negative ion collision-induced dissociation to provide structural information on N-linked glycans containing multiple fucose residues forming the Lewisx and Lewisy epitopes. These epitopes are involved in processes such as cell-cell recognition and are important as cancer biomarkers. Specific information that could be obtained from the intact N-glycans by negative ion CID included the general topology of the glycan such as the presence or absence of a bisecting GlcNAc residue and the branching pattern of the triantennary glycans. Information on the location of the fucose residues was also readily obtainable from ions specific to each antenna. Some isobaric fragment ions produced prior to ion mobility could subsequently be separated and, in some cases, provided additional valuable structural information that was missing from the CID spectra alone. Graphical abstract ᅟ.
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Affiliation(s)
- David J Harvey
- Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Weston B Struwe
- Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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15
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Affiliation(s)
- David J. Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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16
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Frost DC, Li L. Recent advances in mass spectrometry-based glycoproteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 95:71-123. [PMID: 24985770 DOI: 10.1016/b978-0-12-800453-1.00003-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein glycosylation plays fundamental roles in many biological processes as one of the most common, and the most complex, posttranslational modification. Alterations in glycosylation profile are now known to be associated with many diseases. As a result, the discovery and detailed characterization of glycoprotein disease biomarkers is a primary interest of biomedical research. Advances in mass spectrometry (MS)-based glycoproteomics and glycomics are increasingly enabling qualitative and quantitative approaches for site-specific structural analysis of protein glycosylation. While the complexity presented by glycan heterogeneity and the wide dynamic range of clinically relevant samples like plasma, serum, cerebrospinal fluid, and tissue make comprehensive analyses of the glycoproteome a challenging task, the ongoing efforts into the development of glycoprotein enrichment, enzymatic digestion, and separation strategies combined with novel quantitative MS methodologies have greatly improved analytical sensitivity, specificity, and throughput. This review summarizes current MS-based glycoproteomics approaches and highlights recent advances in its application to cancer biomarker and neurodegenerative disease research.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA; Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.
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17
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Struwe WB, Baldauf C, Hofmann J, Rudd PM, Pagel K. Ion mobility separation of deprotonated oligosaccharide isomers - evidence for gas-phase charge migration. Chem Commun (Camb) 2018; 52:12353-12356. [PMID: 27711324 DOI: 10.1039/c6cc06247d] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There has been increasing evidence that certain isomeric glycans can be separated efficiently by ion mobility-mass spectrometry when deprotonated ions are analyzed. To better understand the fundamentals behind these separations, we here investigate the impact of ionisation mode and adduct formation using IM-MS, density-functional theory and ab initio molecular dynamics.
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Affiliation(s)
- W B Struwe
- National Institute of Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Dublin, Ireland.
| | - C Baldauf
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
| | - J Hofmann
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
| | - P M Rudd
- National Institute of Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Dublin, Ireland.
| | - K Pagel
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany. and Institut für Chemie und Biochemie der Freien Universität Berlin, Takustr. 3, 14195 Berlin, Germany.
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18
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Improving the discovery of secondary metabolite natural products using ion mobility-mass spectrometry. Curr Opin Chem Biol 2017; 42:160-166. [PMID: 29287234 DOI: 10.1016/j.cbpa.2017.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/30/2017] [Accepted: 12/11/2017] [Indexed: 02/07/2023]
Abstract
Secondary metabolite discovery requires an unbiased, comprehensive workflow to detect unknown unknowns for which little to no molecular knowledge exists. Untargeted mass spectrometry-based metabolomics is a powerful platform, particularly when coupled with ion mobility for high-throughput gas-phase separations to increase peak capacity and obtain gas-phase structural information. Ion mobility data are described by the amount of time an ion spends in the drift cell, which is directly related to an ion's collision cross section (CCS). The CCS parameter describes the size, shape, and charge of a molecule and can be used to characterize unknown metabolomic species. Here, we describe current and emerging applications of ion mobility-mass spectrometry for prioritization, discovery and structure elucidation, and spatial/temporal characterization.
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19
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Barroso A, Giménez E, Konijnenberg A, Sancho J, Sanz-Nebot V, Sobott F. Evaluation of ion mobility for the separation of glycoconjugate isomers due to different types of sialic acid linkage, at the intact glycoprotein, glycopeptide and glycan level. J Proteomics 2017; 173:22-31. [PMID: 29197583 DOI: 10.1016/j.jprot.2017.11.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023]
Abstract
The study of protein glycosylation can be regarded as an intricate but very important task, making glycomics one of the most challenging and interesting, albeit under-researched, type of "omics" science. Complexity escalates remarkably when considering that carbohydrates can form severely branched structures with many different constituents, which often leads to the formation of multiple isomers. In this regard, ion mobility (IM) spectrometry has recently demonstrated its power for the separation of isomeric compounds. In the present work, the potential of traveling wave IM (TWIMS) for the separation of isomeric glycoconjugates was evaluated, using mouse transferrin (mTf) as model glycoprotein. Particularly, we aim to assess the performance of this platform for the separation of isomeric glycoconjugates due to the type of sialic acid linkage, at the intact glycoprotein, glycopeptide and glycan level. Straightforward separation of isomers was achieved with the analysis of released glycans, as opposed to the glycopeptides which showed a more complex pattern. Finally, the developed methodology was applied to serum samples of mice, to investigate its robustness when analyzing real complex samples. BIOLOGICAL SIGNIFICANCE Ion mobility mass spectrometry is a promising analytical technique for the separation of glycoconjugate isomers due to type of sialic acid linkage. The impact of such a small modification in the glycan structure is more evident in smaller analytes, reason why the analysis of free glycans was easier compared to the intact protein or the glycopeptides. The established methodology could be regarded as starting point in the separation of highly decorated glycoconjugates. This is an important topic nowadays, as differences in the abundance of some glycan isomers could be the key for the early diagnosis, control or differentiation of certain diseases, such as inflammation or cancer.
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Affiliation(s)
- Albert Barroso
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Estela Giménez
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Jaime Sancho
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Armilla, Granada, Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
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20
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D'Atri V, Causon T, Hernandez-Alba O, Mutabazi A, Veuthey JL, Cianferani S, Guillarme D. Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? J Sep Sci 2017; 41:20-67. [PMID: 29024509 DOI: 10.1002/jssc.201700919] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).
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Affiliation(s)
- Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tim Causon
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU Vienna), Vienna, Austria
| | - Oscar Hernandez-Alba
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Aline Mutabazi
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Sarah Cianferani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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21
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Recent advances in ion mobility-mass spectrometry for improved structural characterization of glycans and glycoconjugates. Curr Opin Chem Biol 2017; 42:1-8. [PMID: 29080446 DOI: 10.1016/j.cbpa.2017.10.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/02/2017] [Accepted: 10/06/2017] [Indexed: 12/25/2022]
Abstract
Glycans and glycoconjugates are involved in regulating a vast array of cellular and molecular processes. Despite the importance of glycans in biology and disease, characterization of glycans remains difficult due to their structural complexity and diversity. Mass spectrometry (MS)-based techniques have emerged as the premier analytical tools for characterizing glycans. However, traditional MS-based strategies struggle to distinguish the large number of coexisting isomeric glycans that are indistinguishable by mass alone. Because of this, ion mobility spectrometry coupled to MS (IM-MS) has received considerable attention as an analytical tool for improving glycan characterization due to the capability of IM to resolve isomeric glycans before MS measurements. In this review, we present recent improvements in IM-MS instrumentation and methods for the structural characterization of isomeric glycans. In addition, we highlight recent applications of IM-MS that illustrate the enormous potential of this technology in a variety of research areas, including glycomics, glycoproteomics, and glycobiology.
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22
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Furuki K, Toyo'oka T. Retention of glycopeptides analyzed using hydrophilic interaction chromatography is influenced by charge and carbon chain length of ion-pairing reagent for mobile phase. Biomed Chromatogr 2017; 31. [DOI: 10.1002/bmc.3988] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/15/2017] [Accepted: 04/06/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Kenichiro Furuki
- Process Lab II, Biotechnology Labs, Astellas Pharma Inc; Ibaraki Japan
- School of Pharmaceutical Sciences; University of Shizuoka; Shizuoka Japan
| | - Toshimasa Toyo'oka
- School of Pharmaceutical Sciences; University of Shizuoka; Shizuoka Japan
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23
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Hofmann J, Pagel K. Glykananalyse mittels Ionenmobilitäts-Massenspektrometrie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Johanna Hofmann
- Abteilung Molekülphysik; Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Kevin Pagel
- Institut für Chemie und Biochemie; Freie Universität Berlin; Takustraße 3 Deutschland
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24
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Hofmann J, Pagel K. Glycan Analysis by Ion Mobility-Mass Spectrometry. Angew Chem Int Ed Engl 2017; 56:8342-8349. [DOI: 10.1002/anie.201701309] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/03/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Johanna Hofmann
- Abteilung Molekülphysik; Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Germany
| | - Kevin Pagel
- Institut für Chemie und Biochemie; Freie Universität Berlin; Takustraße 3 Germany
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25
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Gray CJ, Schindler B, Migas LG, Pičmanová M, Allouche AR, Green AP, Mandal S, Motawia MS, Sánchez-Pérez R, Bjarnholt N, Møller BL, Rijs AM, Barran PE, Compagnon I, Eyers CE, Flitsch SL. Bottom-Up Elucidation of Glycosidic Bond Stereochemistry. Anal Chem 2017; 89:4540-4549. [PMID: 28350444 DOI: 10.1021/acs.analchem.6b04998] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The lack of robust, high-throughput, and sensitive analytical strategies that can conclusively map the structure of glycans has significantly hampered progress in fundamental and applied aspects of glycoscience. Resolution of the anomeric α/β glycan linkage within oligosaccharides remains a particular challenge. Here, we show that "memory" of anomeric configuration is retained following gas-phase glycosidic bond fragmentation during tandem mass spectrometry (MS2). These findings allow for integration of MS2 with ion mobility spectrometry (IM-MS2) and lead to a strategy to distinguish α- and β-linkages within natural underivatized carbohydrates. We have applied this fragment-based hyphenated MS technology to oligosaccharide standards and to de novo sequencing of purified plant metabolite glycoconjugates, showing that the anomeric signature is also observable in fragments derived from larger glycans. The discovery of the unexpected anomeric memory effect is further supported by IR-MS action spectroscopy and ab initio calculations. Quantum mechanical calculations provide candidate geometries for the distinct anomeric fragment ions, in turn shedding light on gas-phase dissociation mechanisms of glycosidic linkages.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Baptiste Schindler
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon 69622 Villeurbanne Cedex, France
| | - Lukasz G Migas
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Martina Pičmanová
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences and Center for Synthetic Biology, University of Copenhagen , 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Abdul R Allouche
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon 69622 Villeurbanne Cedex, France
| | - Anthony P Green
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Santanu Mandal
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Mohammed S Motawia
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences and Center for Synthetic Biology, University of Copenhagen , 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Raquel Sánchez-Pérez
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences and Center for Synthetic Biology, University of Copenhagen , 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Nanna Bjarnholt
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences and Center for Synthetic Biology, University of Copenhagen , 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Birger L Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences and Center for Synthetic Biology, University of Copenhagen , 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Anouk M Rijs
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Perdita E Barran
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom.,Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Isabelle Compagnon
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon 69622 Villeurbanne Cedex, France.,Institut Universitaire de France IUF , 103 Boulevard St. Michel, 75005 Paris, France
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Sabine L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
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26
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Boschmans J, Lemière F, Sobott F. Analyzing complex mixtures of drug-like molecules: Ion mobility as an adjunct to existing liquid chromatography-(tandem) mass spectrometry methods. J Chromatogr A 2017; 1490:80-88. [DOI: 10.1016/j.chroma.2017.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/24/2017] [Accepted: 02/09/2017] [Indexed: 12/17/2022]
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27
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Abstract
Glycosylation is one of the most common and essential protein modifications. Glycans conjugated to biomolecules modulate the function of such molecules through both direct recognition of glycan structures and indirect mechanisms that involve the control of protein turnover rates, stability, and conformation. The biological attributes of glycans in numerous biological processes and implications in a number of diseases highlight the necessity for comprehensive characterization of protein glycosylation. This chapter reviews cutting-edge methods and tools developed to facilitate quantitative glycomics. This chapter highlights the different methods employed for the release and purification of glycans from biological samples. The most effective labeling methods developed for sensitive quantitative glycomics are also described and discussed. The chromatographic approaches that have been used effectively in glycomics are also highlighted.
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Affiliation(s)
- L Veillon
- Texas Tech University, Lubbock, TX, United States
| | - S Zhou
- Texas Tech University, Lubbock, TX, United States
| | - Y Mechref
- Texas Tech University, Lubbock, TX, United States.
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28
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Harvey DJ, Scarff CA, Edgeworth M, Pagel K, Thalassinos K, Struwe WB, Crispin M, Scrivens JH. Travelling-wave ion mobility mass spectrometry and negative ion fragmentation of hybrid and complex N-glycans. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1064-1079. [PMID: 27477117 PMCID: PMC5150983 DOI: 10.1002/jms.3828] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 05/20/2023]
Abstract
Nitrogen collisional cross sections (CCSs) of hybrid and complex glycans released from the glycoproteins IgG, gp120 (from human immunodeficiency virus), ovalbumin, α1-acid glycoprotein and thyroglobulin were measured with a travelling-wave ion mobility mass spectrometer using dextran as the calibrant. The utility of this instrument for isomer separation was also investigated. Some isomers, such as Man3 GlcNAc3 from chicken ovalbumin and Man3 GlcNAc3 Fuc1 from thyroglobulin could be partially resolved and identified by their negative ion fragmentation spectra obtained by collision-induced decomposition (CID). Several other larger glycans, however, although existing as isomers, produced only asymmetric rather than separated arrival time distributions (ATDs). Nevertheless, in these cases, isomers could often be detected by plotting extracted fragment ATDs of diagnostic fragment ions from the negative ion CID spectra obtained in the transfer cell of the Waters Synapt mass spectrometer. Coincidence in the drift times of all fragment ions with an asymmetric ATD profile in this work, and in the related earlier paper on high-mannose glycans, usually suggested that separations were because of conformers or anomers, whereas symmetrical ATDs of fragments showing differences in drift times indicated isomer separation. Although some significant differences in CCSs were found for the smaller isomeric glycans, the differences found for the larger compounds were usually too small to be analytically useful. Possible correlations between CCSs and structural types were also investigated, and it was found that complex glycans tended to have slightly smaller CCSs than high-mannose glycans of comparable molecular weight. In addition, biantennary glycans containing a core fucose and/or a bisecting GlcNAc residue fell on different mobility-m/z trend lines to those glycans not so substituted with both of these substituents contributing to larger CCSs. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Charlotte A Scarff
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
- Current address, Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew Edgeworth
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
- MedImmune, Sir Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse. 3, 14159, Berlin, Germany
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - James H Scrivens
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
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29
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Gray C, Thomas B, Upton R, Migas L, Eyers C, Barran P, Flitsch S. Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. Biochim Biophys Acta Gen Subj 2016; 1860:1688-709. [DOI: 10.1016/j.bbagen.2016.02.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/21/2022]
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30
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Yang H, Shi L, Zhuang X, Su R, Wan D, Song F, Li J, Liu S. Identification of structurally closely related monosaccharide and disaccharide isomers by PMP labeling in conjunction with IM-MS/MS. Sci Rep 2016; 6:28079. [PMID: 27306514 PMCID: PMC4910106 DOI: 10.1038/srep28079] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/31/2016] [Indexed: 12/15/2022] Open
Abstract
It remains particularly difficult for gaining unambiguous information on anomer, linkage, and position isomers of oligosaccharides using conventional mass spectrometry (MS) methods. In our laboratory, an ion mobility (IM) shift strategy was employed to improve confidence in the identification of structurally closely related disaccharide and monosaccharide isomers using IMMS. Higher separation between structural isomers was achieved using 1-phenyl-3-methyl-5-pyrazolone (PMP) derivatization in comparison with phenylhydrazine (PHN) derivatization. Furthermore, the combination of pre-IM fragmentation of PMP derivatives provided sufficient resolution to separate the isomers not resolved in the IMMS. To chart the structural variation observed in IMMS, the collision cross sections (CCSs) for the corresponding ions were measured. We analyzed nine disaccharide and three monosaccharide isomers that differ in composition, linkages, or configuration. Our data show that coexisting carbohydrate isomers can be identified by the PMP labeling technique in conjunction with ion-mobility separation and tandem mass spectrometry. The practical application of this rapid and effective method that requires only small amounts of sample is demonstrated by the successful analysis of water-soluble ginseng extract. This demonstrated the potential of this method to measure a variety of heterogeneous sample mixtures, which may have an important impact on the field of glycomics.
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Affiliation(s)
- Hongmei Yang
- Changchun University of Chinese Medicine, Changchun 130117, China
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, China
| | - Lei Shi
- High Temperature Reactor Holdings Co., Ltd., China Nuclear Engineering Group Co., Beijing 100037, China
| | - Xiaoyu Zhuang
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, China
| | - Rui Su
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Debin Wan
- Department of Entomology and Comprehensive Cancer Center, University of California, Davis, CA 95616, United States
| | - Fengrui Song
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, China
| | - Jinying Li
- High Temperature Reactor Holdings Co., Ltd., China Nuclear Engineering Group Co., Beijing 100037, China
| | - Shuying Liu
- Changchun University of Chinese Medicine, Changchun 130117, China
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31
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Zhang P, Woen S, Wang T, Liau B, Zhao S, Chen C, Yang Y, Song Z, Wormald MR, Yu C, Rudd PM. Challenges of glycosylation analysis and control: an integrated approach to producing optimal and consistent therapeutic drugs. Drug Discov Today 2016; 21:740-65. [DOI: 10.1016/j.drudis.2016.01.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/22/2015] [Accepted: 01/14/2016] [Indexed: 12/18/2022]
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32
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Struwe WB, Benesch JL, Harvey DJ, Pagel K. Collision cross sections of high-mannose N-glycans in commonly observed adduct states--identification of gas-phase conformers unique to [M-H](-) ions. Analyst 2016; 140:6799-803. [PMID: 26159123 DOI: 10.1039/c5an01092f] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report collision cross sections (CCS) of high-mannose N-glycans as [M + Na](+), [M + K](+), [M + H](+), [M + Cl](-), [M + H2PO4](-) and [M - H](-) ions, measured by drift tube (DT) ion mobility-mass spectrometry (IM-MS) in helium and nitrogen gases. Further analysis using traveling wave (TW) IM-MS reveal the existence of distinct conformers exclusive to [M - H](-) ions.
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Affiliation(s)
- W B Struwe
- Department of Chemistry, University of Oxford, Oxford, UKOX1 3TA.
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Harvey DJ, Scarff CA, Edgeworth M, Struwe WB, Pagel K, Thalassinos K, Crispin M, Scrivens J. Travelling-wave ion mobility and negative ion fragmentation of high-mannose N-glycans. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:219-35. [PMID: 26956389 PMCID: PMC4821469 DOI: 10.1002/jms.3738] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 05/02/2023]
Abstract
The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility mass spectrometry for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation gave more informative spectra than positive ion spectra with mass-different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra, and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed, but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers or anomers were being separated. Collision cross sections of the isomers in positive and negative fragmentation mode were estimated from travelling-wave ion mobility mass spectrometry data using dextran glycans as calibrant. More complete collision cross section data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross-sectional data, details of the negative ion collision-induced dissociation spectra of all resolved isomers are discussed.
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Affiliation(s)
- David J. Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
| | - Charlotte A. Scarff
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
- Current address, Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew Edgeworth
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
| | - Weston B. Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse. 3, 14159 Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jim Scrivens
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
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34
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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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35
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Dotz V, Haselberg R, Shubhakar A, Kozak RP, Falck D, Rombouts Y, Reusch D, Somsen GW, Fernandes DL, Wuhrer M. Mass spectrometry for glycosylation analysis of biopharmaceuticals. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.04.024] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Harvey DJ, Crispin M, Bonomelli C, Scrivens JH. Ion Mobility Mass Spectrometry for Ion Recovery and Clean-Up of MS and MS/MS Spectra Obtained from Low Abundance Viral Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015. [PMID: 26204966 PMCID: PMC4811024 DOI: 10.1007/s13361-015-1163-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many samples of complex mixtures of N-glycans released from small amounts of material, such as glycoproteins from viruses, present problems for mass spectrometric analysis because of the presence of contaminating material that is difficult to remove by conventional methods without involving sample loss. This study describes the use of ion mobility for extraction of glycan profiles from such samples and for obtaining clean CID spectra when targeted m/z values capture additional ions from those of the target compound. N-glycans were released enzymatically from within SDS-PAGE gels, from the representative recombinant glycoprotein, gp120 of the human immunodeficiency virus, and examined by direct infusion electrospray in negative mode followed by ion mobility with a Waters Synapt G2 mass spectrometer (Waters MS-Technologies, Manchester, UK). Clean profiles of singly, doubly, and triply charged N-glycans were obtained from samples in cases where the raw electrospray spectra displayed only a few glycan ions as the result of low sample concentration or the presence of contamination. Ion mobility also enabled uncontaminated CID spectra to be obtained from glycans when their molecular ions displayed coincidence with ions from fragments or multiply charged ions with similar m/z values. This technique proved to be invaluable for removing extraneous ions from many CID spectra. The presence of such ions often produces spectra that are difficult to interpret. Most CID spectra, even those from abundant glycan constituents, benefited from such clean-up, showing that the extra dimension provided by ion mobility was invaluable for studies of this type.
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Affiliation(s)
- David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK.
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Camille Bonomelli
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jim H Scrivens
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
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37
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Zhu F, Trinidad JC, Clemmer DE. Glycopeptide Site Heterogeneity and Structural Diversity Determined by Combined Lectin Affinity Chromatography/IMS/CID/MS Techniques. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1092-102. [PMID: 25840811 PMCID: PMC4475505 DOI: 10.1007/s13361-015-1110-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 05/10/2023]
Abstract
Glycopeptides from a tryptic digest of chicken ovomucoid were enriched using a simplified lectin affinity chromatography (LAC) platform, and characterized by high-resolution mass spectrometry (MS) as well as ion mobility spectrometry (IMS)-MS. The LAC platform effectively enriched the glycoproteome, from which a total of 117 glycopeptides containing 27 glycan forms were identified for this protein. IMS-MS analysis revealed a high degree of glycopeptide site heterogeneity. Comparison of the IMS distributions of the glycopeptides from different charge states reveals that higher charge states allow more structures to be resolved. Presumably the repulsive interactions between charged sites lead to more open configurations, which are more readily separated compared with the more compact, lower charge state forms of the same groups of species. Combining IMS with collision induced dissociation (CID) made it possible to determine the presence of isomeric glycans and to reconstruct their IMS profiles. This study illustrates a workflow involving hybrid techniques for determining glycopeptide site heterogeneity and evaluating structural diversity of glycans and glycopeptides.
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Affiliation(s)
| | - Jonathan C. Trinidad
- Corresponding authors. J.C.T.: ; Tel: (812) 856-4126. D.E.C.: ; Tel: (812) 855-8259
| | - David E. Clemmer
- Corresponding authors. J.C.T.: ; Tel: (812) 856-4126. D.E.C.: ; Tel: (812) 855-8259
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38
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Ward AB, Wilson IA. Insights into the trimeric HIV-1 envelope glycoprotein structure. Trends Biochem Sci 2015; 40:101-7. [PMID: 25600289 DOI: 10.1016/j.tibs.2014.12.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 01/16/2023]
Abstract
The HIV-1 envelope glycoprotein (Env) trimer is responsible for receptor recognition and viral fusion with CD4(+) T cells, and is the sole target for neutralizing antibodies. Thus, understanding its molecular architecture is of significant interest. However, the Env trimer has proved to be a challenging target for 3D structure determination. Recent electron microscopy (EM) and X-ray structures have at last enabled us to decipher the structural complexity and unique features of the Env trimer, and how it is recognized by an ever-expanding arsenal of potent broadly neutralizing antibodies. We describe our current knowledge of the Env trimer structure in the context of exciting recent developments in the identification and characterization of HIV broadly neutralizing antibodies.
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Affiliation(s)
- Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center and Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center and Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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39
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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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40
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Gaye MM, Kurulugama R, Clemmer DE. Investigating carbohydrate isomers by IMS-CID-IMS-MS: precursor and fragment ion cross-sections. Analyst 2015; 140:6922-32. [DOI: 10.1039/c5an00840a] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fragmentation of melezitose by IMS-CID-IMS-MS.
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Affiliation(s)
- M. M. Gaye
- Department of Chemistry
- Indiana University
- Bloomington
- USA
| | - R. Kurulugama
- Department of Chemistry
- Indiana University
- Bloomington
- USA
| | - D. E. Clemmer
- Department of Chemistry
- Indiana University
- Bloomington
- USA
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41
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Zhu F, Glover MS, Shi H, Trinidad JC, Clemmer DE. Populations of metal-glycan structures influence MS fragmentation patterns. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:25-35. [PMID: 25315458 PMCID: PMC4276451 DOI: 10.1007/s13361-014-1000-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 09/04/2014] [Accepted: 09/07/2014] [Indexed: 05/19/2023]
Abstract
The structures and collision-induced dissociation (CID) fragmentation patterns of the permethylated glycan Man5GlcNAc2 are investigated by a combination of hybrid ion mobility spectrometry (IMS), mass spectrometry (MS), and MS/MS techniques. IMS analysis of eight metal-adducted glycans ([Man5GlcNAc2 + M](2+), where M = Mn, Fe, Co, Ni, Cu, Mg, Ca, and Ba) shows distinct conformer patterns. These conformers appear to arise from individual metals binding at different sites on the glycan. Fragmentation studies suggest that these different binding sites influence the CID fragmentation patterns. This paper describes a series of separation, activation, and fragmentation studies that assess which fragments arise from each of the different gas-phase conformer states. Comparison of the glycan distributions formed under gentle ionization conditions with those obtained after activation of the gas-phase ions suggests that these conformer binding states also appear to exist in solution.
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Affiliation(s)
- Feifei Zhu
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Matthew S. Glover
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Huilin Shi
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Jonathan C. Trinidad
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
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42
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Bitto D, Harvey DJ, Halldorsson S, Doores KJ, Pritchard LK, Huiskonen JT, Bowden TA, Crispin M. Determination of N-linked Glycosylation in Viral Glycoproteins by Negative Ion Mass Spectrometry and Ion Mobility. Methods Mol Biol 2015; 1331:93-121. [PMID: 26169737 PMCID: PMC4817836 DOI: 10.1007/978-1-4939-2874-3_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycan analysis of virion-derived glycoproteins is challenging due to the difficulties in glycoprotein isolation and low sample abundance. Here, we describe how ion mobility mass spectrometry can be used to obtain spectra from virion samples. We also describe how negative ion fragmentation of glycans can be used to probe structural features of virion glycans.
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Affiliation(s)
- David Bitto
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David J. Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Steinar Halldorsson
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Katie J. Doores
- King’s College London, School of Medicine at Guy’s, King’s and St Thomas’ Hospitals, Guy’s Hospital, Great Maze Pond, London, UK
| | - Laura K. Pritchard
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Juha T. Huiskonen
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Thomas A. Bowden
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Max Crispin
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK,To whom correspondence should be addressed, Max Crispin, , Tel: +44(0)1865 285445
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43
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Lazar IM, Deng J, Ikenishi F, Lazar AC. Exploring the glycoproteomics landscape with advanced MS technologies. Electrophoresis 2014; 36:225-37. [PMID: 25311661 DOI: 10.1002/elps.201400400] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/28/2014] [Accepted: 09/29/2014] [Indexed: 12/13/2022]
Abstract
The advance of glycoproteomic technologies has offered unique insights into the importance of glycosylation in determining the functional roles of a protein within a cell. Biologically active glycoproteins include the categories of enzymes, hormones, proteins involved in cell proliferation, cell membrane proteins involved in cell-cell recognition, and communication events or secreted proteins, just to name a few. The recent progress in analytical instrumentation, methodologies, and computational approaches has enabled a detailed exploration of glycan structure, connectivity, and heterogeneity, underscoring the staggering complexity of the glycome repertoire in a cell. A variety of approaches involving the use of spectroscopy, MS, separation, microfluidic, and microarray technologies have been used alone or in combination to tackle the glycoproteome challenge, the research results of these efforts being captured in an overwhelming number of annual publications. This work is aimed at reviewing the major developments and accomplishments in the field of glycoproteomics, with focus on the most recent advancements (2012-2014) that involve the use of capillary separations and MS detection.
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Affiliation(s)
- Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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44
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Dixon EV, Claridge JK, Harvey DJ, Baruah K, Yu X, Vesiljevic S, Mattick S, Pritchard LK, Krishna B, Scanlan CN, Schnell JR, Higgins MK, Zitzmann N, Crispin M. Fragments of bacterial endoglycosidase s and immunoglobulin g reveal subdomains of each that contribute to deglycosylation. J Biol Chem 2014; 289:13876-89. [PMID: 24668806 PMCID: PMC4022860 DOI: 10.1074/jbc.m113.532812] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Endoglycosidase S (EndoS) is a glycoside-hydrolase secreted by the bacterium Streptococcus pyogenes. EndoS preferentially hydrolyzes the N-linked glycans from the Fc region of IgG during infection. This hydrolysis impedes Fc functionality and contributes to the immune evasion strategy of S. pyogenes. Here, we investigate the mechanism of human serum IgG deactivation by EndoS. We expressed fragments of IgG1 and demonstrated that EndoS was catalytically active against all of them including the isolated CH2 domain of the Fc domain. Similarly, we sought to investigate which domains within EndoS could contribute to activity. Bioinformatics analysis of the domain organization of EndoS confirmed the previous predictions of a chitinase domain and leucine-rich repeat but also revealed a putative carbohydrate binding module (CBM) followed by a C-terminal region. Using expressed fragments of EndoS, circular dichroism of the isolated CBM, and a CBM-C-terminal region fusion revealed folded domains dominated by β sheet and α helical structure, respectively. Nuclear magnetic resonance analysis of the CBM with monosaccharides was suggestive of carbohydrate binding functionality. Functional analysis of truncations of EndoS revealed that, whereas the C-terminal of EndoS is dispensable for activity, its deletion impedes the hydrolysis of IgG glycans.
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Affiliation(s)
- Emma V Dixon
- From the Oxford Glycobiology Institute, Department of Biochemistry and
| | - Jolyon K Claridge
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, United Kingdom, and
| | - David J Harvey
- From the Oxford Glycobiology Institute, Department of Biochemistry and School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, United Kingdom
| | - Kavitha Baruah
- From the Oxford Glycobiology Institute, Department of Biochemistry and
| | - Xiaojie Yu
- From the Oxford Glycobiology Institute, Department of Biochemistry and
| | | | - Susan Mattick
- From the Oxford Glycobiology Institute, Department of Biochemistry and
| | - Laura K Pritchard
- From the Oxford Glycobiology Institute, Department of Biochemistry and
| | - Benjamin Krishna
- From the Oxford Glycobiology Institute, Department of Biochemistry and
| | | | - Jason R Schnell
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, United Kingdom, and
| | - Matthew K Higgins
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, United Kingdom, and
| | - Nicole Zitzmann
- From the Oxford Glycobiology Institute, Department of Biochemistry and
| | - Max Crispin
- From the Oxford Glycobiology Institute, Department of Biochemistry and
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45
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Hoffmann W, Hofmann J, Pagel K. Energy-resolved ion mobility-mass spectrometry--a concept to improve the separation of isomeric carbohydrates. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:471-479. [PMID: 24385395 DOI: 10.1007/s13361-013-0780-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 11/01/2013] [Accepted: 11/04/2013] [Indexed: 06/03/2023]
Abstract
Recent works using ion mobility-mass spectrometry (IM-MS) have highlighted the power of this instrumental configuration to tackle one of the greatest challenges in glycomics and glycoproteomics: the existence of isobaric isomers. For a successful separation of species with identical mass but different structure via IM-MS, it is crucial to have sufficient IM resolution. In commercially available IM-MS instruments, however, this resolution is limited by the design of the instrument and usually cannot be increased at-will without extensive modifications. Here, we present a systematic approach to improve the resolving capability of IM-MS instruments using so-called energy-resolved ion mobility-mass spectrometry. The technique utilizes the fact that individual components in an isobaric mixture fragment at considerably different energies when activated in the gas phase via collision-induced dissociation (CID). As a result, certain components can be suppressed selectively at increased CID activation energy. Using a mixture of four isobaric carbohydrates, we show that each of the individual sugars can be resolved and unambiguously identified even when their drift times differ by as little as 3%. However, the presented results also indicate that a certain difference in the gas-phase stability of the individual components is crucial for a successful separation via energy-resolved IM-MS.
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Affiliation(s)
- Waldemar Hoffmann
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
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Hanneman AJ, Strand J, Huang CT. Profiling and Characterization of Sialylated N-glycans by 2D-HPLC (HIAX/PGC) with Online Orbitrap MS/MS and Offline MSn. J Pharm Sci 2014; 103:400-8. [DOI: 10.1002/jps.23792] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/14/2013] [Accepted: 10/30/2013] [Indexed: 01/14/2023]
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Kailemia MJ, Ruhaak LR, Lebrilla CB, Amster IJ. Oligosaccharide analysis by mass spectrometry: a review of recent developments. Anal Chem 2014; 86:196-212. [PMID: 24313268 PMCID: PMC3924431 DOI: 10.1021/ac403969n] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - L. Renee Ruhaak
- Department of Chemistry, University of California at Davis, Davis, CA 95616
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