1
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Hykollari A, Paschinger K, Wilson IBH. Negative-mode mass spectrometry in the analysis of invertebrate, fungal, and protist N-glycans. MASS SPECTROMETRY REVIEWS 2022; 41:945-963. [PMID: 33955035 DOI: 10.1002/mas.21693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
The approaches for analysis of N-glycans have radically altered in the last 20 years or so. Due to increased sensitivity, mass spectrometry has become the predominant method in modern glycomics. Here, we summarize recent studies showing that the improved resolution and detection by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has contributed greatly to the discovery of a large range of anionic and zwitterionic N-glycan structures across the different kingdoms of life, whereby MALDI-TOF MS in negative mode is less widely performed than in positive mode. However, its use enables the detection of key fragments indicative of certain sugar modifications such as sulfate, (methyl) phosphate, phosphoethanolamine, (methyl)aminoethylphosphonate, glucuronic, and sialic acid, thereby enabling certain isobaric glycan variations to be distinguished. As we also discuss in this review, complementary approaches such as negative-mode electrospray ionization-MS/MS, Fourier-transform ion cyclotron resonance MS, and ion mobility MS yield, respectively, cross-linkage fragments, high accuracy masses, and isomeric information, thus adding other components to complete the jigsaw puzzle when defining unusual glycan modifications from lower organisms.
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Affiliation(s)
- Alba Hykollari
- Department für Chemie, Universität für Bodenkultur Wien, Wien, Austria
- VetCore Facility for Research, Veterinärmedizinische Universität Wien, Wien, Austria
| | | | - Iain B H Wilson
- Department für Chemie, Universität für Bodenkultur Wien, Wien, Austria
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2
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Li N, Desiderio DM, Zhan X. The use of mass spectrometry in a proteome-centered multiomics study of human pituitary adenomas. MASS SPECTROMETRY REVIEWS 2022; 41:964-1013. [PMID: 34109661 DOI: 10.1002/mas.21710] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
A pituitary adenoma (PA) is a common intracranial neoplasm, and is a complex, chronic, and whole-body disease with multicausing factors, multiprocesses, and multiconsequences. It is very difficult to clarify molecular mechanism and treat PAs from the single-factor strategy model. The rapid development of multiomics and systems biology changed the paradigms from a traditional single-factor strategy to a multiparameter systematic strategy for effective management of PAs. A series of molecular alterations at the genome, transcriptome, proteome, peptidome, metabolome, and radiome levels are involved in pituitary tumorigenesis, and mutually associate into a complex molecular network system. Also, the center of multiomics is moving from structural genomics to phenomics, including proteomics and metabolomics in the medical sciences. Mass spectrometry (MS) has been extensively used in phenomics studies of human PAs to clarify molecular mechanisms, and to discover biomarkers and therapeutic targets/drugs. MS-based proteomics and proteoform studies play central roles in the multiomics strategy of PAs. This article reviews the status of multiomics, multiomics-based molecular pathway networks, molecular pathway network-based pattern biomarkers and therapeutic targets/drugs, and future perspectives for personalized, predeictive, and preventive (3P) medicine in PAs.
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Affiliation(s)
- Na Li
- Shandong Key Laboratory of Radiation Oncology, Cancer Hospital of Shandong First Medical University, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, Shandong, China
| | - Dominic M Desiderio
- The Charles B. Stout Neuroscience Mass Spectrometry Laboratory, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Cancer Hospital of Shandong First Medical University, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, Shandong, China
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3
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Development and application of a sensitive phosphonium-hydrazide oligosaccharide labelling reagent in capillary electrophoresis- electrospray ionization- mass spectrometry. J Chromatogr A 2022; 1680:463409. [PMID: 35998551 DOI: 10.1016/j.chroma.2022.463409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 07/13/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022]
Abstract
Glycosylation is one of the most ubiquitous post-translational modifications (PTM) of proteins. Although the ionization efficiency of native glycans is fairly low, with the assistance of chemical derivation strategies, mass spectrometry (MS) has been extensively used in glycomics because of its high sensitivity, accuracy, and speed. In this study, a novel glycan labelling reagent, (4-hydrazidebutyl) triphenylphosphonium bromide (P4HZD), with a permanent positive charge was developed. The comprehensive capabilities of P4HZD for MS analysis of oligosaccharides were evaluated in detail using maltodextrin as a standard. This labelling reagent can be used in common biological MS techniques such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometry. The MS signal intensity of maltodextrin species could be enhanced up to 96-fold in MALDI-MS by labelling with P4HZD, making P4HZD favorable for MALDI-MS-based high-throughput screening of oligosaccharides. Moreover, P4HZD-labelled oligosaccharides with a degree of polymerization (DP) from 1 to 18 could be separated and analysed by capillary electrophoresis (CE) combined with positive ion mode ESI-MS. In comparison with a commercialized oligosaccharide tag, Girard's reagent P (GirP), P4HZD was more effective for enhancing the signal of oligosaccharides in the middle or higher mass range using both ESI and MALDI ion sources. Two biologics, immunoglobulin G 2 (IgG 2) and fusion protein (FP), were chosen as model complex biological samples to test the efficacy of detection and separation of oligosaccharides by MALDI-MS and CE-ESI-MS analysis with P4HZD labelling. The results indicated that P4HZD is a promising labelling reagent for the detection of oligosaccharides in complex biological samples. The tandem workflow combines the strengths of MALDI-MS and CE-ESI-MS to fulfil the analytical demands of high-throughput screening, while affording good separation.
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4
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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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5
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Butler KE, Kalmar JG, Muddiman DC, Baker ES. Utilizing liquid chromatography, ion mobility spectrometry, and mass spectrometry to assess INLIGHT™ derivatized N-linked glycans in biological samples. Anal Bioanal Chem 2022; 414:623-637. [PMID: 34347113 PMCID: PMC8336533 DOI: 10.1007/s00216-021-03570-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/06/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
Glycosylation is a ubiquitous co- and post-translational modification involved in the sorting, folding, and trafficking of proteins in biological systems; in humans, >50% of gene products are glycosylated with the cellular machinery of glycosylation compromising ~2% of the genome. Perturbations in glycosylation have been implicated in a variety of diseases including neurodegenerative diseases and certain types of cancer. However, understanding the relationship between a glycan and its biological role is often difficult due to the numerous glycan isomers that exist. To address this challenge, nanoflow liquid chromatography, ion mobility spectrometry, and mass spectrometry (nLC-IMS-MS) were combined with the Individuality Normalization when Labeling with the Isotopic Glycan Hydrazide Tags (INLIGHT™) strategy to study a series of glycan standards and those enzymatically released from the glycoproteins horseradish peroxidase, fetuin, and pooled human plasma. The combination of IMS and the natural (NAT) and stable-isotope label (SIL) in the INLIGHT™ strategy provided additional confidence for each glycan identification due to the mobility aligned NAT- and SIL-labeled glycans and further capabilities for isomer examinations. Additionally, molecular trend lines based on the IMS and MS dimensions were investigated for the INLIGHT™ derivatized glycans, facilitating rapid identification of putative glycans in complex biological samples.
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Affiliation(s)
- Karen E Butler
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jaclyn Gowen Kalmar
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - David C Muddiman
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, 27695, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA.
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27695, USA.
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6
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Harvey DJ, Struwe WB, Behrens AJ, Vasiljevic S, Crispin M. Formation and fragmentation of doubly and triply charged ions in the negative ion spectra of neutral N-glycans from viral and other glycoproteins. Anal Bioanal Chem 2021; 413:7277-7294. [PMID: 34342671 PMCID: PMC8329908 DOI: 10.1007/s00216-021-03480-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/28/2021] [Accepted: 06/15/2021] [Indexed: 11/05/2022]
Abstract
Structural determination of N-glycans by mass spectrometry is ideally performed by negative ion collision-induced dissociation because the spectra are dominated by cross-ring fragments leading to ions that reveal structural details not available by many other methods. Most glycans form [M - H]- or [M + adduct]- ions but larger ones (above approx. m/z 2000) typically form doubly charged ions. Differences have been reported between the fragmentation of singly and doubly charged ions but a detailed comparison does not appear to have been reported. In addition to [M + adduct]- ions (this paper uses phosphate as the adduct) other doubly, triply, and quadruply charged ions of composition [Mn + (H2PO4)n]n- have been observed in mixtures of N-glycans released from viral and other glycoproteins. This paper explores the formation and fragmentation of these different types of multiply charged ions with particular reference to the presence of diagnostic fragments in the CID spectra and comments on how these ions can be used to characterize these glycans.
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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.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
| | - Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- GlycoEra AG, Grabenstrasse 3, 8952, Schlieren, Switzerland
| | - Snezana Vasiljevic
- 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
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
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7
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Trapped ion mobility spectrometry time-of-flight mass spectrometry for high throughput and high resolution characterization of human milk oligosaccharide isomers. Anal Chim Acta 2021; 1180:338878. [PMID: 34538323 DOI: 10.1016/j.aca.2021.338878] [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: 05/04/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022]
Abstract
The microbiome and immune system of infants are shaped by various bioactive components of human breastmilk, notably human milk oligosaccharides (HMOs). HMOs represent the third component of breastmilk and exhibit extremely high structural diversity with many isomers. Here, we propose a high throughput and high resolution approach to characterize main oligosaccharides present in breastmilk with high identification level thanks to ion mobility spectrometry. Four pairs of standard HMO isomers, that are (LNT/LNnT), (LNFP I/LNFP V), (3'-SL/6'-SL) and (2'-FL/3-FL), were first investigated under both positive and negative ionization mode using direct introduction-trapped ion mobility spectrometry-time-of-flight mass spectrometry (TIMS-TOF). By examining all the ionic species formed (i.e. protonated and deprotonated ions as well as adduct species), every isomer pair could be distinguished through the separation of at least one species, even with a small difference in collision cross section values (as small as 1.5%) thanks to the flexible resolution capacity of the TIMS instrument. Although multiple mobility peaks resulting from different glycan anomeric conformers, open-ring and/or different ionic isomer structures (i.e. various charge site locations), could be observed for some HMO species. The reduction at the reducing-end of HMOs did not significantly facilitate the isomer distinction. Finally, the unambiguous identification of the studied HMOs in a breastmilk sample showed the potential of the approach combining ion mobility separation and MS/MS experiments for high throughput distinction of HMO isomers in complex breastmilk samples without laborious sample preparation.
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8
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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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9
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Sharma VK, Sharma I, Glick J. The expanding role of mass spectrometry in the field of vaccine development. MASS SPECTROMETRY REVIEWS 2020; 39:83-104. [PMID: 29852530 PMCID: PMC7027533 DOI: 10.1002/mas.21571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/30/2018] [Indexed: 05/09/2023]
Abstract
Biological mass spectrometry has evolved as a core analytical technology in the last decade mainly because of its unparalleled ability to perform qualitative as well as quantitative profiling of enormously complex biological samples with high mass accuracy, sensitivity, selectivity and specificity. Mass spectrometry-based techniques are also routinely used to assess glycosylation and other post-translational modifications, disulfide bond linkage, and scrambling as well as for the detection of host cell protein contaminants in the field of biopharmaceuticals. The role of mass spectrometry in vaccine development has been very limited but is now expanding as the landscape of global vaccine development is shifting towards the development of recombinant vaccines. In this review, the role of mass spectrometry in vaccine development is presented, some of the ongoing efforts to develop vaccines for diseases with global unmet medical need are discussed and the regulatory challenges of implementing mass spectrometry techniques in a quality control laboratory setting are highlighted.
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Affiliation(s)
| | - Ity Sharma
- Independent CMC ConsultantParamusNew Jersey
| | - James Glick
- Novartis Institutes for BioMedical ResearchEast HanoverNew Jersey
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10
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Zhu H, Aloor A, Ma C, Kondengaden SM, Wang PG. Mass Spectrometric Analysis of Protein Glycosylation. ACS SYMPOSIUM SERIES 2020. [DOI: 10.1021/bk-2020-1346.ch010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- He Zhu
- These authors contributed equally
| | | | | | | | - Peng George Wang
- Current Address: Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P. R. China
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11
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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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12
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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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13
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Shen Y, You Y, Xiao K, Chen Y, Tian Z. Large-Scale Identification and Fragmentation Pathways Analysis of N-Glycans from Mouse Brain. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1254-1261. [PMID: 31098956 DOI: 10.1007/s13361-019-02181-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 02/18/2019] [Accepted: 02/24/2019] [Indexed: 06/09/2023]
Abstract
N-linked glycosylation is one of the most common protein PTMs, and the topological structure (monosaccharide composition and sequence as well as glycosidic linkages) of N-glycans is vital information to understand their biological functions and roles. Tandem mass spectrometry has been widely used for topological structure characterization of N-glycans, where comprehensive understanding of fragmentation pathways and characteristics of product ions are essential to achieve best interpretation of MS/MS data and highest confidence of identification. Here, we report our glycomic study of N-glycome of mouse brain as well as fragmentation pathway analysis of the identified N-glycans. With LC-MS/MS analysis at both the positive and negative ESI modes together with our recently developed N-glycan database search engine GlySeeker, 221 unique N-glycans with putative topological structures were identified with target-decoy searches and number of best hits of 1. Analysis of fragmentation pathways and characteristics of product ions of permethylated N-glycans in the positive mode and native N-glycans in the negative mode were further carried out. The reported N-glycans serve as a basic reference for future glycosylation study of mouse brain; and in general database search of tandem mass spectra of N-glycans, B/Y/Z ions should be preferentially considered for the permethylated form in the positive mode and B/C/Z ions for the native form in the negative mode.
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Affiliation(s)
- Yun Shen
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Yiwen You
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Kaijie Xiao
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China.
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14
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Smith J, Mittermayr S, Váradi C, Bones J. Quantitative glycomics using liquid phase separations coupled to mass spectrometry. Analyst 2018; 142:700-720. [PMID: 28170017 DOI: 10.1039/c6an02715f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Post-translational modification of proteins by the attachment of glycans is governed by a variety of highly specific enzymes and is associated with fundamental impacts on the parent protein's physical, chemical and biological properties. The inherent connection between cellular physiology and specific glycosylation patterns has been shown to offer potential for diagnostic and prognostic monitoring of altered glycosylation in the disease state. Conversely, glycoprotein based biopharmaceuticals have emerged as dominant therapeutic strategies in the treatment of intricate diseases. Glycosylation present on these biopharmaceuticals represents a major critical quality attribute with impacts on both pharmacokinetics and pharmacodynamics. The structural variety of glycans, based upon their non-template driven assembly, poses a significant analytical challenge for both qualitative and quantitative analysis. Labile monosaccharide constituents, isomeric species and often low sample availability from biological sources necessitates meticulous sample handling, ultra-high-resolution analytical separation and sensitive detection techniques, respectively. In this article a critical review of analytical quantitation approaches using liquid phase separations coupled to mass spectrometry for released glycans of biopharmaceutical and biomedical significance is presented. Considerations associated with sample derivatisation strategies, ionisation, relative quantitation through isotopic as well as isobaric labelling, metabolic/enzymatic incorporation and targeted analysis are all thoroughly discussed.
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Affiliation(s)
- Josh Smith
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland. and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590, Ireland
| | - Stefan Mittermayr
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland.
| | - Csaba Váradi
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland.
| | - Jonathan Bones
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland. and School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1 W8, Ireland
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15
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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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16
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Harvey DJ, Watanabe Y, Allen JD, Rudd P, Pagel K, Crispin M, Struwe WB. Collision Cross Sections and Ion Mobility Separation of Fragment Ions from Complex N-Glycans. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1250-1261. [PMID: 29675741 DOI: 10.1007/s13361-018-1930-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/27/2018] [Accepted: 02/27/2018] [Indexed: 05/17/2023]
Abstract
Ion mobility mass spectrometry (IM-MS) holds great potential for structural glycobiology, in particular in its ability to resolve glycan isomers. Generally, IM-MS has largely been applied to intact glycoconjugate ions with reports focusing on the separation of different adduct types. Here, we explore IM separation and report the collision cross section (CCS) of complex type N-glycans and their fragments in negative ion mode following collision-induced dissociation (CID). CCSs of isomeric fragment ions were found, in some cases, to reveal structural details that were not present in CID spectra themselves. Many fragment ions were confirmed as possessing multiple structure, details of which could be obtained by comparing their drift time profiles to different glycans. By using fragmentation both before and after mobility separation, information was gathered on the fragmentation pathways producing some of the ions. These results help demonstrate the utility of IM and will contribute to the growing use of IM-MS for glycomics. Graphical Abstract ᅟ.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Yasunori Watanabe
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Joel D Allen
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Pauline Rudd
- NIBRT GlycoScience Group, The National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
- Institut für Chemie und Biochemie, Freien Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Max Crispin
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK.
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17
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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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18
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Harvey DJ, Seabright GE, Vasiljevic S, Crispin M, Struwe WB. Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:972-988. [PMID: 29508223 PMCID: PMC5940726 DOI: 10.1007/s13361-018-1890-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 01/02/2018] [Accepted: 01/08/2018] [Indexed: 05/15/2023]
Abstract
Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man8GlcNAc2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. Graphical Abstract ᅟ.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Center for Biological Sciences, Faculty of Natural and Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK.
| | - Gemma E Seabright
- Center for Biological Sciences, Faculty of Natural and Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Snezana Vasiljevic
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Max Crispin
- Center for Biological Sciences, Faculty of Natural and Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Weston B Struwe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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19
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Behrens AJ, Kumar A, Medina-Ramirez M, Cupo A, Marshall K, Cruz Portillo VM, Harvey DJ, Ozorowski G, Zitzmann N, Wilson IA, Ward AB, Struwe WB, Moore JP, Sanders RW, Crispin M. Integrity of Glycosylation Processing of a Glycan-Depleted Trimeric HIV-1 Immunogen Targeting Key B-Cell Lineages. J Proteome Res 2018; 17:987-999. [PMID: 29420040 DOI: 10.1021/acs.jproteome.7b00639] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Broadly neutralizing antibodies (bNAbs) that target the trimeric HIV-1 envelope glycoprotein spike (Env) are tools that can guide the design of recombinant Env proteins intended to engage the predicted human germline precursors of bNAbs (gl-bNAbs). The protein components of gl-bNAb epitopes are often masked by glycans, while mature bNAbs can evolve to accommodate or bypass these shielding glycans. The design of germline-targeting Env immunogens therefore includes the targeted deletion of specific glycan sites. However, the processing of glycans on Env trimers can be influenced by the density with which they are packed together, a highly relevant point given the essential contributions under-processed glycans make to multiple bNAb epitopes. We sought to determine the impact of the removal of 15 potential N-glycan sites (5 per protomer) from the germline-targeting soluble trimer, BG505 SOSIP.v4.1-GT1, using quantitative, site-specific N-glycan mass spectrometry analysis. We find that, compared with SOSIP.664, there was little overall change in the glycan profile but only subtle increases in the extent of processing at sites immediately adjacent to where glycans had been deleted. We conclude that multiple glycans can be deleted from BG505 SOSIP trimers without perturbing the overall integrity of the glycan shield.
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Affiliation(s)
- Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Abhinav Kumar
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Max Medina-Ramirez
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam , 1105 AZ Amsterdam, The Netherlands
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York , New York, New York 10021, United States
| | - Kevin Marshall
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York , New York, New York 10021, United States
| | - Victor M Cruz Portillo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York , New York, New York 10021, United States
| | - David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, IAVI Neutralizing Antibody Center and CAVD, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, IAVI Neutralizing Antibody Center and CAVD, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute , La Jolla, California 92037, United States.,Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, IAVI Neutralizing Antibody Center and CAVD, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York , New York, New York 10021, United States
| | - Rogier W Sanders
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam , 1105 AZ Amsterdam, The Netherlands.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York , New York, New York 10021, United States
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom.,Centre for Biological Sciences and Institute for Life Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
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20
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Morrison KA, Clowers BH. Contemporary glycomic approaches using ion mobility-mass spectrometry. Curr Opin Chem Biol 2017; 42:119-129. [PMID: 29248736 DOI: 10.1016/j.cbpa.2017.11.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 10/18/2022]
Abstract
Characterization of complex oligosaccharides has historically required extensive sample handling and separations before analysis using nuclear magnetic resonance spectroscopy and electron impact mass spectra following hydrolysis, derivatization, and gas chromatographic separation. Advances in liquid chromatography separations and tandem mass spectrometry have expanded the range of intact glycan analysis, but carbohydrate structure and conformation-integral chemical characteristics-are often difficult to assess with minimal amounts of sample in a rapid fashion. Because ion mobility spectrometry (IMS) separates analytes based upon an effective 'size-to-charge' ratio, IMS is, by extension, highly applicable to glycomics. Furthermore, the speed of IMS, its growing levels of separation efficiency, and direct compatibility with all forms of mass spectrometry, illustrates is core role in the future of glycomics efforts. This review assesses the current state of ion mobility-mass spectrometry applied to glycan, glycoprotein, and glycoconjugate analysis. Currently, assessing optimal ion polarity and adduct type for a glycan class along with the appropriate tandem mass spectrometry technique underpin many of the current glycan analysis efforts using ion mobility-mass spectrometry (IMMS). Once determined, these parameters have enabled a growing and impressive range of glycomics campaigns employing this technique. Additionally, the combination of IMS with tandem mass spectrometry, and even spectroscopic methods, further expands the dimensionality of hybrid instrumentation to provide a more comprehensive assessment of glycan structure across a wide dynamic range. Continued computational efforts to complement experimental and instrumental advancements also serve as a core component of IMMS workflows applied to glycomics and promise to maximize the information gained from mobility separations.
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Affiliation(s)
- Kelsey A Morrison
- Department of Chemistry, Washington State University, Pullman, WA 99164, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, WA 99164, United States.
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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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Manz C, Pagel K. Glycan analysis by ion mobility-mass spectrometry and gas-phase spectroscopy. Curr Opin Chem Biol 2017; 42:16-24. [PMID: 29107930 DOI: 10.1016/j.cbpa.2017.10.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
Abstract
Due to the existence of numerous isomers, the in-depth analysis of glycans represents a major challenge. Currently, the majority of glycans are analysed using mass spectrometry (MS)-based techniques, which can provide information on regioisomers but usually fail to differentiate stereoisomers. A promising approach to overcome this limitation is to implement ion mobility spectrometry (IMS) as an additional gas-phase separation dimension. This review highlights recent developments in which IM-MS was used as a tool for comprehensive glycan analysis or as rapid screening method for glycan feature analysis. Furthermore, we summarize a series of very recent investigations in which gas-phase spectroscopy is applied to study glycans and discuss the potential of the hyphenation between IM-MS and infrared (IR) spectroscopy as a future tool for glycomics and glycoproteomics.
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Affiliation(s)
- Christian Manz
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany; Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany; Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
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23
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Behrens AJ, Struwe WB, Crispin M. Glycosylation profiling to evaluate glycoprotein immunogens against HIV-1. Expert Rev Proteomics 2017; 14:881-890. [PMID: 28870097 DOI: 10.1080/14789450.2017.1376658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Much of the efforts to develop a vaccine against the human immunodeficiency virus (HIV) have focused on the design of recombinant mimics of the viral attachment glycoprotein (Env). The leading immunogens exhibit native-like antigenic properties and are being investigated for their ability to induce broadly neutralizing antibodies (bNAbs). Understanding the relative abundance of glycans at particular glycosylation sites on these immunogens is important as most bNAbs have evolved to recognize or evade the dense coat of glycans that masks much of the protein surface. Understanding the glycan structures on candidate immunogens enables triaging between native-like conformations and immunogens lacking key structural features as steric constraints limit glycan processing. The sensitivity of the processing state of a particular glycan to its structural environment has led to the need for quantitative glycan profiling and site-specific analysis to probe the structural integrity of immunogens. Areas covered: We review analytical methodologies for HIV immunogen evaluation and discuss how these studies have led to a greater understanding of the structural constraints that control the glycosylation state of the HIV attachment and fusion spike. Expert commentary: Total composition and site-specific glycosylation profiling are emerging as standard methods in the evaluation of Env-based immunogen candidates.
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Affiliation(s)
- Anna-Janina Behrens
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK
| | - Weston B Struwe
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK
| | - Max Crispin
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK.,b Department of Immunology and Microbial Science , The Scripps Research Institute , La Jolla , CA , USA.,c Centre for Biological Sciences and Institute for Life Sciences , University of Southampton , Southampton SO17 1BJ , UK
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24
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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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25
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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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26
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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27
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Morrison KA, Bendiak BK, Clowers BH. Enhanced Mixture Separations of Metal Adducted Tetrasaccharides Using Frequency Encoded Ion Mobility Separations and Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:664-677. [PMID: 27796835 DOI: 10.1007/s13361-016-1505-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 05/16/2023]
Abstract
Using five isomeric tetrasaccharides in combination with seven multivalent metals, the impact on mobility separations and resulting CID spectra were examined using a hybrid ion mobility atmospheric pressure drift tube system coupled with a linear ion trap. By enhancing the duty cycle of the drift tube system using a linearly chirped frequency, the collision-induced dissociation spectra were encoded in the mobility domain according to the drift times of each glycan isomer precursor. Differential fragmentation patterns correlated with precursor drift times ensured direct assignment of fragments with precursor structure whether as individual standards or in a mixture of isomers. In addition to certain metal ions providing higher degrees of separation than others, in select cases more than one arrival time distribution was observed for a single pure carbohydrate isomer. These observations suggest the existence of alternative coordination sites within a single monomeric species, but more interesting was the observation of different fragmentation ion yields for carbohydrate dimers formed through metal adduction. Positive-ion data were also compared with negative-ion species, where dimer formation did not occur and single peaks were observed for each isomeric tetrasaccharide-alditol. This enhanced analytical power has implications not only for carbohydrate molecules but also for a wide variety of complex mixtures of molecules where dissociation spectra may potentially be derived from combinations of monomeric, homodimeric, and heterodimeric species having identical nominal m/z values. Graphical Abstract ᅟ.
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Affiliation(s)
- Kelsey A Morrison
- Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA, 99164, USA
| | - Brad K Bendiak
- Department of Cell and Developmental Biology and Program in Structural Biology and Biochemistry, University of Colorado Health Sciences Center, Mail Stop 8108, 12801 E 17th Ave., Aurora, CO, 80045, USA
| | - Brian H Clowers
- Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA, 99164, USA.
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28
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Molecular Architecture of the Cleavage-Dependent Mannose Patch on a Soluble HIV-1 Envelope Glycoprotein Trimer. J Virol 2017; 91:JVI.01894-16. [PMID: 27807235 DOI: 10.1128/jvi.01894-16] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/25/2016] [Indexed: 01/04/2023] Open
Abstract
The formation of a correctly folded and natively glycosylated HIV-1 viral spike is dependent on protease cleavage of the gp160 precursor protein in the Golgi apparatus. Cleavage induces a compact structure which not only renders the spike capable of fusion but also limits further maturation of its extensive glycosylation. The redirection of the glycosylation pathway to preserve underprocessed oligomannose-type glycans is an important feature in immunogen design, as glycans contribute to or influence the epitopes of numerous broadly neutralizing antibodies. Here we present a quantitative site-specific analysis of a recombinant, trimeric mimic of the native HIV-1 viral spike (BG505 SOSIP.664) compared to the corresponding uncleaved pseudotrimer and the matched gp120 monomer. We present a detailed molecular map of a trimer-associated glycan remodeling that forms a localized subdomain of the native mannose patch. The formation of native trimers is a critical design feature in shaping the glycan epitopes presented on recombinant vaccine candidates. IMPORTANCE The envelope spike of human immunodeficiency virus type 1 (HIV-1) is a target for antibody-based neutralization. For some patients infected with HIV-1, highly potent antibodies have been isolated that can neutralize a wide range of circulating viruses. It is a goal of HIV-1 vaccine research to elicit these antibodies by immunization with recombinant mimics of the viral spike. These antibodies have evolved to recognize the dense array of glycans that coat the surface of the viral molecule. We show how the structure of these glycans is shaped by steric constraints imposed upon them by the native folding of the viral spike. This information is important in guiding the development of vaccine candidates.
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29
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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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30
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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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31
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May JC, Gant-Branum RL, McLean JA. Targeting the untargeted in molecular phenomics with structurally-selective ion mobility-mass spectrometry. Curr Opin Biotechnol 2016; 39:192-197. [PMID: 27132126 DOI: 10.1016/j.copbio.2016.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/06/2016] [Accepted: 04/13/2016] [Indexed: 12/25/2022]
Abstract
Systems-wide molecular phenomics is rapidly expanding through technological advances in instrumentation and bioinformatics. Strategies such as structural mass spectrometry, which utilizes size and shape measurements with molecular weight, serve to characterize the sum of molecular expression in biological contexts, where broad-scale measurements are made that are interpreted through big data statistical techniques to reveal underlying patterns corresponding to phenotype. The data density, data dimensionality, data projection, and data interrogation are all critical aspects of these approaches to turn data into salient information. Untargeted molecular phenomics is already having a dramatic impact in discovery science from drug discovery to synthetic biology. It is evident that these emerging techniques will integrate closely in broad efforts aimed at precision medicine.
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Affiliation(s)
- Jody Christopher May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - Randi Lee Gant-Branum
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - John Allen McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA.
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32
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Planinc A, Bones J, Dejaegher B, Van Antwerpen P, Delporte C. Glycan characterization of biopharmaceuticals: Updates and perspectives. Anal Chim Acta 2016; 921:13-27. [PMID: 27126786 DOI: 10.1016/j.aca.2016.03.049] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/21/2016] [Accepted: 03/29/2016] [Indexed: 02/01/2023]
Abstract
Therapeutic proteins are rapidly becoming the most promising class of pharmaceuticals on the market due to their successful treatment of a vast array of serious diseases, such as cancers and immune disorders. Therapeutic proteins are produced using recombinant DNA technology. More than 60% of therapeutic proteins are posttranslationally modified following biosynthesis by the addition of N- or O-linked glycans. Glycosylation is the most common posttranslational modifications of proteins. However, it is also the most demanding and complex posttranslational modification from the analytical point of view. Moreover, research has shown that glycosylation significantly impacts stability, half-life, mechanism of action and safety of a therapeutic protein. Considering the exponential growth of biotherapeutics, this present review of the literature (2009-2015) focuses on the characterization of protein glycosylation, which has witnessed an improvement in methodology. Furthermore, it discusses current issues in the fields of production and characterization of therapeutic proteins. This review also highlights the problem of non-standard requirements for the approval of biosimilars with regard to their glycosylation and discusses recent developments and perspectives for improved glycan characterization.
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Affiliation(s)
- Ana Planinc
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Universite Libre de Bruxelles (ULB), Brussels, Belgium
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Bieke Dejaegher
- Laboratory of Instrumental Analysis and Bioelectrochemistry, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, B-1050 Brussels, Belgium; Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Faculty of Medicines and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Pierre Van Antwerpen
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Universite Libre de Bruxelles (ULB), Brussels, Belgium
| | - Cédric Delporte
- Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Universite Libre de Bruxelles (ULB), Brussels, Belgium.
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33
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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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34
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Behrens AJ, Vasiljevic S, Pritchard LK, Harvey DJ, Andev RS, Krumm SA, Struwe WB, Cupo A, Kumar A, Zitzmann N, Seabright GE, Kramer HB, Spencer DIR, Royle L, Lee JH, Klasse PJ, Burton DR, Wilson IA, Ward AB, Sanders RW, Moore JP, Doores KJ, Crispin M. Composition and Antigenic Effects of Individual Glycan Sites of a Trimeric HIV-1 Envelope Glycoprotein. Cell Rep 2016; 14:2695-706. [PMID: 26972002 PMCID: PMC4805854 DOI: 10.1016/j.celrep.2016.02.058] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/29/2016] [Accepted: 02/10/2016] [Indexed: 11/25/2022] Open
Abstract
The HIV-1 envelope glycoprotein trimer is covered by an array of N-linked glycans that shield it from immune surveillance. The high density of glycans on the trimer surface imposes steric constraints limiting the actions of glycan-processing enzymes, so that multiple under-processed structures remain on specific areas. These oligomannose glycans are recognized by broadly neutralizing antibodies (bNAbs) that are not thwarted by the glycan shield but, paradoxically, target it. Our site-specific glycosylation analysis of a soluble, recombinant trimer (BG505 SOSIP.664) maps the extremes of simplicity and diversity of glycan processing at individual sites and reveals a mosaic of dense clusters of oligomannose glycans on the outer domain. Although individual sites usually minimally affect the global integrity of the glycan shield, we identify examples of how deleting some glycans can subtly influence neutralization by bNAbs that bind at distant sites. The network of bNAb-targeted glycans should be preserved on vaccine antigens. Quantitative, site-specific N-glycan analysis of a soluble HIV-1 Env trimer A map of the extremes of simplicity and diversity at individual glycan sites The fine structure of the mannose patch area of the Env trimer How individual glycan sites influence HIV-1 Env-pseudovirus neutralization
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Affiliation(s)
- Anna-Janina Behrens
- Oxford Glycobiology Institute and Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Snezana Vasiljevic
- Oxford Glycobiology Institute and Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Laura K Pritchard
- Oxford Glycobiology Institute and Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - David J Harvey
- Oxford Glycobiology Institute and Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Rajinder S Andev
- Department of Infectious Diseases, Faculty of Life Sciences and Medicine, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Stefanie A Krumm
- Department of Infectious Diseases, Faculty of Life Sciences and Medicine, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Weston B Struwe
- Oxford Glycobiology Institute and Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Abhinav Kumar
- Oxford Glycobiology Institute and Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Nicole Zitzmann
- Oxford Glycobiology Institute and Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Gemma E Seabright
- Oxford Glycobiology Institute and Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Holger B Kramer
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | | | - Louise Royle
- Ludger, Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14 3EB, UK
| | - Jeong Hyun Lee
- Department of Integrative Structural and Computational Biology, International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center and CAVD, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Per J Klasse
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, IAVI Neutralizing Antibody Center and CAVD, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, the Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02142, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center and CAVD, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center and CAVD, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rogier W Sanders
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA; Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Katie J Doores
- Department of Infectious Diseases, Faculty of Life Sciences and Medicine, King's College London, Guy's Hospital, London SE1 9RT, UK.
| | - Max Crispin
- Oxford Glycobiology Institute and Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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35
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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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36
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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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37
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Sherrod SD, McLean JA. Systems-Wide High-Dimensional Data Acquisition and Informatics Using Structural Mass Spectrometry Strategies. Clin Chem 2015; 62:77-83. [PMID: 26453699 DOI: 10.1373/clinchem.2015.238261] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/12/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND Untargeted multiomics data sets are obtained for samples in systems, synthetic, and chemical biology by integrating chromatographic separations with ion mobility-mass spectrometry (IM-MS) analysis. The data sets are interrogated using bioinformatics strategies to organize the data for identification prioritization. CONTENT The use of big data approaches for data mining of massive data sets in systems-wide analyses is presented. Untargeted biological data across multiomics dimensions are obtained using a variety of chromatography strategies with structural MS. Separation timescales for different techniques and the resulting data deluge when combined with IM-MS are presented. Data mining self-organizing map strategies are used to rapidly filter the data, highlighting those features describing uniqueness to the query. Examples are provided in longitudinal analyses in synthetic biology and human liver exposure to acetaminophen, and in chemical biology for natural product discovery from bacterial biomes. CONCLUSIONS Matching the separation timescales of different forms of chromatography with IM-MS provides sufficient multiomics selectivity to perform untargeted systems-wide analyses. New data mining strategies provide a means for rapidly interrogating these data sets for feature prioritization and discovery in a range of applications in systems, synthetic, and chemical biology.
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Affiliation(s)
- Stacy D Sherrod
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN.
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38
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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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39
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Cell- and Protein-Directed Glycosylation of Native Cleaved HIV-1 Envelope. J Virol 2015; 89:8932-44. [PMID: 26085151 DOI: 10.1128/jvi.01190-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 06/08/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The gp120/gp41 HIV-1 envelope glycoprotein (Env) is highly glycosylated, with up to 50% of its mass consisting of N-linked glycans. This dense carbohydrate coat has emerged as a promising vaccine target, with its glycans acting as epitopes for a number of potent and broadly neutralizing antibodies (bnAbs). Characterizing the glycan structures present on native HIV-1 Env is thus a critical goal for the design of Env immunogens. In this study, we used a complementary, multistep approach involving ion mobility mass spectrometry and high-performance liquid chromatography to comprehensively characterize the glycan structures present on HIV-1 gp120 produced in peripheral blood mononuclear cells (PBMCs). The capacity of different expression systems, including pseudoviral particles and recombinant cell surface trimers, to reproduce native-like glycosylation was then assessed. A population of oligomannose glycans on gp120 was reproduced across all expression systems, supporting this as an intrinsic property of Env that can be targeted for vaccine design. In contrast, Env produced in HEK 293T cells failed to accurately reproduce the highly processed complex-type glycan structures observed on PBMC-derived gp120, and in particular the precise linkage of sialic acid residues that cap these glycans. Finally, we show that unlike for gp120, the glycans decorating gp41 are mostly complex-type sugars, consistent with the glycan specificity of bnAbs that target this region. These findings provide insights into the glycosylation of native and recombinant HIV-1 Env and can be used to inform strategies for immunogen design and preparation. IMPORTANCE Development of an HIV vaccine is desperately needed to control new infections, and elicitation of HIV bnAbs will likely be an important component of an effective vaccine. Increasingly, HIV bnAbs are being identified that bind to the N-linked glycans coating the HIV envelope glycoproteins gp120 and gp41, highlighting them as important targets for vaccine design. It is therefore important to characterize the glycan structures present on native, virion-associated gp120 and gp41 for development of vaccines that accurately mimic native-Env glycosylation. In this study, we used a number of analytical techniques to precisely study the structures of both the oligomannose and complex-type glycans present on native Env to provide a reference for determining the ability of potential HIV immunogens to accurately replicate the glycosylation pattern on these native structures.
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40
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Glycan Microheterogeneity at the PGT135 Antibody Recognition Site on HIV-1 gp120 Reveals a Molecular Mechanism for Neutralization Resistance. J Virol 2015; 89:6952-9. [PMID: 25878100 DOI: 10.1128/jvi.00230-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/01/2015] [Indexed: 12/16/2022] Open
Abstract
Broadly neutralizing antibodies have been isolated that bind the glycan shield of the HIV-1 envelope spike. One such antibody, PGT135, contacts the intrinsic mannose patch of gp120 at the Asn332, Asn392, and Asn386 glycosylation sites. Here, site-specific glycosylation analysis of recombinant gp120 revealed glycan microheterogeneity sufficient to explain the existence of a minor population of virions resistant to PGT135 neutralization. Target microheterogeneity and antibody glycan specificity are therefore important parameters in HIV-1 vaccine design.
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41
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Li H, Bendiak B, Siems WF, Gang DR, Hill HH. Determining the Isomeric Heterogeneity of Neutral Oligosaccharide-Alditols of Bovine Submaxillary Mucin Using Negative Ion Traveling Wave Ion Mobility Mass Spectrometry. Anal Chem 2015; 87:2228-35. [DOI: 10.1021/ac503754k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hongli Li
- Department
of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brad Bendiak
- Department
of Cell and Developmental Biology, Program in Structural
Biology and Biophysics, University of Colorado, Health Sciences Center, Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - William F. Siems
- Department
of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - David R. Gang
- Institute of Biological
Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Herbert H. Hill
- Department
of Chemistry, Washington State University, Pullman, Washington 99164, United States
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42
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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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43
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May JC, Goodwin CR, McLean JA. Ion mobility-mass spectrometry strategies for untargeted systems, synthetic, and chemical biology. Curr Opin Biotechnol 2014; 31:117-21. [PMID: 25462629 DOI: 10.1016/j.copbio.2014.10.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 12/12/2022]
Abstract
Contemporary strategies that concentrate on only one or a handful of molecular targets limits the utility of the information gained for diagnostic and predictive purposes. Recent advances in the sensitivity, speed, and precision of measurements obtained from ion mobility coupled to mass spectrometry (IM-MS) have accelerated the utility of IM-MS in untargeted, discovery-driven studies in biology. Perhaps most evident is the impact that such wide-scale discovery capabilities have yielded in the areas of systems, synthetic, and chemical biology, where the need for comprehensive, hypothesis-driving studies from multidimensional and unbiased data is required.
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Affiliation(s)
- Jody C May
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - Cody R Goodwin
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - John A McLean
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA.
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Abstract
Uukuniemi virus (UUKV) is a model system for investigating the genus Phlebovirus of the Bunyaviridae. We report the UUKV glycome, revealing differential processing of the Gn and Gc virion glycoproteins. Both glycoproteins display poly-N-acetyllactosamines, consistent with virion assembly in the medial Golgi apparatus, whereas oligomannose-type glycans required for DC-SIGN-dependent cellular attachment are predominant on Gc. Local virion structure and the route of viral egress from the cell leave a functional imprint on the phleboviral glycome.
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45
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Haji-Ghassemi O, Müller-Loennies S, Saldova R, Muniyappa M, Brade L, Rudd PM, Harvey DJ, Kosma P, Brade H, Evans SV. Groove-type recognition of chlamydiaceae-specific lipopolysaccharide antigen by a family of antibodies possessing an unusual variable heavy chain N-linked glycan. J Biol Chem 2014; 289:16644-61. [PMID: 24682362 DOI: 10.1074/jbc.m113.528224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure of the antigen binding fragment of mAb S25-26, determined to 1.95 Å resolution in complex with the Chlamydiaceae family-specific trisaccharide antigen Kdo(2→8)Kdo(2→4)Kdo (Kdo = 3-deoxy-α-d-manno-oct-2-ulopyranosonic acid), displays a germ-line-coded paratope that differs significantly from previously characterized Chlamydiaceae-specific mAbs despite being raised against the identical immunogen. Unlike the terminal Kdo recognition pocket that promotes cross-reactivity in S25-2-type antibodies, S25-26 and the closely related S25-23 utilize a groove composed of germ-line residues to recognize the entire trisaccharide antigen and so confer strict specificity. Interest in S25-23 was sparked by its rare high μm affinity and strict specificity for the family-specific trisaccharide antigen; however, only the related antibody S25-26 proved amenable to crystallization. The structures of three unliganded forms of S25-26 have a labile complementary-determining region H3 adjacent to significant glycosylation of the variable heavy chain on asparagine 85 in Framework Region 3. Analysis of the glycan reveals a heterogeneous mixture with a common root structure that contains an unusually high number of terminal αGal-Gal moieties. One of the few reported structures of glycosylated mAbs containing these epitopes is the therapeutic antibody Cetuximab; however, unlike Cetuximab, one of the unliganded structures in S25-26 shows significant order in the glycan with appropriate electron density for nine residues. The elucidation of the three-dimensional structure of an αGal-containing N-linked glycan on a mAb variable heavy chain has potential clinical interest, as it has been implicated in allergic response in patients receiving therapeutic antibodies.
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Affiliation(s)
- Omid Haji-Ghassemi
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada
| | - Sven Müller-Loennies
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany,
| | - Radka Saldova
- GlycoScience Group, the National Institute for Bioprocessing Research and Training (NIBRT), Mount Merrion, Blackrock, Dublin 4, Ireland
| | - Mohankumar Muniyappa
- GlycoScience Group, the National Institute for Bioprocessing Research and Training (NIBRT), Mount Merrion, Blackrock, Dublin 4, Ireland
| | - Lore Brade
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany
| | - Pauline M Rudd
- GlycoScience Group, the National Institute for Bioprocessing Research and Training (NIBRT), Mount Merrion, Blackrock, Dublin 4, Ireland
| | - David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Paul Kosma
- University of Natural Resources and Life Sciences, Vienna, Austria, and
| | - Helmut Brade
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany
| | - Stephen V Evans
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada,
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46
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Crispin M, Harvey DJ, Bitto D, Bonomelli C, Edgeworth M, Scrivens JH, Huiskonen JT, Bowden TA. Structural plasticity of the Semliki Forest virus glycome upon interspecies transmission. J Proteome Res 2014; 13:1702-12. [PMID: 24467287 PMCID: PMC4428802 DOI: 10.1021/pr401162k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Cross-species
viral transmission subjects parent and progeny alphaviruses
to differential post-translational processing of viral envelope glycoproteins.
Alphavirus biogenesis has been extensively studied, and the Semliki
Forest virus E1 and E2 glycoproteins have been shown to exhibit differing
degrees of processing of N-linked glycans. However the composition
of these glycans, including that arising from different host cells,
has not been determined. Here we determined the chemical composition
of the glycans from the prototypic alphavirus, Semliki Forest virus,
propagated in both arthropod and rodent cell lines, by using ion-mobility
mass spectrometry and collision-induced dissociation analysis. We
observe that both the membrane-proximal E1 fusion glycoprotein and
the protruding E2 attachment glycoprotein display heterogeneous glycosylation
that contains N-linked glycans exhibiting both limited and extensive
processing. However, E1 contained predominantly highly processed glycans
dependent on the host cell, with rodent and mosquito-derived E1 exhibiting
complex-type and paucimannose-type glycosylation, respectively. In
contrast, the protruding E2 attachment glycoprotein primarily contained
conserved under-processed oligomannose-type structures when produced
in both rodent and mosquito cell lines. It is likely that glycan processing
of E2 is structurally restricted by steric-hindrance imposed by local
viral protein structure. This contrasts E1, which presents glycans
characteristic of the host cell and is accessible to enzymes. We integrated
our findings with previous cryo-electron microscopy and crystallographic
analyses to produce a detailed model of the glycosylated mature virion
surface. Taken together, these data reveal the degree to which virally
encoded protein structure and cellular processing enzymes shape the
virion glycome during interspecies transmission of Semliki Forest
virus.
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Affiliation(s)
- Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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47
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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: 266] [Impact Index Per Article: 26.6] [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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48
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Yang S, Yuan W, Yang W, Zhou J, Harlan R, Edwards J, Li S, Zhang H. Glycan analysis by isobaric aldehyde reactive tags and mass spectrometry. Anal Chem 2013; 85:8188-95. [PMID: 23895018 DOI: 10.1021/ac401226d] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycans play significant roles in physiological and pathological processes. Therefore, quantitative analysis of glycans from normal and disease specimens can provide insight into disease onset and progression. Relative glycan quantification usually requires modification of the glycans with either chromogenic or fluorogenic tags for optical measurement or isotopic tags for mass spectrometric analysis. Because of rapid advances in mass spectrometry (MS) instruments in resolution, sensitivity, and speed, MS-based methods have become increasingly popular for glycan analysis in the past decade. However, current isotopic tags for glycan labeling are mostly mass-shift tags generating mass differences in precursor ions for quantification, which can complicate mass spectra. In this study, we report the synthesis and characterization of isobaric aldehyde reactive tags (iARTs) for glycan quantification using tandem MS. We applied iARTs to the relative identification and quantification of glycans of gp120, a glycoprotein from human immunodeficiency virus. The results show that iARTs provide strong signals for glycan identification. Although we only show the synthesis and characterization of two iARTs reagents, iARTs can be readily expanded to six-plex tags for quantitative analysis of six samples concurrently.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, USA
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49
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Harvey DJ, Scarff CA, Edgeworth M, Crispin M, Scanlan CN, Sobott F, Allman S, Baruah K, Pritchard L, Scrivens JH. Travelling wave ion mobility and negative ion fragmentation for the structural determination ofN-linked glycans. Electrophoresis 2013; 34:2368-78. [DOI: 10.1002/elps.201200669] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/05/2013] [Accepted: 03/05/2013] [Indexed: 12/17/2022]
Affiliation(s)
| | | | - Matthew Edgeworth
- Department of Biological Sciences; University of Warwick; Coventry; UK
| | - Max Crispin
- Department of Biochemistry, Oxford Glycobiology Institute; University of Oxford; Oxford; UK
| | - Christopher N. Scanlan
- Department of Biochemistry, Oxford Glycobiology Institute; University of Oxford; Oxford; UK
| | - Frank Sobott
- Department of Chemistry, Center for Proteomics; University of Antwerp; Antwerp; Belgium
| | - Sarah Allman
- Department of Biochemistry, Oxford Glycobiology Institute; University of Oxford; Oxford; UK
| | - Kavitha Baruah
- Department of Biochemistry, Oxford Glycobiology Institute; University of Oxford; Oxford; UK
| | - Laura Pritchard
- Department of Biochemistry, Oxford Glycobiology Institute; University of Oxford; Oxford; UK
| | - James H. Scrivens
- Department of Biological Sciences; University of Warwick; Coventry; UK
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50
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Fellenberg M, Behnken HN, Nagel T, Wiegandt A, Baerenfaenger M, Meyer B. Glycan analysis: scope and limitations of different techniques--a case for integrated use of LC-MS(/MS) and NMR techniques. Anal Bioanal Chem 2013; 405:7291-305. [PMID: 23852147 DOI: 10.1007/s00216-013-7164-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 06/13/2013] [Accepted: 06/19/2013] [Indexed: 01/16/2023]
Abstract
The structure of glycans from glycoproteins is highly relevant for their function. We tightly integrate liquid chromatography-mass spectrometry (LC-MS), MS/MS, and nuclear magnetic resonance (NMR) data to achieve a complete characterization of even isobaric glycans differing in only one linkage position or in the substitution in one branch. As example, we analyzed ten desialylated underivatized glycans from bovine fibrinogen. The molecules were separated on a PGC column, and LC-MS data allowed an assignment of the compositions of the glycans. MS/MS data of the same glycans allowed elucidation of sequence and to some extent of branching and linkage. All MS/MS fragmentation methods led to multiple dissociations, resulting in several cases in ambiguous data. The MS/MS data were interpreted both by scientists and automatically by software, and the differential results are compared. Additional data from a tight integration of LC-MS and NMR data resulted in a complete structural characterization of the glycans. The acquisition of simple 1D (1)H NMR data led--in combination with LC-MS and MS/MS data--to an unambiguous assignment of the isobaric glycans. Compounds that were not separated in the chromatography could easily be assigned structurally by applying the 3D cross-correlation (3DCC) technology to arrive at NMR spectra of the pure components-without actually separating them. By applying LC-MS, MS/MS, 1D (1)H NMR, and 3DCC together, one can assign glycan structures from glycoconjugates with high confidence affording only 200 pmol of glycan material.
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Affiliation(s)
- Meike Fellenberg
- Organic Chemistry, Department of Chemistry, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
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