1
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Marie AL, Gao Y, Ivanov AR. Native N-glycome profiling of single cells and ng-level blood isolates using label-free capillary electrophoresis-mass spectrometry. Nat Commun 2024; 15:3847. [PMID: 38719792 PMCID: PMC11079027 DOI: 10.1038/s41467-024-47772-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
The development of reliable single-cell dispensers and substantial sensitivity improvement in mass spectrometry made proteomic profiling of individual cells achievable. Yet, there are no established methods for single-cell glycome analysis due to the inability to amplify glycans and sample losses associated with sample processing and glycan labeling. In this work, we present an integrated platform coupling online in-capillary sample processing with high-sensitivity label-free capillary electrophoresis-mass spectrometry for N-glycan profiling of single mammalian cells. Direct and unbiased quantitative characterization of single-cell surface N-glycomes are demonstrated for HeLa and U87 cells, with the detection of up to 100 N-glycans per single cell. Interestingly, N-glycome alterations are unequivocally detected at the single-cell level in HeLa and U87 cells stimulated with lipopolysaccharide. The developed workflow is also applied to the profiling of ng-level amounts (5-500 ng) of blood-derived protein, extracellular vesicle, and total plasma isolates, resulting in over 170, 220, and 370 quantitated N-glycans, respectively.
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Affiliation(s)
- Anne-Lise Marie
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US
| | - Yunfan Gao
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US.
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2
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Liew CY, Chen JL, Lin YT, Luo HS, Hung AT, Magoling BJA, Nguan HS, Lai CPK, Ni CK. Chromatograms and Mass Spectra of High-Mannose and Paucimannose N-Glycans for Rapid Isomeric Identifications. J Proteome Res 2024; 23:939-955. [PMID: 38364797 PMCID: PMC10913092 DOI: 10.1021/acs.jproteome.3c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/18/2024]
Abstract
N-Linked glycosylation is one of the most essential post-translational modifications of proteins. However, N-glycan structural determination remains challenging because of the small differences in structures between isomers. In this study, we constructed a database containing collision-induced dissociation MSn mass spectra and chromatograms of high-performance liquid chromatography for the rapid identification of high-mannose and paucimannose N-glycan isomers. These N-glycans include isomers by breaking of arbitrary numbers of glycosidic bonds at arbitrary positions of canonical Man9GlcNAc2 N-glycans. In addition, some GlcMannGlcNAc2 N-glycan isomers were included in the database. This database is particularly useful for the identification of the N-glycans not in conventional N-glycan standards. This study demonstrated the application of the database to structural assignment for high-mannose N-glycans extracted from bovine whey proteins, soybean proteins, human mammary epithelial cells, and human breast carcinoma cells. We found many N-glycans that are not expected to be generated by conventional biosynthetic pathways of multicellular eukaryotes.
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Affiliation(s)
- Chia Yen Liew
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- International
Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei 106216, Taiwan
- Molecular
Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 106216, Taiwan
| | - Jien-Lian Chen
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Yen-Ting Lin
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Hong-Sheng Luo
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Taiwan Normal University, Taipei 116059, Taiwan
| | - An-Ti Hung
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Bryan John Abel Magoling
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Institute
of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106216, Taiwan
- Chemical
Biology and Molecular Biophysics Program, Taiwan International Graduate
Program, Academia Sinica, Taipei 115201, Taiwan
| | - Hock-Seng Nguan
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
| | - Charles Pin-Kuang Lai
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Chemical
Biology and Molecular Biophysics Program, Taiwan International Graduate
Program, Academia Sinica, Taipei 115201, Taiwan
- Genome
and Systems Biology Degree Program, National
Taiwan University and Academia Sinica, Taipei 106216, Taiwan
| | - Chi-Kung Ni
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106216, Taiwan
- Molecular
Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 106216, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
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3
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Ivanov A, Marie AL, Gao Y. In-capillary sample processing coupled to label-free capillary electrophoresis-mass spectrometry to decipher the native N-glycome of single mammalian cells and ng-level blood isolates. RESEARCH SQUARE 2023:rs.3.rs-3500983. [PMID: 38014012 PMCID: PMC10680937 DOI: 10.21203/rs.3.rs-3500983/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The development of reliable single-cell dispensers and substantial sensitivity improvement in mass spectrometry made proteomic profiling of individual cells achievable. Yet, there are no established methods for single-cell glycome analysis due to the inability to amplify glycans and sample losses associated with sample processing and glycan labeling. In this work, we developed an integrated platform coupling online in-capillary sample processing with high-sensitivity label-free capillary electrophoresis-mass spectrometry for N-glycan profiling of single mammalian cells. Direct and unbiased characterization and quantification of single-cell surface N-glycomes were demonstrated for HeLa and U87 cells, with the detection of up to 100 N-glycans per single cell. Interestingly, N-glycome alterations were unequivocally detected at the single-cell level in HeLa and U87 cells stimulated with lipopolysaccharide. The developed workflow was also applied to the profiling of ng-level amounts of blood-derived protein, extracellular vesicle, and total plasma isolates, resulting in over 170, 220, and 370 quantitated N-glycans, respectively.
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4
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Liew CY, Luo HS, Yang TY, Hung AT, Magoling BJA, Lai CPK, Ni CK. Identification of the High Mannose N-Glycan Isomers Undescribed by Conventional Multicellular Eukaryotic Biosynthetic Pathways. Anal Chem 2023. [PMID: 37235553 DOI: 10.1021/acs.analchem.2c05599] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
N-linked glycosylation is one of the most important post-translational modifications of proteins. Current knowledge of multicellular eukaryote N-glycan biosynthesis suggests high mannose N-glycans are generated in the endoplasmic reticulum and Golgi apparatus through conserved biosynthetic pathways. According to conventional biosynthetic pathways, four Man7GlcNAc2 isomers, three Man6GlcNAc2 isomers, and one Man5GlcNAc2 isomer are generated during this process. In this study, we applied our latest mass spectrometry method, logically derived sequence tandem mass spectrometry (LODES/MSn), to re-examine high mannose N-glycans extracted from various multicellular eukaryotes which are not glycosylation mutants. LODES/MSn identified many high mannose N-glycan isomers previously unreported in plantae, animalia, cancer cells, and fungi. A database consisting of retention time and CID MSn mass spectra was constructed for all possible MannGlcNAc2 (n = 5, 6, 7) isomers that include the isomers by removing arbitrary numbers and positions of mannose from canonical N-glycan, Man9GlcNAc2. Many N-glycans in this database are not found in current N-glycan mass spectrum libraries. The database is useful for rapid high mannose N-glycan isomeric identification.
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Affiliation(s)
- Chia Yen Liew
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- International Graduate Program of Molecular Science and Technology, National Taiwan University (NTU-MST), Taipei 10617, Taiwan
- Molecular Science and Technology (MST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 10617, Taiwan
| | - Hong-Sheng Luo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Ting-Yi Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - An-Ti Hung
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Bryan John Abel Magoling
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
| | - Charles Pin-Kuang Lai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Molecular Science and Technology (MST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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5
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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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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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Harvey DJ, Behrens AJ, Crispin M, Struwe WB. Identification of N-glycans with GalNAc-containing antennae from recombinant HIV trimers by ion mobility and negative ion fragmentation. Anal Bioanal Chem 2021; 413:7229-7240. [PMID: 34327564 PMCID: PMC8321768 DOI: 10.1007/s00216-021-03477-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/10/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Negative ion collision-induced dissociation (CID) of underivatized N-glycans has proved to be a simple, yet powerful method for their structural determination. Recently, we have identified a series of such structures with GalNAc rather than the more common galactose capping the antennae of hybrid and complex glycans. As part of a series of publications describing the negative ion fragmentation of different types of N-glycan, this paper describes their CID spectra and estimated nitrogen cross sections recorded by travelling wave ion mobility mass spectrometry (TWIMS). Most of the glycans were derived from the recombinant glycoproteins gp120 and gp41 from the human immunodeficiency virus (HIV), recombinantly derived from human embryonic kidney (HEK 293T) cells. Twenty-six GalNAc-capped hybrid and complex N-glycans were identified by a combination of TWIMS, negative ion CID, and exoglycosidase digestions. They were present as the neutral glycans and their sulfated and α2→3-linked sialylated analogues. Overall, negative ion fragmentation of glycans generates fingerprints that reveal their structural identity.
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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.
| | - 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
| | - 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
| | - 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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Abstract
GlycoStore ( http://www.glycostore.org ) is an open access chromatographic and electrophoretic retention database of glycans characterized from glycoproteins, glycolipids, and biotherapeutics. It is a continuation of the GlycoBase project (Oxford Glycobiology Institute and National Institute for Bioprocessing Research and Training, Ireland) but addresses many of the technological limitations that impacted the growth of GlycoBase, in particular, improvements to the bioinformatics architecture, enhancing data annotations and coverage, and improving connectivity with external resources. The first release of GlycoStore (October 2017) contains over 850 glycan entries accompanied by 8500+ retention positions including data from: (1) fluorescently labelled released glycans determined using hydrophilic interaction chromatography (HILIC) ultrahigh-performance liquid chromatography (U/HPLC) and reversed phase (RP)-U/HPLC; (2) porous graphitized carbon chromatography (PGC) interfaced with ESI-MS/MS; and (3) capillary electrophoresis with laser induced fluorescence detection (CE-LIF). In this chapter, we outline the objectives of GlycoStore, and describe a selection of step-by-step workflows for navigating and browsing the information available. We also provide a short description of informatics tools available to query the database using Semantic technologies. The information presented in this chapter supplements our documentation knowledge base that describes interface improvements, new features and tools, and content updates ( https://unicarbkb.freshdesk.com/ ).
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9
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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10
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Structural identification of N-glycan isomers using logically derived sequence tandem mass spectrometry. Commun Chem 2021; 4:92. [PMID: 36697781 PMCID: PMC9814355 DOI: 10.1038/s42004-021-00532-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/19/2021] [Indexed: 01/28/2023] Open
Abstract
N-linked glycosylation is one of the most important protein post-translational modifications. Despite the importance of N-glycans, the structural determination of N-glycan isomers remains challenging. Here we develop a mass spectrometry method, logically derived sequence tandem mass spectrometry (LODES/MSn), to determine the structures of N-glycan isomers that cannot be determined using conventional mass spectrometry. In LODES/MSn, the sequences of successive collision-induced dissociation are derived from carbohydrate dissociation mechanisms and apply to N-glycans in an ion trap for structural determination. We validate LODES/MSn using synthesized N-glycans and subsequently applied this method to N-glycans extracted from soybean, ovalbumin, and IgY. Our method does not require permethylation, reduction, and labeling of N-glycans, or the mass spectrum databases of oligosaccharides and N-glycan standards. Moreover, it can be applied to all types of N-glycans (high-mannose, hybrid, and complex), as well as the N-glycans degraded from larger N-glycans by any enzyme or acid hydrolysis.
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11
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Pralow A, Cajic S, Alagesan K, Kolarich D, Rapp E. State-of-the-Art Glycomics Technologies in Glycobiotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 175:379-411. [PMID: 33112988 DOI: 10.1007/10_2020_143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycosylation affects the properties of biologics; thus regulatory bodies classified it as critical quality attribute and force biopharma industry to capture and control it throughout all phases, from R&D till end of product lifetime. The shift from originators to biosimilars further increases importance and extent of glycoanalysis, which thus increases the need for technology platforms enabling reliable high-throughput and in-depth glycan analysis. In this chapter, we will first summarize on established glycoanalytical methods based on liquid chromatography focusing on hydrophilic interaction chromatography, capillary electrophoresis focusing on multiplexed capillary gel electrophoresis, and mass spectrometry focusing on matrix-assisted laser desorption; we will then highlight two emerging technologies based on porous graphitized carbon liquid chromatography and on ion-mobility mass spectrometry as both are highly promising tools to deliver an additional level of information for in-depth glycan analysis; additionally we elaborate on the advantages and challenges of different glycoanalytical technologies and their complementarity; finally, we briefly review applications thereof to biopharmaceutical products. This chapter provides an overview of current state-of-the-art analytical approaches for glycan characterization of biopharmaceuticals that can be employed to capture glycoprotein heterogeneity in a biopharmaceutical context.
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Affiliation(s)
- Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Samanta Cajic
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
- ARC Centre of Excellence in Nanoscale Biophotonics, Griffith University, Gold Coast, QLD, Australia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
- glyXera GmbH, Magdeburg, Germany.
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12
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Wei J, Tang Y, Ridgeway ME, Park MA, Costello CE, Lin C. Accurate Identification of Isomeric Glycans by Trapped Ion Mobility Spectrometry-Electronic Excitation Dissociation Tandem Mass Spectrometry. Anal Chem 2020; 92:13211-13220. [PMID: 32865981 DOI: 10.1021/acs.analchem.0c02374] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) has become a powerful tool for glycan structural characterization due to its ability to separate isomers and provide collision cross section (CCS) values that facilitate structural assignment. However, IM-based isomer analysis may be complicated by the presence of multiple gas-phase conformations of a single structure that not only increases difficulty in isomer separation but can also introduce the possibility for misinterpretation of conformers as isomers. Here, the ion mobility behavior of several sets of isomeric glycans, analyzed as their permethylated derivatives, in both nonreduced and reduced forms, was investigated by gated-trapped ion mobility spectrometry (G-TIMS). Notably, reducing-end reduction, commonly performed to remove anomerism-induced chromatographic peak splitting, did not eliminate the conformational heterogeneity of permethylated glycans in the gas phase. At a mobility resolving power of ∼100, 14 out of 22 structures showed more than one conformation. These results highlight the need to use IMS devices with high mobility resolving power for better separation of isomers and to acquire additional structural information that can differentiate isomers from conformers. Online electronic excitation dissociation (EED) MS/MS analysis of isomeric glycan mixtures following G-TIMS separation showed that EED can generate isomer-specific fragments while producing nearly identical tandem mass spectra for conformers, thus allowing confident identification of isomers with minimal evidence of any ambiguity resulting from the presence of conformers. G-TIMS EED MS/MS analysis of N-linked glycans released from ovalbumin revealed that several mobility features previously thought to arise from isomeric structures were conformers of a single structure. Finally, analysis of ovalbumin N-glycans from different sources showed that the G-TIMS EED MS/MS approach can accurately determine the batch-to-batch variations in glycosylation profiles at the isomer level, with confident assignment of each isomeric structure.
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Affiliation(s)
- Juan Wei
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States
| | - Yang Tang
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Mark E Ridgeway
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | - Melvin A Park
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States
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13
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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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14
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Bansal P, Yatsyna V, AbiKhodr AH, Warnke S, Ben Faleh A, Yalovenko N, Wysocki VH, Rizzo TR. Using SLIM-Based IMS-IMS Together with Cryogenic Infrared Spectroscopy for Glycan Analysis. Anal Chem 2020; 92:9079-9085. [PMID: 32456419 PMCID: PMC7349563 DOI: 10.1021/acs.analchem.0c01265] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
Abstract
The isomeric heterogeneity of glycans poses a great challenge for their analysis. While combining ion mobility spectrometry (IMS) with tandem mass spectrometry is a powerful means for identifying and characterizing glycans, it has difficulty distinguishing the subtlest differences between isomers. Cryogenic infrared spectroscopy provides an additional dimension for glycan identification that is extremely sensitive to their structure. Our approach to glycan analysis combines ultrahigh-resolution IMS-IMS using structures for lossless ion manipulation (SLIM) with cryogenic infrared spectroscopy. We present here the design of a SLIM board containing a series of on-board traps in which we perform collision-induced dissociation (CID) at pressures in the millibar range. We characterize the on-board CID process by comparing the fragments generated from a pentapeptide to those obtained on a commercial tandem mass spectrometer. We then apply our new technique to study the mobility and vibrational spectra of CID fragments from two human milk oligosaccharides. Comparison of both the fragment drift times and IR spectra with those of suitable reference compounds allows us to identify their specific isomeric form, including the anomericity of the glycosidic linkage, demonstrating the power of this tool for glycan analysis.
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Affiliation(s)
- Priyanka Bansal
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Vasyl Yatsyna
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
- Department
of Physics, University of Gothenburg, 412 96 Gotheburg, Sweden
| | - Ali H. AbiKhodr
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Stephan Warnke
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Ahmed Ben Faleh
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Natalia Yalovenko
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Thomas R. Rizzo
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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15
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Zhang T, Madunić K, Holst S, Zhang J, Jin C, Ten Dijke P, Karlsson NG, Stavenhagen K, Wuhrer M. Development of a 96-well plate sample preparation method for integrated N- and O-glycomics using porous graphitized carbon liquid chromatography-mass spectrometry. Mol Omics 2020; 16:355-363. [PMID: 32281997 DOI: 10.1039/c9mo00180h] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Changes in glycosylation signatures of cells have been associated with pathological processes in cancer as well as infectious and autoimmune diseases. The current protocols for comprehensive analysis of N-glycomics and O-glycomics derived from cells and tissues often require a large amount of biological material. They also only allow the processing of very limited numbers of samples at a time. Here we established a workflow for sequential release of N-glycans and O-glycans based on PVDF membrane immobilization in 96-well format from 5 × 105 cells. Released glycans are reduced, desalted, purified, and reconstituted, all in 96-well format plates, without additional staining or derivatization. Glycans are then analyzed with porous graphitized carbon nano-liquid chromatography coupled to tandem mass spectrometry using negative-mode electrospray ionization, enabling the chromatographic resolution and structural elucidation of glycan species including many compositional isomers. The approach was demonstrated using glycoprotein standards and further applied to analyze the glycosylation of the murine mammary gland NMuMG cell line. The developed protocol allows the analysis of N- and O-glycans from relatively large numbers of samples in a less time consuming way with high repeatability. Inter- and intraday repeatability of the fetuin N-glycan analysis showed two median intraday coefficients of variations (CVs) of 7.6% and 8.0%, and a median interday CV of 9.8%. Median CVs of 7.9% and 8.7% for the main peaks of N- and O-glycans released from the NMuMG cell line indicate a very good repeatability. The method is applicable to purified glycoproteins as well as to biofluids and cell- or tissue-based samples.
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Affiliation(s)
- Tao Zhang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
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16
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Abrahams JL, Taherzadeh G, Jarvas G, Guttman A, Zhou Y, Campbell MP. Recent advances in glycoinformatic platforms for glycomics and glycoproteomics. Curr Opin Struct Biol 2019; 62:56-69. [PMID: 31874386 DOI: 10.1016/j.sbi.2019.11.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022]
Abstract
Protein glycosylation is the most complex and prevalent post-translation modification in terms of the number of proteins modified and the diversity generated. To understand the functional roles of glycoproteins it is important to gain an insight into the repertoire of oligosaccharides present. The comparison and relative quantitation of glycoforms combined with site-specific identification and occupancy are necessary steps in this direction. Computational platforms have continued to mature assisting researchers with the interpretation of such glycomics and glycoproteomics data sets, but frequently support dedicated workflows and users rely on the manual interpretation of data to gain insights into the glycoproteome. The growth of site-specific knowledge has also led to the implementation of machine-learning algorithms to predict glycosylation which is now being integrated into glycoproteomics pipelines. This short review describes commercial and open-access databases and software with an emphasis on those that are actively maintained and designed to support current analytical workflows.
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Affiliation(s)
- Jodie L Abrahams
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Ghazaleh Taherzadeh
- School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Gabor Jarvas
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary; Horváth Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Andras Guttman
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary; Horváth Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; SCIEX, Brea, CA, USA
| | - Yaoqi Zhou
- School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Matthew P Campbell
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia.
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17
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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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18
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Yang L, Du X, Peng Y, Cai Y, Wei L, Zhang Y, Lu H. Integrated Pipeline of Isotopic Labeling and Selective Enriching for Quantitative Analysis of N-Glycome by Mass Spectrometry. Anal Chem 2018; 91:1486-1493. [DOI: 10.1021/acs.analchem.8b04525] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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19
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Mu Y, Schulz BL, Ferro V. Applications of Ion Mobility-Mass Spectrometry in Carbohydrate Chemistry and Glycobiology. Molecules 2018; 23:molecules23102557. [PMID: 30301275 PMCID: PMC6222328 DOI: 10.3390/molecules23102557] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/26/2018] [Accepted: 10/04/2018] [Indexed: 01/25/2023] Open
Abstract
Carbohydrate analyses are often challenging due to the structural complexity of these molecules, as well as the lack of suitable analytical tools for distinguishing the vast number of possible isomers. The coupled technique, ion mobility-mass spectrometry (IM-MS), has been in use for two decades for the analysis of complex biomolecules, and in recent years it has emerged as a powerful technique for the analysis of carbohydrates. For carbohydrates, most studies have focused on the separation and characterization of isomers in biological samples. IM-MS is capable of separating isomeric ions by drift time, and further characterizing them by mass analysis. Applications of IM-MS in carbohydrate analysis are extremely useful and important for understanding many biological mechanisms and for the determination of disease states, although efforts are still needed for higher sensitivity and resolution.
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Affiliation(s)
- Yuqing Mu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia.
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia.
- Australian Research Council Industrial Transformation Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane 4072, Australia.
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia.
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20
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Ashwood C, Lin CH, Thaysen-Andersen M, Packer NH. Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1194-1209. [PMID: 29603058 DOI: 10.1007/s13361-018-1932-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 06/08/2023]
Abstract
Profiling cellular protein glycosylation is challenging due to the presence of highly similar glycan structures that play diverse roles in cellular physiology. As the anomericity and the exact linkage type of a single glycosidic bond can influence glycan function, there is a demand for improved and automated methods to confirm detailed structural features and to discriminate between structurally similar isomers, overcoming a significant bottleneck in the analysis of data generated by glycomics experiments. We used porous graphitized carbon-LC-ESI-MS/MS to separate and detect released N- and O-glycan isomers from mammalian model glycoproteins using negative mode resonance activation CID-MS/MS. By interrogating similar fragment spectra from closely related glycan isomers that differ only in arm position and sialyl linkage, product fragment ions for discrimination between these features were discovered. Using the Skyline software, at least two diagnostic fragment ions of high specificity were validated for automated discrimination of sialylation and arm position in N-glycan structures, and sialylation in O-glycan structures, complementing existing structural diagnostic ions. These diagnostic ions were shown to be useful for isomer discrimination using both linear and 3D ion trap mass spectrometers when analyzing complex glycan mixtures from cell lysates. Skyline was found to serve as a useful tool for automated assessment of glycan isomer discrimination. This platform-independent workflow can potentially be extended to automate the characterization and quantitation of other challenging glycan isomers. Graphical Abstract ᅟ.
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Affiliation(s)
- Christopher Ashwood
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- Australian Research Council Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, Australia
| | - Chi-Hung Lin
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
- Institute for Glycomics, Griffith University, Southport, Australia
| | | | - Nicolle H Packer
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.
- Australian Research Council Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, Australia.
- Institute for Glycomics, Griffith University, Southport, Australia.
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21
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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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22
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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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23
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Abrahams JL, Campbell MP, Packer NH. Building a PGC-LC-MS N-glycan retention library and elution mapping resource. Glycoconj J 2017; 35:15-29. [PMID: 28905148 DOI: 10.1007/s10719-017-9793-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/10/2017] [Accepted: 08/18/2017] [Indexed: 11/27/2022]
Abstract
Porous graphitised carbon-liquid chromatography (PGC-LC) has been proven to be a powerful technique for the analysis and characterisation of complex mixtures of isomeric and isobaric glycan structures. Here we evaluate the elution behaviour of N-glycans on PGC-LC and thereby provide the potential of using chromatographic separation properties, together with mass spectrometry (MS) fragmentation, to determine glycan structure assignments more easily. We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. Over 100 glycan structures were determined by MS/MS, and together with targeted exoglycosidase digestions, created a N-glycan PGC retention library covering a full spectrum of biologically significant N-glycans from pauci mannose to sialylated tetra-antennary classes. The resultant PGC retention library ( http://www.glycostore.org/showPgc ) incorporates retention times and supporting fragmentation spectra including exoglycosidase digestion products, and provides detailed knowledge on the elution properties of N-glycans by PGC-LC. Consequently, this platform should serve as a valuable resource for facilitating the detailed analysis of the glycosylation of both purified recombinant, and complex mixtures of, glycoproteins using established workflows.
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Affiliation(s)
- Jodie L Abrahams
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia
| | - Matthew P Campbell
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia.
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia.
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24
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Nishikaze T. Sensitive and Structure-Informative N-Glycosylation Analysis by MALDI-MS; Ionization, Fragmentation, and Derivatization. ACTA ACUST UNITED AC 2017; 6:A0060. [PMID: 28794918 DOI: 10.5702/massspectrometry.a0060] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 06/15/2017] [Indexed: 01/02/2023]
Abstract
Mass spectrometry (MS) has become an indispensable tool for analyzing post translational modifications of proteins, including N-glycosylated molecules. Because most glycosylation sites carry a multitude of glycans, referred to as "glycoforms," the purpose of an N-glycosylation analysis is glycoform profiling and glycosylation site mapping. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has unique characteristics that are suited for the sensitive analysis of N-glycosylated products. However, the analysis is often hampered by the inherent physico-chemical properties of N-glycans. Glycans are highly hydrophilic in nature, and therefore tend to show low ion yields in both positive- and negative-ion modes. The labile nature and complicated branched structures involving various linkage isomers make structural characterization difficult. This review focuses on MALDI-MS-based approaches for enhancing analytical performance in N-glycosylation research. In particular, the following three topics are emphasized: (1) Labeling for enhancing the ion yields of glycans and glycopeptides, (2) Negative-ion fragmentation for less ambiguous elucidation of the branched structure of N-glycans, (3) Derivatization for the stabilization and linkage isomer discrimination of sialic acid residues.
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Affiliation(s)
- Takashi Nishikaze
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation
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25
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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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26
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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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27
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Ashwood C, Abrahams JL, Nevalainen H, Packer NH. Enhancing structural characterisation of glucuronidated O-linked glycans using negative mode ion trap higher energy collision-induced dissociation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:851-858. [PMID: 28277614 DOI: 10.1002/rcm.7851] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/20/2017] [Accepted: 03/04/2017] [Indexed: 06/06/2023]
Abstract
RATIONALE High protein production and secretion with eukaryotic glycosylation machinery make T. reesei RUT-C30 a suitable expression host for recombinant proteins. The N-glycosylation of secreted proteins of RUT-C30 is known to vary depending on culture nutrients but O-glycosylation has been less extensively studied. METHODS O-Glycans and glycopeptides from secreted proteins were separated by porous graphitised carbon and C-18 liquid chromatography, respectively. O-Glycans were analysed in negative ion mode by electrospray ionisation linear ion trap mass spectrometry and glycopeptides in positive ion mode by electrospray ionisation hybrid quadrupole-orbitrap mass spectrometry. Tandem mass spectrometry was used on O-glycans and glycopeptides including ion trap higher energy collision-induced dissociation (tHCD) to detect glycan fragments not detectable with standard ion trap fragmentation. tHCD allowed targeted MS3 experiments to be performed on structures containing hexuronic acid, which was not possible with ion trap CID, validating this novel O-glycan composition. Positive mode C18-LC/ESI-MS/MS was used to identify and characterise glycopeptides found to be modified with this class of O-glycans, identifying cellobiohydrolase I as a carrier of these novel O-glycans. RESULTS Negative mode ion trap higher energy collision-induced dissociation allowed detection and targeted MS3 experiments to be performed on the hexuronic acid substituent of O-glycan structures, which was not possible with ion trap CID, validating the novel O-glycan composition to include hexuronic acid. Using glycopeptide analysis, this novel O-glycan composition was found to be present on the catalytic domain of cellobiohydrolase I, the most abundant secreted protein by T. reesei. CONCLUSIONS These are the first reported O-glycans to contain acidic sugars in fungi and they could have significant implications for cellobiohydrolase I structure and activity as well as the activity of recombinant proteins expressed in this host system. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Christopher Ashwood
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jodie L Abrahams
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Helena Nevalainen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW, 2109, Australia
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Hinneburg H, Korać P, Schirmeister F, Gasparov S, Seeberger PH, Zoldoš V, Kolarich D. Unlocking Cancer Glycomes from Histopathological Formalin-fixed and Paraffin-embedded (FFPE) Tissue Microdissections. Mol Cell Proteomics 2017; 16:524-536. [PMID: 28122943 DOI: 10.1074/mcp.m116.062414] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 01/22/2017] [Indexed: 12/22/2022] Open
Abstract
N- and O-glycans are attractive clinical biomarkers as glycosylation changes in response to diseases. The limited availability of defined clinical specimens impedes glyco-biomarker identification and validation in large patient cohorts. Formalin-fixed paraffin-embedded (FFPE) clinical specimens are the common form of sample preservation in clinical pathology, but qualitative and quantitative N- and O-glycomics of such samples has not been feasible to date. Here, we report a highly sensitive and glycan isomer selective method for simultaneous N- and O-glycomics from histopathological slides. As few as 2000 cells isolated from FFPE tissue sections by laser capture microdissection were sufficient for in-depth histopathology-glycomics using porous graphitized carbon nanoLC ESI-MS/MS. N- and O-glycan profiles were similar between unstained and hematoxylin and eosin stained FFPE samples but differed slightly compared with fresh tissue. This method provides the key to unlock glyco-biomarker information from FFPE histopathological tissues archived in pathology laboratories worldwide.
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Affiliation(s)
- Hannes Hinneburg
- From the ‡Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany.,§Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, 14195 Berlin, Germany
| | - Petra Korać
- ¶Faculty of Science, Department of Biology, Division of Molecular Biology, University of Zagreb, Zagreb, Croatia
| | - Falko Schirmeister
- From the ‡Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany.,§Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, 14195 Berlin, Germany
| | - Slavko Gasparov
- ‖Institute for Pathology and Cytology, University Hospital Merkur, Zagreb, Croatia.,**Department of Pathology, Medical School Zagreb, University of Zagreb, Zagreb, Croatia
| | - Peter H Seeberger
- From the ‡Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany.,§Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, 14195 Berlin, Germany
| | - Vlatka Zoldoš
- ¶Faculty of Science, Department of Biology, Division of Molecular Biology, University of Zagreb, Zagreb, Croatia
| | - Daniel Kolarich
- From the ‡Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany;
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29
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Affiliation(s)
- Stefan Gaunitz
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Gabe Nagy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicola L. B. Pohl
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Regional Center for Applied Molecular Oncology, Masaryk Memorial Oncological Institute, 656 53 Brno, Czech Republic
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30
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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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