1
|
Zeng WF, Yan G, Zhao HH, Liu C, Cao W. Uncovering missing glycans and unexpected fragments with pGlycoNovo for site-specific glycosylation analysis across species. Nat Commun 2024; 15:8055. [PMID: 39277585 PMCID: PMC11401942 DOI: 10.1038/s41467-024-52099-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 08/23/2024] [Indexed: 09/17/2024] Open
Abstract
Precision mapping of site-specific glycans using mass spectrometry is vital in glycoproteomics. However, the diversity of glycan compositions across species often exceeds database capacity, hindering the identification of rare glycans. Here, we introduce pGlycoNovo, a software within the pGlyco3 software environment, which employs a glycan first-based full-range Y-ion dynamic searching strategy. pGlycoNovo enables de novo identification of intact glycopeptides with rare glycans by considering all possible monosaccharide combinations, expanding the glycan search space to 16~1000 times compared to non-open search methods, while maintaining accuracy, sensitivity and speed. Reanalysis of SARS Covid-2 spike protein glycosylation data revealed 230 additional site-specific N-glycans and 30 previously unreported O-glycans. pGlycoNovo demonstrated high complementarity to six other tools and superior search speed. It enables characterization of site-specific N-glycosylation across five evolutionarily distant species, contributing to a dataset of 32,549 site-specific glycans on 4602 proteins, including 2409 site-specific rare glycans, and uncovering unexpected glycan fragments.
Collapse
Affiliation(s)
- Wen-Feng Zeng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- Center for Infectious Disease Research & School of Engineering, Westlake University, Hangzhou, China
| | - Guoquan Yan
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Huan-Huan Zhao
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Chao Liu
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Weiqian Cao
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China.
| |
Collapse
|
2
|
Buchowiecka AK. Evidence of Gas Phase Glucosyl Transfer and Glycation in the CID/HCD-Spectra of S-Glucosylated Peptides. Int J Mol Sci 2024; 25:7483. [PMID: 39000590 PMCID: PMC11242366 DOI: 10.3390/ijms25137483] [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: 06/03/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Protein cysteine S-glycosylation is a relatively rare and less well characterized post-translational modification (PTM). Creating reliable model proteins that carry this modification is challenging. The lack of available models or natural S-glycosylated proteins significantly hampers the development of mass-spectrometry-based (MS-based) methodologies for detecting protein cysteine S-glycosylation in real-world proteomic studies. There is also limited MS-sequencing data describing it as easier to create synthetic S-glycopeptides. Here, we present the results of an in-depth manual analysis of automatically annotated CID/HCD spectra for model S-glucopeptides. The CID spectra show a long series of y/b-fragment ions with retained S-glucosylation, regardless of the dominant m/z signals corresponding to neutral loss of 1,2-anhydroglucose from the precursor ions. In addition, the spectra show signals manifesting glucosyl transfer from the cysteine position onto lysine, arginine (Lys, Arg) side chains, and a peptide N-terminus. Other spectral evidence indicates that the N-glucosylated initial products of transfer are converted into N-fructosylated (i.e., glycated) structures due to Amadori rearrangement. We discuss the peculiar transfer of the glucose oxocarbenium ion (Glc+) to positively charged guanidinium residue (ArgH+) and propose a mechanism for the gas-phase Amadori rearrangement involving a 1,2-hydride ion shift.
Collapse
Affiliation(s)
- Alicja K Buchowiecka
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Łódź, Poland
| |
Collapse
|
3
|
DeBono NJ, Moh ESX, Packer NH. Experimentally Determined Diagnostic Ions for Identification of Peptide Glycotopes. J Proteome Res 2024; 23:2661-2673. [PMID: 38888225 DOI: 10.1021/acs.jproteome.3c00858] [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: 06/20/2024]
Abstract
The analysis of the structures of glycans present on glycoproteins is an essential component for determining glycoprotein function; however, detailed glycan structural assignment on glycopeptides from proteomics mass spectrometric data remains challenging. Glycoproteomic analysis by mass spectrometry currently can provide significant, yet incomplete, information about the glycans present, including the glycan monosaccharide composition and in some circumstances the site(s) of glycosylation. Advancements in mass spectrometric resolution, using high-mass accuracy instrumentation and tailored MS/MS fragmentation parameters, coupled with a dedicated definition of diagnostic fragmentation ions have enabled the determination of some glycan structural features, or glycotopes, expressed on glycopeptides. Here we present a collation of diagnostic glycan fragments produced by traditional positive-ion-mode reversed-phase LC-ESI MS/MS proteomic workflows and describe the specific fragmentation energy settings required to identify specific glycotopes presented on N- or O-linked glycopeptides in a typical proteomics MS/MS experiment.
Collapse
Affiliation(s)
- Nicholas J DeBono
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Edward S X Moh
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Nicolle H Packer
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
4
|
Kontodimas V, Yaman M, Greis K, Lettow M, Pagel K, Marianski M. Reinvestigation of the internal glycan rearrangement of Lewis a and blood group type H1 epitopes. Phys Chem Chem Phys 2024; 26:14160-14170. [PMID: 38712976 PMCID: PMC11147448 DOI: 10.1039/d3cp04491b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Protonated ions of fucose-containing oligosaccharides are prone to undergo internal glycan rearrangement which results in chimeric fragments that obfuscate mass-spectrometric analysis. Lack of accessible tools that would facilitate systematic analysis of glycans in the gas phase limits our understanding of this phenomenon. In this work, we use density functional theory modeling to interpret cryogenic IR spectra of Lewis a and blood group type H1 trisaccharides and to establish whether these trisaccharides undergo the rearrangement during gas-phase analysis. Structurally unconstrained search reveals that none of the parent ions constitute a thermodynamic global minimum. In contrast, predicted collision cross sections and anharmonic IR spectra provide a good match to available experimental data which allowed us to conclude that fucose migration does not occur in these antigens. By comparing the predicted structures with those obtained for Lewis x and blood group type H2 epitopes, we demonstrate that the availability of the mobile proton and a large difference in the relative stability of the parent ions and rearrangement products constitute the prerequisites for the rearrangement reaction.
Collapse
Affiliation(s)
- Vasilis Kontodimas
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
| | - Murat Yaman
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Kim Greis
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Maike Lettow
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Mateusz Marianski
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
| |
Collapse
|
5
|
Stadlmann J, Helm J, Mereiter S, Oliveira T, Gattinger A, Markovitz D, Penninger J, Altmann F. Non-targeted isomer-sensitive N-glycome analysis reveals new layers of organ-specific diversity in mice. RESEARCH SQUARE 2024:rs.3.rs-4130712. [PMID: 38659835 PMCID: PMC11042426 DOI: 10.21203/rs.3.rs-4130712/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
N-glycosylation is one of the most common protein modifications in eukaryotes, with immense importance at the molecular, cellular, and organismal level. Accurate and reliable N-glycan analysis is essential to obtain a systems-wide understanding of fundamental biological processes. Due to the structural complexity of glycans, their analysis is still highly challenging. Here we make publicly available a consistent N-glycome dataset of 20 different mouse tissues and demonstrate a multimodal data analysis workflow that allows for unprecedented depth and coverage of N-glycome features. This highly scalable, LC-MS/MS data-driven method integrates the automated identification of N-glycan spectra, the application of non-targeted N-glycome profiling strategies and the isomer-sensitive analysis of glycan structures. Our delineation of critical sub-structural determinants and glycan isomers across the mouse N-glycome uncovered tissue-specific glycosylation patterns, the expression of non-canonical N-glycan structures and highlights multiple layers of N-glycome complexity that derive from organ-specific regulations of glycobiological pathways.
Collapse
Affiliation(s)
| | - Johannes Helm
- University of Natural Resources and Life Sciences Vienna
| | | | - Tiago Oliveira
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)
| | - Anna Gattinger
- Bioinformatics Research Group, University of Applied Sciences Upper Austria
| | | | | | | |
Collapse
|
6
|
Bechtella L, Chunsheng J, Fentker K, Ertürk GR, Safferthal M, Polewski Ł, Götze M, Graeber SY, Vos GM, Struwe WB, Mall MA, Mertins P, Karlsson NG, Pagel K. Ion mobility-tandem mass spectrometry of mucin-type O-glycans. Nat Commun 2024; 15:2611. [PMID: 38521783 PMCID: PMC10960840 DOI: 10.1038/s41467-024-46825-4] [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: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
The dense O-glycosylation of mucins plays an important role in the defensive properties of the mucus hydrogel. Aberrant glycosylation is often correlated with inflammation and pathology such as COPD, cancer, and Crohn's disease. The inherent complexity of glycans and the diversity in the O-core structure constitute fundamental challenges for the analysis of mucin-type O-glycans. Due to coexistence of multiple isomers, multidimensional workflows such as LC-MS are required. To separate the highly polar carbohydrates, porous graphitized carbon is often used as a stationary phase. However, LC-MS workflows are time-consuming and lack reproducibility. Here we present a rapid alternative for separating and identifying O-glycans released from mucins based on trapped ion mobility mass spectrometry. Compared to established LC-MS, the acquisition time is reduced from an hour to two minutes. To test the validity, the developed workflow was applied to sputum samples from cystic fibrosis patients to map O-glycosylation features associated with disease.
Collapse
Affiliation(s)
- Leïla Bechtella
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Jin Chunsheng
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kerstin Fentker
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Güney R Ertürk
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
| | - Marc Safferthal
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Łukasz Polewski
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Michael Götze
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Simon Y Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), associated partner site, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gaël M Vos
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Weston B Struwe
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Marcus A Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), associated partner site, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Berlin Institute of Health, 10178, Berlin, Germany
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany.
| |
Collapse
|
7
|
White MEH, Sinn LR, Jones DM, de Folter J, Aulakh SK, Wang Z, Flynn HR, Krüger L, Tober-Lau P, Demichev V, Kurth F, Mülleder M, Blanchard V, Messner CB, Ralser M. Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics. Nat Biomed Eng 2024; 8:233-247. [PMID: 37474612 DOI: 10.1038/s41551-023-01067-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named 'OxoScan-MS', identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.
Collapse
Affiliation(s)
- Matthew E H White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ludwig R Sinn
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Marc Jones
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Joost de Folter
- Software Engineering and Artificial Intelligence Technology Platform, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ziyue Wang
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Helen R Flynn
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lynn Krüger
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Mülleder
- Core Facility High-throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Véronique Blanchard
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Precision Proteomic Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland.
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
| |
Collapse
|
8
|
Lettow M, Greis K, Mucha E, Lambeth TR, Yaman M, Kontodimas V, Manz C, Hoffmann W, Meijer G, Julian RR, von Helden G, Marianski M, Pagel K. Decoding the Fucose Migration Product during Mass-Spectrometric analysis of Blood Group Epitopes. Angew Chem Int Ed Engl 2023; 62:e202302883. [PMID: 36939315 PMCID: PMC10299593 DOI: 10.1002/anie.202302883] [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: 02/25/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/21/2023]
Abstract
Fucose is a signaling carbohydrate that is attached at the end of glycan processing. It is involved in a range of processes, such as the selectin-dependent leukocyte adhesion or pathogen-receptor interactions. Mass-spectrometric techniques, which are commonly used to determine the structure of glycans, frequently show fucose-containing chimeric fragments that obfuscate the analysis. The rearrangement leading to these fragments-often referred to as fucose migration-has been known for more than 25 years, but the chemical identity of the rearrangement product remains unclear. In this work, we combine ion-mobility spectrometry, radical-directed dissociation mass spectrometry, cryogenic IR spectroscopy of ions, and density-functional theory calculations to deduce the product of the rearrangement in the model trisaccharides Lewis x and blood group H2. The structural search yields the fucose moiety attached to the galactose with an α(1→6) glycosidic bond as the most likely product.
Collapse
Affiliation(s)
- Maike Lettow
- Fritz-Haber-Intitut der Max-Planck-Gesellschaft, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Germany
| | - Kim Greis
- Fritz-Haber-Intitut der Max-Planck-Gesellschaft, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Germany
| | - Eike Mucha
- Fritz-Haber-Intitut der Max-Planck-Gesellschaft, Germany
| | - Tyler R Lambeth
- Department of Chemistry, University of California, Riverside, USA
| | - Murat Yaman
- Department of Chemistry and Biochemistry, Hunter College, The City University of New York, USA
- The PhD Program in Chemistry and Biochemistry, The Graduate Center, The City University of New York, USA
| | - Vasilis Kontodimas
- Department of Chemistry and Biochemistry, Hunter College, The City University of New York, USA
| | - Christian Manz
- Fritz-Haber-Intitut der Max-Planck-Gesellschaft, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Germany
| | - Waldemar Hoffmann
- Fritz-Haber-Intitut der Max-Planck-Gesellschaft, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Germany
| | - Gerard Meijer
- Fritz-Haber-Intitut der Max-Planck-Gesellschaft, Germany
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, USA
| | | | - Mateusz Marianski
- Department of Chemistry and Biochemistry, Hunter College, The City University of New York, USA
- The PhD Program in Chemistry and Biochemistry, The Graduate Center, The City University of New York, USA
| | - Kevin Pagel
- Fritz-Haber-Intitut der Max-Planck-Gesellschaft, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Germany
| |
Collapse
|
9
|
Moge B, Schindler B, Yeni O, Compagnon I. Fucose Migration Pathways Identified Using Infrared Spectroscopy. Angew Chem Int Ed Engl 2023; 62:e202300538. [PMID: 36825496 DOI: 10.1002/anie.202300538] [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: 01/12/2023] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 02/25/2023]
Abstract
Fucose is a ubiquitous monosaccharide associated to major classes of glycans. A main obstacle to the sequencing of fucosylated glycans is the migration of fucose, which leads to misinterpretations in mass spectrometry analysis. Here, using ion vibrational spectroscopy, we resolve the structure of fucosylated fragments of Lewis and blood group H antigen trisaccharides and we unveil the position and linkage of the fucose after migration. Our findings demonstrate that the structure of fragment ions resulting from fucose migration can be characterized. Additionally, we report a new type of fucose migration, which does not feature any change of mass and therefore had not been previously reported: it consists of a local migration where the fucose changes its position remaining on the initial residue. Our approach allows the characterization of glycans, an essential step to interpret glycomics data, as well as to understand underlying processes at play in mass spectrometry.
Collapse
Affiliation(s)
- Baptiste Moge
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, 69622, Villeurbanne, France
| | - Baptiste Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, 69622, Villeurbanne, France
| | - Oznur Yeni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, 69622, Villeurbanne, France
| | - Isabelle Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, 69622, Villeurbanne, France
| |
Collapse
|
10
|
Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth 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 2020. 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. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
Collapse
Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
| |
Collapse
|
11
|
Zappe A, Miller RL, Struwe WB, Pagel K. State-of-the-art glycosaminoglycan characterization. MASS SPECTROMETRY REVIEWS 2022; 41:1040-1071. [PMID: 34608657 DOI: 10.1002/mas.21737] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/02/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Glycosaminoglycans (GAGs) are heterogeneous acidic polysaccharides involved in a range of biological functions. They have a significant influence on the regulation of cellular processes and the development of various diseases and infections. To fully understand the functional roles that GAGs play in mammalian systems, including disease processes, it is essential to understand their structural features. Despite having a linear structure and a repetitive disaccharide backbone, their structural analysis is challenging and requires elaborate preparative and analytical techniques. In particular, the extent to which GAGs are sulfated, as well as variation in sulfate position across the entire oligosaccharide or on individual monosaccharides, represents a major obstacle. Here, we summarize the current state-of-the-art methodologies used for GAG sample preparation and analysis, discussing in detail liquid chromatograpy and mass spectrometry-based approaches, including advanced ion activation methods, ion mobility separations and infrared action spectroscopy of mass-selected species.
Collapse
Affiliation(s)
- Andreas Zappe
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Rebecca L Miller
- Department of Cellular and Molecular Medicine, Copenhagen Centre for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Kevin Pagel
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
12
|
Liew CY, Hsu HC, Nguan HS, Huang YC, Zhong YQ, Hung SC, Ni CK. The Good, the Bad, and the Ugly Memories of Carbohydrate Fragments in Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1891-1903. [PMID: 36111786 DOI: 10.1021/jasms.2c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Collision-induced dissociation (CID) tandem mass spectrometry is commonly used for carbohydrate structural determinations. In the CID tandem mass spectrometry approach, carbohydrates are dissociated into fragments, and this is followed by the structural identification of fragments through subsequent CID. The success of the structural analysis depends on the structural correlation of fragments before and after dissociation, that is, structural memory of fragments. Fragments that completely lose the memory of their original structures cannot be used for structural analysis. By contrast, fragments with extremely strong correlations between the structures before and after fragmentation retain the information on their original structures as well as have memories of their precursors' entire structures. The CID spectra of these fragments depend on their own structures and on the remaining parts of the precursor structures, making structural analysis impractical. For effective structural analysis, the fragments produced from a precursor must have good structural memory, meaning that the structures of these fragments retain their original structure, and they must not be strongly affected by the remaining parts of the precursors. In this study, we found that most of the carbohydrate fragments produced by low-energy CID have good memory in terms of linkage position and anomericity. Fragments with ugly memory, where fragment structures change with the remaining parts of the precursors, can be attributed to C ion formation in a linear form. Fragments with ugly memory can be changed to have good memory by preventing linear C ion generation by using an alternative CID sequence, or the fragments of ugly memory can become useful in structural analysis when the contribution of linear C ions in fragmentation patterns is understood.
Collapse
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
- Taiwan International Graduate Program (TIGP) of Molecular Science and Technology (MST), Academia Sinica, Taipei 10617, Taiwan
| | - Hsu Chen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Yu-Chao Huang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yong-Qing Zhong
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | | | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Taiwan International Graduate Program (TIGP) of Molecular Science and Technology (MST), Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| |
Collapse
|
13
|
Manz C, Mancera-Arteu M, Zappe A, Hanozin E, Polewski L, Giménez E, Sanz-Nebot V, Pagel K. Determination of Sialic Acid Isomers from Released N-Glycans Using Ion Mobility Spectrometry. Anal Chem 2022; 94:13323-13331. [PMID: 36121379 PMCID: PMC9535620 DOI: 10.1021/acs.analchem.2c00783] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Complex carbohydrates are ubiquitous in nature and represent one of the major classes of biopolymers. They can exhibit highly diverse structures with multiple branched sites as well as a complex regio- and stereochemistry. A common way to analytically address this complexity is liquid chromatography (LC) in combination with mass spectrometry (MS). However, MS-based detection often does not provide sufficient information to distinguish glycan isomers. Ion mobility-mass spectrometry (IM-MS)─a technique that separates ions based on their size, charge, and shape─has recently shown great potential to solve this problem by identifying characteristic isomeric glycan features such as the sialylation and fucosylation pattern. However, while both LC-MS and IM-MS have clearly proven their individual capabilities for glycan analysis, attempts to combine both methods into a consistent workflow are lacking. Here, we close this gap and combine hydrophilic interaction liquid chromatography (HILIC) with IM-MS to analyze the glycan structures released from human alpha-1-acid glycoprotein (hAGP). HILIC separates the crude mixture of highly sialylated multi-antennary glycans, MS provides information on glycan composition, and IMS is used to distinguish and quantify α2,6- and α2,3-linked sialic acid isomers based on characteristic fragments. Further, the technique can support the assignment of antenna fucosylation. This feature mapping can confidently assign glycan isomers with multiple sialic acids within one LC-IM-MS run and is fully compatible with existing workflows for N-glycan analysis.
Collapse
Affiliation(s)
- Christian Manz
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstr. 23A, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Montserrat Mancera-Arteu
- Department
of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, 08028 Barcelona, Spain
| | - Andreas Zappe
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstr. 23A, 14195 Berlin, Germany
| | - Emeline Hanozin
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstr. 23A, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Lukasz Polewski
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstr. 23A, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Estela Giménez
- Department
of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, 08028 Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department
of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, 08028 Barcelona, Spain
| | - Kevin Pagel
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstr. 23A, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Towards Mapping of the Human Brain N-Glycome with Standardized Graphitic Carbon Chromatography. Biomolecules 2022; 12:biom12010085. [PMID: 35053234 PMCID: PMC8774104 DOI: 10.3390/biom12010085] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/21/2022] Open
Abstract
The brain N-glycome is known to be crucial for many biological functions, including its involvement in neuronal diseases. Although large structural studies of brain N-glycans were recently carried out, a comprehensive isomer-specific structural analysis has still not been achieved, as indicated by the recent discovery of novel structures with galactosylated bisecting GlcNAc. Here, we present a detailed, isomer-specific analysis of the human brain N-glycome based on standardized porous graphitic carbon (PGC)-LC-MS/MS. To achieve this goal, we biosynthesized glycans with substitutions typically occurring in the brain N-glycome and acquired their normalized retention times. Comparison of these values with the standardized retention times of neutral and desialylated N-glycan fractions of the human brain led to unambiguous isomer specific assignment of most major peaks. Profound differences in the glycan structures between naturally neutral and desialylated glycans were found. The neutral and sialylated N-glycans derive from diverging biosynthetic pathways and are biosynthetically finished end products, rather than just partially processed intermediates. The focus on structural glycomics defined the structure of human brain N-glycans, amongst these are HNK-1 containing glycans, a bisecting sialyl-lactose and structures with fucose and N-acetylgalactosamine on the same arm, the so-called LDNF epitope often associated with parasitic worms.
Collapse
|
16
|
Hong T, Yin JY, Nie SP, Xie MY. Applications of infrared spectroscopy in polysaccharide structural analysis: Progress, challenge and perspective. Food Chem X 2021; 12:100168. [PMID: 34877528 PMCID: PMC8633561 DOI: 10.1016/j.fochx.2021.100168] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/31/2022] Open
Abstract
Functional properties of polysaccharides depend on their structural features. IR spectroscopy is widely used in polysaccharide structural analysis. Classical applications of IR spectroscopy in polysaccharide are reviewed. IR integrating techniques can considerably expand its application scope.
Polysaccharides are important biomacromolecules with numerous beneficial functions and a wide range of industrial applications. Functions and properties of polysaccharides are closely related to their structural features. Infrared (IR) spectroscopy is a well-established technique which has been widely applied in polysaccharide structural analysis. In this paper, the principle of IR and interpretation of polysaccharide IR spectrum are briefly introduced. Classical applications of IR spectroscopy in polysaccharide structural elucidation are reviewed from qualitative and quantitative aspects. Some advanced IR techniques including integrating with mass spectrometry (MS), microscopy and computational chemistry are introduced and their applications are emphasized. These emerging techniques can considerably expand application scope of IR, thus exert a more important effect on carbohydrate characterization. Overall, this review seeks to provide a comprehensive insight to applications of IR spectroscopy in polysaccharide structural analysis and highlights the importance of advanced IR-integrating techniques.
Collapse
Affiliation(s)
- Tao Hong
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Jun-Yi Yin
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Ming-Yong Xie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| |
Collapse
|
17
|
Greis K, Kirschbaum C, von Helden G, Pagel K. Gas-phase infrared spectroscopy of glycans and glycoconjugates. Curr Opin Struct Biol 2021; 72:194-202. [PMID: 34952241 DOI: 10.1016/j.sbi.2021.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/02/2021] [Accepted: 11/21/2021] [Indexed: 11/28/2022]
Abstract
Glycans are intrinsically complex biomolecules that pose particular analytical challenges. Standard workflows for glycan analysis are based on mass spectrometry, often coupled with separation techniques such as liquid chromatography and ion mobility spectrometry. However, this approach does not yield direct structural information and cannot always distinguish between isomers. This gap might be filled in the future by gas-phase infrared spectroscopy, which has emerged as a promising structure-sensitive technique for glycan fingerprinting. This review highlights recent applications of gas-phase infrared spectroscopy for the analysis of synthetic and biological glycans and how they can be integrated into mass spectrometry-based workflows.
Collapse
Affiliation(s)
- Kim Greis
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Carla Kirschbaum
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Kevin Pagel
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
| |
Collapse
|
18
|
Tomek MB, Janesch B, Braun ML, Taschner M, Figl R, Grünwald-Gruber C, Coyne MJ, Blaukopf M, Altmann F, Kosma P, Kählig H, Comstock LE, Schäffer C. A Combination of Structural, Genetic, Phenotypic and Enzymatic Analyses Reveals the Importance of a Predicted Fucosyltransferase to Protein O-Glycosylation in the Bacteroidetes. Biomolecules 2021; 11:1795. [PMID: 34944439 PMCID: PMC8698959 DOI: 10.3390/biom11121795] [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: 10/18/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 12/20/2022] Open
Abstract
Diverse members of the Bacteroidetes phylum have general protein O-glycosylation systems that are essential for processes such as host colonization and pathogenesis. Here, we analyzed the function of a putative fucosyltransferase (FucT) family that is widely encoded in Bacteroidetes protein O-glycosylation genetic loci. We studied the FucT orthologs of three Bacteroidetes species-Tannerella forsythia, Bacteroides fragilis, and Pedobacter heparinus. To identify the linkage created by the FucT of B. fragilis, we elucidated the full structure of its nine-sugar O-glycan and found that l-fucose is linked β1,4 to glucose. Of the two fucose residues in the T. forsythia O-glycan, the fucose linked to the reducing-end galactose was shown by mutational analysis to be l-fucose. Despite the transfer of l-fucose to distinct hexose sugars in the B. fragilis and T. forsythia O-glycans, the FucT orthologs from B. fragilis, T. forsythia, and P. heparinus each cross-complement the B. fragilis ΔBF4306 and T. forsythia ΔTanf_01305 FucT mutants. In vitro enzymatic analyses showed relaxed acceptor specificity of the three enzymes, transferring l-fucose to various pNP-α-hexoses. Further, glycan structural analysis together with fucosidase assays indicated that the T. forsythia FucT links l-fucose α1,6 to galactose. Given the biological importance of fucosylated carbohydrates, these FucTs are promising candidates for synthetic glycobiology.
Collapse
Affiliation(s)
- Markus B. Tomek
- NanoGlycobiology Unit, Institute of Biologically Inspired Materials, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria; (M.B.T.); (B.J.); (M.L.B.); (M.T.)
| | - Bettina Janesch
- NanoGlycobiology Unit, Institute of Biologically Inspired Materials, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria; (M.B.T.); (B.J.); (M.L.B.); (M.T.)
| | - Matthias L. Braun
- NanoGlycobiology Unit, Institute of Biologically Inspired Materials, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria; (M.B.T.); (B.J.); (M.L.B.); (M.T.)
| | - Manfred Taschner
- NanoGlycobiology Unit, Institute of Biologically Inspired Materials, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria; (M.B.T.); (B.J.); (M.L.B.); (M.T.)
| | - Rudolf Figl
- Institute of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, A-1190 Vienna, Austria; (R.F.); (C.G.-G.); (F.A.)
| | - Clemens Grünwald-Gruber
- Institute of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, A-1190 Vienna, Austria; (R.F.); (C.G.-G.); (F.A.)
| | - Michael J. Coyne
- Department of Microbiology and the Duchossois Family Institute, University of Chicago, KCBD, 900 E. 57th Street, Chicago, IL 60637, USA; (M.J.C.); (L.E.C.)
| | - Markus Blaukopf
- Institute of Organic Chemistry, Department of Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, A-1190 Vienna, Austria; (M.B.); (P.K.)
| | - Friedrich Altmann
- Institute of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, A-1190 Vienna, Austria; (R.F.); (C.G.-G.); (F.A.)
| | - Paul Kosma
- Institute of Organic Chemistry, Department of Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, A-1190 Vienna, Austria; (M.B.); (P.K.)
| | - Hanspeter Kählig
- Department of Organic Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 38, A-1090 Vienna, Austria;
| | - Laurie E. Comstock
- Department of Microbiology and the Duchossois Family Institute, University of Chicago, KCBD, 900 E. 57th Street, Chicago, IL 60637, USA; (M.J.C.); (L.E.C.)
| | - Christina Schäffer
- NanoGlycobiology Unit, Institute of Biologically Inspired Materials, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria; (M.B.T.); (B.J.); (M.L.B.); (M.T.)
| |
Collapse
|
19
|
Mookherjee A, Uppal SS, Murphree TA, Guttman M. Linkage Memory in Underivatized Protonated Carbohydrates. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:581-589. [PMID: 33350817 PMCID: PMC8136833 DOI: 10.1021/jasms.0c00440] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Carbohydrates are among the most complex class of biomolecules, and even subtle variations in their structures are attributed to diverse biological functions. Mass spectrometry has been essential for large scale glycomics and glycoproteomics studies, but the gas-phase structures and sometimes anomalous fragmentation properties of carbohydrates present long-standing challenges. Here we investigate the gas-phase properties of a panel of isomeric protonated disaccharides differing in their linkage configurations. Multiple conformations were evident for most of the structures based on their fragment ion abundances by tandem mass spectrometry, their ion mobilities in several gases, and their deuterium uptake kinetics by gas-phase hydrogen-deuterium exchange. Most notably, we find that the properties of the Y-ion fragments are characteristically influenced by the precursor carbohydrate's linkage configuration. This study reveals how protonated carbohydrate fragment ions can retain "linkage memory" that provides structural insight into their intact precursor.
Collapse
|
20
|
Chizhov AO, Filatov AV, Perepelov AV, Knirel YA. A New Example of Rearrangement Observed in the Tandem Mass Spectra of Oligosaccharides. JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1134/s1061934820140075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
21
|
She YM, Tam RY, Li X, Rosu-Myles M, Sauvé S. Resolving Isomeric Structures of Native Glycans by Nanoflow Porous Graphitized Carbon Chromatography-Mass Spectrometry. Anal Chem 2020; 92:14038-14046. [PMID: 32960038 DOI: 10.1021/acs.analchem.0c02951] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Characterization of the structural diversity of glycans by liquid chromatography-tandem mass spectrometry (LC-MS/MS) remains an analytical challenge in large-scale glycomics applications because of the presence of heterogeneous composition, ubiquitous isomers, lability of post-translational glycan modifications, and complexity of data interpretation. High-resolution separation of glycan isomers differentiating from positional, linkage, branching, and anomeric structures is often a prerequisite to ensure the comprehensive glycan identification. Here, we developed a straightforward method using self-packed capillary porous graphitic carbon (PGC) columns for nanoflow LC-MS/MS analyses of native glycans released from glycoproteins. The technique enables highly resolved chromatographic separation of over 20 high-mannose glycan isomers in ribonuclease B and a diverse range of hybrid and complex-type sialoglycoforms of fetuin. The distinct structures of anomeric glycans and linkage sialoglycan isomers, α2,3 and α2,6, were identified by the characteristic MS/MS fragment ions. A glycan sequencing strategy utilizing diagnostic ions and complementary fragments specific to branching residues was established to simplify the MS/MS data interpretation of closely related isomeric structures. To promote the PGC-LC-MS/MS-based method for glycome-wide applications, we extended analyses to native sulfoglycans from the egg-propagated and cell culture-derived influenza vaccines and demonstrate the high-resolution separation and structural characterization of underivatized neutral and anionic glycoforms including oligomannosidic glycan anomers, sialoglycan linkage isomers, and regioisomers of afucosylated and fucosylated sulfoglycans containing sulfated-6-GlcNAc and sulfated-4-GalNAc residues.
Collapse
Affiliation(s)
- Yi-Min She
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Roger Y Tam
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Xuguang Li
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Michael Rosu-Myles
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Simon Sauvé
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| |
Collapse
|
22
|
Porfirio S, Archer-Hartmann S, Moreau GB, Ramakrishnan G, Haque R, Kirkpatrick BD, Petri WA, Azadi P. New strategies for profiling and characterization of human milk oligosaccharides. Glycobiology 2020; 30:774-786. [PMID: 32248230 PMCID: PMC7526734 DOI: 10.1093/glycob/cwaa028] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/19/2022] Open
Abstract
Human breast milk is an incredibly rich and complex biofluid composed of proteins, lipids and complex carbohydrates, including a diverse repertoire of free human milk oligosaccharides (HMOs). Strikingly, HMOs are not digested by the infant but function as prebiotics for bacterial strains associated with numerous benefits. Considering the broad variety of beneficial effects of HMOs, and the vast number of factors that affect breast milk composition, the analysis of HMO diversity and complexity is of utmost relevance. Using human milk samples from a cohort of Bangladeshi mothers participating in a study on malnutrition and stunting in children, we have characterized breast milk oligosaccharide composition by means of permethylation followed by liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-MS/MS) analysis. This approach identified over 100 different glycoforms and showed a wide diversity of milk composition, with a predominance of fucosylated and sialylated HMOs over nonmodified HMOs. We observed that these samples contain on average 80 HMOs, with the highest permethylated masses detected being >5000 mass units. Here we report an easily implemented method developed for the separation, characterization and relative quantitation of large arrays of HMOs, including higher molecular weight sialylated HMOs. Our ultimate goal is to create a simple, high-throughput method, which can be used for full characterization of sialylated and/or fucosylated HMOs. These results demonstrate how current analytical techniques can be applied to characterize human milk composition, providing new tools to help the scientific community shed new light on the impact of HMOs during infant development.
Collapse
Affiliation(s)
- Sara Porfirio
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602, USA
| | | | - G Brett Moreau
- Department of Medicine/Infectious Diseases, University of Virginia, Charlottesville, VA 22903, USA
| | - Girija Ramakrishnan
- Department of Medicine/Infectious Diseases, University of Virginia, Charlottesville, VA 22903, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Beth D Kirkpatrick
- Department of Medicine, University of Vermont, Burlington, VT 05401, USA
| | - William A Petri
- Department of Medicine/Infectious Diseases, University of Virginia, Charlottesville, VA 22903, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
23
|
Rebello OD, Nicolardi S, Lageveen-Kammeijer GSM, Nouta J, Gardner RA, Mesker WE, Tollenaar RAEM, Spencer DIR, Wuhrer M, Falck D. A Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Assay for the Relative Quantitation of Antennary Fucosylated N-Glycans in Human Plasma. Front Chem 2020; 8:138. [PMID: 32185163 PMCID: PMC7059190 DOI: 10.3389/fchem.2020.00138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/14/2020] [Indexed: 12/29/2022] Open
Abstract
Changes in the abundance of antennary fucosylated glycans in human total plasma N-glycome (TPNG) have been associated with several diseases ranging from diabetes to various forms of cancer. However, it is challenging to address this important part of the human glycome. Most commonly, time-consuming chromatographic separations are performed to differentially quantify core and antenna fucosylation. Obtaining sufficient resolution for larger, more complex glycans can be challenging. We introduce a matrix-assisted laser desorption/ionization—mass spectrometry (MALDI-MS) assay for the relative quantitation of antennary fucosylation in TPNG. N-linked glycans are released from plasma by PNGase F and further treated with a core fucosidase before performing a linkage-informative sialic acid derivatization. The core fucosylated glycans are thus depleted while the remaining antennary fucosylated glycans are quantitated. Simultaneous quantitation of α2,3-linked sialic acids and antennary fucosylation allows an estimation of the sialyl-Lewis x motif. The approach is feasible using either ultrahigh-resolution Fourier-transform ion cyclotron resonance mass spectrometry or time-of-flight mass spectrometry. The assay was used to investigate changes of antennary fucosylation as clinically relevant marker in 14 colorectal cancer patients. In accordance with a previous report, we found elevated levels of antennary fucosylation pre-surgery which decreased after tumor resection. The assay has the potential for revealing antennary fucosylation signatures in various conditions including diabetes and different types of cancer.
Collapse
Affiliation(s)
- Osmond D Rebello
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands.,Ludger Ltd, Culham Science Centre, Abingdon, United Kingdom
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Jan Nouta
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Wilma E Mesker
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | | | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - David Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| |
Collapse
|
24
|
Yalovenko N, Yatsyna V, Bansal P, AbiKhodr AH, Rizzo TR. Analyzing glycans cleaved from a biotherapeutic protein using ultrahigh-resolution ion mobility spectrometry together with cryogenic ion spectroscopy. Analyst 2020; 145:6493-6499. [DOI: 10.1039/d0an01206h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new approach for analysis of cleaved glycans.
Collapse
Affiliation(s)
- Natalia Yalovenko
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Vasyl Yatsyna
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Priyanka Bansal
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Ali H. AbiKhodr
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| |
Collapse
|
25
|
Manz C, Grabarics M, Hoberg F, Pugini M, Stuckmann A, Struwe WB, Pagel K. Separation of isomeric glycans by ion mobility spectrometry – the impact of fluorescent labelling. Analyst 2019; 144:5292-5298. [DOI: 10.1039/c9an00937j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bloodgroup oligosaccharides have been derivatized with labels common in HPLC and evaluated regarding their ion mobility behaviour.
Collapse
Affiliation(s)
- Christian Manz
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Fritz Haber Institute of the Max Planck Society
| | - Márkó Grabarics
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Fritz Haber Institute of the Max Planck Society
| | - Friederike Hoberg
- Fritz Haber Institute of the Max Planck Society
- Department of Molecular Physics
- 14195 Berlin
- Germany
| | - Michele Pugini
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Fritz Haber Institute of the Max Planck Society
| | - Alexandra Stuckmann
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Weston B. Struwe
- Oxford Glycobiology Institute
- Department of Biochemistry
- University of Oxford
- Oxford OX1 3QU
- UK
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Fritz Haber Institute of the Max Planck Society
| |
Collapse
|