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Girgis M, Petruncio G, Russo P, Peyton S, Paige M, Campos D, Sanda M. Analysis of N- and O-linked site-specific glycosylation by ion mobility mass spectrometry: State of the art and future directions. Proteomics 2024; 24:e2300281. [PMID: 38171879 DOI: 10.1002/pmic.202300281] [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: 07/18/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
Glycosylation, the major post-translational modification of proteins, significantly increases the diversity of proteoforms. Glycans are involved in a variety of pivotal structural and functional roles of proteins, and changes in glycosylation are profoundly connected to the progression of numerous diseases. Mass spectrometry (MS) has emerged as the gold standard for glycan and glycopeptide analysis because of its high sensitivity and the wealth of fragmentation information that can be obtained. Various separation techniques have been employed to resolve glycan and glycopeptide isomers at the front end of the MS. However, differentiating structures of isobaric and isomeric glycopeptides constitutes a challenge in MS-based characterization. Many reports described the use of various ion mobility-mass spectrometry (IM-MS) techniques for glycomic analyses. Nevertheless, very few studies have focused on N- and O-linked site-specific glycopeptidomic analysis. Unlike glycomics, glycoproteomics presents a multitude of inherent challenges in microheterogeneity, which are further exacerbated by the lack of dedicated bioinformatics tools. In this review, we cover recent advances made towards the growing field of site-specific glycosylation analysis using IM-MS with a specific emphasis on the MS techniques and capabilities in resolving isomeric peptidoglycan structures. Furthermore, we discuss commonly used software that supports IM-MS data analysis of glycopeptides.
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Affiliation(s)
- Michael Girgis
- Department of Bioengineering, College of Engineering & Computing, George Mason University, Fairfax, Virginia, USA
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
| | - Gregory Petruncio
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
- Department of Chemistry & Biochemistry, College of Science, George Mason University, Fairfax, Virginia, USA
| | - Paul Russo
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Steven Peyton
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
| | - Mikell Paige
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
- Department of Chemistry & Biochemistry, College of Science, George Mason University, Fairfax, Virginia, USA
| | - Diana Campos
- Max-Planck-Institut fuer Herz- und Lungenforschung, Bad Nauheim, Germany
| | - Miloslav Sanda
- Max-Planck-Institut fuer Herz- und Lungenforschung, Bad Nauheim, Germany
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Tomris I, Kimpel A, Liang R, van der Woude R, Boons GJ, Li Z, de Vries RP. The HCoV-HKU1 N-terminal domain binds a wide range of 9- O-acetylated sialic acids presented on different glycan cores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595699. [PMID: 38826377 PMCID: PMC11142222 DOI: 10.1101/2024.05.24.595699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Coronaviruses recognize a wide array of protein and glycan receptors using the S1 subunit of the spike (S) glycoprotein. The S1 subunit contains two functional domains: the N-terminal (S1-NTD) and C-terminal (S1-CTD). The S1-NTD of SARS-CoV-2, MERS-CoV, and HCoV-HKU1 possess an evolutionarily conserved glycan binding cleft that facilitates weak interactions with sialic acids on cell surfaces. HCoV-HKU1 employs 9-O-acetylated α2-8-linked disialylated structures for initial binding, followed by TMPRSS2 receptor binding and virus-cell fusion. Here, we demonstrate that HCoV-HKU1 NTD has a broader receptor binding repertoire than previously recognized. We presented HCoV-HKU1 NTD Fc chimeras on a nanoparticle system to mimic the densely decorated surface of HCoV-HKU1. These proteins were expressed by HEK293S GNTI- cells, generating species carrying Man-5 structures, often observed near the receptor binding site of CoVs. This multivalent presentation of high-mannose-containing NTD proteins revealed a much broader receptor binding profile compared to its fully glycosylated counterpart. Using glycan microarrays, we observed that 9-O-acetylated α2-3 linked sialylated LacNAc structures are also bound, comparable to OC43 NTD, suggesting an evolutionarily conserved glycan-binding modality. Further characterization of receptor specificity indicated promiscuous binding towards 9-O-acetylated sialoglycans, independent of the glycan core (glycolipids, N- or O-glycans). We demonstrate that HCoV-HKU1 may employ additional sialoglycan receptors to trigger conformational changes in the spike glycoprotein to expose the S1-CTD for proteinaceous receptor binding.
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Affiliation(s)
- Ilhan Tomris
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Anne Kimpel
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ruonan Liang
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Roosmarijn van der Woude
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Zeshi Li
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Robert P. de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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Li Y, Fu B, Li Y, Li C, Zhai Y, Feng X, Wang J, Zhang Y, Lu H. O-GlycoIsoQuant: A Novel O-Glycome Quantitative Approach through Superbase Release and Isotopic Girard's P Labeling. Anal Chem 2024; 96:7289-7296. [PMID: 38666489 DOI: 10.1021/acs.analchem.4c01300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Quantitative glycosylation analysis serves as an effective tool for detecting changes in glycosylation patterns in cancer and various diseases. However, compared with N-glycans, O-glycans present challenges in both qualitative and quantitative mass spectrometry analysis due to their low abundance, ease of peeling, lack of a universal enzyme, and difficult accessibility. To address this challenge, we developed O-GlycoIsoQuant, a novel O-glycome quantitative approach utilizing superbase release and isotopic Girard's P labeling. This method facilitates rapid and efficient nonreducing β-elimination to dissociate O-glycans from proteins using the organic superbase, 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU), combined with light and heavy isotopic Girard's reagent P (GP) labeling for relative quantification of O-glycans by mass spectrometry. Employing this method, labeled O-glycans exhibit a double peak with a mass difference of 5 Da, suitable for stable relative quantification. The O-GlycoIsoQuant method is characterized by its high labeling efficiency, excellent reproducibility (CV < 20%), and good linearity (R2 > 0.99), across a dynamic range spanning a 100-fold range. This method was applied to various complex sample types, including human serum, porcine spermatozoa, human saliva, and urinary extracellular vesicles, detecting 33, 39, 49, and 37 O-glycans, respectively, thereby demonstrating its broad applicability.
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Affiliation(s)
- Yueyue Li
- Liver Cancer Institute, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Bin Fu
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Yang Li
- Liver Cancer Institute, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Chong Li
- Liver Cancer Institute, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yujia Zhai
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu 610041, China
| | - Xiaoxiao Feng
- Liver Cancer Institute, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jun Wang
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
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Safferthal M, Bechtella L, Zappe A, Vos GM, Pagel K. Labeling of Mucin-Type O-Glycans for Quantification Using Liquid Chromatography and Fluorescence Detection. ACS MEASUREMENT SCIENCE AU 2024; 4:223-230. [PMID: 38645579 PMCID: PMC11027200 DOI: 10.1021/acsmeasuresciau.3c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 04/23/2024]
Abstract
O-glycosylation is a common post-translational modification that is essential for the defensive properties of mucus barriers. Incomplete and altered O-glycosylation is often linked to severe diseases, such as cancer, cystic fibrosis, and chronic obstructive pulmonary disease. Originating from a nontemplate-driven biosynthesis, mucin-type O-glycan structures are very complex. They are often present as heterogeneous mixtures containing multiple isomers. Therefore, the analysis of complex O-glycan mixtures usually requires hyphenation of orthogonal techniques such as liquid chromatography (LC), ion mobility spectrometry, and mass spectrometry (MS). However, MS-based techniques are mainly qualitative. Moreover, LC separation of O-glycans often lacks reproducibility and requires sophisticated data treatment and analysis. Here we present a mucin-type O-glycomics analysis workflow that utilizes hydrophilic interaction liquid chromatography for separation and fluorescence labeling for detection and quantification. In combination with mass spectrometry, a detailed analysis on the relative abundance of specific mucin-type O-glycan compositions and features, such as fucose, sialic acids, and sulfates, is performed. Furthermore, the average number of monosaccharide units of O-glycans in different samples was determined. To demonstrate universal applicability, the method was tested on mucins from different tissue types and mammals, such as bovine submaxillary mucins, porcine gastric mucins, and human milk mucins. To account for day-to-day retention time shifts in O-glycan separations and increase the comparability between different instruments and laboratories, we included fluorescently labeled dextran ladders in our workflow. In addition, we set up a library of glucose unit values for all identified O-glycans, which can be used to simplify the identification process of glycans in future analyses.
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Affiliation(s)
- Marc Safferthal
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Leïla Bechtella
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Andreas Zappe
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Gaël M. Vos
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
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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.
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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.
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