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Onigbinde S, Gutierrez Reyes CD, Sandilya V, Chukwubueze F, Oluokun O, Sahioun S, Oluokun A, Mechref Y. Optimization of glycopeptide enrichment techniques for the identification of clinical biomarkers. Expert Rev Proteomics 2024; 21:431-462. [PMID: 39439029 PMCID: PMC11877277 DOI: 10.1080/14789450.2024.2418491] [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: 06/05/2024] [Revised: 07/28/2024] [Accepted: 10/11/2024] [Indexed: 10/25/2024]
Abstract
INTRODUCTION The identification and characterization of glycopeptides through LC-MS/MS and advanced enrichment techniques are crucial for advancing clinical glycoproteomics, significantly impacting the discovery of disease biomarkers and therapeutic targets. Despite progress in enrichment methods like Lectin Affinity Chromatography (LAC), Hydrophilic Interaction Liquid Chromatography (HILIC), and Electrostatic Repulsion Hydrophilic Interaction Chromatography (ERLIC), issues with specificity, efficiency, and scalability remain, impeding thorough analysis of complex glycosylation patterns crucial for disease understanding. AREAS COVERED This review explores the current challenges and innovative solutions in glycopeptide enrichment and mass spectrometry analysis, highlighting the importance of novel materials and computational advances for improving sensitivity and specificity. It outlines the potential future directions of these technologies in clinical glycoproteomics, emphasizing their transformative impact on medical diagnostics and therapeutic strategies. EXPERT OPINION The application of innovative materials such as Metal-Organic Frameworks (MOFs), Covalent Organic Frameworks (COFs), functional nanomaterials, and online enrichment shows promise in addressing challenges associated with glycoproteomics analysis by providing more selective and robust enrichment platforms. Moreover, the integration of artificial intelligence and machine learning is revolutionizing glycoproteomics by enhancing the processing and interpretation of extensive data from LC-MS/MS, boosting biomarker discovery, and improving predictive accuracy, thus supporting personalized medicine.
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Affiliation(s)
- Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | | | - Vishal Sandilya
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Favour Chukwubueze
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Odunayo Oluokun
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Sarah Sahioun
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Ayobami Oluokun
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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Goumenou A, Delaunay N, Pichon V. Recent Advances in Lectin-Based Affinity Sorbents for Protein Glycosylation Studies. Front Mol Biosci 2021; 8:746822. [PMID: 34778373 PMCID: PMC8585745 DOI: 10.3389/fmolb.2021.746822] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/23/2021] [Indexed: 01/29/2023] Open
Abstract
Glycosylation is one of the most significant post-translational modifications occurring to proteins, since it affects some of their basic properties, such as their half-life or biological activity. The developments in analytical methodologies has greatly contributed to a more comprehensive understanding of the quantitative and qualitative characteristics of the glycosylation state of proteins. Despite those advances, the difficulty of a full characterization of glycosylation still remains, mainly due to the complexity of the glycoprotein and/or glycopeptide mixture especially when they are present in complex biological samples. For this reason, various techniques that allow a prior selective enrichment of exclusively glycosylated proteins or glycopeptides have been developed in the past and are coupled either on- or off- line with separation and detection methods. One of the most commonly implemented enrichment methods includes the use of lectin proteins immobilized on various solid supports. Lectins are a group of different, naturally occurring proteins that share a common characteristic, which concerns their affinity for specific sugar moieties of glycoproteins. This review presents the different formats and conditions for the use of lectins in affinity chromatography and in solid phase extraction, including their use in dispersive mode, along with the recent progress made on either commercial or home-made lectin-based affinity sorbents, which can lead to a fast and automated glycosylation analysis.
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Affiliation(s)
- Anastasia Goumenou
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France
| | - Nathalie Delaunay
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France
| | - Valérie Pichon
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France.,Sorbonne University, Paris, France
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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Deracinois B, Camoin L, Lambert M, Boyer JB, Dupont E, Bastide B, Cieniewski-Bernard C. O-GlcNAcylation site mapping by (azide-alkyne) click chemistry and mass spectrometry following intensive fractionation of skeletal muscle cells proteins. J Proteomics 2018; 186:83-97. [DOI: 10.1016/j.jprot.2018.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/13/2018] [Accepted: 07/03/2018] [Indexed: 12/22/2022]
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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Lee A, Miller D, Henry R, Paruchuri VDP, O'Meally RN, Boronina T, Cole RN, Zachara NE. Combined Antibody/Lectin Enrichment Identifies Extensive Changes in the O-GlcNAc Sub-proteome upon Oxidative Stress. J Proteome Res 2016; 15:4318-4336. [PMID: 27669760 DOI: 10.1021/acs.jproteome.6b00369] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
O-Linked N-acetyl-β-d-glucosamine (O-GlcNAc) is a dynamic post-translational modification that modifies and regulates over 3000 nuclear, cytoplasmic, and mitochondrial proteins. Upon exposure to stress and injury, cells and tissues increase the O-GlcNAc modification, or O-GlcNAcylation, of numerous proteins promoting the cellular stress response and thus survival. The aim of this study was to identify proteins that are differentially O-GlcNAcylated upon acute oxidative stress (H2O2) to provide insight into the mechanisms by which O-GlcNAc promotes survival. We achieved this goal by employing Stable Isotope Labeling of Amino Acids in Cell Culture (SILAC) and a novel "G5-lectibody" immunoprecipitation strategy that combines four O-GlcNAc-specific antibodies (CTD110.6, RL2, HGAC39, and HGAC85) and the lectin WGA. Using the G5-lectibody column in combination with basic reversed phase chromatography and C18 RPLC-MS/MS, 990 proteins were identified and quantified. Hundreds of proteins that were identified demonstrated increased (>250) or decreased (>110) association with the G5-lectibody column upon oxidative stress, of which we validated the O-GlcNAcylation status of 24 proteins. Analysis of proteins with altered glycosylation suggests that stress-induced changes in O-GlcNAcylation cluster into pathways known to regulate the cell's response to injury and include protein folding, transcriptional regulation, epigenetics, and proteins involved in RNA biogenesis. Together, these data suggest that stress-induced O-GlcNAcylation regulates numerous and diverse cellular pathways to promote cell and tissue survival.
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Affiliation(s)
- Albert Lee
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - Devin Miller
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - Roger Henry
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - Venkata D P Paruchuri
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - Robert N O'Meally
- Mass Spectrometry and Proteomics Facility, The Johns Hopkins University School of Medicine , 733 North Broadway Street, Baltimore, Maryland 21205-2185, United States
| | - Tatiana Boronina
- Mass Spectrometry and Proteomics Facility, The Johns Hopkins University School of Medicine , 733 North Broadway Street, Baltimore, Maryland 21205-2185, United States
| | - Robert N Cole
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States.,Mass Spectrometry and Proteomics Facility, The Johns Hopkins University School of Medicine , 733 North Broadway Street, Baltimore, Maryland 21205-2185, United States
| | - Natasha E Zachara
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
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Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA. A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics. Mol Cell Proteomics 2016; 15:2462-75. [PMID: 27114449 DOI: 10.1074/mcp.o115.049627] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 12/28/2022] Open
Abstract
Over the past decades, protein O-GlcNAcylation has been found to play a fundamental role in cell cycle control, metabolism, transcriptional regulation, and cellular signaling. Nevertheless, quantitative approaches to determine in vivo GlcNAc dynamics at a large-scale are still not readily available. Here, we have developed an approach to isotopically label O-GlcNAc modifications on proteins by producing (13)C-labeled UDP-GlcNAc from (13)C6-glucose via the hexosamine biosynthetic pathway. This metabolic labeling was combined with quantitative mass spectrometry-based proteomics to determine protein O-GlcNAcylation turnover rates. First, an efficient enrichment method for O-GlcNAc peptides was developed with the use of phenylboronic acid solid-phase extraction and anhydrous DMSO. The near stoichiometry reaction between the diol of GlcNAc and boronic acid dramatically improved the enrichment efficiency. Additionally, our kinetic model for turnover rates integrates both metabolomic and proteomic data, which increase the accuracy of the turnover rate estimation. Other advantages of this metabolic labeling method include in vivo application, direct labeling of the O-GlcNAc sites and higher confidence for site identification. Concentrating only on nuclear localized GlcNAc modified proteins, we are able to identify 105 O-GlcNAc peptides on 42 proteins and determine turnover rates of 20 O-GlcNAc peptides from 14 proteins extracted from HeLa nuclei. In general, we found O-GlcNAcylation turnover rates are slower than those published for phosphorylation or acetylation. Nevertheless, the rates widely varied depending on both the protein and the residue modified. We believe this methodology can be broadly applied to reveal turnovers/dynamics of protein O-GlcNAcylation from different biological states and will provide more information on the significance of O-GlcNAcylation, enabling us to study the temporal dynamics of this critical modification for the first time.
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Affiliation(s)
- Xiaoshi Wang
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Zuo-Fei Yuan
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Jing Fan
- §Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715
| | - Kelly R Karch
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Lauren E Ball
- ¶Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - John M Denu
- §Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715
| | - Benjamin A Garcia
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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Vercoutter-Edouart AS, El Yazidi-Belkoura I, Guinez C, Baldini S, Leturcq M, Mortuaire M, Mir AM, Steenackers A, Dehennaut V, Pierce A, Lefebvre T. Detection and identification ofO-GlcNAcylated proteins by proteomic approaches. Proteomics 2015; 15:1039-50. [DOI: 10.1002/pmic.201400326] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/03/2014] [Accepted: 11/24/2014] [Indexed: 02/06/2023]
Affiliation(s)
| | | | - Céline Guinez
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Steffi Baldini
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Maïté Leturcq
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Marlène Mortuaire
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Anne-Marie Mir
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Agata Steenackers
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Vanessa Dehennaut
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Annick Pierce
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Tony Lefebvre
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
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Huang BY, Yang CK, Liu CP, Liu CY. Stationary phases for the enrichment of glycoproteins and glycopeptides. Electrophoresis 2014; 35:2091-107. [PMID: 24729282 DOI: 10.1002/elps.201400034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 03/25/2014] [Accepted: 04/04/2014] [Indexed: 12/20/2022]
Abstract
The analysis of protein glycosylation is important for biomedical and biopharmaceutical research. Recent advances in LC-MS analysis have enabled the identification of glycosylation sites, the characterisation of glycan structures and the identification and quantification of glycoproteins and glycopeptides. However, this type of analysis remains challenging due to the low abundance of glycopeptides in complex protein digests, the microheterogeneity at glycosylation sites, ion suppression effects and the competition for ionisation by co-eluting peptides. Specific sample preparation is necessary for comprehensive and site-specific glycosylation analyses using MS. Therefore, researchers continue to pursue new columns to broaden their applications. The current manuscript covers recent literature published from 2008 to 2013. The stationary phases containing various chemical bonding methods or ligands immobilisation strategies on solid supports that selectively enrich N-linked or sialylated N-glycopeptides are categorised with either physical or chemical modes of binding. These categories include lectin affinity, hydrophilic interactions, boronate affinity, titanium dioxide affinity, hydrazide chemistry and other separation techniques. This review should aid in better understanding the syntheses and physicochemical properties of each type of stationary phases for enriching glycoproteins and glycopeptides.
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Affiliation(s)
- Bao-Yu Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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