1
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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2
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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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3
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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4
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Gutierrez Reyes CD, Atashi M, Fowowe M, Onigbinde S, Daramola O, Lubman DM, Mechref Y. Differential expression of N-glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients. Proteomics 2024:e2300620. [PMID: 38602241 DOI: 10.1002/pmic.202300620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024]
Abstract
Mild cognitive impairment (MCI) is an early stage of memory loss that affects cognitive abilities with the aging of individuals, such as language or visual/spatial comprehension. MCI is considered a prodromal phase of more complicated neurodegenerative diseases such as Alzheimer's. Therefore, accurate diagnosis and better understanding of the disease prognosis will facilitate prevention of neurodegeneration. However, the existing diagnostic methods fail to provide precise and well-timed diagnoses, and the pathophysiology of MCI is not fully understood. Alterations of the serum N-glycoproteome expression could represent an essential contributor to the overall pathophysiology of neurodegenerative diseases and be used as a potential marker to assess MCI diagnosis using less invasive procedures. In this approach, we identified N-glycopeptides with different expressions between healthy and MCI patients from serum glycoproteins. Seven of the N-glycopeptides showed outstanding AUC values, among them the antithrombin-III Asn224 + 4-5-0-2 with an AUC value of 1.00 and a p value of 0.0004. According to proteomics and ingenuity pathway analysis (IPA), our data is in line with recent publications, and the glycoproteins carrying the identified N-sites play an important role in neurodegeneration.
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Affiliation(s)
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mojibola Fowowe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Oluwatosin Daramola
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - David M Lubman
- Department of Surgery, The University of Michigan, Ann Arbor, Michigan, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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5
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Onigbinde S, Peng W, Solomon J, Adeniyi M, Nwaiwu J, Fowowe M, Daramola O, Purba W, Mechref Y. O-Glycome Profiling of Breast Cancer Cell Lines to Understand Breast Cancer Brain Metastasis. J Proteome Res 2024; 23:1458-1470. [PMID: 38483275 PMCID: PMC11299836 DOI: 10.1021/acs.jproteome.3c00914] [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] [Indexed: 04/06/2024]
Abstract
Breast cancer is the second leading cause of cancer-related death among women and a major source of brain metastases. Despite the increasing incidence of brain metastasis from breast cancer, the underlying mechanisms remain poorly understood. Altered glycosylation is known to play a role in various diseases including cancer metastasis. However, profiling studies of O-glycans and their isomers in breast cancer brain metastasis (BCBM) are scarce. This study analyzed the expression of O-glycans and their isomers in human breast cancer cell lines (MDA-MB-231, MDA-MB-361, HTB131, and HTB22), a brain cancer cell line (CRL-1620), and a brain metastatic breast cancer cell line (MDA-MB-231BR) using nanoLC-MS/MS, identifying 27 O-glycan compositions. We observed significant upregulation in the expression of HexNAc1Hex1NeuAc2 and HexNAc2Hex3, whereas the expression of HexNAc1Hex1NeuAc1 was downregulated in MDA-MB-231BR compared to other cell lines. In our isomeric analysis, we observed notable alterations in the isomeric forms of the O-glycan structure HexNAc1Hex1NeuAc1 in a comparison of different cell lines. Our analysis of O-glycans and their isomers in cancer cells demonstrated that changes in their distribution can be related to the metastatic process. We believe that our investigation will contribute to an enhanced comprehension of the significance of O-glycans and their isomers in BCBM.
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Affiliation(s)
- Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Joy Solomon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Moyinoluwa Adeniyi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Judith Nwaiwu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Mojibola Fowowe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Oluwatosin Daramola
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Waziha Purba
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
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6
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Bashyal A, Brodbelt JS. Uncommon posttranslational modifications in proteomics: ADP-ribosylation, tyrosine nitration, and tyrosine sulfation. MASS SPECTROMETRY REVIEWS 2024; 43:289-326. [PMID: 36165040 PMCID: PMC10040477 DOI: 10.1002/mas.21811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Posttranslational modifications (PTMs) are covalent modifications of proteins that modulate the structure and functions of proteins and regulate biological processes. The development of various mass spectrometry-based proteomics workflows has facilitated the identification of hundreds of PTMs and aided the understanding of biological significance in a high throughput manner. Improvements in sample preparation and PTM enrichment techniques, instrumentation for liquid chromatography-tandem mass spectrometry (LC-MS/MS), and advanced data analysis tools enhance the specificity and sensitivity of PTM identification. Highly prevalent PTMs like phosphorylation, glycosylation, acetylation, ubiquitinylation, and methylation are extensively studied. However, the functions and impact of less abundant PTMs are not as well understood and underscore the need for analytical methods that aim to characterize these PTMs. This review focuses on the advancement and analytical challenges associated with the characterization of three less common but biologically relevant PTMs, specifically, adenosine diphosphate-ribosylation, tyrosine sulfation, and tyrosine nitration. The advantages and disadvantages of various enrichment, separation, and MS/MS techniques utilized to identify and localize these PTMs are described.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
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7
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Liu Z, Wu Z, Zhou Y, Xia J, Zhang W, Gao S, Li S, Lu Z, Zhang X, Yang S. Hydrophilic Peptide and Glycopeptide as Immobilized Sorbents for Glycosylation Analysis. Anal Chem 2024; 96:1498-1505. [PMID: 38216336 DOI: 10.1021/acs.analchem.3c03944] [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: 01/14/2024]
Abstract
Hydrophilic interaction liquid chromatography (HILIC) is widely used for glycopeptide enrichment in shot-gun glycoproteomics to enhance the glycopeptide signal and minimize the ionization competition of peptides. In this work, we have developed a novel hydrophilic material (glycoHILIC) based on glycopeptides and peptides to provide hydrophilic properties. GlycoHILIC was synthesized by oxidizing cotton and then reacting the resulting aldehyde with the N-terminus of the glycopeptide or peptide by reductive amination. Due to the large amount of hydrophilic carbohydrates and hydrophilic amino acids contained in glycopeptides, glycoHILIC showed significantly better enrichment of glycopeptides than cotton itself. Our results demonstrate that glycoHILIC has high selectivity, a low detection limit, and good stability. Over 257 unique N-linked glycosylation sites in 1477 intact N-glycopeptides from 146 glycoproteins were identified from 1 μL of human serum using glycoHILIC. Serum analysis of pancreatic cancer patients found that 38 N-glycopeptides among 21 glycoproteins changed significantly, of which 7 N-glycopeptides increased and 31 N-glycopeptides decreased. These results demonstrate that glycoHILIC can be used for glycopeptide enrichment and analysis.
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Affiliation(s)
- Zhaoliang Liu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Zhen Wu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yufeng Zhou
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jun Xia
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, China
| | - Wenqi Zhang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang 222005, China
| | - Shuwei Li
- Nanjing Apollomics Biotech, Inc., Nanjing, Jiangsu 210033, China
| | - Zhaohui Lu
- Health Examination Center, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
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8
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Goli M, Jiang P, Fowowe M, Hakim MA, Mechref Y. Hydrophilic Interaction Liquid Chromatography (HILIC) Enrichment of Glycopeptides Using PolyHYDROXYETHYL A. Methods Mol Biol 2024; 2762:267-280. [PMID: 38315371 DOI: 10.1007/978-1-0716-3666-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Glycosylation of proteins is an important post-translational modification that plays a role in a wide range of biological processes, including immune response, intercellular signaling, inflammation, and host-pathogen interaction. Abnormal protein glycosylation has been correlated with various diseases. However, the study of protein glycosylation remains challenging due to its low abundance, microheterogeneity of glycosylation sites, and low ionization efficiency. During the past decade, several methods for enrichment and for isolation of glycopeptides from biological samples have been developed and successfully employed in glycoproteomics research. In this chapter, we discuss the sample preparation protocol and the strategies for effectively isolating and enriching glycopeptides from biological samples, using PolyHYDROXYETHYL A as a hydrophilic interaction liquid chromatography (HILIC) enrichment technique.
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Affiliation(s)
- Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Mojibola Fowowe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Md Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
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9
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Wang J, Onigbinde S, Purba W, Nwaiwu J, Mechref Y. O-Glycoproteomics Sample Preparation and Analysis Using NanoHPLC and Tandem MS. Methods Mol Biol 2024; 2762:281-290. [PMID: 38315372 DOI: 10.1007/978-1-0716-3666-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Glycosylation refers to the biological processes that covalently attach carbohydrates to the peptide backbone after the synthesis of proteins. As one of the most common post-translational modifications (PTMs), glycosylation can greatly affect proteins' features and functions. Moreover, aberrant glycosylation has been linked to various diseases. There are two major types of glycosylation, known as N-linked and O-linked glycosylation. Here, we focus on O-linked glycosylation and thoroughly describe a bottom-up strategy to perform O-linked glycoproteomics studies. The experimental section involves enzymatic digestions using trypsin and O-glycoprotease at 37 °C. The prepared samples containing O-glycopeptides are analyzed using nanoHPLC coupled with tandem mass spectrometry (MS) for accurate identification and quantification.
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Affiliation(s)
- Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Waziha Purba
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Judith Nwaiwu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
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10
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Gutierrez Reyes CD, Sanni A, Adeniyi M, Mogut D, Najera Gonzalez HR, Ahmadi P, Atashi M, Onigbinde S, Mechref Y. Targeted Glycoproteomics Analysis Using MRM/PRM Approaches. Methods Mol Biol 2024; 2762:231-250. [PMID: 38315369 DOI: 10.1007/978-1-0716-3666-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
MS-target analyses are frequently utilized to analyze and validate structural changes of biomolecules across diverse fields of study such as proteomics, glycoproteomics, glycomics, lipidomics, and metabolomics. Targeted studies are commonly conducted using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) techniques. A reliable glycoproteomics analysis in intricate biological matrices is possible with these techniques, which streamline the analytical workflow, lower background interference, and enhance selectivity and specificity.
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Affiliation(s)
| | - Akeem Sanni
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Moyinoluwa Adeniyi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Damir Mogut
- Department of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Hector R Najera Gonzalez
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
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11
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Jiang P, Huang Y, Gutierrez Reyes CD, Zhong J, Mechref Y. Isomeric Separation of α2,3/α2,6-Linked 2-Aminobenzamide (2AB)-Labeled Sialoglycopeptides by C18-LC-MS/MS. Anal Chem 2023; 95:18388-18397. [PMID: 38069741 DOI: 10.1021/acs.analchem.3c03118] [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: 12/20/2023]
Abstract
Determination of the relative expression levels of the α2,3/α2,6-sialic acid linkage isomers on glycoproteins is critical to the analysis of various human diseases such as cancer, inflammation, and viral infection. However, it remains a challenge to separate and differentiate site-specific linkage isomers at the glycopeptide level. Some derivatization methods on the carboxyl group of sialic acid have been developed to generate mass differences between linkage isomers. In this study, we utilized chemical derivatization that occurred on the vicinal diol of sialic acid to separate linkage isomers on a reverse-phase column using a relatively short time. 2-Aminobenzamide (2AB) labeling derivatization, including periodate oxidation and reductive amination, took only ∼3 h and achieved high labeling efficiency (>90%). Within a 66 min gradient, the sialic acid linkage isomers of 2AB-labeled glycopeptides from model glycoproteins can be efficiently resolved compared to native glycopeptides. Two different methods, neuraminidase digestion and higher-energy collision dissociation tandem mass spectrometry (HCD-MS2) fragmentation, were utilized to differentiate those isomeric peaks. By calculating the diagnostic oxonium ion ratio of Gal2ABNeuAc and 2ABNeuAc fragments, significant differences in chromatographic retention times and in mass spectral peak abundances were observed between linkage isomers. Their corresponding MS2 PCA plots also helped to elucidate the linkage information. This method was successfully applied to human blood serum. A total of 514 2AB-labeled glycopeptide structures, including 152 sets of isomers, were identified, proving the applicability of this method in linkage-specific structural characterization and relative quantification of sialic acid isomers.
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Affiliation(s)
- Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Cristian D Gutierrez Reyes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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12
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Jiang P, Peng W, Zhao J, Goli M, Huang Y, Li Y, Mechref Y. Glycan/Protein-Stable Isotope Labeling in Cell Culture for Enabling Concurrent Quantitative Glycomics/Proteomics/Glycoproteomics. Anal Chem 2023; 95:16059-16069. [PMID: 37843510 DOI: 10.1021/acs.analchem.3c00247] [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: 10/17/2023]
Abstract
The complexity and heterogeneity of protein glycosylation present an analytical challenge to the studies of characterization and quantitation. Various LC-MS-based quantitation strategies have emerged in recent decades. Metabolic stable isotope labeling has been developed to enhance the accurate LC/MS-based quantitation between different cell lines. Stable isotope labeling by amino acids in a cell culture (SILAC) is the most widely used metabolic labeling method in proteomic analysis. However, it can only label the peptide backbone and is thus limited in glycomic studies. Here, we present a metabolic isotope labeling strategy, named GlyProSILC (Glycan Protein Stable Isotope Labeling in Cell Culture), that can label both the glycan motif and peptide backbone from the same batch of cells. It was performed by feeding cells with a heavy medium containing amide-15N-glutamine, 13C6-arginine (Arg6), and 13C6-15N2-lysine (Lys8). No significant change of cell line metabolism after GlyProSILC labeling was observed based on transcriptomic, glycomic, and proteomic data. The labeling conditions, labeling efficiency, and quantitation accuracy were investigated. After quantitation correction, we simultaneously quantified 62 N-glycans, 574 proteins, and 344 glycopeptides using the same batch of mixed 231BR/231 cell lines. So far, GlyProSILC provides an accurate and effective quantitation approach for glycomics, proteomics, and glycoproteomics in a cell culture system.
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Affiliation(s)
- Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yunxiang Li
- Division of Chemistry and Biochemistry, Texas Woman's University, Denton, Texas 76204, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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13
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Kumarasamy G, Mohd Salim NH, Mohd Afandi NS, Hazlami Habib MA, Mat Amin ND, Ismail MN, Musa M. Glycoproteomics-based liquid biopsy: translational outlook for colorectal cancer clinical management in Southeast Asia. Future Oncol 2023; 19:2313-2332. [PMID: 37937446 DOI: 10.2217/fon-2023-0704] [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: 11/09/2023] Open
Abstract
Colorectal cancer (CRC) signifies a significant healthcare challenge in Southeast Asia. Despite advancements in screening approaches and treatment modalities, significant medical gaps remain, ranging from prevention and early diagnosis to determining targeted therapy and establishing personalized approaches to managing CRC. There is a need to expand more validated biomarkers in clinical practice. An advanced technique incorporating high-throughput mass spectrometry as a liquid biopsy to unravel a repertoire of glycoproteins and glycans would potentially drive the development of clinical tools for CRC screening, diagnosis and monitoring, and it can be further adapted to the existing standard-of-care procedure. Therefore this review offers a perspective on glycoproteomics-driven liquid biopsy and its potential integration into the clinical care of CRC in the southeast Asia region.
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Affiliation(s)
- Gaayathri Kumarasamy
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Pulau Pinang, 11800, Malaysia
| | - Nurul Hakimah Mohd Salim
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, 16150, Malaysia
| | - Nur Syafiqah Mohd Afandi
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Nor Datiakma Mat Amin
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
- Nature Products Division, Forest Research Institute Malaysia, Kepong, Selangor, 52109, Malaysia
| | - Mohd Nazri Ismail
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Pulau Pinang, 11800, Malaysia
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Marahaini Musa
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, 16150, Malaysia
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14
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Atashi M, Reyes CDG, Sandilya V, Purba W, Ahmadi P, Hakim MA, Kobeissy F, Plazzi G, Moresco M, Lanuzza B, Ferri R, Mechref Y. LC-MS/MS Quantitation of HILIC-Enriched N-glycopeptides Derived from Low-Abundance Serum Glycoproteins in Patients with Narcolepsy Type 1. Biomolecules 2023; 13:1589. [PMID: 38002271 PMCID: PMC10669497 DOI: 10.3390/biom13111589] [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: 09/06/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Glycoproteomic analysis is always challenging because of low abundance and complex site-specific heterogeneity. Glycoproteins are involved in various biological processes such as cell signaling, adhesion, and cell-cell communication and may serve as potential biomarkers when analyzing different diseases. Here, we investigate glycoproteins in narcolepsy type 1 (NT1) disease, a form of narcolepsy characterized by cataplexy-the sudden onset of muscle paralysis that is typically triggered by intense emotions. In this study, 27 human blood serum samples were analyzed, 16 from NT1 patients and 11 from healthy individuals serving as controls. We quantified hydrophilic interaction liquid chromatography (HILIC)-enriched glycopeptides from low-abundance serum samples of controls and NT1 patients via LC-MS/MS. Twenty-eight unique N-glycopeptides showed significant changes between the two studied groups. The sialylated N-glycopeptide structures LPTQNITFQTESSVAEQEAEFQSPK HexNAc6, Hex3, Neu5Ac2 (derived from the ITIH4 protein) and the structure IVLDPSGSMNIYLVLDGSDSIGASNFTGAK HexNAc5, Hex4, Fuc1 (derived from the CFB protein), with p values of 0.008 and 0.01, respectively, were elevated in NT1 samples compared with controls. In addition, the N-glycopeptide protein sources Ceruloplasmin, Complement factor B, and ITH4 were observed to play an important role in the complement activation and acute-phase response signaling pathways. This may explain the possible association between the biomarkers and pathophysiological effects.
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Affiliation(s)
- Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Cristian D. Gutierrez Reyes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Vishal Sandilya
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Waziha Purba
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Md. Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Firas Kobeissy
- Department of biochemistry and molecular genetics, Faculty of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 11072020, Lebanon;
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), Neuroscience Institute, Morehouse School of Medicine, Atlanta, GE 30310, USA
| | - Giuseppe Plazzi
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40124 Bologna, Italy; (G.P.); (M.M.)
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Monica Moresco
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40124 Bologna, Italy; (G.P.); (M.M.)
| | - Bartolo Lanuzza
- Sleep Research Center, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Tronia, Italy; (B.L.); (R.F.)
| | - Raffaele Ferri
- Sleep Research Center, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Tronia, Italy; (B.L.); (R.F.)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
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15
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Reyes CDG, Onigbinde S, Sanni A, Bennett AI, Jiang P, Daramola O, Ahmadi P, Fowowe M, Atashi M, Sandilya V, Hakim MA, Mechref Y. N-Glycome Profile of the Spike Protein S1: Systemic and Comparative Analysis from Eleven Variants of SARS-CoV-2. Biomolecules 2023; 13:1421. [PMID: 37759821 PMCID: PMC10526240 DOI: 10.3390/biom13091421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
The SARS-CoV-2 virus rapidly spread worldwide, threatening public health. Since it emerged, the scientific community has been engaged in the development of effective therapeutics and vaccines. The subunit S1 in the spike protein of SARS-CoV-2 mediates the viral entry into the host and is therefore one of the major research targets. The S1 protein is extensively glycosylated, and there is compelling evidence that glycans protect the virus' active site from the human defense system. Therefore, investigation of the S1 protein glycome alterations in the different virus variants will provide a view of the glycan evolution and its relationship with the virus pathogenesis. In this study, we explored the N-glycosylation expression of the S1 protein for eleven SARS-CoV-2 variants: five variants of concern (VOC), including alpha, beta, gamma, delta, and omicron, and six variants of interest (VOI), including epsilon, eta, iota, lambda, kappa, and mu. The results showed significant differences in the N-glycome abundance of all variants. The N-glycome of the VOC showed a large increase in the abundance of sialofucosylated glycans, with the greatest abundance in the omicron variant. In contrast, the results showed a large abundance of fucosylated glycans for most of the VOI. Two glycan compositions, GlcNAc4,Hex5,Fuc,NeuAc (4-5-1-1) and GlcNAc6,Hex8,Fuc,NeuAc (6-8-1-1), were the most abundant structures across all variants. We believe that our data will contribute to understanding the S1 protein's structural differences between SARS-CoV-2 mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (C.D.G.R.); (S.O.); (A.S.); (A.I.B.); (P.J.); (O.D.); (P.A.); (M.F.); (M.A.); (V.S.); (M.A.H.)
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16
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Le HT, Liu M, Grimes CL. Application of bioanalytical and computational methods in decoding the roles of glycans in host-pathogen interactions. Curr Opin Chem Biol 2023; 74:102301. [PMID: 37080155 PMCID: PMC10296625 DOI: 10.1016/j.cbpa.2023.102301] [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: 12/05/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 04/22/2023]
Abstract
Host-pathogen interactions (HPIs) are complex processes that require tight regulation. A common regulatory mechanism of HPIs is through glycans of either host cells or pathogens. Due to their diverse sequences, complex structures, and conformations, studies of glycans require highly sensitive and powerful tools. Recent improvements in technology have enabled the application of many bioanalytical techniques and modeling methods to investigate glycans and their mechanisms in HPIs. This mini-review highlights how these advances have been used to understand the role glycans play in HPIs in the past 2 years.
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Affiliation(s)
- Ha T Le
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Min Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA.
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17
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Chau TH, Chernykh A, Kawahara R, Thaysen-Andersen M. Critical considerations in N-glycoproteomics. Curr Opin Chem Biol 2023; 73:102272. [PMID: 36758418 DOI: 10.1016/j.cbpa.2023.102272] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023]
Abstract
N-Glycoproteomics, the system-wide study of glycans asparagine-linked to protein carriers, holds a unique and still largely untapped potential to provide deep insights into the complexity and dynamics of the heterogeneous N-glycoproteome. Despite the advent of innovative analytical and informatics tools aiding the analysis, N-glycoproteomics remains challenging and consequently largely restricted to specialised laboratories. Aiming to stimulate discussions of method harmonisation, data standardisation and reporting guidelines to make N-glycoproteomics more reproducible and accessible to the community, we here discuss critical considerations related to the design and execution of N-glycoproteomics experiments and highlight good practices in N-glycopeptide data collection, analysis, interpretation and sharing. Giving the rapid maturation and, expectedly, a wide-spread implementation of N-glycoproteomics capabilities across the community in future years, this piece aims to point out common pitfalls, to encourage good data sharing and documentation practices, and to highlight practical solutions and strategies to enhance the insight into the N-glycoproteome.
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Affiliation(s)
- The Huong Chau
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Anastasia Chernykh
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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18
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Abstract
Tweetable abstract Bottom-up glycoproteomics combined with top-down strategy allows direct analysis of glycoform-mapped glycosylation and its glycans by high-resolution mass spectrometry.
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19
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Barrett K, Dube DH. Chemical tools to study bacterial glycans: a tale from discovery of glycoproteins to disruption of their function. Isr J Chem 2023; 63:e202200050. [PMID: 37324574 PMCID: PMC10266715 DOI: 10.1002/ijch.202200050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Indexed: 01/02/2024]
Abstract
Bacteria coat themselves with a dense array of cell envelope glycans that enhance bacterial fitness and promote survival. Despite the importance of bacterial glycans, their systematic study and perturbation remains challenging. Chemical tools have made important inroads toward understanding and altering bacterial glycans. This review describes how pioneering discoveries from Prof. Carolyn Bertozzi's laboratory inspired our laboratory to develop sugar probes to facilitate the study of bacterial glycans. As described below, we used metabolic glycan labelling to install bioorthogonal reporters into bacterial glycans, ultimately permitting the discovery of a protein glycosylation system, the identification of glycosylation genes, and the development of metabolic glycan inhibitors. Our results have provided an approach to screen bacterial glycans and gain insight into their function, even in the absence of detailed structural information.
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Affiliation(s)
- Katharine Barrett
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011 USA
| | - Danielle H Dube
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011 USA
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20
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Baboo S, Diedrich JK, Martínez-Bartolomé S, Wang X, Schiffner T, Groschel B, Schief WR, Paulson JC, Yates JR. DeGlyPHER: Highly sensitive site-specific analysis of N-linked glycans on proteins. Methods Enzymol 2022; 682:137-185. [PMID: 36948700 PMCID: PMC11032187 DOI: 10.1016/bs.mie.2022.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Traditional mass spectrometry-based glycoproteomic approaches have been widely used for site-specific N-glycoform analysis, but a large amount of starting material is needed to obtain sampling that is representative of the vast diversity of N-glycans on glycoproteins. These methods also often include a complicated workflow and very challenging data analysis. These limitations have prevented glycoproteomics from being adapted to high-throughput platforms, and the sensitivity of the analysis is currently inadequate for elucidating N-glycan heterogeneity in clinical samples. Heavily glycosylated spike proteins of enveloped viruses, recombinantly expressed as potential vaccines, are prime targets for glycoproteomic analysis. Since the immunogenicity of spike proteins may be impacted by their glycosylation patterns, site-specific analysis of N-glycoforms provides critical information for vaccine design. Using recombinantly expressed soluble HIV Env trimer, we describe DeGlyPHER, a modification of our previously reported sequential deglycosylation strategy to yield a "single-pot" process. DeGlyPHER is an ultrasensitive, simple, rapid, robust, and efficient approach for site-specific analysis of protein N-glycoforms, that we developed for analysis of limited quantities of glycoproteins.
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Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States.
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | | | - Xiaoning Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States
| | - Bettina Groschel
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States.
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