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Xin M, Li C, You S, Zhu B, Shen J, Dong W, Xue X, Shi W, Xiong Y, Shi J, Sun S. Site-specific N-glycoproteomic analysis reveals up-regulated fucosylation in seminal plasma of asthenozoospermia. Glycobiology 2024; 34:cwae054. [PMID: 39073901 DOI: 10.1093/glycob/cwae054] [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: 05/17/2024] [Revised: 07/08/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024] Open
Abstract
N-linked glycoproteins are rich in seminal plasma, playing essential roles in supporting sperm function and fertilization process. The alteration of seminal plasma glycans and its correspond glycoproteins may lead to sperm dysfunction and even infertility. In present study, an integrative analysis of glycoproteomic and proteomic was performed to investigate the changes of site-specific glycans and glycoptoteins in seminal plasma of asthenozoospermia. By large scale profiling and quantifying 5,018 intact N-glycopeptides in seminal plasma, we identified 92 intact N-glycopeptides from 34 glycoproteins changed in asthenozoospermia. Especially, fucosylated glycans containing lewis x, lewis y and core fucosylation were significantly up-regulated in asthenozoospermia compared to healthy donors. The up-regulation of fucosylated glycans in seminal plasma may interfere sperm surface compositions and regulation of immune response, which subsequently disrupts sperm function. Three differentiated expression of seminal vesicle-specific glycoproteins (fibronectin, seminogelin-2, and glycodelin) were also detected with fucosylation alteration in seminal plasma of asthenozoospermia. The interpretation of the altered site-specific glycan structures provides data for the diagnosis and etiology analysis of male infertility, as well as providing new insights into the potential therapeutic targets for male infertility.
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Affiliation(s)
- Miaomiao Xin
- The Assisted Reproduction Center, Northwest Women and Children's Hospital, NO. 73, houzaimen, Xincheng Zone, Xi'an 710003, China
- Laboratory for Disease Glycoproteomics, College of Life Sciences, Northwest University, Xi'an 710069, P. R. China
| | - Cheng Li
- Laboratory for Disease Glycoproteomics, College of Life Sciences, Northwest University, Xi'an 710069, P. R. China
| | - Shanshan You
- Laboratory for Disease Glycoproteomics, College of Life Sciences, Northwest University, Xi'an 710069, P. R. China
| | - Bojing Zhu
- Laboratory for Disease Glycoproteomics, College of Life Sciences, Northwest University, Xi'an 710069, P. R. China
| | - Jiechen Shen
- Laboratory for Disease Glycoproteomics, College of Life Sciences, Northwest University, Xi'an 710069, P. R. China
| | - Wenbo Dong
- Laboratory for Disease Glycoproteomics, College of Life Sciences, Northwest University, Xi'an 710069, P. R. China
| | - Xia Xue
- The Assisted Reproduction Center, Northwest Women and Children's Hospital, NO. 73, houzaimen, Xincheng Zone, Xi'an 710003, China
| | - Wenhao Shi
- The Assisted Reproduction Center, Northwest Women and Children's Hospital, NO. 73, houzaimen, Xincheng Zone, Xi'an 710003, China
| | - Yao Xiong
- The Assisted Reproduction Center, Northwest Women and Children's Hospital, NO. 73, houzaimen, Xincheng Zone, Xi'an 710003, China
| | - Juanzi Shi
- The Assisted Reproduction Center, Northwest Women and Children's Hospital, NO. 73, houzaimen, Xincheng Zone, Xi'an 710003, China
| | - Shisheng Sun
- Laboratory for Disease Glycoproteomics, College of Life Sciences, Northwest University, Xi'an 710069, P. R. China
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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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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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Yang Y, Fang Q. Prediction of glycopeptide fragment mass spectra by deep learning. Nat Commun 2024; 15:2448. [PMID: 38503734 PMCID: PMC10951270 DOI: 10.1038/s41467-024-46771-1] [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: 09/13/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Deep learning has achieved a notable success in mass spectrometry-based proteomics and is now emerging in glycoproteomics. While various deep learning models can predict fragment mass spectra of peptides with good accuracy, they cannot cope with the non-linear glycan structure in an intact glycopeptide. Herein, we present DeepGlyco, a deep learning-based approach for the prediction of fragment spectra of intact glycopeptides. Our model adopts tree-structured long-short term memory networks to process the glycan moiety and a graph neural network architecture to incorporate potential fragmentation pathways of a specific glycan structure. This feature is beneficial to model explainability and differentiation ability of glycan structural isomers. We further demonstrate that predicted spectral libraries can be used for data-independent acquisition glycoproteomics as a supplement for library completeness. We expect that this work will provide a valuable deep learning resource for glycoproteomics.
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Affiliation(s)
- Yi Yang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China.
| | - Qun Fang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China.
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China.
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Xin M, You S, Wu J, Xu Y, Li C, Zhu B, Shen J, Chen Z, Dang L, Dan W, Zhang X, Sun S. Evaluation of absorbent cotton for glycopeptide enrichment. Anal Bioanal Chem 2022; 414:8245-8253. [PMID: 36181511 DOI: 10.1007/s00216-022-04353-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022]
Abstract
Selecting proper and efficient glycopeptide enrichment approaches are essential for mass spectrometry-based glycoproteomics since glycopeptides are usually with microheterogeneity and low abundance in most biological samples. Herein, we introduced a cotton hydrophilic interaction liquid chromatography (HILIC) approach for large-scale glycopeptide enrichment with 80% acetonitrile/1% trifluoroacetic acid as the optimal sample loading buffer. The comparison of cotton HILIC with Venusil HILIC and mixed anion-exchange (MAX) approaches indicated that cotton HILIC was superior in overall glycopeptide enrichment, whereas Venusil HILIC preferred in complex glycan structures and MAX performed better with high mannose glycans. Exploration of capacity and recovery rate of cotton HILIC illustrated that 5mg cotton packed in a 200μL tip achieved a reasonable glycopeptide enrichment performance (~6% recovery) from ~0.5mg peptides. In conclusion, cotton HILIC can be used as an optional glycopeptide enrichment approach in glycosylation analysis with its specific merit.
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Affiliation(s)
- Miaomiao Xin
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China.,South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, 38925, Vodnany, Czech Republic
| | - Shanshan You
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Jingyu Wu
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Yintai Xu
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Cheng Li
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Bojing Zhu
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Jiechen Shen
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Zexuan Chen
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Liuyi Dang
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Wei Dan
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Xinwen Zhang
- Department of Medical Genetics, Xi'an Fourth Hospital, Xi'an, Shaanxi Province, 710004, People's Republic of China
| | - Shisheng Sun
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China.
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Olejnik B, Ferens-Sieczkowska M. Seminal Plasma Glycoproteins as Potential Ligands of Lectins Engaged in Immunity Regulation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10489. [PMID: 36078205 PMCID: PMC9518496 DOI: 10.3390/ijerph191710489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Environmental pollution, chronic stress, and unhealthy lifestyle are factors that negatively affect reproductive potential. Currently, 15-20% of couples in industrialized countries face the problem of infertility. This growing health and social problem prompts researchers to explore the regulatory mechanisms that may be important for successful fertilization. In recent years, more attention has been paid to male infertility factors, including the impact of seminal plasma components on regulation of the female immune response to allogenic sperm, embryo and fetal antigens. Directing this response to the tolerogenic pathway is crucial to achieve a healthy pregnancy. According to the fetoembryonic defense hypothesis, the regulatory mechanism may be associated with the interaction of lectins and immunomodulatory glycoepitopes. Such interactions may involve lectins of dendritic cells and macrophages, recruited to the cervical region immediately after intercourse. Carbohydrate binding receptors include C type lectins, such as DC-SIGN and MGL, as well as galectins and siglecs among others. In this article we discuss the expression of the possible lectin ligands, highly fucosylated and high mannose structures, which may be recognized by DC-SIGN, glycans of varying degrees of sialylation, which may differ in their interaction with siglecs, as well as T and Tn antigens in O-glycans.
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