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Li Y, Guo W, Zhang Q, Yang B, Zhang Y, Yang Y, Liu G, Pan L, Zhang W, Kong D. Improved analysis ZIC-HILIC-HCD-Orbitrap method for mapping the glycopeptide by mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1228:123852. [PMID: 37633008 DOI: 10.1016/j.jchromb.2023.123852] [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] [Received: 05/29/2023] [Revised: 07/29/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023]
Abstract
Glycosylation is one of the most common post-translational modifications (PTMs). Protein glycosylation analysis is the bottleneck to deeply understand their functions. At present, the LC-MS analysis of glycosylated post-translational modification is mainly focused on the analysis of glycopeptides. However, the factors affecting the identification of glycopeptides were not fully elucidated. In the paper, we have carefully studied the factors, e.g., HILIC materials, search engines, protein amount, gradient duration, extraction solution, etc. According to the results, HILIC materials were the most important factors affecting the glycopeptides identification, and the amphoteric sulfoalkyl betaine stationary phase enriched glycopeptides 6-fold more compared to the amphiphilic ion-bonded fully porous spherical silica stationary phase. We explored the influence of the extraction solutions on glycan identification. Comparing sodium dodecyl sulfate (SDS) and urea (UA), the results showed that N-glycolylneuraminic acid (NeuGc) type of glycan content was found to be increased 1.4-fold in the SDS compared to UA. Besides, we explored the influence of the search engine on glycopeptide identification. Comparing pGlyco3.0 and MSFragger-Glyco, it was observed that pGlyco3.0 outperformed MSFragger-Glyco in identifying glycopeptides. Then, using our optimized method we found that there was a significant difference in the distribution of monosaccharide types in plasma and brain tissue, e.g., the content of NeuAc in brain was 5-fold higher than that in plasma. To importantly, two glycoproteins (Neurexin-2 and SUN domain-containing protein 2) were also found for the first time by our method. In summary, we have comprehensively studied the factors influencing glycopeptide identification than any previous research, and the optimized method could be widely used for identifying the glycoproteins or glycolpeptides biomarkers for disease detection and therapeutic targets.
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Affiliation(s)
- Yahui Li
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Wenyan Guo
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Qingning Zhang
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Bingkun Yang
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China; School of Pharmacy, Hebei Medical University, Shijiazhuang, China
| | - Yuyu Zhang
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Yi Yang
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China; The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Guangyuan Liu
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Liangyu Pan
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Wei Zhang
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China.
| | - Dezhi Kong
- Department of Pharmacology of Chinese Materia Medica, Institution of Chinese Integrative Medicine, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China.
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Li M, Zhu W, Zheng H, Zhang J. Efficient HCD-pd-EThcD approach for N-glycan mapping of therapeutic antibodies at intact glycopeptide level. Anal Chim Acta 2022; 1189:339232. [PMID: 34815030 DOI: 10.1016/j.aca.2021.339232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 09/30/2021] [Accepted: 10/28/2021] [Indexed: 11/28/2022]
Abstract
N-glycosylation is a critical quality attribute for monoclonal antibody (mAb)-based therapeutics due to its significant impact on drug efficacy and safety. Extensive glycosylation mapping is therefore necessary for mAb drug development and quality control. We utilized a higher-energy dissociation product ions-triggered electron-transfer/higher-energy collision dissociation (HCD-pd-EThcD) approach to mapping N-glycosylation in therapeutic mAbs. Due to the improved duty cycle and targeted ability, HCD-pd-EThcD could provide extensive N-glycan identifications as well as higher quality spectra than EThcD mode. On average, ten types of N-glycan were uncovered in two different lots of trastuzumab, demonstrating a significant increment in N-glycan species compared to only four types identified by EThcD. After integrating pre-enrichment of glycopeptides, up to 16 N-glycans were recognized. Significantly, this strategy facilitated the identification of glycopeptides containing fucosylated and sialylated glycans, meanwhile enabled the recognition of different N-glycan classes (high mannose, hybrid, and complex). Further application in the glycosylation analysis of adalimumab and bevacizumab resulted in 19 and 8 N-glycans species, providing a more comprehensive insight into their glycosylation modification status. We demonstrated the benefits of an integrated strategy in characterizing various N-glycans of mAb therapeutics and offer an alternative approach for their quality control at the intact glycopeptides level.
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Affiliation(s)
- Menglin Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Wenwen Zhu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Hao Zheng
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Jinlan Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China.
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Zhang Y, Zhao W, Mao Y, Chen Y, Zheng S, Cao W, Zhu J, Hu L, Gong M, Cheng J, Yang H. O-Glycosylation Landscapes of SARS-CoV-2 Spike Proteins. Front Chem 2021; 9:689521. [PMID: 34552909 PMCID: PMC8450404 DOI: 10.3389/fchem.2021.689521] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/24/2021] [Indexed: 02/05/2023] Open
Abstract
The densely glycosylated spike (S) proteins that are highly exposed on the surface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) facilitate viral attachment, entry, and membrane fusion. We have previously reported all the 22 N-glycosites and site-specific N-glycans in the S protein protomer. Herein, we report the O-glycosylation landscapes of SARS-CoV-2 S proteins, which were characterized through high-resolution mass spectrometry. Following digestion with trypsin and trypsin/Glu-C, and de-N-glycosylation using PNGase F, we determined the GalNAc-type O-glycosylation pattern of S proteins, including O-glycosites and the six most common O-glycans occupying them, via Byonic identification and manual validation. Finally, 255 intact O-glycopeptides composed of 50 peptides sequences and 43 O-glycosites were discovered by higher energy collision-induced dissociation (HCD), and three O-glycosites were confidently identified by electron transfer/higher energy collision-induced dissociation (EThcD) in the insect cell-expressed S protein. Most glycosites were modified by non-sialylated O-glycans such as HexNAc(1) and HexNAc(1)Hex (1). In contrast, in the human cell-expressed S protein S1 subunit, 407 intact O-glycopeptides composed of 34 peptides sequences and 30 O-glycosites were discovered by HCD, and 11 O-glycosites were unambiguously assigned by EThcD. However, the measurement of O-glycosylation occupancy hasn’t been made. Most glycosites were modified by sialylated O-glycans such as HexNAc(1)Hex (1)NeuAc (1) and HexNAc(1)Hex (1)NeuAc (2). Our results reveal that the SARS-CoV-2 S protein is an O-glycoprotein; the O-glycosites and O-glycan compositions vary with the host cell type. These comprehensive O-glycosylation landscapes of the S protein are expected to provide novel insights into the viral binding mechanism and present a strategy for the development of vaccines and targeted drugs.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yaohui Chen
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Shanshan Zheng
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Cao
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiang Zhu
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Liqiang Hu
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Gong
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Yang
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
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Abstract
Glycosylation is one of the most ubiquitous and complex post-translational modifications (PTMs). It plays pivotal roles in various biological processes. Studies at the glycopeptide level are typically considered as a downstream work resulting from enzymatic digested glycoproteins. Less attention has been focused on glycosylated endogenous signaling peptides due to their low abundance, structural heterogeneity and the lack of enabling analytical tools. Here, protocols are presented to isolate and characterize glycosylated neuropeptides utilizing nanoflow liquid chromatography coupled with mass spectrometry (LC-MS). We first demonstrate how to extract neuropeptides from raw tissues and perform further separation/cleanup before MS analysis. Then we describe hybrid MS methods for glycosylated neuropeptide profiling and site-specific analysis. We also include recommendations for data analysis to identify glycosylated neuropeptides in crustaceans where a complete neuropeptide database is still lacking. Other strategies and future directions are discussed to provide readers with alternative approaches and further unravel biological complexity rendered by glycosylation.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Qinjingwen Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States; School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States.
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Macromolecular properties and partial amino acid sequence of a Kunitz-type protease inhibitor from okra (Abelmoschus esculentus) seeds. J Biosci 2019. [DOI: 10.1007/s12038-019-9859-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Rashid ZM, Mormann M, Steckhan K, Peters A, Esch S, Hensel A. Polysaccharides from lichen Xanthoria parietina: 1,4/1,6-α-d-glucans and a highly branched galactomannan with macrophage stimulating activity via Dectin-2 activation. Int J Biol Macromol 2019; 134:921-935. [PMID: 31078591 DOI: 10.1016/j.ijbiomac.2019.05.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 11/25/2022]
Abstract
Hot-water soluble polysaccharides H-1-3 and H-2-1 were isolated from the thalli of the lichen Xanthoria parietina (L.) Th. Fr. and purified by ion exchange and gel permeation chromatography. Structure elucidation was mainly based on 2D-NMR and nano-ESI-Q-TOF MS/MS experiments. H-1-3 (13.7 kDa) was shown to be linear α-glucan with α-d-Glcp-(1 → [→[4)-α-d-Glcp-(1]2 → [6)-α-d-Glcp-(1]3 → 4)]n core backbone. The (1,4)- and (1,6)-α-d-Glcp linkages were in a 2:3 M ratio. H-2-1 (525 kDa) was characterized as a complex branched β-galacto-α-mannan with →[6)-α-d-Manp-(1 → [2,6)-α-d-Manp-(1]2 → [2)-α-d-Manp-(1]2→]n core units and main side chains of (1,3)-β-d-Galf linked at O-6 to →2)-α-d-Manp-(1→, together with minor terminal units of 1,4/1,6-α-D -Glcp units attached to the core chain at O-6 position and α-L-Rhap linked to Galf side chain at O-2 position (Manp: Galf: Glcp: Rhap linkage ratio = 9:3:2:1). H-2-1 exerted strong immunoactivity in vitro and activated murine RAW macrophages 264.7 towards significantly increased phagocytosis, TNF-α and IL-1β secretion. These effects are due to an interaction of the galactomannan with the transmembrane pattern-recognition protein Dectin-2 of the macrophages.
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Affiliation(s)
- Zalilawati Mat Rashid
- University of Münster, Institute of Pharmaceutical Biology and Phytochemistry, Corrensstrasse 48, D-48149 Münster, Germany
| | - Michael Mormann
- University of Münster, Institute for Hygiene, Robert-Koch-Strasse 41, D-48149 Münster, Germany
| | - Katja Steckhan
- University of Münster, Institute for Hygiene, Robert-Koch-Strasse 41, D-48149 Münster, Germany
| | - Alena Peters
- University of Münster, Institute of Pharmaceutical Biology and Phytochemistry, Corrensstrasse 48, D-48149 Münster, Germany
| | - Stefan Esch
- University of Münster, Institute of Pharmaceutical Biology and Phytochemistry, Corrensstrasse 48, D-48149 Münster, Germany
| | - Andreas Hensel
- University of Münster, Institute of Pharmaceutical Biology and Phytochemistry, Corrensstrasse 48, D-48149 Münster, Germany.
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Chang F, Yue Y, Yang Z, Huang S, Liu Z, Wang K, Peng Y, Chen Y, Ma M, Chen B. The fabrication of poly (polyethylene glycol diacrylate) monolithic porous layer open tubular (mono-PLOT) columns and applications in hydrophilic interaction chromatography and capillary gas chromatography for small molecules. Electrophoresis 2019; 40:521-529. [DOI: 10.1002/elps.201800410] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/28/2018] [Accepted: 11/28/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Feng Chang
- Key Laboratory of Phytochemical R&D of Hunan Province; Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research; Ministry of Education; Hunan Normal University; Changsha P. R. China
| | - Yunfang Yue
- Key Laboratory of Phytochemical R&D of Hunan Province; Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research; Ministry of Education; Hunan Normal University; Changsha P. R. China
| | - Zihui Yang
- Key Laboratory of Phytochemical R&D of Hunan Province; Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research; Ministry of Education; Hunan Normal University; Changsha P. R. China
| | - Si Huang
- Key Laboratory of Phytochemical R&D of Hunan Province; Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research; Ministry of Education; Hunan Normal University; Changsha P. R. China
| | - Zhihua Liu
- Key Laboratory of Tobacco Chemistry of Yunnan Province; Research and Development of Center; China Tobacco Yunnan Industrial Co., Ltd.; Kunming P. R. China
| | - Kunmiao Wang
- Key Laboratory of Tobacco Chemistry of Yunnan Province; Research and Development of Center; China Tobacco Yunnan Industrial Co., Ltd.; Kunming P. R. China
| | - Yan Peng
- College of Economics and Management; Hengyang Normal University; Hengyang P. R. China
| | - Yingzhuang Chen
- Key Laboratory of Phytochemical R&D of Hunan Province; Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research; Ministry of Education; Hunan Normal University; Changsha P. R. China
| | - Ming Ma
- Key Laboratory of Phytochemical R&D of Hunan Province; Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research; Ministry of Education; Hunan Normal University; Changsha P. R. China
| | - Bo Chen
- Key Laboratory of Phytochemical R&D of Hunan Province; Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research; Ministry of Education; Hunan Normal University; Changsha P. R. China
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Chatterjee B, Thakur SS. Investigation of post-translational modifications in type 2 diabetes. Clin Proteomics 2018; 15:32. [PMID: 30258344 PMCID: PMC6154926 DOI: 10.1186/s12014-018-9208-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022] Open
Abstract
The investigation of post-translational modifications (PTMs) plays an important role for the study of type 2 diabetes. The importance of PTMs has been realized with the advancement of analytical techniques. The challenging detection and analysis of post-translational modifications is eased by different enrichment methods and by high throughput mass spectrometry based proteomics studies. This technology along with different quantitation methods provide accurate knowledge about the changes happening in disease conditions as well as in normal conditions. In this review, we have discussed PTMs such as phosphorylation, N-glycosylation, O-GlcNAcylation, acetylation and advanced glycation end products in type 2 diabetes which have been characterized by high throughput mass spectrometry based proteomics analysis.
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Affiliation(s)
- Bhaswati Chatterjee
- 1Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500 037 India
| | - Suman S Thakur
- 2Proteomics and Cell Signaling, Lab E409, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007 India
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Kayili HM, Barlas N, Atakay M, Salih B. Fast purification of glycans and glycopeptides using silk-packed micropipette tip for matrix-assisted laser desorption/ionization-mass spectrometry and high-performance liquid chromatography-fluorescence detection analysis. Microchem J 2018. [DOI: 10.1016/j.microc.2018.03.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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