1
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Park CS, Moon C, Kim M, Kim J, Yang S, Jang L, Jang JY, Jeong CM, Lee HS, Kim DK, Kim HH. Comparison of sialylated and fucosylated N-glycans attached to Asn 6 and Asn 41 with different roles in hyaluronan and proteoglycan link protein 1 (HAPLN1). Int J Biol Macromol 2024; 260:129575. [PMID: 38246450 DOI: 10.1016/j.ijbiomac.2024.129575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
Hyaluronan and proteoglycan link protein 1 (HAPLN1) is an extracellular matrix protein stabilizing interactions between hyaluronan and proteoglycan. Although HAPLN1 is being investigated for various biological roles, its N-glycosylation is poorly understood. In this study, the structure of N-glycopeptides of trypsin-treated recombinant human HAPLN1 (rhHAPLN1) expressed from CHO cells were identified by nano-liquid chromatography-tandem mass spectrometry. A total of 66 N-glycopeptides were obtained, including 16 and 12 N-glycans at sites Asn 6 (located in the N-terminal region) and Asn 41 (located in the Ig-like domain, which interacts with proteoglycan), respectively. The quantities (%) of each N-glycan relative to the totals (100 %) at each site were calculated. Tri- and tetra-sialylation (to resist proteolysis and extend half-life) were more abundant at Asn 6, and di- (core- and terminal-) fucosylation (to increase binding affinity and stability) and sialyl-Lewis X/a epitope (a major ligand for E-selectin) were more abundant at Asn 41. These results indicate that N-glycans attached to Asn 6 (protecting HAPLN1) and Asn 41 (supporting molecular interactions) play different roles in HAPLN1. This is the first study of site-specific N-glycosylation in rhHAPLN1, which will be useful for understanding its molecular interactions in the extracellular matrix.
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Affiliation(s)
- Chi Soo Park
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chulmin Moon
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Mirae Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Jieun Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Subin Yang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Leeseul Jang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Ji Yeon Jang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chang Myeong Jeong
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Han Seul Lee
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Dae Kyong Kim
- Department of Environmental & Health Chemistry, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Ha Hyung Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea.
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2
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Yang Y, Qiao L. Profiling Serum Intact N-Glycopeptides Using Data-Independent Acquisition Mass Spectrometry. Methods Mol Biol 2023; 2628:365-391. [PMID: 36781798 DOI: 10.1007/978-1-0716-2978-9_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data-independent acquisition (DIA) mass spectrometry is an emerging technology with deep proteome coverage as well as accurate quantitative capability for large-scale proteomics studies and has also been applied to the field of glycoproteomics. In this protocol, we describe how to analyze data from a DIA experiment for profiling serum intact N-glycopeptides. We present a comprehensive data analysis workflow using GproDIA, including glycopeptide spectral library building, chromatographic feature extraction from the DIA data, and feature scoring with appropriate statistical control of error rates. We anticipate that this method could provide a powerful tool to explore the serum glycoproteome.
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Affiliation(s)
- Yi Yang
- Department of Chemistry and Shanghai Stomatological Hospital, Fudan University, Shanghai, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Liang Qiao
- Department of Chemistry and Shanghai Stomatological Hospital, Fudan University, Shanghai, China.
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3
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Sun Z, Fu B, Wang G, Zhang L, Xu R, Zhang Y, Lu H. High-throughput site-specific N-glycoproteomics reveals glyco-signatures for liver disease diagnosis. Natl Sci Rev 2023; 10:nwac059. [PMID: 36879659 PMCID: PMC9985154 DOI: 10.1093/nsr/nwac059] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
The glycoproteome has emerged as a prominent target for screening biomarkers, as altered glycosylation is a hallmark of cancer cells. In this work, we incorporated tandem mass tag labeling into quantitative glycoproteomics by developing a chemical labeling-assisted complementary dissociation method for the multiplexed analysis of intact N-glycopeptides. Benefiting from the complementary nature of two different mass spectrometry dissociation methods for identification and multiplex labeling for quantification of intact N-glycopeptides, we conducted the most comprehensive site-specific and subclass-specific N-glycosylation profiling of human serum immunoglobulin G (IgG) to date. By analysing the serum of 90 human patients with varying severities of liver diseases, as well as healthy controls, we identified that the combination of IgG1-H3N5F1 and IgG4-H4N3 can be used for distinguishing between different stages of liver diseases. Finally, we used targeted parallel reaction monitoring to successfully validate the expression changes of glycosylation in liver diseases in a different sample cohort that included 45 serum samples.
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Affiliation(s)
- Zhenyu Sun
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Bin Fu
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Guoli Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ruofan Xu
- Eleanor Roosevelt College, University of California San Diego, La Jolla, CA92093, USA
| | - Ying Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
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4
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Kim H, Bang G, Park YE, Park M, Choi JH, Oh MJ, An HJ, Yoo JS, Park YH, Kim JY, Hwang H. Advanced assessment through intact glycopeptide analysis of Infliximab’s biologics and biosimilar. Front Mol Biosci 2022; 9:1006866. [DOI: 10.3389/fmolb.2022.1006866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/26/2022] [Indexed: 11/30/2022] Open
Abstract
Characterization of therapeutic monoclonal antibodies (mAbs) represents a major challenge for analytical sciences due to their heterogeneity associated with post-translational modifications (PTMs). The protein glycosylation requires comprehensive identification, which could influence on the mAbs’ structure and their function. Here, we demonstrated high-resolution tandem mass spectrometry with an ultra-high-performance liquid chromatography for characterization and comparison between biologics and biosimilar of infliximab at an advanced level. Comparing the N- and O-glycopeptides profiles, a total of 49 and 54 glycopeptides was identified for each product of the biologics and biosimilar, respectively. We also discovered one novel N-glycosylation site at the light chain from both biopharmaceuticals and one novel O-glycopeptide at the heavy chain from only biosimilar. Site-specific glycopeptide analysis process will be a robust and useful technique for evaluating therapeutic mAbs and complex glycoprotein products.
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5
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San Clemente H, Jamet E. N-glycoproteins in Plant Cell Walls: A Survey. Plants (Basel) 2022; 11:3204. [PMID: 36501244 PMCID: PMC9738366 DOI: 10.3390/plants11233204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Cell walls are an extracellular compartment specific to plant cells, which are not found in animal cells. Their composition varies between cell types, plant species, and physiological states. They are composed of a great diversity of polymers, i.e., polysaccharides, proteins, and lignins. Cell wall proteins (CWPs) are major players involved in the plasticity of cell walls which support cell growth and differentiation, as well as adaptation to environmental changes. In order to reach the extracellular space, CWPs are transported through the secretory pathway where they may undergo post-translational modifications, including N-glycosylations on the Asn residues in specific motifs (Asn-X-Ser/Thr-X, with X≠Pro). This review aims at providing a survey of the present knowledge related to cell wall N-glycoproteins with (i) an overview of the experimental workflows, (ii) a selection of relevant articles dedicated to N-glycoproteomics, (iii) a description of the diversity of N-glycans, and (iv) a focus on the importance of N-glycans for CWP structure and/or function.
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6
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Remoroza CA, Burke MC, Yang X, Sheetlin S, Mirokhin Y, Markey SP, Tchekhovskoi DV, Stein SE. Mass Spectral Library Methods for Analysis of Site-Specific N-Glycosylation: Application to Human Milk Proteins. J Proteome Res 2022; 21:2421-2434. [DOI: 10.1021/acs.jproteome.2c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Concepcion A. Remoroza
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Meghan C. Burke
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Xiaoyu Yang
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Sergey Sheetlin
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Yuri Mirokhin
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Sanford P. Markey
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Dmitrii V. Tchekhovskoi
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Stephen E. Stein
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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7
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Tomnikova A, Kozlík P, Křížek T. Monosaccharide profiling of glycoproteins by capillary electrophoresis with contactless conductivity detection. Electrophoresis 2022; 43:1963-1970. [DOI: 10.1002/elps.202200033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/01/2022] [Accepted: 08/09/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Alice Tomnikova
- Faculty of Science, Department of Analytical Chemistry Charles University Prague Czech Republic
| | - Petr Kozlík
- Faculty of Science, Department of Analytical Chemistry Charles University Prague Czech Republic
| | - Tomáš Křížek
- Faculty of Science, Department of Analytical Chemistry Charles University Prague Czech Republic
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8
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Kinoshita M, Yamada K. Recent advances and trends in sample preparation and chemical modification for glycan analysis. J Pharm Biomed Anal 2022; 207:114424. [PMID: 34653745 DOI: 10.1016/j.jpba.2021.114424] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/26/2022]
Abstract
Growing significance of glycosylation in protein functions has accelerated the development of methodologies for detection, identification, and characterization of protein glycosylation. In the past decade, glycobiology research has been advanced by innovative techniques with further progression in the post-genome era. Although significant technical progress has been made in terms of analytical throughput, comprehensiveness, and sensitivity, most methods for glycosylation analysis still require laborious and time-consuming sample preparation tasks. Additionally, sample preparation methods that are focused on specific glycan(s) require an in-depth understanding of various issues in glycobiology. In this review, modern sample preparation and chemical modification methods for the structural and quantitative glycan analyses together with the challenges and advantages of recent sample preparation methods are summarized. The techniques presented herein can facilitate the exploration of biomarkers, understanding of unknown glycan functions, and development of biopharmaceuticals.
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9
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Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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10
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Yang Y, Yan G, Kong S, Wu M, Yang P, Cao W, Qiao L. GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control. Nat Commun 2021; 12:6073. [PMID: 34663801 PMCID: PMC8523693 DOI: 10.1038/s41467-021-26246-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) is an emerging technology with deep proteome coverage and accurate quantitative capability in proteomics studies, but is still in the early stage of development in the field of glycoproteomics. We propose GproDIA, a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact glycopeptides using wide isolation windows. We further utilize a semi-empirical spectrum prediction strategy to expand the coverage of spectral libraries of glycopeptides. We benchmark our method for N-glycopeptide profiling on DIA data of yeast and human serum samples, demonstrating that DIA with GproDIA outperforms the data-dependent acquisition-based methods for glycoproteomics in terms of capacity and data completeness of identification, as well as accuracy and precision of quantification. We expect that this work can provide a powerful tool for glycoproteomic studies.
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Affiliation(s)
- Yi Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Siyuan Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Mengxi Wu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
- The Shanghai Key Laboratory of Medical Epigenetics, Fudan University, Shanghai, 200000, China
- The International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, 200000, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200000, China
| | - Weiqian Cao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China.
- The Shanghai Key Laboratory of Medical Epigenetics, Fudan University, Shanghai, 200000, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, 200000, China.
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200000, China.
| | - Liang Qiao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China.
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11
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HIOKI M, KOBAYASHI H, KINOSHITA M, YAMAMOTO S, SUZUKI S. Chromatographic Performance of an Amine/amino-bonded Column and a Monolithic Reversed-Phase Column for the Separation of Fluorescently Labeled Glycoprotein Glycans. CHROMATOGRAPHY 2021. [DOI: 10.15583/jpchrom.2021.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Maho HIOKI
- Faculty of Pharmaceutical Sciences, Kindai University
| | | | | | | | - Shigeo SUZUKI
- Faculty of Pharmaceutical Sciences, Kindai University
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12
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Shen Z, Wang Y, Xu H, Zhang Q, Sha C, Sun B, Li Q. Analytical comparability assessment on glycosylation of ziv-aflibercept and the biosimilar candidate. Int J Biol Macromol 2021; 180:494-509. [PMID: 33684428 DOI: 10.1016/j.ijbiomac.2021.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022]
Abstract
Ziv-aflibercept (aflibercept) is a recombinant fusion protein which combines the portions of human vascular endothelial growth factor receptors extracellular domains fused to the Fc portion of human IgG1. It is a highly sialylated glycoprotein with 5 N-glycosylation sites. In this study, a comprehensive strategy for comparability study of the complex glycosylation was developed between aflibercept and the biosimilar candidate including the investigations on N-glycosylation sites, site occupancy, site-specific glycoforms, released glycans and sialic acids. The results indicated that same N-glycosylation sites were identified, site occupancy were 100% except N68 site, site-specific glycoforms and released glycans showed similar glycan species, contents of NANA were at a same level for two products. Minor differences were found between two products. The biosimilar candidate presented lower level of aglycosylation, lower level of glycans containing one terminal sialic acid, higher level of glycans containing two terminal sialic acids, higher level of G0F and Man5, lower level of G1F and G2F compared with aflibercept. However, further studies exhibited no differences were observed in the cell-based biological potency and Fc effector function. Moreover, the biosimilar candidate showed a similar pharmacokinetics curve and bioequivalence compared with aflibercept.
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Affiliation(s)
- Zhenduo Shen
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Yanhong Wang
- Department of Pharmacy, Shandong Drug and Food Vocational College, Weihai, China
| | - Huarong Xu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Qian Zhang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Chunjie Sha
- Analytical Department, Shandong Boan Biotechnology Co., Ltd, Yantai, China
| | - Baiping Sun
- Analytical Department, Shandong Boan Biotechnology Co., Ltd, Yantai, China
| | - Qing Li
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China.
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13
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Abstract
Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism. Intact glycopeptide analysis is a blossoming field that has received increasing attention in recent years. MS-based strategies and relative software tools are major drivers that have greatly facilitated the analysis of intact glycopeptides, particularly intact N-glycopeptides. This article provides a systematic review of the intact glycopeptide-identification process using MS data generated in shotgun proteomic experiments, which typically focus on N-glycopeptide analysis. Particular attention is paid to the software tools that have been recently developed in the last decade for the interpretation and quality control of glycopeptide spectra acquired using different MS strategies. The review also provides information about the characteristics and applications of these software tools, discusses their advantages and disadvantages, and concludes with a discussion of outstanding tools.
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Affiliation(s)
- Weiqian Cao
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China; The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China.
| | - Mingqi Liu
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Siyuan Kong
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mengxi Wu
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; Department of Chemistry, Fudan University, Shanghai, China
| | - Yang Zhang
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China
| | - Pengyuan Yang
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China; The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China; Department of Chemistry, Fudan University, Shanghai, China.
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14
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Abstract
Exosomes represent a class of secreted biological vesicles, which have recently gained attention due to their function as intertissue and interorganism transporters of genetic materials, small molecules, lipids, and proteins. Although the protein constituents of these exosomes are often glycosylated, a large-scale characterization of the glycoproteome has not yet been completed. This study identified 3144 unique glycosylation events belonging to 378 glycoproteins and 604 unique protein sites of glycosylation. With these data, we investigated the level of glycan microheterogeneity within the urinary exosomes, finding on average 5.9 glycans per site. The glycan family abundance on individual proteins showed subtle differences, providing an additional level of molecular characterization compared to the unmodified proteome. Finally, we show protein site-specific changes in regard to the common urinary glycoprotein, uromodulin. While uromodulin is an individual case, these same site-specific analyses provide a way forward for developing diagnostic glycoprotein biomarkers with urine as a noninvasive biological fluid. This study represents an important first step in understanding the functional urinary glycoproteome.
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Affiliation(s)
- Christopher J Brown
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Stefan Gaunitz
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Ziyu Wang
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Lena Strindelius
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Stephen C Jacobson
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Milos V Novotny
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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15
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Duivelshof BL, Murisier A, Camperi J, Fekete S, Beck A, Guillarme D, D'Atri V. Therapeutic Fc-fusion proteins: Current analytical strategies. J Sep Sci 2020; 44:35-62. [PMID: 32914936 DOI: 10.1002/jssc.202000765] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/27/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Fc-Fusion proteins represent a successful class of biopharmaceutical products, with already 13 drugs approved in the European Union and United States as well as three biosimilar versions of etanercept. Fc-Fusion products combine tailored pharmacological properties of biological ligands, together with multiple functions of the fragment crystallizable domain of immunoglobulins. There is a great diversity in terms of possible biological ligands, including the extracellular domains of natural receptors, functionally active peptides, recombinant enzymes, and genetically engineered binding constructs acting as cytokine traps. Due to their highly diverse structures, the analytical characterization of Fc-Fusion proteins is far more complex than that of monoclonal antibodies and requires the use and development of additional product-specific methods over conventional generic/platform methods. This can be explained, for example, by the presence of numerous sialic acids, leading to high diversity in terms of isoelectric points and complex glycosylation profiles including multiple N- and O-linked glycosylation sites. In this review, we highlight the wide range of analytical strategies used to fully characterize Fc-fusion proteins. We also present case studies on the structural assessment of all commercially available Fc-fusion proteins, based on the features and critical quality attributes of their ligand-binding domains.
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Affiliation(s)
- Bastiaan L Duivelshof
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Amarande Murisier
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Julien Camperi
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Szabolcs Fekete
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Alain Beck
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
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16
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Kelly MI, Dodds ED. Parallel Determination of Polypeptide and Oligosaccharide Connectivities by Energy-Resolved Collison-Induced Dissociation of Protonated O-Glycopeptides Derived from Nonspecific Proteolysis. J Am Soc Mass Spectrom 2020; 31:624-632. [PMID: 32126781 PMCID: PMC7164384 DOI: 10.1021/jasms.9b00065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Collision-induced dissociation (CID) is by far the most broadly applied dissociation method used for tandem mass spectrometry (MS/MS). This includes MS/MS-based structural interrogation of glycopeptides for applications in glycoproteomics. The end goal of such measurements is to determine the monosaccharide connectivity of the glycan, the amino acid sequence of the peptide, and the site of glycosylation for each glycopeptide of interest. In turn, this allows inferences with respect to the glycoprofile of the intact glycoprotein. For glycopeptide analysis, CID is best known for the ability to determine glycosidic topology of the oligosaccharide group; however, CID has also been shown to produce amide bond cleavage of the polypeptide group. Whether structural information is obtained for the glycan or the peptide has been found to depend on the applied collision energy. While these energy-resolved fragmentation pathways have been the subject of several studies on N-linked glycopeptides, there remains a dearth of similar work on O-linked glycopeptides. In this study, MS/MS via CID was shown to provide substantial peptide backbone fragmentation, in addition to glycosidic fragmentation, in an energy-dependent manner. While qualitatively similar to previous findings for N-glycopeptides, the energy-resolved CID (ER-CID) of O-glycopeptides was found to be substantially more sensitive to the collision energy setting. Thus, deliberately obtaining either glycan or peptide dissociation is a more delicate undertaking for O-glycopeptides. Establishing a more complete understanding of O-glycopeptide ER-CID is likely to have a substantive impact on how O-glycoproteomic analysis is approached in the future.
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Affiliation(s)
- Maia I. Kelly
- Department of Chemistry, University of Nebraska – Lincoln, Lincoln, NE, 68588-0304, USA
| | - Eric D. Dodds
- Department of Chemistry, University of Nebraska – Lincoln, Lincoln, NE, 68588-0304, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska – Lincoln, Lincoln, NE, 68588-0304, USA
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17
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Gelb AS, Lai R, Li H, Dodds ED. Composition and charge state influence on the ion-neutral collision cross sections of protonated N-linked glycopeptides: an experimental and theoretical deconstruction of coulombic repulsion vs. charge solvation effects. Analyst 2020; 144:5738-5747. [PMID: 31453603 DOI: 10.1039/c9an00875f] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ion mobility spectrometry (IMS) is of significant interest as a platform for glycoanalysis. While much attention has been focused on the resolution of isomeric carbohydrates and glycoconjugates, another appealing aspect of IMS is the ability to sort different classes of biomolecules into distinct regions of mass vs. mobility space. This capability has potential to greatly simplify glycoproteomic analyses, as glycosylated and non-glycosylated peptides can be rapidly partitioned in the gas phase. Nevertheless, the physical and chemical characteristics of glycopeptides that dictate their mass vs. mobility loci have yet to be systematically investigated. This report presents an IMS study of model protonated glycopeptide ions with systematically varied oligosaccharide topologies, polypeptide sequences, and charge states. In all, over 110 ion-neutral collision cross sections (CCSs) were measured and analyzed in the context of the physicochemical characteristics of the analytes. Glycan size and composition emerged as a decisive factor in dictating the CCS space occupied by the glycopeptides and exerted this influence in a charge state dependent fashion. Furthermore, elongation of the glycan group was found to either increase or decrease glycopeptide CCSs depending on the ion charge state and the size of the glycan. Molecular dynamics (MD) simulations of the gas phase structures and CCSs of selected glycopeptides revealed that the experimental observations were consistent with a glycan size and charge state dependent interplay between destabilizing coulombic repulsion effects (tending to result in more extended structures) and stabilizing charge solvation effects in which the glycan plays a major role (tending to result in more compact structures). Taken together, these IMS and MD findings suggest the possibility of predicting and delineating glycopeptide-enriched regions of mass vs. mobility space for applications in glycoproteomics.
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Affiliation(s)
- Abby S Gelb
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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18
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Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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19
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Zhang S, Cao X, Liu C, Li W, Zeng W, Li B, Chi H, Liu M, Qin X, Tang L, Yan G, Ge Z, Liu Y, Gao Q, Lu H. N-glycopeptide Signatures of IgA 2 in Serum from Patients with Hepatitis B Virus-related Liver Diseases. Mol Cell Proteomics 2019; 18:2262-2272. [PMID: 31501225 PMCID: PMC6823847 DOI: 10.1074/mcp.ra119.001722] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Indexed: 12/11/2022] Open
Abstract
N-glycosylation alteration has been reported in liver diseases. Characterizing N-glycopeptides that correspond to N-glycan structure with specific site information enables better understanding of the molecular pathogenesis of liver damage and cancer. Here, unbiased quantification of N-glycopeptides of a cluster of serum glycoproteins with 40-55 kDa molecular weight (40-kDa band) was investigated in hepatitis B virus (HBV)-related liver diseases. We used an N-glycopeptide method based on 18O/16O C-terminal labeling to obtain 82 comparisons of serum from patients with HBV-related hepatocellular carcinoma (HCC) and liver cirrhosis (LC). Then, multiple reaction monitoring (MRM) was performed to quantify N-glycopeptide relative to the protein content, especially in the healthy donor-HBV-LC-HCC cascade. TPLTAN205ITK (H5N5S1F1) and (H5N4S2F1) corresponding to the glycopeptides of IgA2 were significantly elevated in serum from patients with HBV infection and even higher in HBV-related LC patients, as compared with healthy donor. In contrast, the two glycopeptides of IgA2 fell back down in HBV-related HCC patients. In addition, the variation in the abundance of two glycopeptides was not caused by its protein concentration. The altered N-glycopeptides might be part of a unique glycan signature indicating an IgA-mediated mechanism and providing potential diagnostic clues in HBV-related liver diseases.
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Affiliation(s)
- Shu Zhang
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Xinyi Cao
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Chao Liu
- Beijing Advanced Innovation Center for Precision Medicine, Beihang University, Beijing 100083, China
| | - Wei Li
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wenfeng Zeng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Baiwen Li
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai 201620, China
| | - Hao Chi
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Mingqi Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xue Qin
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Lingyi Tang
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Guoquan Yan
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zefan Ge
- State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210046, China
| | - Yinkun Liu
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qiang Gao
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China.
| | - Haojie Lu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Chemistry, Fudan University, Shanghai 200433, China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China.
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20
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Zhao B, Reilly CP, Reilly JP. ETD-Cleavable Linker for Confident Cross-linked Peptide Identifications. J Am Soc Mass Spectrom 2019; 30:1631-1642. [PMID: 31098958 DOI: 10.1007/s13361-019-02227-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Peptide cross-links formed using the homobifunctional-linker diethyl suberthioimidate (DEST) are shown to be ETD-cleavable. DEST has a spacer arm consisting of a 6-carbon alkyl chain and it cleaves at the amidino groups created upon reaction with primary amines. In ETD MS2 spectra, DEST cross-links can be recognized based on mass pairs consisting of peptide-NH2• and peptide+linker+NH3 ions, and backbone cleavages are more equally distributed over the two constituent peptides compared with collisional activation. Dead ends that are often challenging to distinguish from cross-links are diagnosed by intense reporter ions. ETD mass pairs can be used in MS3 experiments to confirm cross-link identifications. These features provide a simple but reliable approach to identify cross-links that should facilitate studies of protein complexes.
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Affiliation(s)
- Bingqing Zhao
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Colin P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA.
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21
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Kolli V, Schumacher KN, Dodds ED. Ion mobility-resolved collision-induced dissociation and electron transfer dissociation of N-glycopeptides: gathering orthogonal connectivity information from a single mass-selected precursor ion population. Analyst 2018; 142:4691-4702. [PMID: 29119999 DOI: 10.1039/c7an01196b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glycopeptide-level mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses are commonly performed to establish site-specific protein glycosylation profiles that are of central importance to gaining structure-function insights on glycoproteins. Confoundingly, the complete characterization of glycopeptide connectivity usually requires the acquisition of multiple MS/MS fragmentation spectra. Complementary ion fragmentation techniques such as collision-induced dissociation (CID) and electron transfer dissociation (ETD) are often applied in concert to address this need. While structurally informative, the requirement for acquisition of two MS/MS spectra per analyte places considerable limitations upon the breadth and depth of large-scale glycoproteomic inquiry. Here, a previously developed method of multiplexing CID and ETD is applied to the study of glycopeptides for the first time. Integration of the two dissociation methods was accomplished through addition of an ion mobility (IM) dimension that disperses the two stages of MS/MS in time. This allows the two MS/MS spectra to be acquired within a few milliseconds of one another, and to be deconvoluted in post-processing. Furthermore, the method allows both fragmentation readouts to be obtained from the same precursor ion packet, thus reducing the inefficiencies imposed by separate CID and ETD acquisitions and the relatively poor precursor ion to fragment ion conversion typical of ETD. N-Linked glycopeptide ions ranging in molecular weight from 1.8 to 6.5 kDa were generated from four model glycoproteins that collectively encompassed paucimannosidic, high mannose, and complex types of N-glycosylation. In each case, IM-resolved CID and ETD events provided complete coverage of the glycan topology and peptide sequence coverages ranging from 48.4% (over 32 amino acid residues) to 85.7% (over eight amino acid residues). The potential of this method for large-scale glycoproteomic analysis is discussed.
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Affiliation(s)
- Venkata Kolli
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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22
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Aboufazeli F, Dodds ED. Precursor ion survival energies of protonated N-glycopeptides and their weak dependencies on high mannose N-glycan composition in collision-induced dissociation. Analyst 2018; 143:4459-4468. [PMID: 30151520 PMCID: PMC6131044 DOI: 10.1039/c8an00830b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fully realizing the capabilities of tandem mass spectrometry (MS/MS) for analysis of glycosylated peptides will require further understanding of the unimolecular dissociation chemistry that dictates their fragmentation pathways. In this context, the overall composition of a given glycopeptide ion is a key characteristic; however, the extent to which the carbohydrate moiety influences the preferred dissociation channels has received relatively little study. Here, the effect of glycan composition on energy-resolved collision-induced dissociation (CID) behavior was studied for a select menu of 30 protonated high mannose type N-linked glycopeptide ions. Groups of analytes which shared a common charge state, polypeptide sequence, and glycosylation site exhibited 50% precursor ion survival energies that varied only slightly as the size and composition of the oligosaccharide was varied. This was found to be true regardless of whether the precursor ion survival energies were normalized for the number of available vibrational degrees of freedom. The practical consequence of this was that a given collision energy brought about highly similar levels of precursor ion depletion and structural information despite systematic variation of the glycan identity. This lack of sensitivity to oligosaccharide composition stands in contrast to other physicochemical properties of glycopeptide ions (e.g., polypeptide composition, charge state, charge carrier) which sharply influence their energy-resolved CID characteristics. On the whole, these findings imply that the deliberate selection of CID energies to bring about a desired range of fragmentation pathways does not necessarily hinge on the nature of the glycan.
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Affiliation(s)
- Forouzan Aboufazeli
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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23
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Yin H, An M, So P, Wong M, Lubman DM, Yao Z. The analysis of alpha-1-antitrypsin glycosylation with direct LC-MS/MS. Electrophoresis 2018; 39:2351-2361. [PMID: 29405331 PMCID: PMC6077116 DOI: 10.1002/elps.201700426] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 12/11/2022]
Abstract
A liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based methodology has been developed to differentiate core- and antennary-fucosylated glycosylation of glycopeptides. Both the glycosylation sites (heterogeneity) and multiple possible glycan occupancy at each site (microheterogeneity) can be resolved via intact glycopeptide analysis. The serum glycoprotein alpha-1-antitrypsin (A1AT) which contains both core- and antennary-fucosylated glycosites was used in this study. Sialidase was used to remove the sialic acids in order to simplify the glycosylation microheterogeneity and to enhance the MS signal of glycopeptides with similar glycan structures. β1-3,4 galactosidase was used to differentiate core- and antennary-fucosylation. In-source dissociation was found to severely affect the identification and quantification of glycopeptides with low abundance glycan modification. The settings of the mass spectrometer were therefore optimized to minimize the in-source dissociation. A three-step mass spectrometry fragmentation strategy was used for glycopeptide identification, facilitated by pGlyco software annotation and manual checking. The collision energy used for initial glycopeptide fragmentation was found to be crucial for improved detection of oxonium ions and better selection of Y1 ion (peptide+GlcNAc). Structural assignments revealed that all three glycosylation sites of A1AT glycopeptides contain complex N-glycan structures: site Asn70 contains biantennary glycans without fucosylation; site Asn107 contains bi-, tri- and tetra-antennary glycans with both core- and antennary-fucosylation; site Asn271 contains bi- and tri-antennary glycans with both core- and antennary-fucosylation. The relative intensity of core- and antennary-fucosylation on Asn107 was similar to that of the A1AT protein indicating that the glycosylation level of Asn107 is much larger than the other two sites.
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Affiliation(s)
- Haidi Yin
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, PR China
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Mingrui An
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI 48109
| | - Puikin So
- University Research Facility in Life Sciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Melody Wong
- University Research Facility in Chemical and Environmental Analysis, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - David M. Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI 48109
| | - Zhongping Yao
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, PR China
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24
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Yang H, Yang C, Sun T. Characterization of glycopeptides using a stepped higher-energy C-trap dissociation approach on a hybrid quadrupole orbitrap. Rapid Commun Mass Spectrom 2018; 32:1353-1362. [PMID: 29873418 DOI: 10.1002/rcm.8191] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/23/2018] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Accurate characterization of glycopeptides without a prior glycan cleavage could provide valuable information on site-specific glycosylation, which is critical to reveal the biological functions of protein glycosylation. However, due to the distinct nature of oligosaccharides and ploypeptides, it is usually difficult to effectively fragment glycopeptides in mass spectrometry analysis. METHODS Here we applied a stepped normalized collisional energy (NCE) approach, which is able to combine fragment ions from three different collision energies, in a hybrid quadrupole orbitrap (Q Exactive Plus) to characterize glycopeptides. A systematic evaluation was firstly performed to find optimal NCE values for the fragmentation of glycan chains and peptide backbones from glycopeptides. Guided by the results of the systematic evaluation, the stepped NCE method was optimized and employed to analyze glycopeptides enriched from human serum. RESULTS The stepped NCE approach was found to effectively fragment both the glycan chains and peptide backbones from glycopeptides and record these fragments in a single MS/MS spectrum. In comparison with the regular HCD methods, the stepped NCE method identified more glycopeptides with higher scores from human serum samples. CONCLUSIONS Our studies demonstrate the capability of stepped NCE for the effective characterization of glycopeptides on a large scale.
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Affiliation(s)
- Hong Yang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
| | - Chenxi Yang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
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25
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Abstract
The characterization of glycosylation is required for many protein therapeutics. The emergence of antibody and antibody-like molecules with multiple glycan attachment sites has rendered glycan analysis increasingly more complicated. Reliance on site-specific glycopeptide analysis is therefore necessary to fully analyze multi-glycosylated biotherapeutics. Established glycopeptide methodologies have generally utilized a priori knowledge of the glycosylation states of the investigated protein(s), database searching of results generated from data-dependent liquid chromatography–tandem mass spectrometry workflows, and extracted ion quantitation of the individual identified species. However, the inherent complexity of glycosylation makes predicting all glycoforms on all glycosylation sites extremely challenging, if not impossible. That is, only the “knowns” are assessed. Here, we describe an agnostic methodology to qualitatively and quantitatively assess both “known” and “unknown” site-specific glycosylation for biotherapeutics that contain multiple glycosylation sites. The workflow uses data-independent, all ion fragmentation to generate glycan oxonium ions, which are then extracted across the entirety of the chromatographic timeline to produce a glycan-specific “fingerprint” of the glycoprotein sample. We utilized both HexNAc and sialic acid oxonium ion profiles to quickly assess the presence of Fab glycosylation in a therapeutic monoclonal antibody, as well as for high-throughput comparisons of multi-glycosylated protein drugs derived from different clones to a reference product. An automated method was created to rapidly assess oxonium profiles between samples, and to provide a quantitative assessment of similarity.
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Affiliation(s)
- James A Madsen
- a Pharmaceutical Sciences and Research , Momenta Pharmaceuticals , Cambridge , MA , USA
| | - Victor Farutin
- a Pharmaceutical Sciences and Research , Momenta Pharmaceuticals , Cambridge , MA , USA
| | - Yin Yin Lin
- a Pharmaceutical Sciences and Research , Momenta Pharmaceuticals , Cambridge , MA , USA
| | - Stephen Smith
- a Pharmaceutical Sciences and Research , Momenta Pharmaceuticals , Cambridge , MA , USA
| | - Ishan Capila
- a Pharmaceutical Sciences and Research , Momenta Pharmaceuticals , Cambridge , MA , USA
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26
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. Mass Spectrom Rev 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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27
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Kim KH, Lee SY, Hwang H, Lee JY, Ji ES, An HJ, Kim JY, Yoo JS. Direct Monitoring of Fucosylated Glycopeptides of Alpha-Fetoprotein in Human Serum for Early Hepatocellular Carcinoma by Liquid Chromatography-Tandem Mass Spectrometry with Immunoprecipitation. Proteomics Clin Appl 2018; 12:e1800062. [PMID: 29888876 DOI: 10.1002/prca.201800062] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/29/2018] [Indexed: 12/17/2022]
Abstract
PURPOSE Alpha-fetoprotein (AFP) is a widely used serological marker that is associated with hepatocellular carcinoma (HCC). Although the level of AFP is increased in HCC, its sensitivity for diagnosis is poor because AFP levels are also increased in liver diseases. Changes in glycoform, especially fucosylation, have been reported to be associated with the development of HCC. EXPERIMENTAL DESIGN The authors introduce the monitoring of fucosylated glycopeptides by liquid chromatography (LC)-mass spectrometry (MS) combined with immunoprecipitation, where glycan-cleaved fragments with an amino acid sequence are used as transitions. Furthermore, neuraminidase for desialylation is useful to improve the MS detection limit (limit of detection [LOD] <2 ng mL-1 ) in 0.1 μL of serum. RESULTS The performance of the relative percentage of fucosylated AFP (AFP-fuc%) for differentiating between early HCC and cirrhosis is better than that of serum AFP levels as indicated by a greater area under the receiver operator characteristic curve (area under the curve = 0.962 vs. 0.628) and sensitivity (92.3% vs. 53.9%), respectively. Furthermore, the inter- and intraday repeatability of AFP-fuc% in serum is less than 2.1%. CONCLUSIONS AND CLINICAL RELEVANCE These findings suggest that glycopeptide-based LC-MS/MS is a promising method and that AFP-fuc% is a clinically useful parameter for differentiating between early HCC and liver cirrhosis.
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Affiliation(s)
- Kwang Hoe Kim
- Biomedical Omics Research Group, Korea Basic Science Institute, Cheongju, Ochang-eup, 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Soo-Youn Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Heeyoun Hwang
- Biomedical Omics Research Group, Korea Basic Science Institute, Cheongju, Ochang-eup, 28119, Republic of Korea
| | - Ju Yeon Lee
- Biomedical Omics Research Group, Korea Basic Science Institute, Cheongju, Ochang-eup, 28119, Republic of Korea
| | - Eun Sun Ji
- Biomedical Omics Research Group, Korea Basic Science Institute, Cheongju, Ochang-eup, 28119, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Research Group, Korea Basic Science Institute, Cheongju, Ochang-eup, 28119, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Research Group, Korea Basic Science Institute, Cheongju, Ochang-eup, 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
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28
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Khatri K, Pu Y, Klein JA, Wei J, Costello CE, Lin C, Zaia J. Comparison of Collisional and Electron-Based Dissociation Modes for Middle-Down Analysis of Multiply Glycosylated Peptides. J Am Soc Mass Spectrom 2018; 29:1075-1085. [PMID: 29663256 PMCID: PMC6004259 DOI: 10.1007/s13361-018-1909-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/09/2018] [Accepted: 01/29/2018] [Indexed: 05/12/2023]
Abstract
Analysis of singly glycosylated peptides has evolved to a point where large-scale LC-MS analyses can be performed at almost the same scale as proteomics experiments. While collisionally activated dissociation (CAD) remains the mainstay of bottom-up analyses, it performs poorly for the middle-down analysis of multiply glycosylated peptides. With improvements in instrumentation, electron-activated dissociation (ExD) modes are becoming increasingly prevalent for proteomics experiments and for the analysis of fragile modifications such as glycosylation. While these methods have been applied for glycopeptide analysis in isolated studies, an organized effort to compare their efficiencies, particularly for analysis of multiply glycosylated peptides (termed here middle-down glycoproteomics), has not been made. We therefore compared the performance of different ExD modes for middle-down glycopeptide analyses. We identified key features among the different dissociation modes and show that increased electron energy and supplemental activation provide the most useful data for middle-down glycopeptide analysis. Graphical Abstract.
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Affiliation(s)
- Kshitij Khatri
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Yi Pu
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Joshua A Klein
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Juan Wei
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Catherine E Costello
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Cheng Lin
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA.
- Boston University Medical Campus, 670 Albany St., Suite 504, Boston, MA, 02118, USA.
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA.
- Program in Bioinformatics, Boston University, Boston, MA, USA.
- Boston University Medical Campus, 670 Albany St., Suite 504, Boston, MA, 02118, USA.
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29
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Togayachi A, Tomioka A, Fujita M, Sukegawa M, Noro E, Takakura D, Miyazaki M, Shikanai T, Narimatsu H, Kaji H. Identification of Poly-N-Acetyllactosamine-Carrying Glycoproteins from HL-60 Human Promyelocytic Leukemia Cells Using a Site-Specific Glycome Analysis Method, Glyco-RIDGE. J Am Soc Mass Spectrom 2018; 29:1138-1152. [PMID: 29675740 PMCID: PMC6004004 DOI: 10.1007/s13361-018-1938-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 05/15/2023]
Abstract
To elucidate the relationship between the protein function and the diversity and heterogeneity of glycans conjugated to the protein, glycosylation sites, glycan variation, and glycan proportions at each site of the glycoprotein must be analyzed. Glycopeptide-based structural analysis technology using mass spectrometry has been developed; however, complicated analyses of complex spectra obtained by multistage fragmentation are necessary, and sensitivity and throughput of the analyses are low. Therefore, we developed a liquid chromatography/mass spectrometry (MS)-based glycopeptide analysis method to reveal the site-specific glycome (Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile, Glyco-RIDGE). This method used accurate masses and retention times of glycopeptides, without requiring MS2, and could be applied to complex mixtures. To increase the number of identified peptide, fractionation of sample glycopeptides for reduction of sample complexity is required. Therefore, in this study, glycopeptides were fractionated into four fractions by hydrophilic interaction chromatography, and each fraction was analyzed using the Glyco-RIDGE method. As a result, many glycopeptides having long glycans were enriched in the highest hydrophilic fraction. Based on the monosaccharide composition, these glycans were thought to be poly-N-acetyllactosamine (polylactosamine [pLN]), and 31 pLN-carrier proteins were identified in HL-60 cells. Gene ontology enrichment analysis revealed that pLN carriers included many molecules related to signal transduction, receptors, and cell adhesion. Thus, these findings provided important insights into the analysis of the glycoproteome using our novel Glyco-RIDGE method. Graphical Abstract ᅟ.
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Affiliation(s)
- Akira Togayachi
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Azusa Tomioka
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Mika Fujita
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Masako Sukegawa
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Erika Noro
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Daisuke Takakura
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Michiyo Miyazaki
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Toshihide Shikanai
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Hisashi Narimatsu
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
| | - Hiroyuki Kaji
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
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Abstract
INTRODUCTION Though eukaryotic glycoproteins have been studied since their discovery in the 1930s, the first bacterial glycoprotein was not identified until the 1970s. As a result, their role in bacterial pathogenesis is still not well understood and they remain an understudied component of bacterial virulence. In recent years, mass spectrometry has emerged as a leading technology for the study of bacterial glycoproteins, largely due to its sensitivity and versatility. Areas covered: Identification and comprehensive characterization of bacterial glycoproteins usually requires multiple complementary mass spectrometry approaches, including intact protein analysis, top-down analysis, and bottom-up methods used in combination with specialized liquid chromatography. This review provides an overview of liquid chromatography separation technologies, as well as current and emerging mass spectrometry approaches used specifically for bacterial glycoprotein identification and characterization. Expert commentary: Bacterial glycoproteins may have significant clinical utility as a result of their unique structures and exposure on the surface of the cells. Better understanding of these glycoconjugates is an essential first step towards that goal. These often unique structures, and by extension the key enzymes involved in their synthesis, represent promising targets for novel antimicrobials, while unique carbohydrate structures may be used as antigens in vaccines or as biomarkers.
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Affiliation(s)
- Kelly M Fulton
- a Human Health Therapeutics Portfolio , National Research Council Canada , Ottawa , Canada
| | - Jianjun Li
- a Human Health Therapeutics Portfolio , National Research Council Canada , Ottawa , Canada
| | - Juan M Tomas
- b Departament de Microbiologia, Facultat de Biologia , Universitat de Barcelona , Barcelona , Spain
| | - Jeffrey C Smith
- c Department of Chemistry , Carleton University , Ottawa , Canada
| | - Susan M Twine
- a Human Health Therapeutics Portfolio , National Research Council Canada , Ottawa , Canada
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31
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King SR, Hecht ES, Muddiman DC. Demonstration of hydrazide tagging for O-glycans and a central composite design of experiments optimization using the INLIGHT™ reagent. Anal Bioanal Chem 2017; 410:1409-1415. [PMID: 29279989 DOI: 10.1007/s00216-017-0828-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 11/25/2022]
Abstract
The INLIGHT™ strategy for N-linked glycan derivatization has been shown to overcome many of the challenges associated with glycan analysis. The hydrazide tag reacts efficiently with the glycans, increasing their non-polar surface area, allowing for reversed-phase separations and increased ionization efficiency. We have taken the INLIGHT™ strategy and adopted it for use with O-linked glycans. A central composite design was utilized to find optimized tagging conditions (45% acetic acid, 0.1 μg/μL tag concentration, 37 C, 1.75 h). Derivatization at optimized conditions was much quicker than any hydrazide derivatization strategy used previously. Human immunoglobulin A (IgA) and bovine submaxillary mucin (BSM) were then deglycosylated through hydrazinolysis and the removed glycans were tagged under optimum conditions. XIC of tagged glycans and MS2 data show successful hydrazide tagging of O-linked glycans for the first time. Graphical abstract The INLIGHT™ hydrazide tag was optimized using a central composite design for derivatization of O-linked glycans. Two glycoprotein standards were deglycosylated through hydrazinolysis and tagged at the optimized conditions. MS/MS data shows INLIGHT™ derivatization of glycans demonstrating successful hydrazide tagging of O-glycans for the first time.
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Affiliation(s)
- Samuel R King
- W. M. Keck FTMS Laboratory from Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Elizabeth S Hecht
- W. M. Keck FTMS Laboratory from Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - David C Muddiman
- W. M. Keck FTMS Laboratory from Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
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32
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Zeng W, Ford KL, Bacic A, Heazlewood JL. N-linked Glycan Micro-heterogeneity in Glycoproteins of Arabidopsis. Mol Cell Proteomics 2017; 17:413-421. [PMID: 29237727 DOI: 10.1074/mcp.ra117.000165] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/21/2017] [Indexed: 01/01/2023] Open
Abstract
N-glycosylation is one of the most common protein post-translational modifications in eukaryotes and has a relatively conserved core structure between fungi, animals and plants. In plants, the biosynthesis of N-glycans has been extensively studied with all the major biosynthetic enzymes characterized. However, few studies have applied advanced mass spectrometry to profile intact plant N-glycopeptides. In this study, we use hydrophilic enrichment, high-resolution tandem mass spectrometry with complementary and triggered fragmentation to profile Arabidopsis N-glycopeptides from microsomal membranes of aerial tissues. A total of 492 N-glycosites were identified from 324 Arabidopsis proteins with extensive N-glycan structural heterogeneity revealed through 1110 N-glycopeptides. To demonstrate the precision of the approach, we also profiled N-glycopeptides from the mutant (xylt) of β-1,2-xylosyltransferase, an enzyme in the N-glycan biosynthetic pathway. This analysis represents the most comprehensive and unbiased collection of Arabidopsis N-glycopeptides revealing an unsurpassed level of detail on the micro-heterogeneity present in N-glycoproteins of Arabidopsis. Data are available via ProteomeXchange with identifier PXD006270.
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Affiliation(s)
- Wei Zeng
- From the ‡ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia.,§Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, China
| | - Kristina L Ford
- From the ‡ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Antony Bacic
- From the ‡ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Joshua L Heazlewood
- From the ‡ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; .,¶Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94702
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33
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Lakbub JC, Su X, Hua D, Go EP, Desaire H. Dissecting the Dissociation Patterns of Fucosylated Glycopeptides Undergoing CID: A Case Study in Improving Automated Glycopeptide Analysis Scoring Algorithms. Anal Methods 2017; 10:256-262. [PMID: 29662551 PMCID: PMC5898446 DOI: 10.1039/c7ay02687k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The need to investigate the fragmentation of fucosylated glycopeptides is driven by recent work showing that at least one, and perhaps many, glycopeptide analysis scoring algorithms are less effective at identifying fucosylated glycopeptides than non-fucosylated glycopeptides. Herein, we study the CID fragmentation characteristics of fucosylated glycopeptides and the scoring rules of the glycopeptide analysis software, GlycoPep Grader, in an effort to improve automated assignments of these important glycopeptides. We identified some prominent product ions from a common fragmentation pathway of fucosylated glycopeptides that were not accounted for in the scoring rules. Based on this finding, we propose new scoring rules for fucosylated glycopeptides that can be incorporated into GlycoPep Grader and other similar analysis software tools to more accurately identify these species. The approach used here, to improve one particular scoring algorithm, could henceforth be used to improve any other algorithm that assigns glycopeptides based on their MS/MS data.
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Affiliation(s)
- Jude C. Lakbub
- Ralph N Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas-66047, United States
| | - Xiaomeng Su
- Ralph N Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas-66047, United States
| | - David Hua
- Ralph N Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas-66047, United States
| | - Eden P. Go
- Ralph N Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas-66047, United States
| | - Heather Desaire
- Ralph N Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas-66047, United States
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34
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O'Flaherty R, Trbojević-Akmačić I, Greville G, Rudd PM, Lauc G. The sweet spot for biologics: recent advances in characterization of biotherapeutic glycoproteins. Expert Rev Proteomics 2017; 15:13-29. [PMID: 29130774 DOI: 10.1080/14789450.2018.1404907] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Glycosylation is recognized as a Critical Quality Attribute for therapeutic glycoproteins such as monoclonal antibodies, fusion proteins and therapeutic replacement enzymes. Hence, efficient and quantitative glycan analysis techniques have been increasingly important for their discovery, development and quality control. The aim of this review is to highlight relevant and recent advances in analytical technologies for characterization of biotherapeutic glycoproteins. Areas covered: The review gives an overview of the glycosylation trends of biotherapeutics approved in 2016 and 2017 by FDA. It describes current and novel analytical technologies for characterization of therapeutic glycoproteins and is explored in the context of released glycan, glycopeptide or intact glycoprotein analysis. Ultra performance liquid chromatography, mass spectrometry and capillary electrophoresis technologies are explored in this context. Expert commentary: There is a need for the biopharmaceutical industry to incorporate novel state of the art analytical technologies into existing and new therapeutic glycoprotein workflows for safer and more efficient biotherapeutics and for the improvement of future biotherapeutic design. Additionally, at present, there is no 'gold-standard' approach to address all the regulatory requirements and as such this will involve the use of orthogonal glycoanalytical technologies with a view to gain diagnostic information about the therapeutic glycoprotein.
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Affiliation(s)
- Róisín O'Flaherty
- a NIBRT GlycoScience Group , National Institute for Bioprocessing, Research and Training , Blackrock, Co. Dublin , Ireland
| | | | - Gordon Greville
- a NIBRT GlycoScience Group , National Institute for Bioprocessing, Research and Training , Blackrock, Co. Dublin , Ireland
| | - Pauline M Rudd
- a NIBRT GlycoScience Group , National Institute for Bioprocessing, Research and Training , Blackrock, Co. Dublin , Ireland
| | - Gordan Lauc
- b Genos Glycoscience Research Laboratory , 10000 , Zagreb , Croatia.,c Faculty of Pharmacy and Biochemistry , University of Zagreb , Zagreb , Croatia
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35
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Mastrangeli R, Satwekar A, Cutillo F, Ciampolillo C, Palinsky W, Longobardi S. In-vivo biological activity and glycosylation analysis of a biosimilar recombinant human follicle-stimulating hormone product (Bemfola) compared with its reference medicinal product (GONAL-f). PLoS One 2017; 12:e0184139. [PMID: 28880909 PMCID: PMC5589168 DOI: 10.1371/journal.pone.0184139] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 08/18/2017] [Indexed: 02/03/2023] Open
Abstract
Recombinant human follicle-stimulating hormone (r-hFSH) is widely used in fertility treatment. Although biosimilar versions of r-hFSH (follitropin alfa) are currently on the market, given their structural complexity and manufacturing process, it is important to thoroughly evaluate them in comparison with the reference product. This evaluation should focus on how they differ (e.g., active component molecular characteristics, impurities and potency), as this could be associated with clinical outcome. This study compared the site-specific glycosylation profile and batch-to-batch variability of the in-vivo bioactivity of Bemfola, a biosimilar follitropin alfa, with its reference medicinal product GONAL-f. The focus of this analysis was the site-specific glycosylation at asparagine (Asn) 52 of the α-subunit of FSH, owing to the pivotal role of Asn52 glycosylation in FSH receptor (FSHR) activation/signalling. Overall, Bemfola had bulkier glycan structures and greater sialylation than GONAL-f. The nominal specific activity for both Bemfola and GONAL-f is 13,636 IU/mg. Taking into account both the determined potency and the nominal amount the average specific activity of Bemfola was 14,522 IU/mg (105.6% of the nominal value), which was greater than the average specific activity observed for GONAL-f (13,159 IU/mg; 97.3% of the nominal value; p = 0.0048), although this was within the range stated in the product label. A higher batch-to-batch variability was also observed for Bemfola versus GONAL-f (coefficient of variation: 8.3% vs 5.8%). A different glycan profile was observed at Asn52 in Bemfola compared with GONAL-f (a lower proportion of bi-antennary structures [~53% vs ~77%], and a higher proportion of tri-antennary [~41% vs ~23%] and tetra-antennary structures [~5% vs <1%]). These differences in the Asn52 glycan profile might potentially lead to differences in FSHR activation. This, together with the greater bioactivity and higher batch-to-batch variability of Bemfola, could partly explain the reported differences in clinical outcomes. The clinical relevance of the differences observed between GONAL-f and Bemfola should be further investigated.
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Affiliation(s)
- Renato Mastrangeli
- Biotech Development Programme, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Guidonia Montecelio, Rome, Italy
- * E-mail:
| | - Abhijeet Satwekar
- Pharamceutical & Analytical Development Biotech Products, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Guidonia Montecelio, Rome, Italy
| | - Francesca Cutillo
- Pharamceutical & Analytical Development Biotech Products, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Guidonia Montecelio, Rome, Italy
| | - Cinzia Ciampolillo
- Analytical BQC, Merck RBM S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Ivrea, Turin, Italy
| | - Wolf Palinsky
- Biotech Development Programme, Merck Biopharma (an affiliate of Merck KGaA, Darmstadt, Germany), Aubonne, Switzerland
| | - Salvatore Longobardi
- Global Medical Affairs Fertility, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Guidonia Montecelio, Rome, Italy
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36
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Liu MQ, Zeng WF, Fang P, Cao WQ, Liu C, Yan GQ, Zhang Y, Peng C, Wu JQ, Zhang XJ, Tu HJ, Chi H, Sun RX, Cao Y, Dong MQ, Jiang BY, Huang JM, Shen HL, Wong CCL, He SM, Yang PY. pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification. Nat Commun 2017; 8:438. [PMID: 28874712 PMCID: PMC5585273 DOI: 10.1038/s41467-017-00535-2] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
The precise and large-scale identification of intact glycopeptides is a critical step in glycoproteomics. Owing to the complexity of glycosylation, the current overall throughput, data quality and accessibility of intact glycopeptide identification lack behind those in routine proteomic analyses. Here, we propose a workflow for the precise high-throughput identification of intact N-glycopeptides at the proteome scale using stepped-energy fragmentation and a dedicated search engine. pGlyco 2.0 conducts comprehensive quality control including false discovery rate evaluation at all three levels of matches to glycans, peptides and glycopeptides, improving the current level of accuracy of intact glycopeptide identification. The N-glycoproteome of samples metabolically labeled with 15N/13C were analyzed quantitatively and utilized to validate the glycopeptide identification, which could be used as a novel benchmark pipeline to compare different search engines. Finally, we report a large-scale glycoproteome dataset consisting of 10,009 distinct site-specific N-glycans on 1988 glycosylation sites from 955 glycoproteins in five mouse tissues. Protein glycosylation is a heterogeneous post-translational modification that generates greater proteomic diversity that is difficult to analyze. Here the authors describe pGlyco 2.0, a workflow for the precise one step identification of intact N-glycopeptides at the proteome scale.
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Affiliation(s)
- Ming-Qi Liu
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China.,Department of Systems Biology for Medicine, Basic Medical College, Fudan University, Shanghai, 20032, China
| | - Wen-Feng Zeng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pan Fang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Wei-Qian Cao
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Chao Liu
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China
| | - Guo-Quan Yan
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Yang Zhang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Chao Peng
- National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai, 201210, China
| | - Jian-Qiang Wu
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Jin Zhang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui-Jun Tu
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Chi
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China
| | - Rui-Xiang Sun
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China
| | - Yong Cao
- National Institute of Biological Sciences (Beijing), Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences (Beijing), Beijing, 102206, China
| | - Bi-Yun Jiang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Jiang-Ming Huang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Hua-Li Shen
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China
| | - Catherine C L Wong
- National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai, 201210, China.
| | - Si-Min He
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peng-Yuan Yang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, China. .,Department of Systems Biology for Medicine, Basic Medical College, Fudan University, Shanghai, 20032, China.
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37
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Hu H, Khatri K, Zaia J. Algorithms and design strategies towards automated glycoproteomics analysis. Mass Spectrom Rev 2017; 36:475-498. [PMID: 26728195 PMCID: PMC4931994 DOI: 10.1002/mas.21487] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/30/2015] [Indexed: 05/09/2023]
Abstract
Glycoproteomics involves the study of glycosylation events on protein sequences ranging from purified proteins to whole proteome scales. Understanding these complex post-translational modification (PTM) events requires elucidation of the glycan moieties (monosaccharide sequences and glycosidic linkages between residues), protein sequences, as well as site-specific attachment of glycan moieties onto protein sequences, in a spatial and temporal manner in a variety of biological contexts. Compared with proteomics, bioinformatics for glycoproteomics is immature and many researchers still rely on tedious manual interpretation of glycoproteomics data. As sample preparation protocols and analysis techniques have matured, the number of publications on glycoproteomics and bioinformatics has increased substantially; however, the lack of consensus on tool development and code reuse limits the dissemination of bioinformatics tools because it requires significant effort to migrate a computational tool tailored for one method design to alternative methods. This review discusses algorithms and methods in glycoproteomics, and refers to the general proteomics field for potential solutions. It also introduces general strategies for tool integration and pipeline construction in order to better serve the glycoproteomics community. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:475-498, 2017.
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Affiliation(s)
- Han Hu
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Kshitij Khatri
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
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Kammeijer GSM, Jansen BC, Kohler I, Heemskerk AAM, Mayboroda OA, Hensbergen PJ, Schappler J, Wuhrer M. Sialic acid linkage differentiation of glycopeptides using capillary electrophoresis - electrospray ionization - mass spectrometry. Sci Rep 2017; 7:3733. [PMID: 28623326 DOI: 10.1038/s41598-017-03838-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Sialylation is a glycosylation feature that occurs in different linkages at the non-reducing end of a glycan moiety, the linkage isomers are often differentially associated with various biological processes. Due to very similar physico-chemical properties, the separation of isomeric sialylated glycopeptides remains challenging but of utmost importance in the biomedicine and biotechnology, including biomarker discovery, glyco-engineering and biopharmaceutical characterization. This study presents the implementation of a high-resolution separation platform based on capillary electrophoresis - mass spectrometry (CE-MS) allowing for the selective analysis of α2,3- and α2,6-sialylated glycopeptides. These differentially linked glycopeptides showed an identical fragmentation pattern (collision induced dissociation) but different electrophoretic mobilities, allowing for baseline separation of the different linkages without the need for an extensive sample preparation. The different migration behavior between the two moieties was found to correlate with differences in pKa values. Using a novel methodology adapted from the so-called internal standard CE approach, a relative difference of 3.4·10-2 in pKa unit was determined. This approach was applied for the analysis of tryptic glycopeptides of prostate specific antigen, which shows highly complex and heterogeneous glycosylation. The developed platform therefore appears attractive for the identification of differentially linked sialic acids that may be related to pathological conditions.
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Zhang S, Li W, Lu H, Liu Y. Quantification of N-glycosylation site occupancy status based on labeling/label-free strategies with LC-MS/MS. Talanta 2017; 170:509-13. [PMID: 28501204 DOI: 10.1016/j.talanta.2017.04.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 12/30/2022]
Abstract
Protein N-glycosylation plays important roles in physiological and pathological processes. Characterizing the site-specific N-glycosylation including N-glycan macroheterogeneity (glycosylation site occupancy) and microheterogeneity (site-specific glycan structure) is important for understanding of glycoprotein biosynthesis and function. N-Glycan macroheterogeneity is a physiological property of glycoprotein and the technical obstacles have restricted research into the regulation and functions of this heterogeneity. Quantification of N-glycosylation site occupancy would uncover the critical role of macroheterogeneity in a variety of biological properties. Liquid chromatography (LC)- mass spectrometry (MS)-based quantification is emerging as a powerful tool for glycosylation characterization. This review summarizes the labeling and label-free quantitative MS approaches for quantifying N-glycosylation site occupancy, including its quantification for target glycoproteins in recent years.
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Yu Z, Zhao X, Tian F, Zhao Y, Zhang Y, Huang Y, Qian X, Ying W. Sequential fragment ion filtering and endoglycosidase-assisted identification of intact glycopeptides. Anal Bioanal Chem 2017; 409:3077-87. [PMID: 28258464 DOI: 10.1007/s00216-017-0195-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/20/2016] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
Abstract
Detailed characterization of glycoprotein structures requires determining both the sites of glycosylation as well as the glycan structures associated with each site. In this work, we developed an analytical strategy for characterization of intact N-glycopeptides in complex proteome samples. In the first step, tryptic glycopeptides were enriched using ZIC-HILIC. Secondly, a portion of the glycopeptides was treated with endoglycosidase H (Endo H) to remove high-mannose (Man) and hybrid N-linked glycans. Thirdly, a fraction of the Endo H-treated glycopeptides was further subjected to PNGase F treatment in 18O water to remove the remaining complex glycans. The intact glycopeptides and deglycosylated peptides were analyzed by nano-RPLC-MS/MS, and the glycan structures and the peptide sequences were identified by using the Byonic or pFind tools. Sequential digestion by endoglycosidase provided candidate glycosites information and indication of the glycoforms on each glycopeptide, thus helping to confine the database search space and improve the confidence regarding intact glycopeptide identification. We demonstrated the effectiveness of this approach using RNase B and IgG and applied this sequential digestion strategy for the identification of glycopeptides from the HepG2 cell line. We identified 4514 intact glycopeptides coming from 947 glycosites and 1011 unique peptide sequences from HepG2 cells. The intensity of different glycoforms at a specific glycosite was obtained to reach the occupancy ratios of site-specific glycoforms. These results indicate that our method can be used for characterizing site-specific protein glycosylation in complex samples. Graphical abstract Through integrating the information of intact glycopeptide, fragment ions filters and endoglycosidase digestion, the reliability of the identification could be significantly improved. We quantified the site-specific glycoforms occupancy ratios through the MS response signaling of each glycopeptide at the same time.
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Ribela MTCP, Damiani R, Silva FD, Lima ER, Oliveira JE, Peroni CN, Torjesen PA, Soares CR, Bartolini P. N-Glycoprofiling Analysis for Carbohydrate Composition and Site-Occupancy Determination in a Poly-Glycosylated Protein: Human Thyrotropin of Different Origins. Int J Mol Sci 2017; 18:ijms18020131. [PMID: 28165356 PMCID: PMC5343769 DOI: 10.3390/ijms18020131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/22/2016] [Accepted: 12/28/2016] [Indexed: 11/16/2022] Open
Abstract
Human thyrotropin (hTSH) is a glycoprotein with three potential glycosylation sites: two in the α-subunit and one in the β-subunit. These sites are not always occupied and occupancy is frequently neglected in glycoprotein characterization, even though it is related to folding, trafficking, initiation of inflammation and host defense, as well as congenital disorders of glycosylation (CDG). For the first time N-glycoprofiling analysis was applied to the site-occupancy determination of two native pituitary hTSH, in comparison with three recombinant preparations of hTSH, a widely used biopharmaceutical. A single methodology provided the: (i) average N-glycan mass; (ii) mass fraction of each monosaccharide and of sulfate; and (iii) percent carbohydrate. The results indicate that the occupancy (65%–87%) and carbohydrate mass (12%–19%) can be up to 34%–57% higher in recombinant hormones. The average glycan mass is 24% lower in pituitary hTSH and contains ~3-fold fewer moles of galactose (p < 0.005) and sialic acid (p < 0.01). One of the two native preparations, which had the smallest glycan mass together with the lowest occupancy and GalNAc, sulfate, Gal and sialic acid contents, also presented the lowest in vivo bioactivity and circulatory half-life. The methodology described, comparing a recombinant biopharmaceutical to its native equivalent, can be applied to any physiologically or clinical relevant glycoprotein.
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Affiliation(s)
- Maria Teresa C P Ribela
- Biotechnology Center, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP-Avenida Prof. Lineu Prestes, 2242-Cidade Universitária, 05508-000 São Paulo, Brazil.
| | - Renata Damiani
- Biotechnology Center, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP-Avenida Prof. Lineu Prestes, 2242-Cidade Universitária, 05508-000 São Paulo, Brazil.
| | - Felipe D Silva
- Biotechnology Center, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP-Avenida Prof. Lineu Prestes, 2242-Cidade Universitária, 05508-000 São Paulo, Brazil.
| | - Eliana R Lima
- Biotechnology Center, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP-Avenida Prof. Lineu Prestes, 2242-Cidade Universitária, 05508-000 São Paulo, Brazil.
| | - João E Oliveira
- Biotechnology Center, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP-Avenida Prof. Lineu Prestes, 2242-Cidade Universitária, 05508-000 São Paulo, Brazil.
| | - Cibele N Peroni
- Biotechnology Center, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP-Avenida Prof. Lineu Prestes, 2242-Cidade Universitária, 05508-000 São Paulo, Brazil.
| | - Peter A Torjesen
- Hormone Laboratory, Oslo University Hospital, 0424 Oslo, Norway.
| | - Carlos R Soares
- Biotechnology Center, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP-Avenida Prof. Lineu Prestes, 2242-Cidade Universitária, 05508-000 São Paulo, Brazil.
| | - Paolo Bartolini
- Biotechnology Center, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP-Avenida Prof. Lineu Prestes, 2242-Cidade Universitária, 05508-000 São Paulo, Brazil.
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Stavenhagen K, Hinneburg H, Kolarich D, Wuhrer M. Site-Specific N- and O-Glycopeptide Analysis Using an Integrated C18-PGC-LC-ESI-QTOF-MS/MS Approach. Methods Mol Biol 2017; 1503:109-119. [PMID: 27743362 DOI: 10.1007/978-1-4939-6493-2_9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The vast heterogeneity of protein glycosylation, even of a single glycoprotein with only one glycosylation site, can give rise to a set of macromolecules with different physicochemical properties. Thus, the use of orthogonal approaches for comprehensive characterization of glycoproteins is a key requirement. This chapter describes a universal workflow for site-specific N- and O-glycopeptide analysis. In a first step glycoproteins are treated with Pronase to generate glycopeptides containing small peptide sequences for enhanced glycosylation site assignment and characterization. These glycopeptides are then separated and detected using an integrated C18-porous graphitized carbon-liquid chromatography (PGC-LC) setup online coupled to a high-resolution electrospray ionization (ESI)-quadrupole time-of-flight (QTOF)-mass spectrometer operated in a combined higher- and lower-energy CID (stepping-energy CID) mode. The LC-setup allows retention of more hydrophobic glycopeptides on C18 followed by subsequent capturing of C18-unbound (glyco)peptides by a downstream placed PGC stationary phase. Glycopeptides eluted from both columns are then analyzed within a single analysis in a combined data acquisition mode. Stepping-energy CID results in B- and Y-ion fragments originating from the glycan moiety as well as b- and y-ions derived from the peptide part. This allows simultaneous site-specific identification of the glycan and peptide sequence of a glycoprotein.
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Affiliation(s)
- Kathrin Stavenhagen
- Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, Amsterdam, 1081, HV, The Netherlands.,Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333, ZA, The Netherlands
| | - Hannes Hinneburg
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, 14424, Germany.,Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, 14195, Germany
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids andInterfaces, Am Mühlenberg 1, Potsdam, 14476, Germany
| | - Manfred Wuhrer
- Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, Amsterdam, 1081, HV, The Netherlands. .,Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333, ZA, The Netherlands.
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44
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Vreeker GC, Wuhrer M. Reversed-phase separation methods for glycan analysis. Anal Bioanal Chem 2017; 409:359-78. [PMID: 27888305 DOI: 10.1007/s00216-016-0073-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 10/26/2016] [Accepted: 10/31/2016] [Indexed: 12/21/2022]
Abstract
Reversed-phase chromatography is a method that is often used for glycan separation. For this, glycans are often derivatized with a hydrophobic tag to achieve retention on hydrophobic stationary phases. The separation and elution order of glycans in reversed-phase chromatography is highly dependent on the hydrophobicity of the tag and the contribution of the glycan itself to the retention. The contribution of the different monosaccharides to the retention strongly depends on the position and linkage, and isomer separation may be achieved. The influence of sialic acids and fucoses on the retention of glycans is still incompletely understood and deserves further study. Analysis of complex samples may come with incomplete separation of glycan species, thereby complicating reversed-phase chromatography with fluorescence or UV detection, whereas coupling with mass spectrometry detection allows the resolution of complex mixtures. Depending on the column properties, eluents, and run time, separation of isomeric and isobaric structures can be accomplished with reversed-phase chromatography. Alternatively, porous graphitized carbon chromatography and hydrophilic interaction liquid chromatography are also able to separate isomeric and isobaric structures, generally without the necessity of glycan labeling. Hydrophilic interaction liquid chromatography, porous graphitized carbon chromatography, and reversed-phase chromatography all serve different research purposes and thus can be used for different research questions. A great advantage of reversed-phase chromatography is its broad distribution as it is used in virtually every bioanalytical research laboratory, making it an attracting platform for glycan analysis. Glycan isomer separation by reversed phase liquid chromatography ![]()
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45
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Abstract
Glycoproteins influence numerous indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to the development of proteome informatics tools that facilitate the MS analysis of glycans and glycopeptides. Here we report on the development of gFinder, a web-based bioinformatics tool that analyzes mixtures of native N-glycopeptides that have been profiled by tandem MS. gFinder not only enables the simultaneous integration of collision-induced dissociation (CID) and high-energy collisional dissociation (HCD) fragmentation but also merges the spectra for high-throughput analysis. These merged spectra expedite the identification of both glycans and N-glycopeptide backbones in tandem MS data using the glycan database and a proteomic search tool (e.g., Mascot). These data can be used to simultaneously characterize peptide backbone sequences and possible N-glycan structures using assigned scores. gFinder also provides many convenient functions that make it easy to perform manual calculations while viewing the spectrum on-screen. We used gFinder to detect an additional protein (Q8N9B8) that was missed from the previously published data set containing N-linked glycosylation. For N-glycan analysis, we used the GlycomeDB glycan structure database, which integrates the structural and taxonomic data from all of the major carbohydrate databases available in the public domain. Thus, gFinder is a convenient, high-throughput analytical tool for interpreting the tandem mass spectra of N-glycopeptides, which can then be used for identification of potential missing proteins having glycans. gFinder is available publicly at http://gFinder.proteomix.org/ .
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Affiliation(s)
- Ju-Wan Kim
- Graduate Program in Functional Genomics, College of Life Sciences and Biotechnology, Yonsei University , Seoul 03722, Korea.,Yonsei Proteome Research Center , Seoul 03722, Korea
| | - Heeyoun Hwang
- Korea Basic Science Institute , Ochang 28199, Chungbuk, Korea
| | - Jong-Sun Lim
- Yonsei Proteome Research Center , Seoul 03722, Korea
| | | | - Seul-Ki Jeong
- Yonsei Proteome Research Center , Seoul 03722, Korea
| | - Jong Shin Yoo
- Korea Basic Science Institute , Ochang 28199, Chungbuk, Korea
| | - Young-Ki Paik
- Graduate Program in Functional Genomics, College of Life Sciences and Biotechnology, Yonsei University , Seoul 03722, Korea.,Yonsei Proteome Research Center , Seoul 03722, Korea
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46
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Hu W, Su X, Zhu Z, Go EP, Desaire H. GlycoPep MassList: software to generate massive inclusion lists for glycopeptide analyses. Anal Bioanal Chem 2016; 409:561-570. [PMID: 27614974 DOI: 10.1007/s00216-016-9896-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/12/2016] [Accepted: 08/19/2016] [Indexed: 12/14/2022]
Abstract
Protein glycosylation drives many biological processes and serves as markers for disease; therefore, the development of tools to study glycosylation is an essential and growing area of research. Mass spectrometry can be used to identify both the glycans of interest and the glycosylation sites to which those glycans are attached, when proteins are proteolytically digested and their glycopeptides are analyzed by a combination of high-resolution mass spectrometry (MS) and tandem mass spectrometry (MS/MS) methods. One major challenge in these experiments is collecting the requisite MS/MS data. The digested glycopeptides are often present in complex mixtures and in low abundance, and the most commonly used approach to collect MS/MS data on these species is data-dependent acquisition (DDA), where only the most intense precursor ions trigger MS/MS. DDA results in limited glycopeptide coverage. Semi-targeted data acquisition is an alternative experimental approach that can alleviate this difficulty. However, due to the massive heterogeneity of glycopeptides, it is not obvious how to expediently generate inclusion lists for these types of analyses. To solve this problem, we developed the software tool GlycoPep MassList, which can be used to generate inclusion lists for liquid chromatography tandem-mass spectrometry (LC-MS/MS) experiments. The utility of the software was tested by conducting comparisons between semi-targeted and untargeted data-dependent analysis experiments on a variety of proteins, including IgG, a protein whose glycosylation must be characterized during its production as a biotherapeutic. When the GlycoPep MassList software was used to generate inclusion lists for LC-MS/MS experiments, more unique glycopeptides were selected for fragmentation. Generally, ∼30 % more unique glycopeptides can be analyzed per protein, in the simplest cases, with low background. In cases where background ions from proteins or other interferents are high, usage of an inclusion list is even more advantageous. The software is freely publically accessible. Graphical abstract Software increases the number of glycopeptides that get selected for MS/MS analysis.
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Affiliation(s)
- Wenting Hu
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Xiaomeng Su
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Zhikai Zhu
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Eden P Go
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA.
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47
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Qing G, Li X, Xiong P, Chen C, Zhan M, Liang X, Sun T. Dipeptide-Based Carbohydrate Receptors and Polymers for Glycopeptide Enrichment and Glycan Discrimination. ACS Appl Mater Interfaces 2016; 8:22084-92. [PMID: 27500750 DOI: 10.1021/acsami.6b07863] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Glycoproteomics identifies and catalogs protein glycosylation and explores its impact on protein conformations and biofunctions. However, these studies are restricted by the bottleneck to enrich low-abundance glycopeptides from complex biosamples and the difficulties in analyzing glycan structures by mass spectrometry. Here, we report dipeptide as a simple but promising carbohydrate binding platform to tackle these problems. We build a hydropathy-index-based strategy for sequence optimization and screen out three optimal dipeptide sequences from 54 types of dipeptides. The optimized dipeptide-based homopolymers display excellent performance (e.g., selectivity up to ∼70% for real biosamples and strong anti-interference capacity capable of resisting 1000-fold bovine serum albumin interference) in glycopeptide enrichment. Meanwhile, our polymers exhibit high-efficiency chromatographic separation toward oligosaccharides with different compositions, polymerization degrees and even their linkage isomers. This brings another attractive feature that our materials can discriminate subtly variable glycan structures of glycopeptides, especially, isomeric glycosidic linkages. These features provide a solid foundation to analyze the complex glycan structures and glycosites simultaneously, which will benefit future development of glycoproteomics and glycobiology.
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Affiliation(s)
- Guangyan Qing
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, People's Republic of China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, People's Republic of China
| | - Peng Xiong
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, People's Republic of China
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, People's Republic of China
| | - Mimi Zhan
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, People's Republic of China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, People's Republic of China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, People's Republic of China
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, People's Republic of China
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48
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Abstract
The last 6 years have witnessed an explosion of discoveries at the interface of glycobiology and immunology. Binding of clustered oligosaccharides has turned out to be a very frequent mode by which human antibodies have developed broadly neutralizing activity against HIV. This mini-review will cover many recent developments in the HIV antibody field, as well as emerging data about Dengue broadly neutralizing antibodies.
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Affiliation(s)
- Isaac J Krauss
- Department of Chemistry, Brandeis University, Waltham, MA 02454, USA
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Pai PJ, Hu Y, Lam H. Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching. Anal Chim Acta 2016; 934:152-62. [DOI: 10.1016/j.aca.2016.05.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/24/2016] [Accepted: 05/30/2016] [Indexed: 11/24/2022]
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Yamamoto S, Kinoshita M, Suzuki S. Current landscape of protein glycosylation analysis and recent progress toward a novel paradigm of glycoscience research. J Pharm Biomed Anal 2016; 130:273-300. [PMID: 27461579 DOI: 10.1016/j.jpba.2016.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 07/09/2016] [Accepted: 07/09/2016] [Indexed: 12/25/2022]
Abstract
This review covers the basics and some applications of methodologies for the analysis of glycoprotein glycans. Analytical techniques used for glycoprotein glycans, including liquid chromatography (LC), capillary electrophoresis (CE), mass spectrometry (MS), and high-throughput analytical methods based on microfluidics, were described to supply the essentials about biopharmaceutical and biomarker glycoproteins. We will also describe the MS analysis of glycoproteins and glycopeptides as well as the chemical and enzymatic releasing methods of glycans from glycoproteins and the chemical reactions used for the derivatization of glycans. We hope the techniques have accommodated most of the requests from glycoproteomics researchers.
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Affiliation(s)
- Sachio Yamamoto
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1, Kowakae, Higashi-osaka, Osaka, 577-8502, Japan.
| | - Mitsuhiro Kinoshita
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1, Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
| | - Shigeo Suzuki
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1, Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
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