1
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Huang C, Wang H, Zhou J, Huang Y, Ren Y, Zhao K, Wang Y, Hou M, Zhang J, Liu Y, Ma X, Yan J, Bu D, Chai W, Sun S, Li Y. Protocol for automated N-glycan sequencing using mass spectrometry and computer-assisted intelligent fragmentation. STAR Protoc 2024; 5:102976. [PMID: 38635398 PMCID: PMC11043862 DOI: 10.1016/j.xpro.2024.102976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/22/2024] [Accepted: 03/07/2024] [Indexed: 04/20/2024] Open
Abstract
Biological functions of glycans are intimately linked to fine details in branches and linkages, which make structural identification extremely challenging. Here, we present a protocol for automated N-glycan sequencing using multi-stage mass spectrometry (MSn). We describe steps for release/purification and derivation of glycans and procedures for MSn scanning. We then detail "glycan intelligent precursor selection" to computationally guide MSn experiments. The protocol can be used for both discrete individual glycans and isomeric glycan mixtures. For complete details on the use and execution of this protocol, please refer to Sun et al.,1 Huang et al.,2 and Huang et al.3.
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Affiliation(s)
- Chuncui Huang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; Western Institute of Health Data Science, 28 High Tech Avenue, Chongqing 401329, China
| | - Hui Wang
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay Ne Laboratory, Kowloon, Hong Kong SAR, China
| | - Jinyu Zhou
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Yikang Huang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yihui Ren
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Keli Zhao
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China; Western Institute of Health Data Science, 28 High Tech Avenue, Chongqing 401329, China
| | - Yaojun Wang
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Meijie Hou
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
| | - Jingwei Zhang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
| | - Yaming Liu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Xinyue Ma
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jingyu Yan
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Key Laboratory of Separation Science for Analytical Chemistry, Dalian 116023, China
| | - Dongbo Bu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Wengang Chai
- Glycosciences Laboratory, Department of Medicine, Imperial College London, W120NN London, UK.
| | - Shiwei Sun
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China.
| | - Yan Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Western Institute of Health Data Science, 28 High Tech Avenue, Chongqing 401329, China.
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2
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Wei J, Papanastasiou D, Kosmopoulou M, Smyrnakis A, Hong P, Tursumamat N, Klein JA, Xia C, Tang Y, Zaia J, Costello CE, Lin C. De novo glycan sequencing by electronic excitation dissociation MS 2-guided MS 3 analysis on an Omnitrap-Orbitrap hybrid instrument. Chem Sci 2023; 14:6695-6704. [PMID: 37350811 PMCID: PMC10284134 DOI: 10.1039/d3sc00870c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023] Open
Abstract
Comprehensive de novo glycan sequencing remains an elusive goal due to the structural diversity and complexity of glycans. Present strategies employing collision-induced dissociation (CID) and higher energy collisional dissociation (HCD)-based multi-stage tandem mass spectrometry (MSn) or MS/MS combined with sequential exoglycosidase digestions are inherently low-throughput and difficult to automate. Compared to CID and HCD, electron transfer dissociation (ETD) and electron capture dissociation (ECD) each generate more cross-ring cleavages informative about linkage positions, but electronic excitation dissociation (EED) exceeds the information content of all other methods and is also applicable to analysis of singly charged precursors. Although EED can provide extensive glycan structural information in a single stage of MS/MS, its performance has largely been limited to FTICR MS, and thus it has not been widely adopted by the glycoscience research community. Here, the effective performance of EED MS/MS was demonstrated on a hybrid Orbitrap-Omnitrap QE-HF instrument, with high sensitivity, fragmentation efficiency, and analysis speed. In addition, a novel EED MS2-guided MS3 approach was developed for detailed glycan structural analysis. Automated topology reconstruction from MS2 and MS3 spectra could be achieved with a modified GlycoDeNovo software. We showed that the topology and linkage configurations of the Man9GlcNAc2 glycan can be accurately determined from first principles based on one EED MS2 and two CID-EED MS3 analyses, without reliance on biological knowledge, a structure database or a spectral library. The presented approach holds great promise for autonomous, comprehensive and de novo glycan sequencing.
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Affiliation(s)
- Juan Wei
- Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
| | | | | | | | - Pengyu Hong
- Department of Computer Science, Brandeis University Waltham MA 02454 USA
| | - Nafisa Tursumamat
- Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Joshua A Klein
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
| | - Chaoshuang Xia
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
| | - Yang Tang
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
- Department of Chemistry, Boston University Boston MA 02215 USA
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
- Department of Chemistry, Boston University Boston MA 02215 USA
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine Boston MA 02118 USA
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3
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An Integrative Glycomic Approach for Quantitative Meat Species Profiling. Foods 2022; 11:foods11131952. [PMID: 35804766 PMCID: PMC9265272 DOI: 10.3390/foods11131952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 02/05/2023] Open
Abstract
It is estimated that food fraud, where meat from different species is deceitfully labelled or contaminated, has cost the global food industry around USD 6.2 to USD 40 billion annually. To overcome this problem, novel and robust quantitative methods are needed to accurately characterise and profile meat samples. In this study, we use a glycomic approach for the profiling of meat from different species. This involves an O-glycan analysis using LC-MS qTOF, and an N-glycan analysis using a high-resolution non-targeted ultra-performance liquid chromatography-fluorescence-mass spectrometry (UPLC-FLR-MS) on chicken, pork, and beef meat samples. Our integrated glycomic approach reveals the distinct glycan profile of chicken, pork, and beef samples; glycosylation attributes such as fucosylation, sialylation, galactosylation, high mannose, α-galactose, Neu5Gc, and Neu5Ac are significantly different between meat from different species. The multi-attribute data consisting of the abundance of each O-glycan and N-glycan structure allows a clear separation between meat from different species through principal component analysis. Altogether, we have successfully demonstrated the use of a glycomics-based workflow to extract multi-attribute data from O-glycan and N-glycan analysis for meat profiling. This established glycoanalytical methodology could be extended to other high-value biotechnology industries for product authentication.
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4
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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5
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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: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [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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6
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Lukassen MV, Franc V, Hevler JF, Heck AJR. Similarities and differences in the structures and proteoform profiles of the complement proteins C6 and C7. Proteomics 2021; 21:e2000310. [PMID: 34241972 DOI: 10.1002/pmic.202000310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 11/08/2022]
Abstract
The human complement system provides a first line of defence against pathogens. It requires a well-orchestrated sequential assembly of an array of terminal complement components (C5, C6, C7, C8, and C9), ultimately forming the membrane attack complex (MAC). Although much information about MAC assembly is available, the structure of the soluble C7 has remained elusive. The complement proteins C7 and C6 share very high sequence homology and exhibit several conserved domains, disulphide bridges, and C-mannosylation sites. Here, we used an integrative structural MS-based approach combining native MS, glycopeptide-centric MS, in-gel cross-linking MS (IGX-MS) and structural modelling to describe structural features, including glycosylation, of human serum soluble C7. We compare this data with structural and glycosylation data for human serum C6. The new structural model for C7 shows that it adopts a compact conformation in solution. Although C6 and C7 share many similarities, our data reveals distinct O-, and N-linked glycosylation patterns in terms of location and glycan composition. Cumulatively, our data provide valuable new insight into the structure and proteoforms of C7, solving an essential piece of the puzzle in our understanding of MAC assembly.
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Affiliation(s)
- Marie V Lukassen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, The Netherlands.,Netherlands Proteomics Center, The Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, The Netherlands.,Netherlands Proteomics Center, The Netherlands
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, The Netherlands.,Netherlands Proteomics Center, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, The Netherlands.,Netherlands Proteomics Center, The Netherlands
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7
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Kurz S, Sheikh MO, Lu S, Wells L, Tiemeyer M. Separation and Identification of Permethylated Glycan Isomers by Reversed Phase NanoLC-NSI-MS n. Mol Cell Proteomics 2021; 20:100045. [PMID: 33376194 PMCID: PMC8724860 DOI: 10.1074/mcp.ra120.002266] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 01/18/2023] Open
Abstract
HPLC has been employed for decades to enhance detection sensitivity and quantification of complex analytes within biological mixtures. Among these analytes, glycans released from glycoproteins and glycolipids have been characterized as underivatized or fluorescently tagged derivatives by HPLC coupled to various detection methods. These approaches have proven extremely useful for profiling the structural diversity of glycoprotein and glycolipid glycosylation but require the availability of glycan standards and secondary orthogonal degradation strategies to validate structural assignments. A robust method for HPLC separation of glycans as their permethylated derivatives, coupled with in-line multidimensional ion fragmentation (MSn) to assign structural features independent of standards, would significantly enhance the depth of knowledge obtainable from biological samples. Here, we report an optimized workflow for LC-MS analysis of permethylated glycans that includes sample preparation, mobile phase optimization, and MSn method development to resolve structural isomers on-the-fly. We report baseline separation and MSn of isomeric N- and O-glycan structures, aided by supplementing mobile phases with Li+, which simplifies adduct heterogeneity and facilitates cross-ring fragmentation to obtain valuable monosaccharide linkage information. Our workflow has been adapted from standard proteomics-based workflows and, therefore, provides opportunities for laboratories with expertise in proteomics to acquire glycomic data with minimal deviation from existing buffer systems, chromatography media, and instrument configurations. Furthermore, our workflow does not require a mass spectrometer with high-resolution/accurate mass capabilities. The rapidly evolving appreciation of the biological significance of glycans for human health and disease requires the implementation of high-throughput methods to identify and quantify glycans harvested from sample sets of sufficient size to achieve appropriately powered statistical significance. The LC-MSn approach we report generates glycan isomeric separations and robust structural characterization and is amenable to autosampling with associated throughput enhancements.
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Affiliation(s)
- Simone Kurz
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - M Osman Sheikh
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Shan Lu
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
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8
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Wang Y, Bu D, Huang C, Wang H, Zhou J, Dong J, Pan W, Zhang J, Zhang Q, Li Y, Sun S. Best-first search guided multistage mass spectrometry-based glycan identification. Bioinformatics 2020; 35:2991-2997. [PMID: 30689704 DOI: 10.1093/bioinformatics/btz056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/02/2019] [Accepted: 01/19/2019] [Indexed: 12/22/2022] Open
Abstract
MOTIVATION Glycan identification has long been hampered by complicated branching patterns and various isomeric structures of glycans. Multistage mass spectrometry (MSn) is a promising glycan identification technique as it generates multiple-level fragments of a glycan, which can be explored to deduce branching pattern of the glycan and further distinguish it from other candidates with identical mass. However, the automatic glycan identification still remains a challenge since it mainly relies on expertise to guide a MSn instrument to generate spectra. RESULTS Here, we proposed a novel method, named bestFSA, based on a best-first search algorithm to guide the process of spectrum producing in glycan identification using MSn. BestFSA is able to select the most appropriate peaks for next round of experiments and complete the identification using as few experimental rounds. Our analysis of seven representative glycans shows that bestFSA correctly distinguishes actual glycans efficiently and suggested bestFSA could be used in practical glycan identification. The combination of the MSn technology coupled with bestFSA should greatly facilitate the automatic identification of glycan branching patterns, with significantly improved identification sensitivity, and reduce time and cost of MSn experiments. AVAILABILITY AND IMPLEMENTATION http://glycan.ict.ac.cn. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yaojun Wang
- Key Lab of Intelligent Information Processing, Institute of Computing and Technology, Chinese Academy of Sciences, Beijing, China.,Guanghua School of Management, Peking University, Beijing, China
| | - Dongbo Bu
- Key Lab of Intelligent Information Processing, Institute of Computing and Technology, Chinese Academy of Sciences, Beijing, China
| | - Chuncui Huang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hui Wang
- Key Lab of Intelligent Information Processing, Institute of Computing and Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jinyu Zhou
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Junchuan Dong
- Key Lab of Intelligent Information Processing, Institute of Computing and Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Weiyi Pan
- Key Lab of Intelligent Information Processing, Institute of Computing and Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingwei Zhang
- Key Lab of Intelligent Information Processing, Institute of Computing and Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qi Zhang
- Key Lab of Intelligent Information Processing, Institute of Computing and Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shiwei Sun
- Key Lab of Intelligent Information Processing, Institute of Computing and Technology, Chinese Academy of Sciences, Beijing, China
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9
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Multistage mass spectrometry with intelligent precursor selection for N-glycan branching pattern analysis. Carbohydr Polym 2020; 237:116122. [DOI: 10.1016/j.carbpol.2020.116122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 02/10/2020] [Accepted: 03/03/2020] [Indexed: 12/28/2022]
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10
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Wang H, Zhang J, Dong J, Hou M, Pan W, Bu D, Zhou J, Zhang Q, Wang Y, Zhao K, Li Y, Huang C, Sun S. Identification of glycan branching patterns using multistage mass spectrometry with spectra tree analysis. J Proteomics 2020; 217:103649. [PMID: 31978548 DOI: 10.1016/j.jprot.2020.103649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/02/2020] [Accepted: 01/16/2020] [Indexed: 12/11/2022]
Abstract
Glycans are crucial to a wide range of biological processes, and their biological activities are closely related to the branching patterns of structures. Different from the simple linear chains of proteins, branching patterns of glycans are more complicated, making their identification extremely challenging. Tandem mass spectrometry (MS2) cannot provide sufficient structural information to deduce glycan branching patterns even with the assistance of various bioinformatic tools and algorithms.The promising technology to identify glycan branching patterns is multi-stage mass spectrometry (MSn). The production-relationship among MSn spectra of a glycan is essentially a tree, making deducing glycan structures from MSn spectra a great challenge. In the present study, we report an approach called glyBranch (glycan Branching pattern identification based on spectra tree) to fully exploit the information contained in the MSn spectra tree for glycan identification. Using 14 glycan standards, including 2 pairs with isomeric sequence, and 16 complex N-glycans isolated from RNase B and IgG, we demonstrated the successful application of glyBranch to branching pattern analysis. The source code of glyBranch is available at https://github.com/bigict/glyBranch/. We have also developed a web-server, which is freely accessible at http://glycan.ict.ac.cn/glyBranch/. SIGNIFICANCE: Glycans are crucial in various biological processes and their functions are closely related to the details of their structures; thus, the identification of glycan branching patterns is of great significance to biological studies. Multistage mass spectrometry (MSn) can provide detailed structural information by generating multiple-level fragments through consecutive fragmentation; however, the interpretation of numerous MSn spectra is extremely challenging. In this study, we present an approach called glyBranch (glycan Branching pattern identification based on spectra tree) to exploit the information contained in MSn spectra tree for glycan identification. This approach will greatly facilitate the automated identification of glycan structures and related biological studies.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingwei Zhang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA
| | - Junchuan Dong
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meijie Hou
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyi Pan
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongbo Bu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyu Zhou
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Zhang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaojun Wang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; College of Information and Electrical Engineering, China Agricultural University, 100083,China
| | - Keli Zhao
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuncui Huang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shiwei Sun
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Gao X, Lu Y, Wei M, Yang M, Zheng C, Wang C, Zhang Y, Huang L, Wang Z. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Analysis of Human Milk Neutral and Sialylated Free Oligosaccharides Using Girard's Reagent P On-Target Derivatization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8958-8966. [PMID: 31334644 DOI: 10.1021/acs.jafc.9b02635] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The functional role of human milk oligosaccharides (HMOs) is closely associated with their type, composition, and structure. However, a detailed analysis of HMOs is difficult because neutral oligosaccharides (NHMOs) are mixed with sialylated oligosaccharides (SHMOs) in milk. Here, NHMOs were separated from SHMOs by DEAE-52 anion chromatography, and lactose was removed by graphite carbon solid-phase extraction. Lactose-free NHMOs were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) based on Girard's reagent P on-target derivatization (GPOD), and SHMOs were analyzed by MALDI-TOF-MS following selective sialic acid derivatization and GPOD. Sixty-four oligosaccharides were detected: 36 NHMOs, of which 28 were fucosylated, and 28 SHMOs, of which 8 with α-2,3-linked monosialic acid, 2 with α-2,3-linked disialic acid, 10 with α-2,6-linked monosialic acid, 2 with α-2,6-linked disialic acid, and 5 with both α-2,3- and α-2,6-linked disialic acid. These findings provide the groundwork for further characterization of the structure and activity of HMOs.
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Affiliation(s)
| | | | | | | | - CaiXia Zheng
- The Second Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710069 , China
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12
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Sun S, Huang C, Wang Y, Liu Y, Zhang J, Zhou J, Gao F, Yang F, Chen R, Mulloy B, Chai W, Li Y, Bu D. Toward Automated Identification of Glycan Branching Patterns Using Multistage Mass Spectrometry with Intelligent Precursor Selection. Anal Chem 2018; 90:14412-14422. [DOI: 10.1021/acs.analchem.8b03967] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shiwei Sun
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Chuncui Huang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Yaojun Wang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yaming Liu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jingwei Zhang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jinyu Zhou
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Feng Gao
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Fei Yang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Runsheng Chen
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Barbara Mulloy
- Glycosciences Laboratory, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Wengang Chai
- Glycosciences Laboratory, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Dongbo Bu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
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13
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Zhang Y, Wang B, Jin W, Wen Y, Nan L, Yang M, Liu R, Zhu Y, Wang C, Huang L, Song X, Wang Z. Sensitive and robust MALDI-TOF-MS glycomics analysis enabled by Girard's reagent T on-target derivatization (GTOD) of reducing glycans. Anal Chim Acta 2018; 1048:105-114. [PMID: 30598139 DOI: 10.1016/j.aca.2018.10.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/01/2018] [Accepted: 10/07/2018] [Indexed: 12/31/2022]
Abstract
Sensitive glycomics analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is of great importance but significantly hampered by their low ionization efficiency and labile sialic acid moieties. Chemical derivatization offers a viable way to improve both the ionization efficiency and analytical sensitivity of the glycans in MS analysis by altering their hydrophobicity or charge property. Here we employed Girard's reagent T (GT) for on-target derivatization (GTOD) of reducing glycan under mild acid condition to form stable hydrazones at room temperature, allowing rapid and sensitive identification of neutral and sialylated glycans in positive-ion mode as only permanently positive charged molecular ions without multiple ion adducts by MALDI-TOF-MS. The MS signal intensities of lactose, sialylated N-glycans derived from bovine fetuin and neutral N-glycans derived from RNaseB and ovalbumin were boosted by 7.44, 9.13, 12.96 and 13.47 folds on average (n = 3), respectively. More importantly, after GTOD strategy, unwanted desialylation of sialylated glycans during MS was suppressed. The detection limit of the assay is desirable since the nanogram of N-glycans derived from 0.16 μg ovalbumin could be detected. The assay demonstrated good stability (RSD≤2.95%, within 10 days), reliable reproducibility (RSD = 2.96%, n = 7) and a desirable linear dynamic range from 78 nmol/mL to 10 μmol/mL. The strategy has been successfully applied to MS analysis of reducing glycans from human milks, neutral and sialylated O-, N-glycans from glycoproteins, and reducing glycans derived from glycosphingolipids, presenting neater [M]+ signals which allow detection of more low-abundance glycans and assignation of Neu5Ac vs. Neu5Gc or fucose vs. hexose in glycans due to the absence of the ambiguous interpretation from multiple peaks (ion adducts [M+Na]+ and [M+K]+). Moreover, the GTOD assay prevents desialylation during MALDI-TOF-MS profiling and enables distinct linkage-specific characterization of terminal sialic acids of N-glycans derived from human serum protein when combines with an esterification.
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Affiliation(s)
- Ying Zhang
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, 229 Northern Taibai Road, Xi'an, 710069, PR China
| | - Bo Wang
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, 229 Northern Taibai Road, Xi'an, 710069, PR China
| | - Wanjun Jin
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, 229 Northern Taibai Road, Xi'an, 710069, PR China
| | - Yanan Wen
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, 229 Northern Taibai Road, Xi'an, 710069, PR China
| | - Lijing Nan
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, 229 Northern Taibai Road, Xi'an, 710069, PR China
| | - Mingming Yang
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, 229 Northern Taibai Road, Xi'an, 710069, PR China
| | - Rendan Liu
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, 229 Northern Taibai Road, Xi'an, 710069, PR China
| | - Yuyang Zhu
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Chengjian Wang
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, 229 Northern Taibai Road, Xi'an, 710069, PR China
| | - Linjuan Huang
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, 229 Northern Taibai Road, Xi'an, 710069, PR China
| | - Xuezheng Song
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA.
| | - Zhongfu Wang
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, 229 Northern Taibai Road, Xi'an, 710069, PR China.
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14
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Mookherjee A, Uppal SS, Guttman M. Dissection of Fragmentation Pathways in Protonated N-Acetylhexosamines. Anal Chem 2018; 90:11883-11891. [PMID: 30216047 DOI: 10.1021/acs.analchem.8b01963] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Structural characterization of carbohydrates by mass spectrometry necessitates a detailed understanding of their gas phase behavior, particularly for protonated carbohydrates that can undergo complex structural rearrangements during fragmentation. Here we utilize tandem mass spectrometry, isotopic labeling, gas-phase hydrogen/deuterium exchange, and ion mobility measurements to characterize structures of the various product ions of protonated N-acetylhexosamines. Following the facile loss of the reducing end hydroxyl group, we identify two primary fragmentation pathways. Detailed mapping of each step in the fragmentation pathway provides new insight into the mechanisms that drive collision-induced dissociation of protonated carbohydrates. Several of the smaller fragment ions are mixtures of structural isomers, and the relative distributions of these structures reveals information about the stereochemistry of the precursor molecule.
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Affiliation(s)
- Abhigya Mookherjee
- Department of Medicinal Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Sanjit S Uppal
- Department of Medicinal Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Miklos Guttman
- Department of Medicinal Chemistry , University of Washington , Seattle , Washington 98195 , United States
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15
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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 SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [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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16
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Wang C, Lu Y, Han J, Jin W, Li L, Zhang Y, Song X, Huang L, Wang Z. Simultaneous Release and Labeling of O- and N-Glycans Allowing for Rapid Glycomic Analysis by Online LC-UV-ESI-MS/MS. J Proteome Res 2018; 17:2345-2357. [DOI: 10.1021/acs.jproteome.8b00038] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chengjian Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Yu Lu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Jianli Han
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Wanjun Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Lingmei Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Ying Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Xuezheng Song
- Department of Biochemistry, Emory University School of Medicine, O. Wayne Rollins Research Center, 1510 Clifton Road, Suite 4117, Atlanta, Georgia 30322, United States
| | - Linjuan Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Zhongfu Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an 710069, China
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17
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Advanced LC-MS Methods for N-Glycan Characterization. ADVANCES IN THE USE OF LIQUID CHROMATOGRAPHY MASS SPECTROMETRY (LC-MS) - INSTRUMENTATION DEVELOPMENTS AND APPLICATIONS 2018. [DOI: 10.1016/bs.coac.2017.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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18
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Liu Y, Palma AS, Feizi T, Chai W. Insights Into Glucan Polysaccharide Recognition Using Glucooligosaccharide Microarrays With Oxime-Linked Neoglycolipid Probes. Methods Enzymol 2018; 598:139-167. [DOI: 10.1016/bs.mie.2017.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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19
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Chen JY, Huang HH, Yu SY, Wu SJ, Kannagi R, Khoo KH. Concerted mass spectrometry-based glycomic approach for precision mapping of sulfo sialylated N-glycans on human peripheral blood mononuclear cells and lymphocytes. Glycobiology 2017; 28:9-20. [DOI: 10.1093/glycob/cwx091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/20/2017] [Indexed: 12/14/2022] Open
Affiliation(s)
- Jian-You Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Hsin-Hung Huang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Shin-Yi Yu
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Shang-Ju Wu
- Hematology Division, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Reiji Kannagi
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
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20
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Hsiao CT, Wang PW, Chang HC, Chen YY, Wang SH, Chern Y, Khoo KH. Advancing a High Throughput Glycotope-centric Glycomics Workflow Based on nanoLC-MS 2-product Dependent-MS 3 Analysis of Permethylated Glycans. Mol Cell Proteomics 2017; 16:2268-2280. [PMID: 29066631 DOI: 10.1074/mcp.tir117.000156] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/21/2017] [Indexed: 01/08/2023] Open
Abstract
The intrinsic nature of glycosylation, namely nontemplate encoded, stepwise elongation and termination with a diverse range of isomeric glyco-epitopes (glycotopes), translates into ambiguity in most cases of mass spectrometry (MS)-based glycomic mapping. It is arguable that whether one needs to delineate every single glycomic entity, which may be counterproductive. Instead, one should focus on identifying as many structural features as possible that would collectively define the glycomic characteristics of a cell or tissue, and how these may change in response to self-programmed development, immuno-activation, and malignant transformation. We have been pursuing this line of analytical strategy that homes in on identifying the terminal sulfo-, sialyl, and/or fucosylated glycotopes by comprehensive nanoLC-MS2-product dependent MS3 analysis of permethylated glycans, in conjunction with development of a data mining computational tool, GlyPick, to enable an automated, high throughput, semi-quantitative glycotope-centric glycomic mapping amenable to even nonexperts. We demonstrate in this work that diagnostic MS2 ions can be relied on to inform the presence of specific glycotopes, whereas their possible isomeric identities can be resolved at MS3 level. Both MS2 and associated MS3 data can be acquired exhaustively and processed automatically by GlyPick. The high acquisition speed, resolution, and mass accuracy afforded by top-notch Orbitrap Fusion MS system now allow a sensible spectral count and/or summed ion intensity-based glycome-wide glycotope quantification. We report here the technical aspects, reproducibility and optimization of such an analytical approach that uses the same acidic reverse phase C18 nanoLC conditions fully compatible with proteomic analysis to allow rapid hassle-free switching. We further show how this workflow is particularly effective when applied to larger, multiply sialylated and fucosylated N-glycans derived from mouse brain. The complexity of their terminal glycotopes including variants of fucosylated and disialylated type 1 and 2 chains would otherwise not be adequately delineated by any conventional LC-MS/MS analysis.
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Affiliation(s)
- Cheng-Te Hsiao
- From the ‡Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.,§Institute of Biological Chemistry and
| | | | | | - Yen-Ying Chen
- From the ‡Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | | | - Yijuang Chern
- ¶Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Kay-Hooi Khoo
- From the ‡Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan; .,§Institute of Biological Chemistry and
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21
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Abrahams JL, Campbell MP, Packer NH. Building a PGC-LC-MS N-glycan retention library and elution mapping resource. Glycoconj J 2017; 35:15-29. [PMID: 28905148 DOI: 10.1007/s10719-017-9793-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/10/2017] [Accepted: 08/18/2017] [Indexed: 11/27/2022]
Abstract
Porous graphitised carbon-liquid chromatography (PGC-LC) has been proven to be a powerful technique for the analysis and characterisation of complex mixtures of isomeric and isobaric glycan structures. Here we evaluate the elution behaviour of N-glycans on PGC-LC and thereby provide the potential of using chromatographic separation properties, together with mass spectrometry (MS) fragmentation, to determine glycan structure assignments more easily. We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. Over 100 glycan structures were determined by MS/MS, and together with targeted exoglycosidase digestions, created a N-glycan PGC retention library covering a full spectrum of biologically significant N-glycans from pauci mannose to sialylated tetra-antennary classes. The resultant PGC retention library ( http://www.glycostore.org/showPgc ) incorporates retention times and supporting fragmentation spectra including exoglycosidase digestion products, and provides detailed knowledge on the elution properties of N-glycans by PGC-LC. Consequently, this platform should serve as a valuable resource for facilitating the detailed analysis of the glycosylation of both purified recombinant, and complex mixtures of, glycoproteins using established workflows.
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Affiliation(s)
- Jodie L Abrahams
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia
| | - Matthew P Campbell
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia.
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia.
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22
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Yang S, Hu Y, Sokoll L, Zhang H. Simultaneous quantification of N- and O-glycans using a solid-phase method. Nat Protoc 2017; 12:1229-1244. [PMID: 28518173 PMCID: PMC5877797 DOI: 10.1038/nprot.2017.034] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glycosylation has a pivotal role in a diverse range of biological activities, modulating the structure and function of proteins. Glycogens coupled to the nitrogen atom (N-linked) of asparagine side chains or to the oxygen atom (O-linked) of serine and threonine side chains represent the two major protein glycosylation forms. N-glycans can be released by glycosidases, whereas O-glycans are often cleaved by chemical reaction. However, it is challenging to combine these enzymatic and chemical reactions in order to analyze both N- and O-glycans. We recently developed a glycoprotei n immobilization for glycan extraction (GIG) method that allows for the simultaneous analysis of N- and O-glycans on a solid support. GIG enables quantitative analysis of N-glycans and O-glycans from a single specimen and can be applied to a high-throughput automated platform. Here we provide a step-by-step GIG protocol that includes procedures for (i) protein immobilization on an aldehyde-active solid support by reductive amination; (ii) stabilization of fragile sialic acids by carbodiimide coupling; (iii) release of N-glycans by PNGase F digestion; (iv) release of O-glycans by β-elimination using ammonia in the presence of 1-phenyl-3-methyl-5-pyrazolone (PMP) to prevent alditol peeling from O-glycans; (v) mass spectrometry (MS) analysis; and (vi) data analysis for identification of glycans using in-house developed software (GIG Tool; free to download via http://www.biomarkercenter.org/gigtool). The GIG tool extracts precursor masses, oxonium ions and glycan fragments from tandem (liquid chromatography (LC)-MS/MS) mass spectra for glycan identification, and reporter ions from quaternary amine containing isobaric tag for glycan (QUANTITY) isobaric tags are used for quantification of the relative abundance of N-glycans. The GIG protocol takes ∼3 d.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lori Sokoll
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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23
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Uppal SS, Beasley SE, Scian M, Guttman M. Gas-Phase Hydrogen/Deuterium Exchange for Distinguishing Isomeric Carbohydrate Ions. Anal Chem 2017; 89:4737-4742. [PMID: 28304155 DOI: 10.1021/acs.analchem.7b00683] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The structural diversity of carbohydrates presents a major challenge for glycobiology and the analysis of glycoconjugates. Mass spectrometry has become a primary tool for glycan analysis thanks to its speed and sensitivity, but the information content regarding the glycan structure of protonated glycoconjugates is hindered by the inability to differentiate linkage and stereoisomers. Here, we examine a variety of protonated carbohydrate structures by gas-phase hydrogen/deuterium exchange (HDX) to discover that the exchange rates are distinct for isomeric carbohydrates with even subtle structural differences. By incorporating an internal exchange standard, HDX could effectively distinguish all linkage and stereoisomers that were examined and presents a mass spectrometry-based approach for glycan structural analysis with immense potential.
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Affiliation(s)
- Sanjit S Uppal
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Sarah E Beasley
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Michele Scian
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195, United States
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24
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Chaffey PK, Guan X, Wang LX, Tan Z. Introduction: General Aspects of the Chemical Biology of Glycoproteins. CHEMICAL BIOLOGY OF GLYCOPROTEINS 2017. [DOI: 10.1039/9781782623823-00001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This chapter is meant to serve as an introduction to the remainder of the book by providing general background on the chemical biology of glycoproteins as well as a brief review of the chapters that follow. The purpose here is to introduce some basic concepts common to many forms of glycosylation for those readers who may be unfamiliar with the field. We begin with a discussion of the strategies and methods used to study protein glycosylation. During the overview, an effort is made to highlight a few relevant aspects of chemical glycobiology, including glycoprotein biosynthesis and a brief description of the synthesis and function of glycoproteins. Finally, we have a summary of the contributions from chemical biology over the years. It is our hope that, after reading this introductory chapter, the reader will have a broad view of the chemical glycobiology field as it currently stands and a deeper appreciation for some of the unique ideas that chemical biology brings to the field.
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Affiliation(s)
- Patrick K. Chaffey
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Xiaoyang Guan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland College Park MD 20742 USA
| | - Zhongping Tan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
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25
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Bora de Oliveira K, Spencer D, Barton C, Agarwal N. Site-specific monitoring of N-Glycosylation profiles of a CTLA4-Fc-fusion protein from the secretory pathway to the extracellular environment. Biotechnol Bioeng 2017; 114:1550-1560. [PMID: 28186328 DOI: 10.1002/bit.26266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/31/2017] [Accepted: 02/06/2017] [Indexed: 01/18/2023]
Abstract
Glycosylation often plays a key role in the safety and efficacy of therapeutic proteins to patients, thus underlying the need for consistent control of this important post-translational modification during biologics production. In this study, we profiled the site-specific evolution of N-glycans on a CTLA4-Fc-fusion protein, from the intracellular secretory pathway to the conditioned medium (CM) in fed-batch cell culture. For this, we developed an approach that combined sub-cellular fractionation with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. The study revealed that there was a significant amount of heterogeneity in the glycans displayed amongst the three distinct N-glycosylation sites. Furthermore, 54-60% of the intracellular protein was characterized by Man8 and Man9 glycans on day 10, when the cell density peaks, indicative of a significant bottleneck between the endoplasmic reticulum (ER) and the cis-Golgi. At longer culture duration, the accumulation of intracellular protein with bi-antennary-fucosylated GlcNAc-terminated residues identified the formation of another bottleneck in the medial and trans-Golgi compartments, which subsequently led to a decrease in sialylated species in the secreted protein. Glucose deprivation caused a reduction in the Man8 and Man9 glycans in favor of Man5 glycans and bi-antennary-fucosylated GlcNAc-terminated residues in the organellar pool of the Fc-fusion protein. However, transient deprivation of glucose did not lead to major differences in the glycan profile of proteins secreted into the CM. The approach developed here allows us to probe the secretory pathway and sheds light on the site-specific intracellular processing of glycans during fed-batch cell culture, thus serving as an initial step towards their rational control. Biotechnol. Bioeng. 2017;114: 1550-1560. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
| | - David Spencer
- MedImmune LLC., One MedImmune Way, Gaithersburg, Maryland 20878
| | | | - Nitin Agarwal
- MedImmune LLC., One MedImmune Way, Gaithersburg, Maryland 20878
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26
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Hofmann J, Stuckmann A, Crispin M, Harvey DJ, Pagel K, Struwe WB. Identification of Lewis and Blood Group Carbohydrate Epitopes by Ion Mobility-Tandem-Mass Spectrometry Fingerprinting. Anal Chem 2017; 89:2318-2325. [PMID: 28192913 DOI: 10.1021/acs.analchem.6b03853] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Glycans have several elements that contribute to their structural complexity, involving a range of monosaccharide building blocks, configuration of linkages between residues and various degrees of branching on a given structure. Their analysis remains challenging and resolving minor isomeric variants can be difficult, in particular terminal fucosylated Lewis and blood group antigens present on N- and O-glycans. Accurately characterizing these isomeric structures by current techniques is not straightforward and typically requires a combination of methods and/or sample derivatization. Yet the ability to monitor the occurrence of these epitopes is important as structural changes are associated with several human diseases. The use of ion mobility-mass spectrometry (IM-MS), which separates ions in the gas phase based on their size, charge and shape, offers a new potential tool for glycan analysis and recent reports have demonstrated its potential for glycomics. Here we show that Lewis and blood group isomers, which have identical fragmentation spectra, exhibit very distinctive IM drift times and collision cross sections (CCS). We show that IM-MS/MS analysis can rapidly and accurately differentiate epitopes from parotid gland N-glycans and milk oligosaccharides based on fucosylated fragment ions with characteristic CCSs.
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Affiliation(s)
- Johanna Hofmann
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freien Universität Berlin , Takustrasse 3, 14195 Berlin, Germany
| | - Alexandra Stuckmann
- Institut für Chemie und Biochemie, Freien Universität Berlin , Takustrasse 3, 14195 Berlin, Germany
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , OX1 3QU Oxford, United Kingdom
| | - David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , OX1 3QU Oxford, United Kingdom
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany.,Institut für Chemie und Biochemie, Freien Universität Berlin , Takustrasse 3, 14195 Berlin, Germany
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , OX1 3QU Oxford, United Kingdom
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Yang S, Höti N, Yang W, Liu Y, Chen L, Li S, Zhang H. Simultaneous analyses of N-linked and O-linked glycans of ovarian cancer cells using solid-phase chemoenzymatic method. Clin Proteomics 2017; 14:3. [PMID: 28100988 PMCID: PMC5237303 DOI: 10.1186/s12014-017-9137-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/29/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Glycans play critical roles in a number of biological activities. Two common types of glycans, N-linked and O-linked, have been extensively analyzed in the last decades. N-glycans are typically released from glycoproteins by enzymes, while O-glycans are released from glycoproteins by chemical methods. It is important to identify and quantify both N- and O-linked glycans of glycoproteins to determine the changes of glycans. METHODS The effort has been dedicated to study glycans from ovarian cancer cells treated with O-linked glycosylation inhibitor qualitatively and quantitatively. We used a solid-phase chemoenzymatic approach to systematically identify and quantify N-glycans and O-glycans in the ovarian cancer cells. It consists of three steps: (1) immobilization of proteins from cells and derivatization of glycans to protect sialic acids; (2) release of N-glycans by PNGase F and quantification of N-glycans by isobaric tags; (3) release and quantification of O-glycans by β-elimination in the presence of 1-phenyl-3-methyl-5-pyrazolone (PMP). RESULTS We used ovarian cancer cell lines to study effect of O-linked glycosylation inhibitor on protein glycosylation. Results suggested that the inhibition of O-linked glycosylation reduced the levels of O-glycans. Interestingly, it appeared to increase N-glycan level in a lower dose of the O-linked glycosylation inhibitor. The sequential release and analyses of N-linked and O-linked glycans using chemoenzymatic approach are a platform for studying N-glycans and O-glycans in complex biological samples. CONCLUSION The solid-phase chemoenzymatic method was used to analyze both N-linked and O-linked glycans sequentially released from the ovarian cancer cells. The biological studies on O-linked glycosylation inhibition indicate the effects of O-glycosylation inhibition to glycan changes in both O-linked and N-linked glycan expression.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Naseruddin Höti
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Yang Liu
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD 20850 USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins Medicine, Smith Bldg 4013, 400 N. Broadway, Baltimore, MD 21287 USA
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28
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Zhou S, Dong X, Veillon L, Huang Y, Mechref Y. LC-MS/MS analysis of permethylated N-glycans facilitating isomeric characterization. Anal Bioanal Chem 2017; 409:453-466. [PMID: 27796453 PMCID: PMC5444817 DOI: 10.1007/s00216-016-9996-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/23/2016] [Accepted: 09/29/2016] [Indexed: 12/18/2022]
Abstract
The biosynthesis of glycans is a template-free process; hence compositionally identical glycans may contain highly heterogeneous structures. Meanwhile, the functions of glycans in biological processes are significantly influenced by the glycan structure. Structural elucidation of glycans is an essential component of glycobiology. Although NMR is considered the most powerful approach for structural glycan studies, it suffers from low sensitivity and requires highly purified glycans. Although mass spectrometry (MS)-based methods have been applied in numerous glycan structure studies, there are challenges in preserving glycan structure during ionization. Permethylation is an efficient derivatization method that improves glycan structural stability. In this report, permethylated glycans are isomerically separated; thus facilitating structural analysis of a mixture of glycans by LC-MS/MS. Separation by porous graphitic carbon liquid chromatography at high temperatures in conjunction with tandem mass spectrometry (PGC-LC-MS/MS) was utilized for unequivocal characterization of glycan isomers. Glycan fucosylation sites were confidently determined by eliminating fucose rearrangement and assignment of diagnostic ions, achieved by permethylation and PGC-LC at high temperatures, respectively. Assigning monosaccharide residues to specific glycan antennae was also achieved. Galactose linkages were also distinguished from each other by CID/HCD tandem MS. This was attainable because of the different bond energies associated with monosaccharide linkages. Graphical Abstract LC-MS and tandem MS of terminal galactose isomers.
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Affiliation(s)
- Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle & Boston, Box 41061, Lubbock, TX, 79409-1061, USA
| | - Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle & Boston, Box 41061, Lubbock, TX, 79409-1061, USA
| | - Lucas Veillon
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle & Boston, Box 41061, Lubbock, TX, 79409-1061, USA
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle & Boston, Box 41061, Lubbock, TX, 79409-1061, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle & Boston, Box 41061, Lubbock, TX, 79409-1061, USA.
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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] [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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30
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Goldsmith F, O'Sullivan A, Smilowitz JT, Freeman SL. Lactation and Intestinal Microbiota: How Early Diet Shapes the Infant Gut. J Mammary Gland Biol Neoplasia 2015; 20:149-58. [PMID: 26227402 DOI: 10.1007/s10911-015-9335-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/07/2015] [Indexed: 01/15/2023] Open
Abstract
Breast milk is a multifunctional biofluid that provides nutrients along with highly diverse non-nutritive bioactive components such as antibodies, glycans, bacteria, and immunomodulatory proteins. Research over the past decade has confirmed the essential role of breast milk bioactives in the establishment a healthy intestinal microbiota within the infant. The intestinal microbiota of an exclusively breastfed baby is dominated by several species of Bifidobacteria - the most influential member of which is Bifidobacterium longum subspecies infantis (B. infantis) - and is referred to as the milk-oriented microbiome (MOM). MOM is associated with reduced risk of infection in infancy as well as a reduced risk of certain chronic illnesses in adulthood. Establishment and persistence of MOM is dependent on the selective digestion of complex sugar structures in breast milk that are otherwise indigestible to the infant by B. infantis and its relatives. This review focuses primarily on the influence of breast milk glycans and glycosylated proteins on the development of the intestinal microbiome, and how maternal phenotype may influence the development of MOM providing a framework to understand how variation in diet shapes a protective intestinal microbiome.
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Affiliation(s)
- Felicia Goldsmith
- Department of Food Science and Technology, Foods for Health Institute, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA
| | - Aifric O'Sullivan
- Institute of Food and Health, University College Dublin, 2.05 Science Centre, South, Belfield, Dublin 4, Ireland
| | - Jennifer T Smilowitz
- Department of Food Science and Technology, Foods for Health Institute, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA
| | - Samara L Freeman
- Department of Food Science and Technology, Foods for Health Institute, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA.
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31
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Orthogonal Technologies for NISTmAb N-Glycan Structure Elucidation and Quantitation. ACTA ACUST UNITED AC 2015. [DOI: 10.1021/bk-2015-1201.ch004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
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32
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He Y, Xie Q, Wang Y, Liang Y, Xu X, Li Y, Miao J, Chen Z, Li Y. Liquid chromatography mass spectrometry-based O-glycomics to evaluate glycosylation alterations in gastric cancer. Proteomics Clin Appl 2015; 10:206-15. [PMID: 26255982 DOI: 10.1002/prca.201500041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/06/2015] [Accepted: 08/03/2015] [Indexed: 02/02/2023]
Abstract
PURPOSE Gastric cancer is the fourth most common malignant cancer worldwide. Important for tumorigenesis and progression, aberrant glycosylation occurs frequently in cancers. We investigated the differences in O-glycosylation in the serum of 157 gastric cancer patients (GC) and 144 healthy donors. EXPERIMENTAL DESIGN We used the method of labeling O-glycans (released from proteins) with 1-phenyl-3-methyl-5-pyrazolone followed by LC-MS analysis. Analyzing the LC-MS data by partial least squares discriminant and unpaired Student t test, combined with the structural information of O-glycans from LC-MS/MS in positive mode. RESULTS The expression level of core1, core2, ST antigen, and core2 complex O-glycans (m/z 733.33, m/z 809.42) were increased significantly (p < 0.0001), whereas m/z 529.75 and diST-antigen were decreased in the serum of GC compared with controls (p < 0.001). In addition, there were significant correlations between the abundance of the O-glycans and glycoproteins (MUC1, CEA) in the serum of GC. CONCLUSION AND CLINICAL RELEVANCE Glycomics approaches identified multiple candidate antigens for patients with GC. The O-glycan structures are increased in the serum of GC, they may be candidates for carbohydrate tumor markers.
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Affiliation(s)
- Yun He
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, P. R. China
| | - Qin Xie
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, P. R. China
| | - Yanping Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, P. R. China
| | - Yong Liang
- Clinical Laboratory, Huai'an Hospital Affiliated of Xuzhou Medical College, Huaian, P. R. China
| | - Xiukun Xu
- Suzhou Zhongying Medical Sciences and Technologies Company, Suzhou, P. R. China
| | - Yong Li
- Suzhou Pharmavan Cancer Research Center Company, Suzhou, P. R. China
| | - Jinsheng Miao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, P. R. China
| | - Zijun Chen
- Department of Chinese Pharmaceutics, School of Chinese Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, P. R. China
| | - Yunsen Li
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, P. R. China
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33
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Park D, Brune KA, Mitra A, Marusina AI, Maverakis E, Lebrilla CB. Characteristic Changes in Cell Surface Glycosylation Accompany Intestinal Epithelial Cell (IEC) Differentiation: High Mannose Structures Dominate the Cell Surface Glycome of Undifferentiated Enterocytes. Mol Cell Proteomics 2015; 14:2910-21. [PMID: 26355101 DOI: 10.1074/mcp.m115.053983] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Indexed: 12/26/2022] Open
Abstract
Changes in cell surface glycosylation occur during the development and differentiation of cells and have been widely correlated with the progression of several diseases. Because of their structural diversity and sensitivity to intra- and extracellular conditions, glycans are an indispensable tool for analyzing cellular transformations. Glycans present on the surface of intestinal epithelial cells (IEC) mediate interactions with billions of native microorganisms, which continuously populate the mammalian gut. A distinct feature of IECs is that they differentiate as they migrate upwards from the crypt base to the villus tip. In this study, nano-LC/ESI QTOF MS profiling was used to characterize the changes in glycosylation that correspond to Caco-2 cell differentiation. As Caco-2 cells differentiate to form a brush border membrane, a decrease in high mannose type glycans and a concurrent increase in fucosylated and sialylated complex/hybrid type glycans were observed. At day 21, when cells appear to be completely differentiated, remodeling of the cell surface glycome ceases. Differential expression of glycans during IEC maturation appears to play a key functional role in regulating the membrane-associated hydrolases and contributes to the mucosal surface innate defense mechanisms. Developing methodologies to rapidly identify changes in IEC surface glycans may lead to a rapid screening approach for a variety of disease states affecting the GI tract.
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Affiliation(s)
- Dayoung Park
- From the ‡Department of Chemistry, University of California, Davis, California 95616
| | - Kristin A Brune
- From the ‡Department of Chemistry, University of California, Davis, California 95616
| | - Anupam Mitra
- §Department of Dermatology, University of California, Davis School of Medicine, Sacramento, California 95816
| | - Alina I Marusina
- §Department of Dermatology, University of California, Davis School of Medicine, Sacramento, California 95816
| | - Emanual Maverakis
- §Department of Dermatology, University of California, Davis School of Medicine, Sacramento, California 95816
| | - Carlito B Lebrilla
- From the ‡Department of Chemistry, University of California, Davis, California 95616;
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34
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Brito AE, Kletter D, Singhal M, Bern M. Benchmark study of automatic annotation of MALDI-TOF N-glycan profiles. J Proteomics 2015; 129:71-77. [PMID: 26047718 DOI: 10.1016/j.jprot.2015.05.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 05/08/2015] [Accepted: 05/25/2015] [Indexed: 12/29/2022]
Abstract
Human experts can annotate peaks in MALDI-TOF profiles of detached N-glycans with some degree of accuracy. Even though MALDI-TOF profiles give only intact masses without any fragmentation information, expert knowledge of the most common glycans and biosynthetic pathways in the biological system can point to a small set of most likely glycan structures at the "cartoon" level of detail. Cartoonist is a recently developed, fully automatic annotation tool for MALDI-TOF glycan profiles. Here we benchmark Cartoonist's automatic annotations against human expert annotations on human and mouse N-glycan data from the Consortium for Functional Glycomics. We find that Cartoonist and expert annotations largely agree, but the expert tends to annotate more specifically, meaning fewer suggested structures per peak, and Cartoonist more comprehensively, meaning more annotated peaks. On peaks for which both Cartoonist and the expert give unique cartoons, the two cartoons agree in over 90% of all cases. This article is part of a Special Issue entitled: Computational Proteomics.
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35
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Chen CH, Lin YP, Lin JL, Li ST, Ren CT, Wu CY, Chen CH. Rapid Identification of Terminal Sialic Acid Linkage Isomers by Pseudo-MS3Mass Spectrometry. Isr J Chem 2015. [DOI: 10.1002/ijch.201400141] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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36
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Goldman R, Sanda M. Targeted methods for quantitative analysis of protein glycosylation. Proteomics Clin Appl 2015; 9:17-32. [PMID: 25522218 PMCID: PMC5780646 DOI: 10.1002/prca.201400152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/15/2014] [Accepted: 12/11/2014] [Indexed: 12/17/2022]
Abstract
Quantification of proteins by LC-MS/MS-MRM has become a standard method with broad projected clinical applicability. MRM quantification of protein modifications is, however, far less utilized, especially in the case of glycoproteins. This review summarizes current methods for quantitative analysis of protein glycosylation with a focus on MRM methods. We describe advantages of this quantitative approach, analytical parameters that need to be optimized to achieve reliable measurements, and point out the limitations. Differences between major classes of N- and O-glycopeptides are described and class-specific glycopeptide assays are demonstrated.
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Affiliation(s)
- Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
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37
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Metabolomics and Milk: The Development of the Microbiota in Breastfed Infants. MOLECULAR AND INTEGRATIVE TOXICOLOGY 2015. [DOI: 10.1007/978-1-4471-6539-2_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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38
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Gao X, Zhang L, Zhang W, Zhao L. Design and application of an open tubular capillary reactor for solid-phase permethylation of glycans in glycoprotein. Analyst 2015; 140:1566-71. [DOI: 10.1039/c4an01045k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The permethylation derivatization method for structural analysis of glycans is important for characterizing glycoproteins in the study of glycomics.
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Affiliation(s)
- Xiaodi Gao
- Shanghai Key Laboratory of Functional Materials Chemistry
- East China University of Science and Technology
- Shanghai 200237
- PR China
| | - Lingyi Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry
- East China University of Science and Technology
- Shanghai 200237
- PR China
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry
- East China University of Science and Technology
- Shanghai 200237
- PR China
| | - Liang Zhao
- State Key Laboratory of Proteomics
- Beijing Proteome Research Center
- Beijing Institute of Radiation Medicine
- Beijing 102206
- PR China
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39
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Zhang H, Ashline DJ, Reinhold VN. Tools to MSn Sequence and Document the Structures of Glycan Epitopes. DISCOVERING THE SUBTLETIES OF SUGARS : PROCEEDINGS OF THE 3RD BEILSTEIN GLYCO-BIOINFORMATICS SYMPOSIUM : JUNE 10TH - 14TH, 2013, POTSDAM, GERMANY. INTERNATIONAL BEILSTEIN SYMPOSIUM ON GLYCO-BIOINFORMATICS (3RD : 2013 : POTSDAM, GERMANY) 2014; 2013:117-131. [PMID: 27110600 PMCID: PMC4840838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Sequential disassembly (MSn) has been applied to fully characterise and document native samples containing glycan epitopes with their synthetic analogues. Both sample types were prepared by methylation, solvent phase extracted, directly infused and spatially resolved. Product ions of all samples were compiled and contrasted using management tools prepared for the fragment ion library. Each of the epitopes was further disassembled to confirm the multiple structural isomers probable within component substructures of linkage and branching. All native samples tested proved to be matched with their synthetic analogues and reasonably identical on either linear or cylindrical ion traps. Not surprisingly, spectra of mixed epitopes fragment independently, being uninfluenced by similarities. The approach has been coupled with computational tools for data handling and presentation.
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Affiliation(s)
- Hailong Zhang
- The Glycomics Center, University of New Hampshire, Durham, NH 03824, USA
| | | | - Vernon N. Reinhold
- The Glycomics Center, University of New Hampshire, Durham, NH 03824, USA
- Glycan Connections, LLC, Lee, NH 03861, USA
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40
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Smilowitz JT, Lebrilla CB, Mills DA, German JB, Freeman SL. Breast milk oligosaccharides: structure-function relationships in the neonate. Annu Rev Nutr 2014; 34:143-69. [PMID: 24850388 DOI: 10.1146/annurev-nutr-071813-105721] [Citation(s) in RCA: 269] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In addition to providing complete postnatal nutrition, breast milk is a complex biofluid that delivers bioactive components for the growth and development of the intestinal and immune systems. Lactation is a unique opportunity to understand the role of diet in shaping the intestinal environment including the infant microbiome. Of considerable interest is the diversity and abundance of milk glycans that are energetically costly for the mammary gland to produce yet indigestible by infants. Milk glycans comprise free oligosaccharides, glycoproteins, glycopeptides, and glycolipids. Emerging technological advances are enabling more comprehensive, sensitive, and rapid analyses of these different classes of milk glycans. Understanding the impact of inter- and intraindividual glycan diversity on function is an important step toward interventions aimed at improving health and preventing disease. This review discusses the state of technology for glycan analysis and how specific structure-function knowledge is enhancing our understanding of early nutrition in the neonate.
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41
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Baycin Hizal D, Wolozny D, Colao J, Jacobson E, Tian Y, Krag SS, Betenbaugh MJ, Zhang H. Glycoproteomic and glycomic databases. Clin Proteomics 2014; 11:15. [PMID: 24725457 PMCID: PMC3996109 DOI: 10.1186/1559-0275-11-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/20/2014] [Indexed: 11/17/2022] Open
Abstract
Protein glycosylation serves critical roles in the cellular and biological processes of many organisms. Aberrant glycosylation has been associated with many illnesses such as hereditary and chronic diseases like cancer, cardiovascular diseases, neurological disorders, and immunological disorders. Emerging mass spectrometry (MS) technologies that enable the high-throughput identification of glycoproteins and glycans have accelerated the analysis and made possible the creation of dynamic and expanding databases. Although glycosylation-related databases have been established by many laboratories and institutions, they are not yet widely known in the community. Our study reviews 15 different publicly available databases and identifies their key elements so that users can identify the most applicable platform for their analytical needs. These databases include biological information on the experimentally identified glycans and glycopeptides from various cells and organisms such as human, rat, mouse, fly and zebrafish. The features of these databases - 7 for glycoproteomic data, 6 for glycomic data, and 2 for glycan binding proteins are summarized including the enrichment techniques that are used for glycoproteome and glycan identification. Furthermore databases such as Unipep, GlycoFly, GlycoFish recently established by our group are introduced. The unique features of each database, such as the analytical methods used and bioinformatical tools available are summarized. This information will be a valuable resource for the glycobiology community as it presents the analytical methods and glycosylation related databases together in one compendium. It will also represent a step towards the desired long term goal of integrating the different databases of glycosylation in order to characterize and categorize glycoproteins and glycans better for biomedical research.
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Affiliation(s)
- Deniz Baycin Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Daniel Wolozny
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joseph Colao
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Elena Jacobson
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yuan Tian
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Sharon S Krag
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
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Ashline DJ, Hanneman AJS, Zhang H, Reinhold VN. Structural documentation of glycan epitopes: sequential mass spectrometry and spectral matching. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:444-53. [PMID: 24385394 PMCID: PMC3950938 DOI: 10.1007/s13361-013-0776-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/09/2013] [Accepted: 10/09/2013] [Indexed: 05/27/2023]
Abstract
Documenting mass spectral data is a fundamental aspect of accepted protocols. In this report, we contrast MS(n) sequential disassembly spectra obtained from natural and synthetic glycan epitopes. The epitopes considered are clusters found on conjugate termini of lipids and N- and O-glycans of proteins. The latter are most frequently pendant through a CID-labile HexNAc glycosidic linkage. The synthetic samples were supplied by collaborating colleagues and commercial sources and usually possessed a readily released reducing-end linker, a by-product of synthesis. All samples were comparably methylated, extracted, and MS(n) disassembled to compare their linkage and branching spectral details. Both sample types provide B-ion type fragments early in a disassembly pathway and their compositions are a suggestion of structure. Further steps of disassembly are necessary to confirm the details of linkage and branching. Included in this study were various Lewis and H antigens, 3- and 6-linked sialyl-lactosamine, NeuAc-2,8-NeuAc dimer, and Galα1,3Gal. Sample infusion provided high quality spectral data whereas disassembly to small fragments generates reproducible high signal/noise spectra for spectral matching. All samples were analyzed as sodium adducted positive ions. This study includes comparability statistics and evaluations on several mass spectrometers.
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Affiliation(s)
| | | | - Hailong Zhang
- The Glycomics Center, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824
| | - Vernon N. Reinhold
- The Glycomics Center, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824
- Glycan Connections, LLC, Lee, New Hampshire, 03861
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Hanneman AJ, Strand J, Huang CT. Profiling and Characterization of Sialylated N-glycans by 2D-HPLC (HIAX/PGC) with Online Orbitrap MS/MS and Offline MSn. J Pharm Sci 2014; 103:400-8. [DOI: 10.1002/jps.23792] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/14/2013] [Accepted: 10/30/2013] [Indexed: 01/14/2023]
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Kailemia MJ, Ruhaak LR, Lebrilla CB, Amster IJ. Oligosaccharide analysis by mass spectrometry: a review of recent developments. Anal Chem 2014; 86:196-212. [PMID: 24313268 PMCID: PMC3924431 DOI: 10.1021/ac403969n] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - L. Renee Ruhaak
- Department of Chemistry, University of California at Davis, Davis, CA 95616
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45
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Lichti CF, Wildburger NC, Emmett MR, Mostovenko E, Shavkunov AS, Strain SK, Nilsson CL. Post-translational Modifications in the Human Proteome. TRANSLATIONAL BIOINFORMATICS 2014. [DOI: 10.1007/978-94-017-9202-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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46
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Live D, Wells L, Boons GJ. Dissecting the molecular basis of the role of the O-mannosylation pathway in disease: α-dystroglycan and forms of muscular dystrophy. Chembiochem 2013; 14:2392-402. [PMID: 24318691 DOI: 10.1002/cbic.201300417] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Indexed: 11/10/2022]
Abstract
Dystroglycanopathies form a subgroup of muscular dystrophies that arise from defects in enzymes that are implicated in the recently elucidated O-mannosylation pathway, thereby resulting in underglycosylation of α-dystroglycan. The emerging identification of additional brain proteins modified by O-mannosylation provides a broader context for interpreting the range of neurological consequences associated with dystroglycanopathies. This form of glycosylation is associated with protein mucin-like domains that present numerous serine and threonine residues as possible sites for modification. Furthermore, the O-Man glycans coexist in this region with O-GalNAc glycans (conventionally associated with such protein sequences), thus resulting in a complex glycoconjugate landscape. Sorting out the relationships between the various molecular defects in glycosylation and the modes of disease presentation, as well as the regulatory interplay among the O-Man glycans and the effects on other modes of glycosylation in the same domain, is challenging. Here we provide a perspective on chemical biology approaches employing synthetic and analytical methods to address these questions.
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Affiliation(s)
- David Live
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 (USA)
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Madsen JA, Ko BJ, Xu H, Iwashkiw JA, Robotham SA, Shaw JB, Feldman MF, Brodbelt JS. Concurrent automated sequencing of the glycan and peptide portions of O-linked glycopeptide anions by ultraviolet photodissociation mass spectrometry. Anal Chem 2013; 85:9253-61. [PMID: 24006841 DOI: 10.1021/ac4021177] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
O-Glycopeptides are often acidic owing to the frequent occurrence of acidic saccharides in the glycan, rendering traditional proteomic workflows that rely on positive mode tandem mass spectrometry (MS/MS) less effective. In this report, we demonstrate the utility of negative mode ultraviolet photodissociation (UVPD) MS for the characterization of acidic O-linked glycopeptide anions. This method was evaluated for a series of singly and multiply deprotonated glycopeptides from the model glycoprotein kappa casein, resulting in production of both peptide and glycan product ions that afforded 100% sequence coverage of the peptide and glycan moieties from a single MS/MS event. The most abundant and frequent peptide sequence ions were a/x-type products which, importantly, were found to retain the labile glycan modifications. The glycan-specific ions mainly arose from glycosidic bond cleavages (B, Y, C, and Z ions) in addition to some less common cross-ring cleavages. On the basis of the UVPD fragmentation patterns, an automated database searching strategy (based on the MassMatrix algorithm) was designed that is specific for the analysis of glycopeptide anions by UVPD. This algorithm was used to identify glycopeptides from mixtures of glycosylated and nonglycosylated peptides, sequence both glycan and peptide moieties simultaneously, and pinpoint the correct site(s) of glycosylation. This methodology was applied to uncover novel site-specificity of the O-linked glycosylated OmpA/MotB from the "superbug" A. baumannii to help aid in the elucidation of the functional role that protein glycosylation plays in pathogenesis.
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Affiliation(s)
- James A Madsen
- Department of Chemistry, The University of Texas at Austin , 1 University Station A5300, Austin, Texas, 78712 United States
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Zhou H, Hanneman AJ, Chasteen ND, Reinhold VN. Anomalous N-glycan structures with an internal fucose branched to GlcA and GlcN residues isolated from a mollusk shell-forming fluid. J Proteome Res 2013; 12:4547-55. [PMID: 23919883 DOI: 10.1021/pr4006734] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This report describes the structural details of a unique N-linked valence epitope on the major protein within the extrapallial (EP) fluid of the mollusk, Mytilus edulis. Fluids from this area are considered to be responsible for shell expansion by a self-assembly process that provides an organic framework for the growth of CaCO3 crystals. Previous reports from our laboratories have described the purification and amino acid sequence of this EP protein, which was found to be a glycoprotein (EPG) of approximately 28 KDa with 14.3% carbohydrate on a single N-linked consensus site. Described herein is the de novo sequence of the major glycan and its glycomers. The sequence was determined by ion trap sequential mass spectrometry (ITMS(n)) resolving structure by tracking precursor-product relationships through successive rounds of collision induced disassociation (CID), thereby spatially resolving linkage and branching details within the confines of the ion trap. Three major glycomers were detected, each possessing a 6-linked fucosylated N-linked core. Two glycans possessed four and five identical antennae, while the third possessed four antennas, but with an additional methylfucose 2-linked to the glucuronic acid moiety, forming a pentasaccharide. The tetrasaccharide structure was: 4-O-methyl-GlcA(1-4)[GlcNAc(1-3)]Fuc(1-4)GlcNAc, while the pentasaccharide was shown to be as follows: mono-O-methyl-Fuc(1-2)-4-O-methyl-GlcA(1-4)[GlcNAc(1-3)]Fuc(1-4)GlcNAc. Samples were differentially deuteriomethylated (CD3/CH3) to localize indigenous methylation, further analyzed by high resolution mass spectrometry (HRMS) to confirm monomer compositions, and finally gas chromatography mass spectrometry (GC-MS) to assign structural and stereoisomers. The interfacial shell surface location of this major extrapallial glycoprotein, its calcium and heavy metal binding properties and unique structure suggests a probable role in shell formation and possibly metal ion detoxification. A closely related terminal tetrasaccharide structure has been reported in spermatozoan glycolipids of freshwater bivalves.
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Affiliation(s)
- Hui Zhou
- Glycomics Center, University of New Hampshire , 35 Colovos Road, Durham, New Hampshire 03824, United States
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