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Farsang R, Jarvas G, Guttman A. Purification free N-glycan analysis by capillary zone electrophoresis: Hunt for the lost glycans. J Pharm Biomed Anal 2024; 238:115812. [PMID: 37926036 DOI: 10.1016/j.jpba.2023.115812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
Capillary gel electrophoresis is a widely used method for rapid separation of fluorophore labeled carbohydrates. Even though, many publications conferred about this popular technique, no report yet investigated the possible sample losses during the purification process of the fluorophore labeling reaction mixture. In the present work, normal polarity capillary zone electrophoresis separation mode was applied to take advantage of the opposite migration directions of the electroosmotic flow and the negatively charged sample components using Tris-hexanoic acid running buffer at basic pH. For purification free oligosaccharide analysis, the separation parameters were designed in such a way that the triple charged labeling reagent of aminopyrenetrisulfonate (APTS) could not enter the separation capillary in contrary to the labeled sample components of interest, therefore, the APTS did not have to be removed before analysis. The method was used to show electrophoretic profile differences possibly caused by the cleanup process that was immediately apparent by comparing the electropherograms of the purified and non-purified APTS labeled maltooligosaccharides. Furthermore, qualitative and quantitative N-glycosylation profile alterations were revealed during CZE separation of the fluorophore labeling reaction mixtures before and after purification along with the analysis of the consecutively used washing solutions for the well characterized standard glycoproteins of IgG, ribonuclease B and fetuin.
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Affiliation(s)
- Robert Farsang
- Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprem, Hungary
| | - Gabor Jarvas
- Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprem, Hungary
| | - Andras Guttman
- Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprem, Hungary; Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Hungary.
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2
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Streety X, Obike JC, Townsend SD. A Hitchhiker's Guide to Problem Selection in Carbohydrate Synthesis. ACS CENTRAL SCIENCE 2023; 9:1285-1296. [PMID: 37521800 PMCID: PMC10375882 DOI: 10.1021/acscentsci.3c00507] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Indexed: 08/01/2023]
Abstract
Oligosaccharides are ubiquitous in molecular biology and are used for functions ranging from governing protein folding to intercellular communication. Perhaps paradoxically, the exact role of the glycan in most of these settings is not well understood. One reason for this contradiction concerns the fact that carbohydrates often appear in heterogeneous form in nature. These mixtures complicate the isolation of pure material and characterization of structure-activity relationships. As a result, a major bottleneck in glycoscience research is the synthesis and modification of pure materials. While synthetic and chemoenzymatic methods have enabled access to homogeneous tool compounds, a central problem, particularly for newer synthetic chemists, is the matter of problem selection. This outlook aims to provide an entry level overview of fundamental principles in carbohydrate chemistry with an eye toward enabling solutions to frontier challenges.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth 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 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of 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. Most of the applications are 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. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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4
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Torok R, Horompoly K, Szigeti M, Guttman A, Vitai M, Koranyi L, Jarvas G. N-Glycosylation Profiling of Human Blood in Type 2 Diabetes by Capillary Electrophoresis: A Preliminary Study. Molecules 2021; 26:6399. [PMID: 34770808 PMCID: PMC8586923 DOI: 10.3390/molecules26216399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
Currently, diagnosing type 2 diabetes (T2D) is a great challenge. Thus, there is a need to find rapid, simple, and reliable analytical methods that can detect the disease at an early stage. The aim of this work was to shed light on the importance of sample collection options, sample preparation conditions, and the applied capillary electrophoresis bioanalytical technique, for a high-resolution determination of the N-glycan profile in human blood samples of patients with type 2 diabetes (T2D). To achieve the profile information of these complex oligosaccharides, linked by asparagine to hIgG in the blood, the glycoproteins of the samples needed to be cleaved, labelled, and purified with sufficient yield and selectivity. The resulting samples were analyzed by capillary electrophoresis, with laser-induced fluorescence detection. After separation parameter optimization, the capillary electrophoresis technique was implemented for efficient N-glycan profiling of whole blood samples from the diabetic patients. Our results revealed that there were subtle differences between the N-glycan profiles of the diabetic and control samples; in particular, two N-glycan structures were identified as potential glycobiomarkers that could reveal significant changes between the untreated/treated type 2 diabetic and control samples. By analyzing the resulting oligosaccharide profiles, clinically relevant information was obtained, revealing the differences between the untreated and HMG-CoA reductase-inhibitor-treated diabetic patients on changes in the N-glycan profile in the blood. In addition, the information from specific IgG N-glycosylation profiles in T2D could shed light on underlying inflammatory pathophysiological processes and lead to drug targets.
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Affiliation(s)
- Rebeka Torok
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 8200 Veszprem, Hungary; (R.T.); (K.H.); (M.S.); (A.G.)
| | - Klaudia Horompoly
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 8200 Veszprem, Hungary; (R.T.); (K.H.); (M.S.); (A.G.)
| | - Marton Szigeti
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 8200 Veszprem, Hungary; (R.T.); (K.H.); (M.S.); (A.G.)
| | - Andras Guttman
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 8200 Veszprem, Hungary; (R.T.); (K.H.); (M.S.); (A.G.)
- Horvath Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Marta Vitai
- DRC Drug Research Center Ltd., 8230 Balatonfured, Hungary; (M.V.); (L.K.)
| | - Laszlo Koranyi
- DRC Drug Research Center Ltd., 8230 Balatonfured, Hungary; (M.V.); (L.K.)
| | - Gabor Jarvas
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 8200 Veszprem, Hungary; (R.T.); (K.H.); (M.S.); (A.G.)
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5
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Shakyawar SK, Pandey S, Harvey DJ, Bousfield G, Guda C. FGDB: Database of follicle stimulating hormone glycans. Comput Struct Biotechnol J 2021; 19:1635-1640. [PMID: 33897975 PMCID: PMC8050109 DOI: 10.1016/j.csbj.2021.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 11/12/2022] Open
Abstract
Glycomics, the study of the entire complement of sugars of an organism has received significant attention in the recent past due to the advances made in high throughput mass spectrometry technologies. These analytical advancements have facilitated the characterization of glycans associated with the follicle-stimulating hormones (FSH), which play a central role in the human reproductive system both in males and females utilizing regulating gonadal (testicular and ovarian) functions. The irregularities in FSH activity are also directly linked with osteoporosis. The glycoanalytical studies have been tremendously helpful in understanding the biological roles of FSH. Subsequently, the increasing number of characterized FSH glycan structures and related glycoform data has thrown a challenge to the glycoinformatics community in terms of data organization, storage and access. Also, a user-friendly platform is needed for providing easy access to the database and performing integrated analysis using a high volume of experimental data to accelerate FSH-focused research. FSH Glycans DataBase (FGDB) serves as a comprehensive and unique repository of structures, features, and related information of glycans associated with FSH. Apart from providing multiple search options, the database also facilitates an integrated user-friendly interface to perform the glycan abundance and comparative analyses using experimental data. The automated integrated pipelines present the possible structures of glycans and variants of FSH based on the input data, and allow the user to perform various analyses. The potential application of FGDB will significantly help both glycoinformaticians as well as wet-lab researchers to stimulate the research in this area. FGDB web access: https://fgdb.unmc.edu/.
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Affiliation(s)
- Sushil K Shakyawar
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Sanjit Pandey
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, United Kingdom
| | - George Bousfield
- Fairmount College of Liberal Arts and Sciences, Wichita State University, KS 67260, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
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6
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Szigeti M, Meszaros-Matwiejuk A, Molnar-Gabor D, Guttman A. Rapid capillary gel electrophoresis analysis of human milk oligosaccharides for food additive manufacturing in-process control. Anal Bioanal Chem 2021; 413:1595-1603. [PMID: 33558961 PMCID: PMC7921066 DOI: 10.1007/s00216-020-03119-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 11/10/2022]
Abstract
Industrial production of human milk oligosaccharides (HMOs) represents a recently growing interest since they serve as key ingredients in baby formulas and are also utilized as dietary supplements for all age groups. Despite their short oligosaccharide chain lengths, HMO analysis is challenging due to extensive positional and linkage variations. Capillary gel electrophoresis primarily separates analyte molecules based on their hydrodynamic volume to charge ratios, thus, offers excellent resolution for most of such otherwise difficult-to-separate isomers. In this work, two commercially available gel compositions were evaluated on the analysis of a mixture of ten synthetic HMOs. The relevant respective separation matrices were then applied to selected analytical in-process control examples. The conventionally used carbohydrate separation matrix was applied for the in-process analysis of bacteria-mediated production of 3-fucosyllactose, lacto-N-tetraose, and lacto-N-neotetraose. The other example showed the suitability of the method for the in vivo in-process control of a shake flask and fermentation approach of 2′-fucosyllactose production. In this latter instance, borate complexation was utilized to efficiently separate the 2′- and 3-fucosylated lactose positional isomers. In all instances, the analysis of the HMOs of interest required only a couple of minutes with high resolution and excellent migration time and peak area reproducibility (average RSD 0.26% and 3.56%, respectively), features representing high importance in food additive manufacturing in-process control. ![]()
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Affiliation(s)
- Marton Szigeti
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, 4032, Hungary.,Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprem, 8200, Hungary
| | | | | | - Andras Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, 4032, Hungary. .,Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprem, 8200, Hungary.
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7
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Machine Learning Based Analysis of Human Serum N-glycome Alterations to Follow up Lung Tumor Surgery. Cancers (Basel) 2020; 12:cancers12123700. [PMID: 33317143 PMCID: PMC7764602 DOI: 10.3390/cancers12123700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Globally, there were around 2.1 million lung cancer cases and 1.8 million deaths in 2018. Hungary—where this study was carried out—had the highest rate of lung cancer in the same year. We developed a new analytical method which can be readily used to follow up the tumor surgery by investigating the glycan (sugar) structures of proteins. As the results of such investigations are very complex, computer-assisted machine learning methods were utilized for data interpretation. Abstract The human serum N-glycome is a valuable source of biomarkers for malignant diseases, already utilized in multiple studies. In this paper, the N-glycosylation changes in human serum proteins were analyzed after surgical lung tumor resection. Seventeen lung cancer patients were involved in this study and the N-glycosylation pattern of their serum samples was analyzed before and after the surgery using capillary electrophoresis separation with laser-induced fluorescent detection. The relative peak areas of 21 N-glycans were evaluated from the acquired electropherograms using machine learning-based data analysis. Individual glycans as well as their subclasses were taken into account during the course of evaluation. For the data analysis, both discrete (e.g., smoker or not) and continuous (e.g., age of the patient) clinical parameters were compared against the alterations in these 21 N-linked carbohydrate structures. The classification tree analysis resulted in a panel of N-glycans, which could be used to follow up on the effects of lung tumor surgical resection.
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Walls AC, Fiala B, Schäfer A, Wrenn S, Pham MN, Murphy M, Tse LV, Shehata L, O'Connor MA, Chen C, Navarro MJ, Miranda MC, Pettie D, Ravichandran R, Kraft JC, Ogohara C, Palser A, Chalk S, Lee EC, Guerriero K, Kepl E, Chow CM, Sydeman C, Hodge EA, Brown B, Fuller JT, Dinnon KH, Gralinski LE, Leist SR, Gully KL, Lewis TB, Guttman M, Chu HY, Lee KK, Fuller DH, Baric RS, Kellam P, Carter L, Pepper M, Sheahan TP, Veesler D, King NP. Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2. Cell 2020; 183:1367-1382.e17. [PMID: 33160446 PMCID: PMC7604136 DOI: 10.1016/j.cell.2020.10.043] [Citation(s) in RCA: 378] [Impact Index Per Article: 94.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/10/2020] [Accepted: 10/26/2020] [Indexed: 11/25/2022]
Abstract
A safe, effective, and scalable vaccine is needed to halt the ongoing SARS-CoV-2 pandemic. We describe the structure-based design of self-assembling protein nanoparticle immunogens that elicit potent and protective antibody responses against SARS-CoV-2 in mice. The nanoparticle vaccines display 60 SARS-CoV-2 spike receptor-binding domains (RBDs) in a highly immunogenic array and induce neutralizing antibody titers 10-fold higher than the prefusion-stabilized spike despite a 5-fold lower dose. Antibodies elicited by the RBD nanoparticles target multiple distinct epitopes, suggesting they may not be easily susceptible to escape mutations, and exhibit a lower binding:neutralizing ratio than convalescent human sera, which may minimize the risk of vaccine-associated enhanced respiratory disease. The high yield and stability of the assembled nanoparticles suggest that manufacture of the nanoparticle vaccines will be highly scalable. These results highlight the utility of robust antigen display platforms and have launched cGMP manufacturing efforts to advance the SARS-CoV-2-RBD nanoparticle vaccine into the clinic.
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Affiliation(s)
- Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Samuel Wrenn
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Longping V Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Laila Shehata
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Megan A O'Connor
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Washington National Primate Research Center, Seattle, WA 98121, USA
| | - Chengbo Chen
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA; Biological Physics Structure and Design Program, University of Washington, Seattle, WA 91895, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - John C Kraft
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cassandra Ogohara
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Anne Palser
- Kymab Ltd., Babraham Research Campus, Cambridge, UK
| | - Sara Chalk
- Kymab Ltd., Babraham Research Campus, Cambridge, UK
| | - E-Chiang Lee
- Kymab Ltd., Babraham Research Campus, Cambridge, UK
| | - Kathryn Guerriero
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Washington National Primate Research Center, Seattle, WA 98121, USA
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Edgar A Hodge
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Brieann Brown
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Washington National Primate Research Center, Seattle, WA 98121, USA
| | - Jim T Fuller
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Kendra L Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Thomas B Lewis
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Washington National Primate Research Center, Seattle, WA 98121, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA; Biological Physics Structure and Design Program, University of Washington, Seattle, WA 91895, USA
| | - Deborah H Fuller
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Washington National Primate Research Center, Seattle, WA 98121, USA; Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Paul Kellam
- Kymab Ltd., Babraham Research Campus, Cambridge, UK; Department of Infectious Disease, Imperial College, London, UK
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Marion Pepper
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
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9
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Harvey DJ. NEGATIVE ION MASS SPECTROMETRY FOR THE ANALYSIS OF N-LINKED GLYCANS. MASS SPECTROMETRY REVIEWS 2020; 39:586-679. [PMID: 32329121 DOI: 10.1002/mas.21622] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/13/2019] [Accepted: 12/22/2019] [Indexed: 05/03/2023]
Abstract
N-glycans from glycoproteins are complex, branched structures whose structural determination presents many analytical problems. Mass spectrometry, usually conducted in positive ion mode, often requires extensive sample manipulation, usually by derivatization such as permethylation, to provide the necessary structure-revealing fragment ions. The newer but, so far, lesser used negative ion techniques, on the contrary, provide a wealth of structural information not present in positive ion spectra that greatly simplify the analysis of these compounds and can usually be conducted without the need for derivatization. This review describes the use of negative ion mass spectrometry for the structural analysis of N-linked glycans and emphasises the many advantages that can be gained by this mode of operation. Biosynthesis and structures of the compounds are described followed by methods for release of the glycans from the protein. Methods for ionization are discussed with emphasis on matrix-assisted laser desorption/ionization (MALDI) and methods for producing negative ions from neutral compounds. Acidic glycans naturally give deprotonated species under most ionization conditions. Fragmentation of negative ions is discussed next with particular reference to those ions that are diagnostic for specific features such as the branching topology of the glycans and substitution positions of moieties such as fucose and sulfate, features that are often difficult to identify easily by conventional techniques such as positive ion fragmentation and exoglycosidase digestions. The advantages of negative over positive ions for this structural work are emphasised with an example of a series of glycans where all other methods failed to produce a structure. Fragmentation of derivatized glycans is discussed next, both with respect to derivatives at the reducing terminus of the molecules, and to methods for neutralization of the acidic groups on sialic acids to both stabilize them for MALDI analysis and to produce the diagnostic fragments seen with the neutral glycans. The use of ion mobility, combined with conventional mass spectrometry is described with emphasis on its use to extract clean glycan spectra both before and after fragmentation, to separate isomers and its use to extract additional information from separated fragment ions. A section on applications follows with examples of the identification of novel structures from lower organisms and tables listing the use of negative ions for structural identification of specific glycoproteins, glycans from viruses and uses in the biopharmaceutical industry and in medicine. The review concludes with a summary of the advantages and disadvantages of the technique. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
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10
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Hurják B, Kovács Z, Döncző B, Katona É, Haramura G, Erdélyi F, Housang Shemirani A, Sadeghi F, Muszbek L, Guttman A. N-glycosylation of blood coagulation factor XIII subunit B and its functional consequence. J Thromb Haemost 2020; 18:1302-1309. [PMID: 32168410 DOI: 10.1111/jth.14792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/23/2020] [Accepted: 03/10/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND The protective/inhibitory B subunits of coagulation factor XIII (FXIII-B) is a ~80 kDa glycoprotein containing two N-glycosylation sites. Neither the structure nor the functional role of the glycans on FXIII-B has been explored. OBJECTIVE To reveal the glycan structures linked to FXIII-B, to design a method for deglycosylating the native protein, to find out if deglycosylation influences the dimeric structure of FXIII-B and its clearance from the circulation. METHODS Asparagine-linked carbohydrates were released from human FXIIII-B by PNGase F digestion. The released N-linked oligosaccharides were fluorophore labeled and analyzed by capillary electrophoresis. Structural identification utilized glycan database search and exoglycosidase digestion based sequencing. The structure of deglycosylated FXIII-B was investigated by gel filtration. The clearance of deglycosylated and native FXIII-B from plasma was compared in FXIII-B knock out mice. RESULTS PNGase F completely removed N-glycans from the denatured protein. Deglycosylation of the native protein was achieved by repeated digestion at elevated PNGase F concentration. The total N-glycan profile of FXIII-B featured nine individual structures; three were fucosylated and each structure contained at least one sialic acid. Deglycosylation did not change the native dimeric structure of FXIII-B, but accelerated its clearance from the circulation of FXIII-B knock out mice. CONCLUSION Characterization of the glycan moieties attached to FXIII-B is reported for the first time. Complete deglycosylation of the native protein was achieved by a deglycosylation workflow. The associated glycan structure is not required for FXIII-B dimer formation, but it very likely prolongs the half-life of FXIII-B in the plasma.
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Affiliation(s)
- Boglárka Hurják
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Kálmán Laki Doctoral School of Biomedical and Clinical Sciences, University of Debrecen, Debrecen, Hungary
| | - Zsuzsanna Kovács
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Boglarka Döncző
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Éva Katona
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gizella Haramura
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ferenc Erdélyi
- Medical Gene Technology Unit, Institute of Experimental Medicine, Budapest, Hungary
| | - Amir Housang Shemirani
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Farzaneh Sadeghi
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Kálmán Laki Doctoral School of Biomedical and Clinical Sciences, University of Debrecen, Debrecen, Hungary
| | - László Muszbek
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - András Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprem, Hungary
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11
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Quantitative comparison of the N-glycosylation of therapeutic glycoproteins using the Glycosimilarity Index. A tutorial. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Filep C, Borza B, Jarvas G, Guttman A. N-glycosylation analysis of biopharmaceuticals by multicapillary gel electrophoresis: Generation and application of a new glucose unit database. J Pharm Biomed Anal 2020; 178:112892. [DOI: 10.1016/j.jpba.2019.112892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
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13
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Comparative analysis of the human serum N-glycome in lung cancer, COPD and their comorbidity using capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1137:121913. [DOI: 10.1016/j.jchromb.2019.121913] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/13/2019] [Accepted: 11/29/2019] [Indexed: 12/31/2022]
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14
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Szigeti M, Guttman A. Sample Preparation Scale-Up for Deep N-glycomic Analysis of Human Serum by Capillary Electrophoresis and CE-ESI-MS. Mol Cell Proteomics 2019; 18:2524-2531. [PMID: 31628258 PMCID: PMC6885710 DOI: 10.1074/mcp.tir119.001669] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/15/2019] [Indexed: 12/21/2022] Open
Abstract
We introduce an efficient sample preparation workflow to facilitate deep N-glycomics analysis of the human serum by capillary electrophoresis with laser induced fluorescence (CE-LIF) detection and to accommodate the higher sample concentration requirement of electrospray ionization mass spectrometry connected to capillary electrophoresis (CE-ESI-MS). A novel, temperature gradient denaturing protocol was applied on amine functionalized magnetic bead partitioned glycoproteins to circumvent the otherwise prevalent precipitation issue. During this process, the free sugar content of the serum was significantly decreased as well, accommodating enhanced PNGase F mediated release of the N-linked carbohydrates. The liberated oligosaccharides were tagged with aminopyrene-trisulfonate, utilizing a modified evaporative labeling protocol. Processing the samples with this new workflow enabled deep CE-LIF analysis of the human serum N-glycome and provided the appropriate amount of material for CE-ESI-MS analysis in negative ionization mode.
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Affiliation(s)
- Marton Szigeti
- MTA-PE Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprem, 8200, Hungary; Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Doctoral School of Molecular Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., Debrecen, 4032, Hungary
| | - Andras Guttman
- MTA-PE Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprem, 8200, Hungary; Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Doctoral School of Molecular Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., Debrecen, 4032, Hungary.
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15
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Bousfield GR, Harvey DJ. Follicle-Stimulating Hormone Glycobiology. Endocrinology 2019; 160:1515-1535. [PMID: 31127275 PMCID: PMC6534497 DOI: 10.1210/en.2019-00001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/16/2019] [Indexed: 01/13/2023]
Abstract
FSH glycosylation varies in two functionally important aspects: microheterogeneity, resulting from oligosaccharide structure variation, and macroheterogeneity, arising from partial FSHβ subunit glycosylation. Although advances in mass spectrometry permit extensive characterization of FSH glycan populations, microheterogeneity remains difficult to illustrate, and comparisons between different studies are challenging because no standard format exists for rendering oligosaccharide structures. FSH microheterogeneity is illustrated using a consistent glycan diagram format to illustrate the large array of structures associated with one hormone. This is extended to commercially available recombinant FSH preparations, which exhibit greatly reduced microheterogeneity at three of four glycosylation sites. Macroheterogeneity is demonstrated by electrophoretic mobility shifts due to the absence of FSHβ glycans that can be assessed by Western blotting of immunopurified FSH. Initially, macroheterogeneity was hoped to matter more than microheterogeneity. However, it now appears that both forms of carbohydrate heterogeneity have to be taken into consideration. FSH glycosylation can reduce its apparent affinity for its cognate receptor by delaying initial interaction with the receptor and limiting access to all of the available binding sites. This is followed by impaired cellular signaling responses that may be related to reduced receptor occupancy or biased signaling. To resolve these alternatives, well-characterized FSH glycoform preparations are necessary.
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Affiliation(s)
- George R Bousfield
- Department of Biological Sciences, Wichita State University, Wichita, Kansas
- Correspondence: George R. Bousfield, PhD, Department of Biological Sciences, Wichita State University, 1845 Fairmount Street, Wichita, Kansas 67260. E-mail: ; or David J. Harvey, DSc, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford. Roosevelt Drive, Oxford OX3 7FZ, United Kingdom. E-mail:
| | - David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
- Correspondence: George R. Bousfield, PhD, Department of Biological Sciences, Wichita State University, 1845 Fairmount Street, Wichita, Kansas 67260. E-mail: ; or David J. Harvey, DSc, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford. Roosevelt Drive, Oxford OX3 7FZ, United Kingdom. E-mail:
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16
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Bale S, Martiné A, Wilson R, Behrens AJ, Le Fourn V, de Val N, Sharma SK, Tran K, Torres JL, Girod PA, Ward AB, Crispin M, Wyatt RT. Cleavage-Independent HIV-1 Trimers From CHO Cell Lines Elicit Robust Autologous Tier 2 Neutralizing Antibodies. Front Immunol 2018; 9:1116. [PMID: 29881382 PMCID: PMC5976746 DOI: 10.3389/fimmu.2018.01116] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/03/2018] [Indexed: 01/12/2023] Open
Abstract
Native flexibly linked (NFL) HIV-1 envelope glycoprotein (Env) trimers are cleavage-independent and display a native-like, well-folded conformation that preferentially displays broadly neutralizing determinants. The NFL platform simplifies large-scale production of Env by eliminating the need to co-transfect the precursor-cleaving protease, furin that is required by the cleavage-dependent SOSIP trimers. Here, we report the development of a CHO-M cell line that expressed BG505 NFL trimers at a high level of homogeneity and yields of ~1.8 g/l. BG505 NFL trimers purified by single-step lectin-affinity chromatography displayed a native-like closed structure, efficient recognition by trimer-preferring bNAbs, no recognition by non-neutralizing CD4 binding site-directed and V3-directed antibodies, long-term stability, and proper N-glycan processing. Following negative-selection, formulation in ISCOMATRIX adjuvant and inoculation into rabbits, the trimers rapidly elicited potent autologous tier 2 neutralizing antibodies. These antibodies targeted the N-glycan "hole" naturally present on the BG505 Env proximal to residues at positions 230, 241, and 289. The BG505 NFL trimers that did not expose V3 in vitro, elicited low-to-no tier 1 virus neutralization in vivo, indicating that they remained intact during the immunization process, not exposing V3. In addition, BG505 NFL and BG505 SOSIP trimers expressed from 293F cells, when formulated in Adjuplex adjuvant, elicited equivalent BG505 tier 2 autologous neutralizing titers. These titers were lower in potency when compared to the titers elicited by CHO-M cell derived trimers. In addition, increased neutralization of tier 1 viruses was detected. Taken together, these data indicate that both adjuvant and cell-type expression can affect the elicitation of tier 2 and tier 1 neutralizing responses in vivo.
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Affiliation(s)
- Shridhar Bale
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | | | - Richard Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Anna-Janina Behrens
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, United Kingdom
| | | | - Natalia de Val
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Shailendra K Sharma
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Karen Tran
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Jonathan L Torres
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | | | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Max Crispin
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, United Kingdom.,Centre for Biological Sciences, Institute of Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Richard T Wyatt
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
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17
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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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18
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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19
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Campbell MP, Peterson RA, Gasteiger E, Mariethoz J, Lisacek F, Packer NH. Navigating the Glycome Space and Connecting the Glycoproteome. Methods Mol Biol 2017; 1558:139-158. [PMID: 28150237 DOI: 10.1007/978-1-4939-6783-4_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
UniCarbKB ( http://unicarbkb.org ) is a comprehensive resource for mammalian glycoprotein and annotation data. In particular, the database provides information on the oligosaccharides characterized from a glycoprotein at either the global or site-specific level. This evidence is accumulated from a peer-reviewed and manually curated collection of information on oligosaccharides derived from membrane and secreted glycoproteins purified from biological fluids and/or tissues. This information is further supplemented with experimental method descriptions that summarize important sample preparation and analytical strategies. A new release of UniCarbKB is published every three months, each includes a collection of curated data and improvements to database functionality. In this Chapter, we outline the objectives of UniCarbKB, and describe a selection of step-by-step workflows for navigating the information available. We also provide a short description of web services available and future plans for improving data access. The information presented in this Chapter supplements content available in our knowledgebase including regular updates on interface improvements, new features, and revisions to the database content ( http://confluence.unicarbkb.org ).
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Affiliation(s)
- Matthew P Campbell
- Department of Chemistry and Biomolecular Sciences, Research Drive, Building E8C, Macquarie University, North Ryde, Sydney, 2109, NSW, Australia
| | - Robyn A Peterson
- Department of Chemistry and Biomolecular Sciences, Research Drive, Building E8C, Macquarie University, North Ryde, Sydney, 2109, NSW, Australia
| | - Elisabeth Gasteiger
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland
| | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland
- Computer Science Department, University of Geneva, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Research Drive, Building E8C, Macquarie University, North Ryde, Sydney, 2109, NSW, Australia.
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20
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Akune Y, Lin CH, Abrahams JL, Zhang J, Packer NH, Aoki-Kinoshita KF, Campbell MP. Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database. Carbohydr Res 2016; 431:56-63. [PMID: 27318307 DOI: 10.1016/j.carres.2016.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/23/2016] [Accepted: 05/29/2016] [Indexed: 02/06/2023]
Abstract
Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database.
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Affiliation(s)
- Yukie Akune
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia; Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236, Tangi, Hachioji, 192-8577, Tokyo, Japan
| | - Chi-Hung Lin
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia
| | - Jodie L Abrahams
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia
| | - Jingyu Zhang
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia
| | - Kiyoko F Aoki-Kinoshita
- Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236, Tangi, Hachioji, 192-8577, Tokyo, Japan
| | - Matthew P Campbell
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia.
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21
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Meher BR, Dixit A, Bousfield GR, Lushington GH. Glycosylation Effects on FSH-FSHR Interaction Dynamics: A Case Study of Different FSH Glycoforms by Molecular Dynamics Simulations. PLoS One 2015; 10:e0137897. [PMID: 26402790 PMCID: PMC4581761 DOI: 10.1371/journal.pone.0137897] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/23/2015] [Indexed: 12/20/2022] Open
Abstract
The gonadotropin known as follicle-stimulating hormone (FSH) plays a key role in regulating reproductive processes. Physiologically active FSH is a glycoprotein that can accommodate glycans on up to four asparagine residues, including two sites in the FSHα subunit that are critical for biochemical function, plus two sites in the β subunit, whose differential glycosylation states appear to correspond to physiologically distinct functions. Some degree of FSHβ hypo-glycosylation seems to confer advantages toward reproductive fertility of child-bearing females. In order to identify possible mechanistic underpinnings for this physiological difference we have pursued computationally intensive molecular dynamics simulations on complexes between the high affinity site of the gonadal FSH receptor (FSHR) and several FSH glycoforms including fully-glycosylated (FSH24), hypo-glycosylated (e.g., FSH15), and completely deglycosylated FSH (dgFSH). These simulations suggest that deviations in FSH/FSHR binding profile as a function of glycosylation state are modest when FSH is adorned with only small glycans, such as single N-acetylglucosamine residues. However, substantial qualitative differences emerge between FSH15 and FSH24 when FSH is decorated with a much larger, tetra-antennary glycan. Specifically, the FSHR complex with hypo-glycosylated FSH15 is observed to undergo a significant conformational shift after 5-10 ns of simulation, indicating that FSH15 has greater conformational flexibility than FSH24 which may explain the more favorable FSH15 kinetic profile. FSH15 also exhibits a stronger binding free energy, due in large part to formation of closer and more persistent salt-bridges with FSHR.
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Affiliation(s)
- Biswa Ranjan Meher
- Bioinformatics Core Facility, University of Kansas, Lawrence, Kansas, United States of America
- * E-mail: (BRM); (GHL)
| | - Anshuman Dixit
- Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India
| | - George R. Bousfield
- Department of Biological Sciences, Wichita State University, Wichita, Kansas, United States of America
| | - Gerald H. Lushington
- LiS Consulting, Lawrence, Kansas, United States of America
- * E-mail: (BRM); (GHL)
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22
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Struwe WB, Pagel K, Benesch JLP, Harvey DJ, Campbell MP. GlycoMob: an ion mobility-mass spectrometry collision cross section database for glycomics. Glycoconj J 2015; 33:399-404. [PMID: 26314736 DOI: 10.1007/s10719-015-9613-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/21/2015] [Accepted: 07/27/2015] [Indexed: 12/29/2022]
Abstract
Ion mobility mass spectrometry (IM-MS) is a promising analytical technique for glycomics that separates glycan ions based on their collision cross section (CCS) and provides glycan precursor and fragment masses. It has been shown that isomeric oligosaccharide species can be separated by IM and identified on basis of their CCS and fragmentation. These results indicate that adding CCSs information for glycans and glycan fragments to searchable databases and analysis pipelines will increase identification confidence and accuracy. We have developed a freely accessible database, GlycoMob ( http://www.glycomob.org ), containing over 900 CCSs values of glycans, oligosaccharide standards and their fragments that will be continually updated. We have measured the absolute CCSs of calibration standards, biologically derived and synthetic N-glycans ionized with various adducts in positive and negative mode or as protonated (positive ion) and deprotonated (negative ion) ions.
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Affiliation(s)
- Weston B Struwe
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK.
| | - Kevin Pagel
- Free University Chemistry, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, 14195, Berlin, Germany
| | | | - David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Matthew P Campbell
- Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW 2109, Australia.
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23
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Jiang C, Hou X, Wang C, May JV, Butnev VY, Bousfield GR, Davis JS. Hypoglycosylated hFSH Has Greater Bioactivity Than Fully Glycosylated Recombinant hFSH in Human Granulosa Cells. J Clin Endocrinol Metab 2015; 100:E852-60. [PMID: 25915568 PMCID: PMC4454802 DOI: 10.1210/jc.2015-1317] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CONTEXT Previous studies suggest that aging in women is associated with a reduction in hypoglycosylated forms of FSH. OBJECTIVE Experiments were performed to determine whether glycosylation of the FSHβ subunit modulates the biological activity of FSH in human granulosa cells. DESIGN AND SETTING Recombinant human FSH (hFSH) derived from GH3 pituitary cells was purified into fractions containing hypoglycosylated hFSH(21/18) and fully glycosylated hFSH(24). The response to FSH glycoforms was evaluated using the well-characterized, FSH-responsive human granulosa cell line, KGN at an academic medical center. INTERVENTIONS Granulosa cells were treated with increasing concentrations of fully- or hypoglycosylated FSH glycoforms for periods up to 48 hours. MAIN OUTCOME MEASURE(S) The main outcomes were indices of cAMP-dependent cell signaling and estrogen and progesterone synthesis. RESULTS We observed that hypoglycosylated FSH(21/18) was significantly more effective than fully glycosylated FSH(24) at stimulating cAMP accumulation, protein kinase A (PKA) activity, and cAMP response element binding protein (CREB) (S133) phosphorylation. FSH(21/18) was also much more effective than hFSH(24) on the stimulation CREB-response element-mediated transcription, expression of aromatase and STAR proteins, and synthesis of estrogen and progesterone. Adenoviral-mediated expression of the endogenous inhibitor of PKA, inhibited FSH(21/18)- and FSH(24)-stimulated CREB phosphorylation, and steroidogenesis. CONCLUSIONS Hypoglycosylated FSH(21/18) has greater bioactivity than fully glycosylated hFSH(24), suggesting that age-dependent decreases in hypoglycosylated hFSH contribute to reduced ovarian responsiveness. Hypoglycosylated FSH may be useful in follicle stimulation protocols for older patients using assisted reproduction technologies.
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Affiliation(s)
- Chao Jiang
- The Olson Center for Women's Health, Department of Obstetrics and Gynecology (C.J., X.H., C.W., J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198; Nebraska-Northwest Iowa VA Medical Center (X.H., J.S.D.), Omaha, Nebraska 68105; Department of Biological Sciences (J.V.M., V.Y.B., G.R.B.), Wichita State University, Wichita, Kansas 67260; and Department of Biochemistry and Molecular Biology (J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Xiaoying Hou
- The Olson Center for Women's Health, Department of Obstetrics and Gynecology (C.J., X.H., C.W., J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198; Nebraska-Northwest Iowa VA Medical Center (X.H., J.S.D.), Omaha, Nebraska 68105; Department of Biological Sciences (J.V.M., V.Y.B., G.R.B.), Wichita State University, Wichita, Kansas 67260; and Department of Biochemistry and Molecular Biology (J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Cheng Wang
- The Olson Center for Women's Health, Department of Obstetrics and Gynecology (C.J., X.H., C.W., J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198; Nebraska-Northwest Iowa VA Medical Center (X.H., J.S.D.), Omaha, Nebraska 68105; Department of Biological Sciences (J.V.M., V.Y.B., G.R.B.), Wichita State University, Wichita, Kansas 67260; and Department of Biochemistry and Molecular Biology (J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Jeffrey V May
- The Olson Center for Women's Health, Department of Obstetrics and Gynecology (C.J., X.H., C.W., J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198; Nebraska-Northwest Iowa VA Medical Center (X.H., J.S.D.), Omaha, Nebraska 68105; Department of Biological Sciences (J.V.M., V.Y.B., G.R.B.), Wichita State University, Wichita, Kansas 67260; and Department of Biochemistry and Molecular Biology (J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Viktor Y Butnev
- The Olson Center for Women's Health, Department of Obstetrics and Gynecology (C.J., X.H., C.W., J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198; Nebraska-Northwest Iowa VA Medical Center (X.H., J.S.D.), Omaha, Nebraska 68105; Department of Biological Sciences (J.V.M., V.Y.B., G.R.B.), Wichita State University, Wichita, Kansas 67260; and Department of Biochemistry and Molecular Biology (J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - George R Bousfield
- The Olson Center for Women's Health, Department of Obstetrics and Gynecology (C.J., X.H., C.W., J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198; Nebraska-Northwest Iowa VA Medical Center (X.H., J.S.D.), Omaha, Nebraska 68105; Department of Biological Sciences (J.V.M., V.Y.B., G.R.B.), Wichita State University, Wichita, Kansas 67260; and Department of Biochemistry and Molecular Biology (J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - John S Davis
- The Olson Center for Women's Health, Department of Obstetrics and Gynecology (C.J., X.H., C.W., J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198; Nebraska-Northwest Iowa VA Medical Center (X.H., J.S.D.), Omaha, Nebraska 68105; Department of Biological Sciences (J.V.M., V.Y.B., G.R.B.), Wichita State University, Wichita, Kansas 67260; and Department of Biochemistry and Molecular Biology (J.S.D.), University of Nebraska Medical Center, Omaha, Nebraska 68198
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24
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Váradi C, Holló Z, Póliska S, Nagy L, Szekanecz Z, Váncsa A, Palatka K, Guttman A. Combination of IgG N-glycomics and corresponding transcriptomics data to identify anti-TNF-α treatment responders in inflammatory diseases. Electrophoresis 2015; 36:1330-5. [PMID: 25639738 DOI: 10.1002/elps.201400575] [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: 12/04/2014] [Revised: 01/06/2015] [Accepted: 01/06/2015] [Indexed: 12/14/2022]
Abstract
Prediction of responsiveness in biological therapies is an important and challenging issue in different diseases. Analyzing glycosylation pattern changes of key serum glycoproteins is one of the possible avenues to follow disease remission. The aim of this study was to investigate the changes of serum IgG glycoforms in Crohn's disease (CD) and rheumatoid arthritis patients in response to antitumor necrosis factor alpha (anti-TNF-α) treatment. IgG was isolated from patient serum samples using Protein A affinity pull-down, followed by the release of N-glycans with peptide-N-glycosidase F. The released glycans were fluorescently tagged with 8-aminopyrene-1,3,6-trisulfonate and analyzed by CGE with laser-induced fluorescent detection. Significant alterations were detected between responders and nonresponders in both disease groups. In CD patients, disease-specific alteration was found in response to anti-TNF-α therapy, which was also confirmed by transcriptomics data analysis of the corresponding glycosyltransferases and glycosidases.
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Affiliation(s)
- Csaba Váradi
- Horváth Laboratory of Bioseparation Sciences, School of Medicine, MMKK, University of Debrecen, Debrecen, Hungary
| | | | - Szilárd Póliska
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - László Nagy
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Zoltán Szekanecz
- Department of Rheumatology, School of Medicine, University of Debrecen, Debrecen, Hungary
| | - Andrea Váncsa
- Department of Rheumatology, School of Medicine, University of Debrecen, Debrecen, Hungary
| | - Károly Palatka
- Department of Internal Medicine, University of Debrecen, Debrecen, Hungary
| | - András Guttman
- Horváth Laboratory of Bioseparation Sciences, School of Medicine, MMKK, University of Debrecen, Debrecen, Hungary.,MTA-PE Translational Glycomics Research Group, MUKKI, University of Pannonia, Veszprém, Hungary
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25
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Abrahams JL, Packer NH, Campbell MP. Relative quantitation of multi-antennary N-glycan classes: combining PGC-LC-ESI-MS with exoglycosidase digestion. Analyst 2015; 140:5444-9. [DOI: 10.1039/c5an00691k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In the search for N-glycan disease biomarkers current glycoanalytical methods may not be revealing a complete picture of precious samples, and we may be missing valuable structural information that fall outside analysis windows.
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Affiliation(s)
- J. L. Abrahams
- Department of Chemistry and Biomolecular Sciences
- Macquarie University
- Sydney
- Australia
| | - N. H. Packer
- Department of Chemistry and Biomolecular Sciences
- Macquarie University
- Sydney
- Australia
| | - M. P. Campbell
- Department of Chemistry and Biomolecular Sciences
- Macquarie University
- Sydney
- Australia
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26
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Bousfield GR, Butnev VY, White WK, Hall AS, Harvey DJ. Comparison of Follicle-Stimulating Hormone Glycosylation Microheterogenity by Quantitative Negative Mode Nano-Electrospray Mass Spectrometry of Peptide-N Glycanase-Released Oligosaccharides. ACTA ACUST UNITED AC 2015; 5. [PMID: 25960929 DOI: 10.4172/2153-0637.1000129] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Glycans from six highly purified hFSH preparations were released by peptide-N-glycanase digestion and analyzed by negative mode nano-ESI mass spectrometry before and after neuraminidase digestion. Pituitary glycan structures were mainly high-mannose, di-, tri-, and tetra-antennary, and their abundance largely paralleled that reported by other investigators using different approaches. For most of the FSH preparations, the differences in glycosylation appeared to be restricted to relative abundances of the major glycan families, as defined by their neutral core oligosaccharide structures. Qualitative differences between glycan populations were largely relegated to those species that were lowest in abundance. Significant qualitative differences were noted in two cases. Recombinant GH3-hFSH triantennary glycans appeared to have the third antenna exclusively on the mannose6-branch, in contrast to all pituitary and urinary hFSH triantennary glycans, in which this antenna was exclusively attached to the mannose3-branch. The hypo-glycosylated hFSH preparation isolated from purified hLH was decorated with high mannose glycans that accounted for over 40% of the total in this population. As this preparation was found to be consistently 20-fold more active than hFSH24 in FSH receptor-binding assays, it appears that both macroheterogeneity and microheterogeneity in FSH preparations need to be taken into account.
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Affiliation(s)
- George R Bousfield
- Department of Biological Sciences, Wichita State University, Wichita, KS 67260
| | - Vladimir Y Butnev
- Department of Biological Sciences, Wichita State University, Wichita, KS 67260
| | - William K White
- Department of Biological Sciences, Wichita State University, Wichita, KS 67260
| | - Aaron Smalter Hall
- Molecular Graphics and Modeling Laboratory, University of Kansas, Lawrence, KS 66045
| | - David J Harvey
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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27
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Campbell MP, Royle L, Rudd PM. GlycoBase and autoGU: resources for interpreting HPLC-glycan data. Methods Mol Biol 2015; 1273:17-28. [PMID: 25753700 DOI: 10.1007/978-1-4939-2343-4_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological relevance of protein glycosylation has made glycomics, the comprehensive study to identify all glycans in an organism, indispensable in many research fields. Determining the structure and functional relationship of glycoproteins requires the comprehensive characterization of glycan structures by a range of analytical methods. High performance liquid chromatography (HPLC) is a well-established technology commonly used for the complete structural elucidation of N- and O-linked glycans; however, the analysis of data is a major bottleneck and robust bioinformatic solutions are required. This chapter describes the availability of databases and tools, GlycoBase and autoGU developed in conjunction with the EUROCarbDB initiative, to assist the interpretation of HPLC-glycan data collections.
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Affiliation(s)
- Matthew P Campbell
- Biomolecular Frontiers Research Centre, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia,
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28
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Theodoratou E, Campbell H, Ventham NT, Kolarich D, Pučić-Baković M, Zoldoš V, Fernandes D, Pemberton IK, Rudan I, Kennedy NA, Wuhrer M, Nimmo E, Annese V, McGovern DPB, Satsangi J, Lauc G. The role of glycosylation in IBD. Nat Rev Gastroenterol Hepatol 2014; 11:588-600. [PMID: 24912389 DOI: 10.1038/nrgastro.2014.78] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A number of genetic and immunological studies give impetus for investigating the role of glycosylation in IBD. Experimental mouse models have helped to delineate the role of glycosylation in intestinal mucins and to explore the putative pathogenic role of glycosylation in colitis. These experiments have been extended to human studies investigating the glycosylation patterns of intestinal mucins as well as levels of glycans of serum glycoproteins and expression of glycan receptors. These early human studies have generated interesting hypotheses regarding the pathogenic role of glycans in IBD, but have generally been restricted to fairly small underpowered studies. Decreased glycosylation has been observed in the intestinal mucus of patients with IBD, suggesting that a defective inner mucus layer might lead to increased bacterial contact with the epithelium, potentially triggering inflammation. In sera, decreased galactosylation of IgG has been suggested as a diagnostic marker for IBD. Advances in glycoprofiling technology make it technically feasible and affordable to perform high-throughput glycan pattern analyses and to build on previous work investigating a much wider range of glycan parameters in large numbers of patients.
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Affiliation(s)
- Evropi Theodoratou
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, EH8 9AG, Edinburgh, UK
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, EH8 9AG, Edinburgh, UK
| | - Nicholas T Ventham
- Centre for Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Edinburgh, UK
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1 OT Golm, 14476, Potsdam, Germany
| | | | - Vlatka Zoldoš
- University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
| | | | - Iain K Pemberton
- IP Research Consulting SAS, 34 Rue Carnot, 93160 Noisy-le-Grand, Paris, France
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, EH8 9AG, Edinburgh, UK
| | - Nicholas A Kennedy
- Centre for Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Edinburgh, UK
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Elaine Nimmo
- Centre for Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Edinburgh, UK
| | - Vito Annese
- Department of Medical and Surgical Specialities, Division of Gastroenterology, AOU Careggi University Hospital, Largo Brambilla 13, 50139 Florence, Italy
| | - Dermot P B McGovern
- F.Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Suite D4063, Los Angeles, CA 90048, USA
| | - Jack Satsangi
- Centre for Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Edinburgh, UK
| | - Gordan Lauc
- Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry, Trg maršala Tita 14, 10000 Zagreb, Croatia
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29
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Kozak RP, Royle L, Gardner RA, Bondt A, Fernandes DL, Wuhrer M. Improved nonreductive O-glycan release by hydrazinolysis with ethylenediaminetetraacetic acid addition. Anal Biochem 2014; 453:29-37. [PMID: 24613257 DOI: 10.1016/j.ab.2014.02.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 02/23/2014] [Accepted: 02/26/2014] [Indexed: 10/25/2022]
Abstract
The study of protein O-glycosylation is receiving increasing attention in biological, medical, and biopharmaceutical research. Improved techniques are required to allow reproducible and quantitative analysis of O-glycans. An established approach for O-glycan analysis relies on their chemical release in high yield by hydrazinolysis, followed by fluorescent labeling at the reducing terminus and high-performance liquid chromatography (HPLC) profiling. However, an unwanted degradation known as "peeling" often compromises hydrazinolysis for O-glycan analysis. Here we addressed this problem using low-molarity solutions of ethylenediaminetetraacetic acid (EDTA) in hydrazine for O-glycan release. O-linked glycans from a range of different glycoproteins were analyzed, including bovine fetuin, bovine submaxillary gland mucin, and serum immunoglobulin A (IgA). The data for the O-glycans released by hydrazine with anhydrous EDTA or disodium salt dihydrate EDTA show high yields of the native O-glycans compared with the peeled product, resulting in a markedly increased robustness of the O-glycan profiling method. The presented method for O-glycan release demonstrates significant reduction in peeling and reduces the number of sample handling steps prior to release.
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Affiliation(s)
| | - Louise Royle
- Ludger, Culham Science Centre, Oxfordshire OX14 3EB, UK
| | | | - Albert Bondt
- Department of Rheumatology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | | | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
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30
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Campbell MP, Ranzinger R, Lütteke T, Mariethoz J, Hayes CA, Zhang J, Akune Y, Aoki-Kinoshita KF, Damerell D, Carta G, York WS, Haslam SM, Narimatsu H, Rudd PM, Karlsson NG, Packer NH, Lisacek F. Toolboxes for a standardised and systematic study of glycans. BMC Bioinformatics 2014; 15 Suppl 1:S9. [PMID: 24564482 PMCID: PMC4016020 DOI: 10.1186/1471-2105-15-s1-s9] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. Methods Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. Results Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. Conclusions Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics.
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31
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Stavenhagen K, Hinneburg H, Thaysen-Andersen M, Hartmann L, Varón Silva D, Fuchser J, Kaspar S, Rapp E, Seeberger PH, Kolarich D. Quantitative mapping of glycoprotein micro-heterogeneity and macro-heterogeneity: an evaluation of mass spectrometry signal strengths using synthetic peptides and glycopeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:627-39. [PMID: 23722953 DOI: 10.1002/jms.3210] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/08/2013] [Accepted: 03/24/2013] [Indexed: 05/04/2023]
Abstract
Mass spectrometry (MS) is used to quantify the relative distribution of glycans attached to particular protein glycosylation sites (micro-heterogeneity) and evaluate the molar site occupancy (macro-heterogeneity) in glycoproteomics. However, the accuracy of MS for such quantitative measurements remains to be clarified. As a key step towards this goal, a panel of related tryptic peptides with and without complex, biantennary, disialylated N-glycans was chemically synthesised by solid-phase peptide synthesis. Peptides mimicking those resulting from enzymatic deglycosylation using PNGase F/A and endo D/F/H were synthetically produced, carrying aspartic acid and N-acetylglucosamine-linked asparagine residues, respectively, at the glycosylation site. The MS ionisation/detection strengths of these pure, well-defined and quantified compounds were investigated using various MS ionisation techniques and mass analysers (ESI-IT, ESI-Q-TOF, MALDI-TOF, ESI/MALDI-FT-ICR-MS). Depending on the ion source/mass analyser, glycopeptides carrying complex-type N-glycans exhibited clearly lower signal strengths (10-50% of an unglycosylated peptide) when equimolar amounts were analysed. Less ionisation/detection bias was observed when the glycopeptides were analysed by nano-ESI and medium-pressure MALDI. The position of the glycosylation site within the tryptic peptides also influenced the signal response, in particular if detected as singly or doubly charged signals. This is the first study to systematically and quantitatively address and determine MS glycopeptide ionisation/detection strengths to evaluate glycoprotein micro-heterogeneity and macro-heterogeneity by label-free approaches. These data form a much needed knowledge base for accurate quantitative glycoproteomics.
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Affiliation(s)
- Kathrin Stavenhagen
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
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32
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Everest-Dass AV, Abrahams JL, Kolarich D, Packer NH, Campbell MP. Structural feature ions for distinguishing N- and O-linked glycan isomers by LC-ESI-IT MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:895-906. [PMID: 23605685 DOI: 10.1007/s13361-013-0610-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/22/2013] [Accepted: 02/28/2013] [Indexed: 05/13/2023]
Abstract
Glycomics is the comprehensive study of glycan expression in an organism, cell, or tissue that relies on effective analytical technologies to understand glycan structure-function relationships. Owing to the macro- and micro-heterogeneity of oligosaccharides, detailed structure characterization has required an orthogonal approach, such as a combination of specific exoglycosidase digestions, LC-MS/MS, and the development of bioinformatic resources to comprehensively profile a complex biological sample. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) has emerged as a key tool in the structural analysis of oligosaccharides because of its high sensitivity, resolution, and robustness. Here, we present a strategy that uses LC-ESI-MS/MS to characterize over 200 N- and O-glycans from human saliva glycoproteins, complemented by sequential exoglycosidase treatment, to further verify the annotated glycan structures. Fragment-specific substructure diagnostic ions were collated from an extensive screen of the literature available on the detailed structural characterization of oligosaccharides and, together with other specific glycan structure feature ions derived from cross-ring and glycosidic-linkage fragmentation, were used to characterize the glycans and differentiate isomers. The availability of such annotated mass spectrometric fragmentation spectral libraries of glycan structures, together with such substructure diagnostic ions, will be key inputs for the future development of the automated elucidation of oligosaccharide structures from MS/MS data.
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Affiliation(s)
- Arun V Everest-Dass
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
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33
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Campbell MP, Nguyen-Khuong T, Hayes CA, Flowers SA, Alagesan K, Kolarich D, Packer NH, Karlsson NG. Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:108-16. [PMID: 23624262 DOI: 10.1016/j.bbapap.2013.04.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 04/01/2013] [Accepted: 04/16/2013] [Indexed: 10/26/2022]
Abstract
The UniCarb-DB database is an emerging public glycomics data repository, containing over 500 tandem mass spectra (as of March 2013) of glycans released from glycoproteins. A major challenge in glycomics research is to provide and maintain high-quality datasets that will offer the necessary diversity to support the development of accurate bioinformatics tools for data deposition and analysis. The role of UniCarb-DB, as an archival database, is to provide the glycomics community with open-access to a comprehensive LC MS/MS library of N- and O- linked glycans released from glycoproteins that have been annotated with glycosidic and cross-ring fragmentation ions, retention times, and associated experimental metadata descriptions. Here, we introduce the UniCarb-DB data submission pipeline and its practical application to construct a library of LC-MS/MS glycan standards that forms part of this database. In this context, an independent consortium of three laboratories was established to analyze the same 23 commercially available oligosaccharide standards, all by using graphitized carbon-liquid chromatography (LC) electrospray ionization (ESI) ion trap mass spectrometry in the negative ion mode. A dot product score was calculated for each spectrum in the three sets of data as a measure of the comparability that is necessary for use of such a collection in library-based spectral matching and glycan structural identification. The effects of charge state, de-isotoping and threshold levels on the quality of the input data are shown. The provision of well-characterized oligosaccharide fragmentation data provides the opportunity to identify determinants of specific glycan structures, and will contribute to the confidence level of algorithms that assign glycan structures to experimental MS/MS spectra. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.
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Affiliation(s)
- Matthew P Campbell
- Biomolecular Frontiers Research Centre, Macquarie University, Sydney, New South Wales, Australia
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34
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Lazar IM, Lee W, Lazar AC. Glycoproteomics on the rise: established methods, advanced techniques, sophisticated biological applications. Electrophoresis 2012; 34:113-25. [PMID: 23161435 DOI: 10.1002/elps.201200445] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 10/07/2012] [Accepted: 10/07/2012] [Indexed: 02/05/2023]
Abstract
Glycosylation is the most complex form of protein PTMs. Affected proteins may carry dozens of glycosylation sites with tens to hundreds of glycan residues attached to every site. Glycosylated proteins have many important functions in biology, from cellular to organismal levels, being involved in cell-cell signaling, cell adhesion, immune response, host-pathogen interactions, and development and growth. Glycosylation, however, expands the biological functional diversity of proteins at the expense of a tremendous increase in structural heterogeneity. Aberrant glycosylation of cell surface proteins, as well as their detectable fingerprint in plasma samples, has been associated with cancer, inflammatory and degenerative diseases, and congenital disorders of glycosylation. Therefore, there are on-going efforts directed toward developing new technologies and approaches for glycan sequencing and high-throughput analysis of glycosylated proteins in complex samples with simultaneous characterization of both the protein and glycan moieties. This work is aimed primarily at pinpointing the challenges associated with the large-scale analysis of glycoproteins and the latest developments in glycoproteomic research, with focus on recent advancements (2011-2012) in microcolumn separations and MS detection.
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Affiliation(s)
- Iulia M Lazar
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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35
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Marginean I, Kronewitter SR, Moore RJ, Slysz GW, Monroe ME, Anderson G, Tang K, Smith RD. Improving N-glycan coverage using HPLC-MS with electrospray ionization at subambient pressure. Anal Chem 2012; 84:9208-13. [PMID: 23025344 DOI: 10.1021/ac301961u] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human serum glycan profiling with mass spectrometry (MS) has been employed to study several disease conditions and is demonstrating promise in, for example, clinical biomarker discovery. However, the low glycan ionization efficiency and the large dynamic range of glycan concentrations in human sera can hinder comprehensive profiling. In particular, large glycans are problematic because they are present at low concentrations and are prone to fragmentation. Here we show that, following liquid chromatographic separation on graphite columns, subambient pressure ionization with nanoelectrospray (SPIN)-MS can expand the serum glycome profile in comparison with the conventional atmospheric pressure electrospray ionization (ESI)-MS with a heated capillary inlet. Notably, the ions generated by the SPIN interface were observed at higher charge states for approximately half of the annotated glycans. Out of a total of 130 detected glycans, 34 were only detected with the SPIN-MS, resulting in improved coverage of glycan families as well as of glycans with larger numbers of labile monosaccharides.
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Affiliation(s)
- Ioan Marginean
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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