201
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Jin T, Xiong Z, Zhu X, Mehio N, Chen Y, Hu J, Zhang W, Zou H, Liu H, Dai S. Template-Free Synthesis of Mesoporous Polymers for Highly Selective Enrichment of Glycopeptides. ACS Macro Lett 2015; 4:570-574. [PMID: 35596295 DOI: 10.1021/acsmacrolett.5b00235] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A facile template-free strategy for the synthesis of mesoporous phenolic polymers with attractive porosities, nitrogen-containing functionalities, and intrinsic hydrophilic skeletons is presented. The resultant polymer has a high BET surface area (548 m2 g-1) and mesopore size (13 nm) and exhibits superior glycopeptide-capturing performance, thus, revealing the potential application of mesoporous polymers in highly selective glycopeptide enrichment. This general capture protocol may open up new opportunities for the development of glycoproteomes.
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Affiliation(s)
- Tian Jin
- State
Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Zhichao Xiong
- State
Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Key
Laboratory of Separation Sciences for Analytical Chemistry, Dalian
Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian, P. R. China
| | - Xiang Zhu
- State
Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Department
of Chemistry and Food Chemistry, Technische Universitat Dresden, Dresden 01062, Germany
| | - Nada Mehio
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Yajing Chen
- State
Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jun Hu
- State
Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Weibing Zhang
- State
Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Hanfa Zou
- Key
Laboratory of Separation Sciences for Analytical Chemistry, Dalian
Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian, P. R. China
| | - Honglai Liu
- State
Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Sheng Dai
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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202
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Prudden AR, Chinoy ZS, Wolfert MA, Boons GJ. A multifunctional anomeric linker for the chemoenzymatic synthesis of complex oligosaccharides. Chem Commun (Camb) 2015; 50:7132-5. [PMID: 24854112 DOI: 10.1039/c4cc02222j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new anomeric linker has been developed that facilitates the purification of glycans prepared by chemoenzymatic approaches and can readily give compounds that are appropriately modified for microarray development or glycan derivatives with a free reducing end that are needed as standards for the development of analytical protocols.
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Affiliation(s)
- Anthony R Prudden
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA.
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203
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Hushegyi A, Bertok T, Damborsky P, Katrlik J, Tkac J. An ultrasensitive impedimetric glycan biosensor with controlled glycan density for detection of lectins and influenza hemagglutinins. Chem Commun (Camb) 2015; 51:7474-7. [PMID: 25828081 PMCID: PMC4883646 DOI: 10.1039/c5cc00922g] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An impedimetric glycan biosensor with optimised glycan density was applied for the detection of lectins and influenza hemagglutinins down to attomolar concentrations (aM).
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Affiliation(s)
- A Hushegyi
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia.
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204
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Liu G, Neelamegham S. Integration of systems glycobiology with bioinformatics toolboxes, glycoinformatics resources, and glycoproteomics data. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:163-81. [PMID: 25871730 DOI: 10.1002/wsbm.1296] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/08/2015] [Accepted: 03/04/2015] [Indexed: 12/22/2022]
Abstract
The glycome constitutes the entire complement of free carbohydrates and glycoconjugates expressed on whole cells or tissues. 'Systems Glycobiology' is an emerging discipline that aims to quantitatively describe and analyse the glycome. Here, instead of developing a detailed understanding of single biochemical processes, a combination of computational and experimental tools are used to seek an integrated or 'systems-level' view. This can explain how multiple biochemical reactions and transport processes interact with each other to control glycome biosynthesis and function. Computational methods in this field commonly build in silico reaction network models to describe experimental data derived from structural studies that measure cell-surface glycan distribution. While considerable progress has been made, several challenges remain due to the complex and heterogeneous nature of this post-translational modification. First, for the in silico models to be standardized and shared among laboratories, it is necessary to integrate glycan structure information and glycosylation-related enzyme definitions into the mathematical models. Second, as glycoinformatics resources grow, it would be attractive to utilize 'Big Data' stored in these repositories for model construction and validation. Third, while the technology for profiling the glycome at the whole-cell level has been standardized, there is a need to integrate mass spectrometry derived site-specific glycosylation data into the models. The current review discusses progress that is being made to resolve the above bottlenecks. The focus is on how computational models can bridge the gap between 'data' generated in wet-laboratory studies with 'knowledge' that can enhance our understanding of the glycome.
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Affiliation(s)
- Gang Liu
- Department of Chemical and Biological Engineering, State University of New York, Buffalo, NY, USA
| | - Sriram Neelamegham
- Department of Chemical and Biological Engineering, State University of New York, Buffalo, NY, USA
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205
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Tkac J, Bertok T, Nahalka J, Gemeiner P. Perspectives in glycomics and lectin engineering. Methods Mol Biol 2015; 1200:421-45. [PMID: 25117256 DOI: 10.1007/978-1-4939-1292-6_37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This chapter would like to provide a short survey of the most promising concepts applied recently in analysis of glycoproteins based on lectins. The first part describes the most exciting analytical approaches used in the field of glycoprofiling based on integration of nanoparticles, nanowires, nanotubes, or nanochannels or using novel transducing platforms allowing to detect very low levels of glycoproteins in a label-free mode of operation. The second part describes application of recombinant lectins containing several tags applied for oriented and ordered immobilization of lectins. Besides already established concepts of glycoprofiling several novel aspects, which we think will be taken into account for future, more robust glycan analysis, are described including modified lectins, peptide lectin aptamers, and DNA aptamers with lectin-like specificity introduced by modified nucleotides. The last part of the chapter describes a novel concept of a glycocodon, which can lead to a better understanding of glycan-lectin interaction and for design of novel lectins with unknown specificities and/or better affinities toward glycan target or for rational design of peptide lectin aptamers or DNA aptamers.
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Affiliation(s)
- Jan Tkac
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38, Bratislava, Slovakia
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206
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Aboufazeli F, Kolli V, Dodds ED. A comparison of energy-resolved vibrational activation/dissociation characteristics of protonated and sodiated high mannose N-glycopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:587-595. [PMID: 25582509 DOI: 10.1007/s13361-014-1070-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/11/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Fragmentation of glycopeptides in tandem mass spectrometry (MS/MS) plays a pivotal role in site-specific protein glycosylation profiling by allowing specific oligosaccharide compositions and connectivities to be associated with specific loci on the corresponding protein. Although MS/MS analysis of glycopeptides has been successfully performed using a number of distinct ion dissociation methods, relatively little is known regarding the fragmentation characteristics of glycopeptide ions with various charge carriers. In this study, energy-resolved vibrational activation/dissociation was examined via collision-induced dissociation for a group of related high mannose tryptic glycopeptides as their doubly protonated, doubly sodiated, and hybrid protonated sodium adduct ions. The doubly protonated glycopeptide ions with various compositions were found to undergo fragmentation over a relatively low but wide range of collision energies compared with the doubly sodiated and hybrid charged ions, and were found to yield both glycan and peptide fragmentation depending on the applied collision energy. By contrast, the various doubly sodiated glycopeptides were found to dissociate over a significantly higher but narrow range of collision energies, and exhibited only glycan cleavages. Interestingly, the hybrid protonated sodium adduct ions were consistently the most stable of the precursor ions studied, and provided fragmentation information spanning both the glycan and the peptide moieties. Taken together, these findings illustrate the influence of charge carrier over the energy-resolved vibrational activation/dissociation characteristics of glycopeptides, and serve to suggest potential strategies that exploit the analytically useful features uniquely afforded by specific charge carriers or combinations thereof.
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Affiliation(s)
- Forouzan Aboufazeli
- Department of Chemistry, University of Nebraska-Lincoln, 711 Hamilton Hall, Lincoln, NE, 68588-0304, USA
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207
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Yuan H, Wu Y, Liu W, Liu Y, Gao X, Lin J, Zhao Y. Mass spectrometry-based method to investigate the natural selectivity of sucrose as the sugar transport form for plants. Carbohydr Res 2015; 407:5-9. [DOI: 10.1016/j.carres.2015.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/28/2022]
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208
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Goyallon A, Cholet S, Chapelle M, Junot C, Fenaille F. Evaluation of a combined glycomics and glycoproteomics approach for studying the major glycoproteins present in biofluids: Application to cerebrospinal fluid. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:461-473. [PMID: 26160412 DOI: 10.1002/rcm.7125] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/08/2014] [Accepted: 12/14/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE Glycosylation is one of the most complex types of post-translational modifications of proteins. The alteration of glycans bound to proteins from cerebrospinal fluid (CSF) in relation to disorders of the central nervous system is a highly relevant subject, but only few studies have focused on the glycosylation of CSF proteins. METHODS Reproducible profiles of CSF N-glycans were first obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry after permethylation. Tryptic glycopeptides from CSF proteins were also enriched by hydrophilic interaction, and the resulting extracts divided into two equal aliquots. A first aliquot was enzymatically deglycosylated and analyzed by nano-liquid chromatography/tandem mass spectrometry while the second one, containing intact enriched glycopeptides, was directly analyzed. Site-specific data were obtained by combining the data from these three experiments. RESULTS We describe the development of a versatile approach for obtaining site-specific information on the N-glycosylation of CSF glycoproteins. Under these conditions, 124 N-glycopeptides representing 55 N-glycosites from 36 glycoproteins were tentatively identified. Special emphasis was placed on the analysis of glycoproteins/glycopeptides bearing 'brain-type' N-glycans, representing potential biologically relevant structures in the field of neurodegenerative disorders. Using our workflow, only a few proteins were shown to carry such particular glycan motifs. CONCLUSIONS We developed an approach combining N-glycomics and N-glycoproteomics and underline its usefulness to study the site-specific glycosylation of major human CSF proteins. The final rather long-term objective is to combine these data with those from other omics approaches to delve deeper into the understanding of particular neurological disorders.
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Affiliation(s)
- Arnaud Goyallon
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | - Sophie Cholet
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | | | - Christophe Junot
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | - François Fenaille
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
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209
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Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
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210
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Goldman R, Sanda M. Targeted methods for quantitative analysis of protein glycosylation. Proteomics Clin Appl 2015; 9:17-32. [PMID: 25522218 PMCID: PMC5780646 DOI: 10.1002/prca.201400152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/15/2014] [Accepted: 12/11/2014] [Indexed: 12/17/2022]
Abstract
Quantification of proteins by LC-MS/MS-MRM has become a standard method with broad projected clinical applicability. MRM quantification of protein modifications is, however, far less utilized, especially in the case of glycoproteins. This review summarizes current methods for quantitative analysis of protein glycosylation with a focus on MRM methods. We describe advantages of this quantitative approach, analytical parameters that need to be optimized to achieve reliable measurements, and point out the limitations. Differences between major classes of N- and O-glycopeptides are described and class-specific glycopeptide assays are demonstrated.
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Affiliation(s)
- Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
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211
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Lynn KS, Chen CC, Lih TM, Cheng CW, Su WC, Chang CH, Cheng CY, Hsu WL, Chen YJ, Sung TY. MAGIC: An Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 Approach. Anal Chem 2015; 87:2466-73. [DOI: 10.1021/ac5044829] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ke-Shiuan Lynn
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Chen-Chun Chen
- Genomics
Research Center, Academia Sinica, Taipei 11529, Taiwan
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - T. Mamie Lih
- Bioinformatics
Program, Taiwan International Graduate Program, Institute of Information
Science, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Cheng-Wei Cheng
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Wan-Chih Su
- Institute
of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Hao Chang
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Ying Cheng
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Lian Hsu
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
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212
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Zhang YW, Zhao MZ, Liu JX, Zhou YL, Zhang XX. Double-layer poly(vinyl alcohol)-coated capillary for highly sensitive and stable capillary electrophoresis and capillary electrophoresis with mass spectrometry glycan analysis. J Sep Sci 2015; 38:475-82. [DOI: 10.1002/jssc.201401025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/12/2014] [Accepted: 11/13/2014] [Indexed: 01/15/2023]
Affiliation(s)
- Yi-Wei Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS); MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering; College of Chemistry, Peking University; Beijing China
| | - Ming-Zhe Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS); MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering; College of Chemistry, Peking University; Beijing China
| | - Jing-Xin Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS); MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering; College of Chemistry, Peking University; Beijing China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS); MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering; College of Chemistry, Peking University; Beijing China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS); MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering; College of Chemistry, Peking University; Beijing China
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213
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Abstract
Glycans are chains of carbohydrates attached to proteins (glycoproteins and proteoglycans) or lipids (glycolipids). Glycosylation is a posttranslational modification and glycans have a wide range of functions in a human body including involvement in oncological diseases. Change in a glycan structure cannot only indicate presence of a pathological process, but more importantly in some cases also its stage. Thus, a glycan analysis has a potential to be an effective and reliable tool in cancer diagnostics. Lectins are proteins responsible for natural biorecognition of glycans, even carbohydrate moieties still attached to proteins or whole cells can be recognized by lectins, what makes them an ideal candidate for designing label-free biosensors for glycan analysis. In this review we would like to summarize evidence that glycoprofiling of biomarkers by lectin-based biosensors can be really helpful in detecting prostate cancer.
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Affiliation(s)
- Štefan Belický
- Department of Glycobiotechnology, Center for Glycomics, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, SK - 845 38, Slovakia
| | - Jan Tkac
- Department of Glycobiotechnology, Center for Glycomics, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, SK - 845 38, Slovakia
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214
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Pihíková D, Kasák P, Tkac J. Glycoprofiling of cancer biomarkers: Label-free electrochemical lectin-based biosensors. OPEN CHEM 2015; 13:636-655. [PMID: 27275016 PMCID: PMC4892350 DOI: 10.1515/chem-2015-0082] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Glycosylation of biomolecules is one of the most prevalent post- and co-translational modification in a human body, with more than half of all human proteins being glycosylated. Malignant transformation of cells influences glycosylation machinery resulting in subtle changes of the glycosylation pattern within the cell populations as a result of cancer. Thus, an altered terminal glycan motif on glycoproteins could provide a warning signal about disease development and progression and could be applied as a reliable biomarker in cancer diagnostics. Among all highly effective glycoprofiling tools, label-free electrochemical impedance spectroscopy (EIS)-based biosensors have emerged as especially suitable tool for point-of-care early-stage cancer detection. Herein, we highlight the current challenges in glycoprofiling of various cancer biomarkers by ultrasensitive impedimetric-based biosensors with low sample consumption, low cost fabrication and simple miniaturization. Additionally, this review provides a short introduction to the field of glycomics and lectinomics and gives a brief overview of glycan alterations in different types of cancer.
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Affiliation(s)
- Dominika Pihíková
- Department of Glycobiotechnology, Institute of Chemistry, Slovak
Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava,
Slovakia
| | - Peter Kasák
- Center for Advanced Materials, Qatar University, P.O.Box 2713 Doha,
Qatar
| | - Jan Tkac
- Department of Glycobiotechnology, Institute of Chemistry, Slovak
Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava,
Slovakia
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215
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Jia Y, Li J. Molecular assembly of Schiff Base interactions: construction and application. Chem Rev 2014; 115:1597-621. [PMID: 25543900 DOI: 10.1021/cr400559g] [Citation(s) in RCA: 294] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yi Jia
- Beijing National Laboratory for Molecular Sciences, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing, 100190, China
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216
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High-Throughput Analysis and Automation for Glycomics Studies. Chromatographia 2014; 78:321-333. [PMID: 25814696 PMCID: PMC4363487 DOI: 10.1007/s10337-014-2803-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/17/2014] [Accepted: 10/17/2014] [Indexed: 11/12/2022]
Abstract
This review covers advances in analytical technologies for high-throughput (HTP) glycomics. Our focus is on structural studies of glycoprotein glycosylation to support biopharmaceutical realization and the discovery of glycan biomarkers for human disease. For biopharmaceuticals, there is increasing use of glycomics in Quality by Design studies to help optimize glycan profiles of drugs with a view to improving their clinical performance. Glycomics is also used in comparability studies to ensure consistency of glycosylation both throughout product development and between biosimilars and innovator drugs. In clinical studies there is as well an expanding interest in the use of glycomics—for example in Genome Wide Association Studies—to follow changes in glycosylation patterns of biological tissues and fluids with the progress of certain diseases. These include cancers, neurodegenerative disorders and inflammatory conditions. Despite rising activity in this field, there are significant challenges in performing large scale glycomics studies. The requirement is accurate identification and quantitation of individual glycan structures. However, glycoconjugate samples are often very complex and heterogeneous and contain many diverse branched glycan structures. In this article we cover HTP sample preparation and derivatization methods, sample purification, robotization, optimized glycan profiling by UHPLC, MS and multiplexed CE, as well as hyphenated techniques and automated data analysis tools. Throughout, we summarize the advantages and challenges with each of these technologies. The issues considered include reliability of the methods for glycan identification and quantitation, sample throughput, labor intensity, and affordability for large sample numbers.
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217
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Trefulka M, Paleček E. Direct chemical modification and voltammetric detection of glycans in glycoproteins. Electrochem commun 2014. [DOI: 10.1016/j.elecom.2014.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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218
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Klukova L, Bertok T, Petrikova M, Sediva A, Mislovicova D, Katrlik J, Vikartovska A, Filip J, Kasak P, Andicsová-Eckstein A, Mosnáček J, Lukáč J, Rovenský J, Imrich R, Tkac J. Glycoprofiling as a novel tool in serological assays of systemic sclerosis: a comparative study with three bioanalytical methods. Anal Chim Acta 2014; 853:555-562. [PMID: 25467503 DOI: 10.1016/j.aca.2014.10.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/18/2014] [Accepted: 10/24/2014] [Indexed: 11/15/2022]
Abstract
Systemic sclerosis (SSc) is an autoimmune disease seriously affecting patient's quality of life. The heterogeneity of the disease also means that identification and subsequent validation of biomarkers of the disease is quite challenging. A fully validated single biomarker for diagnosis, prognosis, disease activity and assessment of response to therapy is not yet available. The main aim of this study was to apply an alternative assay protocol to the immunoassay-based analysis of this disease by employment of sialic acid recognizing lectin Sambucus nigra agglutinin (SNA) to glycoprofile serum samples. To our best knowledge this is the first study describing direct lectin-based glycoprofiling of serum SSc samples. Three different analytical methods for glycoprofiling of serum samples relying on application of lectins are compared here from a bioanalytical point of view including traditional ELISA-like lectin-based method (ELLA), novel fluorescent lectin microarrays and ultrasensitive impedimetric lectin biosensors. Results obtained by all three bioanalytical methods consistently showed differences in the level of sialic acid present on glycoproteins, when serum from healthy people was compared to the one from patients having SSc. Thus, analysis of sialic acid content in human serum could be of a diagnostic value for future detection of SSc, but further work is needed to enhance selectivity of assays for example by glycoprofiling of a fraction of human serum enriched in antibodies for individual diagnostics.
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Affiliation(s)
- Ludmila Klukova
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - Tomas Bertok
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - Miroslava Petrikova
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - Alena Sediva
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - Danica Mislovicova
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - Jaroslav Katrlik
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - Alica Vikartovska
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - Jaroslav Filip
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - Peter Kasak
- Center for Advanced Materials, Qatar University, P.O. Box 2713, Doha, Qatar; Department for Biomaterial Research, Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 41, Slovakia
| | - Anita Andicsová-Eckstein
- Department of Synthesis and Characterization of Polymers, Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 41, Slovakia
| | - Jaroslav Mosnáček
- Department of Synthesis and Characterization of Polymers, Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 41, Slovakia
| | - Jozef Lukáč
- National Institute of Rheumatic Diseases, Nábr. I. Krasku 4, Piešt'any 921 12, Slovakia
| | - Jozef Rovenský
- National Institute of Rheumatic Diseases, Nábr. I. Krasku 4, Piešt'any 921 12, Slovakia
| | - Richard Imrich
- Laboratory of Human Endocrinology, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Vlárska 3, Bratislava 833 06, Slovakia
| | - Jan Tkac
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia.
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219
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Zhang W, Liu W, Li P, Xiao H, Wang H, Tang B. A Fluorescence Nanosensor for Glycoproteins with Activity Based on the Molecularly Imprinted Spatial Structure of the Target and Boronate Affinity. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405634] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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220
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Zhang W, Liu W, Li P, Xiao H, Wang H, Tang B. A Fluorescence Nanosensor for Glycoproteins with Activity Based on the Molecularly Imprinted Spatial Structure of the Target and Boronate Affinity. Angew Chem Int Ed Engl 2014; 53:12489-93. [DOI: 10.1002/anie.201405634] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/09/2014] [Indexed: 11/09/2022]
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221
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Hushegyi A, Tkac J. Are glycan biosensors an alternative to glycan microarrays? ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2014; 6:6610-6620. [PMID: 27231487 PMCID: PMC4878710 DOI: 10.1039/c4ay00692e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Complex carbohydrates (glycans) play an important role in nature and study of their interaction with proteins or intact cells can be useful for understanding many physiological and pathological processes. Such interactions have been successfully interrogated in a highly parallel way using glycan microarrays, but this technique has some limitations. Thus, in recent years glycan biosensors in numerous progressive configurations have been developed offering distinct advantages compared to glycan microarrays. Thus, in this review advances achieved in the field of label-free glycan biosensors are discussed.
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Affiliation(s)
- A Hushegyi
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - J Tkac
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
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222
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Song E, Zhu R, Hammoud ZT, Mechref Y. LC-MS/MS quantitation of esophagus disease blood serum glycoproteins by enrichment with hydrazide chemistry and lectin affinity chromatography. J Proteome Res 2014; 13:4808-20. [PMID: 25134008 PMCID: PMC4227547 DOI: 10.1021/pr500570m] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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Changes
in glycosylation have been shown to have a profound correlation
with development/malignancy in many cancer types. Currently, two major
enrichment techniques have been widely applied in glycoproteomics,
namely, lectin affinity chromatography (LAC)-based and hydrazide chemistry
(HC)-based enrichments. Here we report the LC–MS/MS quantitative
analyses of human blood serum glycoproteins and glycopeptides associated
with esophageal diseases by LAC- and HC-based enrichment. The separate
and complementary qualitative and quantitative data analyses of protein
glycosylation were performed using both enrichment techniques. Chemometric
and statistical evaluations, PCA plots, or ANOVA test, respectively,
were employed to determine and confirm candidate cancer-associated
glycoprotein/glycopeptide biomarkers. Out of 139, 59 common glycoproteins
(42% overlap) were observed in both enrichment techniques. This overlap
is very similar to previously published studies. The quantitation
and evaluation of significantly changed glycoproteins/glycopeptides
are complementary between LAC and HC enrichments. LC–ESI–MS/MS
analyses indicated that 7 glycoproteins enriched by LAC and 11 glycoproteins
enriched by HC showed significantly different abundances between disease-free
and disease cohorts. Multiple reaction monitoring quantitation resulted
in 13 glycopeptides by LAC enrichment and 10 glycosylation sites by
HC enrichment to be statistically different among disease cohorts.
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Affiliation(s)
- Ehwang Song
- Department of Chemistry and Biochemistry, Texas Tech University , Memorial Circle & Boston, Lubbock, Texas 79409, United States
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223
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Zhang Y, Yu M, Zhang C, Ma W, Zhang Y, Wang C, Lu H. Highly Selective and Ultra Fast Solid-Phase Extraction of N-Glycoproteome by Oxime Click Chemistry Using Aminooxy-Functionalized Magnetic Nanoparticles. Anal Chem 2014; 86:7920-4. [DOI: 10.1021/ac5018666] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ying Zhang
- Shanghai Cancer Center and Key Laboratory of Glycoconjuates Research
Ministry of Public Health, Fudan University, Shanghai, 200032, People’s Republic of China
- Institutes
of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Meng Yu
- State Key Laboratory of Molecular Engineering of Polymers
and Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai, 200433, People’s Republic of China
| | - Cheng Zhang
- Institutes
of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Wanfu Ma
- State Key Laboratory of Molecular Engineering of Polymers
and Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai, 200433, People’s Republic of China
| | - Yuting Zhang
- State Key Laboratory of Molecular Engineering of Polymers
and Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai, 200433, People’s Republic of China
| | - Changchun Wang
- State Key Laboratory of Molecular Engineering of Polymers
and Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai, 200433, People’s Republic of China
| | - Haojie Lu
- Shanghai Cancer Center and Key Laboratory of Glycoconjuates Research
Ministry of Public Health, Fudan University, Shanghai, 200032, People’s Republic of China
- Institutes
of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200032, People’s Republic of China
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224
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Kluková L, Bertók T, Kasák P, Tkac J. Nanoscale controlled architecture for development of ultrasensitive lectin biosensors applicable in glycomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2014; 6:4922-4931. [PMID: 27231486 PMCID: PMC4878709 DOI: 10.1039/c4ay00495g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In this Minireview the most advanced patterning protocols and transducing schemes for development of ultrasensitive label-free and label-based lectin biosensors for glycoprofiling of disease markers and some cancerous cells are described. Performance of such lectin biosensors with interfacial properties tuned at a nanoscale are critically compared to the most sensitive immunoassay format of analysis and challenges ahead in the field are discussed. Moreover, key elements for future advances of such devices on the way to enhance robustness and practical applicability of lectin biosensors are revealed.
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Affiliation(s)
- L Kluková
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - T Bertók
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - P Kasák
- Center for Advanced Materials, Qatar University, P.O. Box 2713, Doha, Qatar; Department for Biomaterial Research, Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - J Tkac
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
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225
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Yang W, Shah P, Toghi Eshghi S, Yang S, Sun S, Ao M, Rubin A, Jackson JB, Zhang H. Glycoform analysis of recombinant and human immunodeficiency virus envelope protein gp120 via higher energy collisional dissociation and spectral-aligning strategy. Anal Chem 2014; 86:6959-67. [PMID: 24941220 PMCID: PMC4215848 DOI: 10.1021/ac500876p] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
Envelope
protein gp120 of human immunodeficiency virus (HIV) is
armored with a dense glycan shield, which plays critical roles in
envelope folding, immune-evasion, infectivity, and immunogenicity.
Site-specific glycosylation profiling of recombinant gp120 is very
challenging. Therefore, glycoproteomic analysis of native viral gp120
is still formidable to date. This challenge promoted us to employ
a Q-Exactive mass spectrometer to identify low abundant glycopeptides
from virion-associated gp120. To search the HCD-MS data for glycopeptides,
a novel spectral-aligning strategy was developed. This strategy depends
on the observation that glycopeptides and the corresponding deglycosylated
peptides share very similar MS/MS pattern in terms of b- and y-ions
that do not contain the site of glycosylation. Moreover, glycopeptides
with an identical peptide backbone show nearly resembling spectra
regardless of the attached glycan structures. For the recombinant
gp120, this “copy–paste” spectral pattern of
glycopeptides facilitated identification of 2224 spectra using only
18 spectral templates, and after precursor mass correction, 1268 (57%)
spectra were assigned to 460 unique glycopeptides accommodating 19
N-linked and one O-linked glycosylation sites (glycosites). Strikingly,
we were able to observe five N- and one O-linked glycosites in native
gp120. We further revealed that except for Asn276 in the C2 region,
glycans were processed to contain both high mannose and hybrid/complex
glycans; an additional four N-linked glycosites were decorated with
high mannose type. Core 1 O-linked glycan Gal1GalNAc1 was seen for the O-linked glycosite at Thr499. This direct
observation of site-specific glycosylation of virion-derived gp120
has implications in HIV glycobiology and vaccine design.
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Affiliation(s)
- Weiming Yang
- Department of Pathology, School of Medicine, Johns Hopkins University , 1550 Orleans Street , Baltimore, Maryland 21205, United States
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226
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Sang LJ, Wang HF. Aminophenylboronic-acid-conjugated polyacrylic acid-Mn-doped ZnS quantum dot for highly sensitive discrimination of glycoproteins. Anal Chem 2014; 86:5706-12. [PMID: 24854708 DOI: 10.1021/ac501020b] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Discrimination of glycoproteins with different glycans is a significant but difficult issue. We presented here a new strategy for strengthening the discrimination of glycoproteins by introducing a new signaling channel, fluorescence polarization (FP), into a "single probe with three signaling channels" sensor array. The single probe was aminophenylboronic-acid-conjugated poly(acrylic acid)-Mn-doped ZnS quantum dots, and the three signaling channels were FP, room temperature phosphorescence and light scattering. Ten glycoproteins, including ovalbumin, fibrinogen, transferrin, horseradish peroxidase, vascular endothelial growth factor, immunoglobulin G, avidin, hyaluronidase, cellulase R-10, and glucose oxidase, were involved for evaluating the discriminating capability. The introduction of the FP signaling channel improved the discriminating power of the sensor array, so that the 10 glycoproteins at 0.15 μM could be well discriminated both in PBS buffer and in the presence of human serum sample. The identification accuracy of the unknown samples was 96.25% (77 out of 80) at the 0.15 μM level and 97.50% (78 out of 80) at the 0.2 μM level. The integration of the signaling patterns with different responsive principles was demonstrated as the promising way to enhance the discrimination power of the single-probe-based sensor arrays.
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Affiliation(s)
- Li-Jia Sang
- State Key Laboratory of Medicinal Chemical Biology, and Research Center for Analytical Sciences, College of Chemistry, Nankai University , Tianjin 300071, China
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227
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Shang TQ, Saati A, Toler KN, Mo J, Li H, Matlosz T, Lin X, Schenk J, Ng CK, Duffy T, Porter TJ, Rouse JC. Development and application of a robust N-glycan profiling method for heightened characterization of monoclonal antibodies and related glycoproteins. J Pharm Sci 2014; 103:1967-1978. [PMID: 24840237 DOI: 10.1002/jps.24004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/07/2014] [Accepted: 04/17/2014] [Indexed: 01/22/2023]
Abstract
A highly robust hydrophilic interaction liquid chromatography (HILIC) method that involves both fluorescence and mass spectrometric detection was developed for profiling and characterizing enzymatically released and 2-aminobenzamide (2-AB)-derivatized mAb N-glycans. Online HILIC/mass spectrometry (MS) with a quadrupole time-of-flight mass spectrometer provides accurate mass identifications of the separated, 2-AB-labeled N-glycans. The method features a high-resolution, low-shedding HILIC column with acetonitrile and water-based mobile phases containing trifluoroacetic acid (TFA) as a modifier. This column and solvent system ensures the combination of robust chromatographic performance and full compatibility and sensitivity with online MS in addition to the baseline separation of all typical mAb N-glycans. The use of TFA provided distinct advantages over conventional ammonium formate as a mobile phase additive, such as, optimal elution order for sialylated N-glycans, reproducible chromatographic profiles, and matching total ion current chromatograms, as well as minimal signal splitting, analyte adduction, and fragmentation during HILIC/MS, maximizing sensitivity for trace-level species. The robustness and selectivity of HILIC for N-glycan analyses allowed for method qualification. The method is suitable for bioprocess development activities, heightened characterization, and clinical drug substance release. Application of this HILIC/MS method to the detailed characterization of a marketed therapeutic mAb, Rituxan(®), is described.
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Affiliation(s)
- Tanya Q Shang
- Analytical Research and Development, Biotherapeutics Pharmaceutical SciencesPfizer, Inc.AndoverMassachusetts 01810
| | - Andrew Saati
- Analytical Research and Development, Biotherapeutics Pharmaceutical SciencesPfizer, Inc.AndoverMassachusetts 01810
| | - Kelly N Toler
- Genzyme, A Sanofi Company, FraminghamMassachusetts01701
| | - Jianming Mo
- Analytical R&D, Pfizer, Inc.St. LouisMissouri63017
| | - Heyi Li
- Analytical R&D, Pfizer, Inc., Pearl RiverNew York10965
| | - Tonya Matlosz
- Analytical R&D, Pfizer, Inc., Pearl RiverNew York10965
| | - Xi Lin
- Analytical R&D, Pfizer, Inc., Pearl RiverNew York10965
| | - Jennifer Schenk
- Analytical Research and Development, Biotherapeutics Pharmaceutical SciencesPfizer, Inc.AndoverMassachusetts 01810
| | - Chee-Keng Ng
- Analytical Research and Development, Biotherapeutics Pharmaceutical SciencesPfizer, Inc.AndoverMassachusetts 01810
| | - Toni Duffy
- Analytical Research and Development, Biotherapeutics Pharmaceutical SciencesPfizer, Inc.AndoverMassachusetts 01810
| | - Thomas J Porter
- Analytical Research and Development, Biotherapeutics Pharmaceutical SciencesPfizer, Inc.AndoverMassachusetts 01810
| | - Jason C Rouse
- Analytical Research and Development, Biotherapeutics Pharmaceutical SciencesPfizer, Inc.AndoverMassachusetts 01810.
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228
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Nishikaze T, Kawabata SI, Tanaka K. In-Depth Structural Characterization of N-Linked Glycopeptides Using Complete Derivatization for Carboxyl Groups Followed by Positive- and Negative-Ion Tandem Mass Spectrometry. Anal Chem 2014; 86:5360-9. [DOI: 10.1021/ac500340t] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Takashi Nishikaze
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho,
Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shin-ichirou Kawabata
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho,
Nakagyo-ku, Kyoto 604-8511, Japan
| | - Koichi Tanaka
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho,
Nakagyo-ku, Kyoto 604-8511, Japan
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229
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Thaysen-Andersen M, Packer NH. Advances in LC-MS/MS-based glycoproteomics: getting closer to system-wide site-specific mapping of the N- and O-glycoproteome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1437-52. [PMID: 24830338 DOI: 10.1016/j.bbapap.2014.05.002] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 04/23/2014] [Accepted: 05/05/2014] [Indexed: 12/22/2022]
Abstract
Site-specific structural characterization of glycoproteins is important for understanding the exact functional relevance of protein glycosylation. Resulting partly from the multiple layers of structural complexity of the attached glycans, the system-wide site-specific characterization of protein glycosylation, defined as glycoproteomics, is still far from trivial leaving the N- and O-linked glycoproteomes significantly under-defined. However, recent years have seen significant advances in glycoproteomics driven, in part, by the developments of dedicated workflows and efficient sample preparation, including glycopeptide enrichment and prefractionation. In addition, glycoproteomics has benefitted from the continuous performance enhancement and more intelligent use of liquid chromatography and tandem mass spectrometry (LC-MS/MS) instrumentation and a wider selection of specialized software tackling the unique challenges of glycoproteomics data. Together these advances promise more streamlined N- and O-linked glycoproteome analysis. Tangible examples include system-wide glycoproteomics studies detecting thousands of intact glycopeptides from hundreds of glycoproteins from diverse biological samples. With a strict focus on the system-wide site-specific analysis of protein N- and O-linked glycosylation, we review the recent advances in LC-MS/MS based glycoproteomics. The review opens with a more general discussion of experimental designs in glycoproteomics and sample preparation prior to LC-MS/MS based data acquisition. Although many challenges still remain, it becomes clear that glycoproteomics, one of the last frontiers in proteomics, is gradually maturing enabling a wider spectrum of researchers to access this new emerging research discipline. The next milestone in analytical glycobiology is being reached allowing the glycoscientist to address the functional importance of protein glycosylation in a system-wide yet protein-specific manner.
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Affiliation(s)
- Morten Thaysen-Andersen
- Biomolecular Frontiers Research Centre, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.
| | - Nicolle H Packer
- Biomolecular Frontiers Research Centre, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
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230
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Liu H, Zhang N, Wan D, Cui M, Liu Z, Liu S. Mass spectrometry-based analysis of glycoproteins and its clinical applications in cancer biomarker discovery. Clin Proteomics 2014; 11:14. [PMID: 24722010 PMCID: PMC3984494 DOI: 10.1186/1559-0275-11-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/19/2014] [Indexed: 02/08/2023] Open
Abstract
Glycosylation is one of the most important posttranslational modifications of proteins and plays essential roles in various biological processes. Aberration in the glycan moieties of glycoproteins is associated with many diseases. It is especially critical to develop the rapid and sensitive methods for analysis of aberrant glycoproteins associated with diseases. Mass spectrometry (MS) has become a powerful tool for glycoprotein analysis. Especially, tandem mass spectrometry can provide highly informative fragments for structural identification of glycoproteins. This review provides an overview of the development of MS technologies and their applications in identification of abnormal glycoproteins and glycans in human serum to screen cancer biomarkers in recent years.
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Affiliation(s)
| | | | | | - Meng Cui
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P, R, China.
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231
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Chen W, Smeekens JM, Wu R. A universal chemical enrichment method for mapping the yeast N-glycoproteome by mass spectrometry (MS). Mol Cell Proteomics 2014; 13:1563-72. [PMID: 24692641 DOI: 10.1074/mcp.m113.036251] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycosylation is one of the most common and important protein modifications in biological systems. Many glycoproteins naturally occur at low abundances, which makes comprehensive analysis extremely difficult. Additionally, glycans are highly heterogeneous, which further complicates analysis in complex samples. Lectin enrichment has been commonly used, but each lectin is inherently specific to one or several carbohydrates, and thus no single or collection of lectin(s) can bind to all glycans. Here we have employed a boronic acid-based chemical method to universally enrich glycopeptides. The reaction between boronic acids and sugars has been extensively investigated, and it is well known that the interaction between boronic acid and diols is one of the strongest reversible covalent bond interactions in an aqueous environment. This strong covalent interaction provides a great opportunity to catch glycopeptides and glycoproteins by boronic acid, whereas the reversible property allows their release without side effects. More importantly, the boronic acid-diol recognition is universal, which provides great capability and potential for comprehensively mapping glycosylation sites in complex biological samples. By combining boronic acid enrichment with PNGase F treatment in heavy-oxygen water and MS, we have identified 816 N-glycosylation sites in 332 yeast proteins, among which 675 sites were well-localized with greater than 99% confidence. The results demonstrated that the boronic acid-based chemical method can effectively enrich glycopeptides for comprehensive analysis of protein glycosylation. A general trend seen within the large data set was that there were fewer glycosylation sites toward the C termini of proteins. Of the 332 glycoproteins identified in yeast, 194 were membrane proteins. Many proteins get glycosylated in the high-mannose N-glycan biosynthetic and GPI anchor biosynthetic pathways. Compared with lectin enrichment, the current method is more cost-efficient, generic, and effective. This method can be extensively applied to different complex samples for the comprehensive analysis of protein glycosylation.
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Affiliation(s)
- Weixuan Chen
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Johanna M Smeekens
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- From the ‡School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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232
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Simone G. Micro analysis to map the glycome code. Proteomics 2014; 14:994-1000. [DOI: 10.1002/pmic.201300324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Giuseppina Simone
- Center for Advanced Biomaterials for Health Care Italian Institute of Technology @ CRIB; Largo Barsanti e Matteucci; Italy
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233
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Recent methodological advances in MALDI mass spectrometry. Anal Bioanal Chem 2014; 406:2261-78. [PMID: 24652146 DOI: 10.1007/s00216-014-7646-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/17/2014] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is widely used for characterization of large, thermally labile biomolecules. Advantages of this analytical technique are high sensitivity, robustness, high-throughput capacity, and applicability to a wide range of compound classes. For some years, MALDI-MS has also been increasingly used for mass spectrometric imaging as well as in other areas of clinical research. Recently, several new concepts have been presented that have the potential to further advance the performance characteristics of MALDI. Among these innovations are novel matrices with low proton affinities for particularly efficient protonation of analyte molecules, use of wavelength-tunable lasers to achieve optimum excitation conditions, and use of liquid matrices for improved quantification. Instrumental modifications have also made possible MALDI-MS imaging with cellular resolution as well as an efficient generation of multiply charged MALDI ions by use of heated vacuum interfaces. This article reviews these recent innovations and gives the author's personal outlook of possible future developments.
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234
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Hoffmann W, Hofmann J, Pagel K. Energy-resolved ion mobility-mass spectrometry--a concept to improve the separation of isomeric carbohydrates. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:471-479. [PMID: 24385395 DOI: 10.1007/s13361-013-0780-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 11/01/2013] [Accepted: 11/04/2013] [Indexed: 06/03/2023]
Abstract
Recent works using ion mobility-mass spectrometry (IM-MS) have highlighted the power of this instrumental configuration to tackle one of the greatest challenges in glycomics and glycoproteomics: the existence of isobaric isomers. For a successful separation of species with identical mass but different structure via IM-MS, it is crucial to have sufficient IM resolution. In commercially available IM-MS instruments, however, this resolution is limited by the design of the instrument and usually cannot be increased at-will without extensive modifications. Here, we present a systematic approach to improve the resolving capability of IM-MS instruments using so-called energy-resolved ion mobility-mass spectrometry. The technique utilizes the fact that individual components in an isobaric mixture fragment at considerably different energies when activated in the gas phase via collision-induced dissociation (CID). As a result, certain components can be suppressed selectively at increased CID activation energy. Using a mixture of four isobaric carbohydrates, we show that each of the individual sugars can be resolved and unambiguously identified even when their drift times differ by as little as 3%. However, the presented results also indicate that a certain difference in the gas-phase stability of the individual components is crucial for a successful separation via energy-resolved IM-MS.
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Affiliation(s)
- Waldemar Hoffmann
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
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235
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Sandra K, Vandenheede I, Sandra P. Modern chromatographic and mass spectrometric techniques for protein biopharmaceutical characterization. J Chromatogr A 2014; 1335:81-103. [DOI: 10.1016/j.chroma.2013.11.057] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 10/25/2022]
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236
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Chen W, Smeekens JM, Wu R. Comprehensive Analysis of Protein N-Glycosylation Sites by Combining Chemical Deglycosylation with LC–MS. J Proteome Res 2014; 13:1466-73. [DOI: 10.1021/pr401000c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Weixuan Chen
- School
of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Johanna M. Smeekens
- School
of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School
of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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237
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Hudak JE, Bertozzi CR. Glycotherapy: new advances inspire a reemergence of glycans in medicine. CHEMISTRY & BIOLOGY 2014; 21:16-37. [PMID: 24269151 PMCID: PMC4111574 DOI: 10.1016/j.chembiol.2013.09.010] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 09/16/2013] [Accepted: 09/30/2013] [Indexed: 12/21/2022]
Abstract
The beginning of the 20(th) century marked the dawn of modern medicine with glycan-based therapies at the forefront. However, glycans quickly became overshadowed as DNA- and protein-focused treatments became readily accessible. The recent development of new tools and techniques to study and produce structurally defined carbohydrates has spurred renewed interest in the therapeutic applications of glycans. This review focuses on advances within the past decade that are bringing glycan-based treatments back to the forefront of medicine and the technologies that are driving these efforts. These include the use of glycans themselves as therapeutic molecules as well as engineering protein and cell surface glycans to suit clinical applications. Glycan therapeutics offer a rich and promising frontier for developments in the academic, biopharmaceutical, and medical fields.
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Affiliation(s)
- Jason E Hudak
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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238
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Kolli V, Dodds ED. Energy-resolved collision-induced dissociation pathways of model N-linked glycopeptides: implications for capturing glycan connectivity and peptide sequence in a single experiment. Analyst 2014; 139:2144-53. [DOI: 10.1039/c3an02342g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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239
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Arriens C, Mohan C. Systemic lupus erythematosus diagnostics in the 'omics' era. ACTA ACUST UNITED AC 2013; 8:671-687. [PMID: 24860621 DOI: 10.2217/ijr.13.59] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Systemic lupus erythematosus is a complex autoimmune disease affecting multiple organ systems. Currently, diagnosis relies upon meeting at least four out of eleven criteria outlined by the ACR. The scientific community actively pursues discovery of novel diagnostics in the hope of better identifying susceptible individuals in early stages of disease. Comprehensive studies have been conducted at multiple biological levels including: DNA (or genomics), mRNA (or transcriptomics), protein (or proteomics) and metabolites (or metabolomics). The 'omics' platforms allow us to re-examine systemic lupus erythematosus at a greater degree of molecular resolution. More importantly, one is hopeful that these 'omics' platforms may yield newer biomarkers for systemic lupus erythematosus that can help clinicians track the disease course with greater sensitivity and specificity.
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Affiliation(s)
- Cristina Arriens
- Rheumatic Diseases Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-8884, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Blvd, Room 2018, Houston, TX 77204, USA
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240
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Alley WR, Mann BF, Hruska V, Novotny MV. Isolation and purification of glycoconjugates from complex biological sources by recycling high-performance liquid chromatography. Anal Chem 2013; 85:10408-16. [PMID: 24070405 DOI: 10.1021/ac4023814] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Among of the most urgent needs of the glycobiology community is to generate libraries of pure carbohydrate standards. While many oligosaccharides have recently been synthesized, some glycans of biomedical importance are still missing in existing collections or are available in only limited amounts. To address this need, we demonstrate the use of the relatively unexplored technique of recycling high-performance liquid chromatography (R-HPLC) to isolate and purify glycoconjugates from several natural sources. We were able to routinely achieve purities greater than 98%. In several cases, we were able to obtain isomerically pure substances, particularly for glycans with different positional isomerism. These purified substances can then be used in different analytical applications, for example, as standards for mass spectrometry (MS) and capillary-based separations. Moreover, using a bifunctional aromatic amine, the same derivatization agent can be used to enable UV detection of oligosaccharides during their purification and link the isolated molecules to functionalized surfaces and potentially create glycan arrays.
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Affiliation(s)
- William R Alley
- Department of Chemistry Indiana University Bloomington, Indiana 47405, United States
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241
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Novotny MV, Alley WR. Recent trends in analytical and structural glycobiology. Curr Opin Chem Biol 2013; 17:832-40. [PMID: 23790311 DOI: 10.1016/j.cbpa.2013.05.029] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/24/2013] [Indexed: 12/22/2022]
Abstract
The great complexity of glycosylated biomolecules necessitates a set of powerful analytical methodologies to reveal functionally important structural features. Mass spectrometry (MS), with its different ionization techniques, mass analyzers, and detection strategies, has become the most important analytical method in glycomic and glycoproteomic investigations. In combination with MS, microscale separations (based on capillary chromatography and electrophoresis) and carbohydrate microchemistry, we feature here conceptually important applications of the recent years. This review focuses on methodological advances pertaining to disease biomarker research, immunology, developmental biology, and measurements of importance to biopharmaceuticals. High-sensitivity determinations and sample enrichment/preconcentration are particularly emphasized in glycomic and glycoproteomic profiling.
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Affiliation(s)
- Milos V Novotny
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States.
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