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Yang S, Onigman P, Wu WW, Sjogren J, Nyhlen H, Shen RF, Cipollo J. Deciphering Protein O-Glycosylation: Solid-Phase Chemoenzymatic Cleavage and Enrichment. Anal Chem 2018; 90:8261-8269. [DOI: 10.1021/acs.analchem.8b01834] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Shuang Yang
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Philip Onigman
- Genovis Inc., Cambridge, Massachusetts 02142, United States
| | - Wells W. Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | | | | | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - John Cipollo
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
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2
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You X, Qin H, Ye M. Recent advances in methods for the analysis of protein o-glycosylation at proteome level. J Sep Sci 2017; 41:248-261. [PMID: 28988430 DOI: 10.1002/jssc.201700834] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 12/12/2022]
Abstract
O-Glycosylation, which refers to the glycosylation of the hydroxyl group of side chains of Serine/Threonine/Tyrosine residues, is one of the most common post-translational modifications. Compared with N-linked glycosylation, O-glycosylation is less explored because of its complex structure and relatively low abundance. Recently, O-glycosylation has drawn more and more attention for its various functions in many sophisticated biological processes. To obtain a deep understanding of O-glycosylation, many efforts have been devoted to develop effective strategies to analyze the two most abundant types of O-glycosylation, i.e. O-N-acetylgalactosamine and O-N-acetylglucosamine glycosylation. In this review, we summarize the proteomics workflows to analyze these two types of O-glycosylation. For the large-scale analysis of mucin-type glycosylation, the glycan simplification strategies including the ''SimpleCell'' technology were introduced. A variety of enrichment methods including lectin affinity chromatography, hydrophilic interaction chromatography, hydrazide chemistry, and chemoenzymatic method were introduced for the proteomics analysis of O-N-acetylgalactosamine and O-N-acetylglucosamine glycosylation.
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Affiliation(s)
- Xin You
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
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3
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Skeene K, Walker M, Clarke G, Bergström E, Genever P, Ungar D, Thomas-Oates J. One Filter, One Sample, and the N- and O-Glyco(proteo)me: Toward a System to Study Disorders of Protein Glycosylation. Anal Chem 2017; 89:5840-5849. [DOI: 10.1021/acs.analchem.7b00143] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | | | - Graham Clarke
- Bristol-Myers Squibb, Reeds Lane, Moreton, Wirral, CH46 1QW, United Kingdom
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4
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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5
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Turyan I, Hronowski X, Sosic Z, Lyubarskaya Y. Comparison of two approaches for quantitative O-linked glycan analysis used in characterization of recombinant proteins. Anal Biochem 2014; 446:28-36. [DOI: 10.1016/j.ab.2013.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 11/30/2022]
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6
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Alley WR, Mann BF, Novotny MV. High-sensitivity analytical approaches for the structural characterization of glycoproteins. Chem Rev 2013; 113:2668-732. [PMID: 23531120 PMCID: PMC3992972 DOI: 10.1021/cr3003714] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- William R. Alley
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
| | - Benjamin F. Mann
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
- Indiana University School of Medicine, Indiana University, Indianapolis, Indiana, United States
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7
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Alley WR, Novotny MV. Structural glycomic analyses at high sensitivity: a decade of progress. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:237-65. [PMID: 23560930 PMCID: PMC3992932 DOI: 10.1146/annurev-anchem-062012-092609] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The field of glycomics has recently advanced in response to the urgent need for structural characterization and quantification of complex carbohydrates in biologically and medically important applications. The recent success of analytical glycobiology at high sensitivity reflects numerous advances in biomolecular mass spectrometry and its instrumentation, capillary and microchip separation techniques, and microchemical manipulations of carbohydrate reactivity. The multimethodological approach appears to be necessary to gain an in-depth understanding of very complex glycomes in different biological systems.
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Affiliation(s)
- William R. Alley
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
- Department of Medicine, Indiana University, Indianapolis, Indiana 46202
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8
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Maniatis S, Zhou H, Reinhold V. Rapid de-O-glycosylation concomitant with peptide labeling using microwave radiation and an alkyl amine base. Anal Chem 2010; 82:2421-5. [PMID: 20178317 DOI: 10.1021/ac902734w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Procedures are detailed for a quantitative release of O-linked glycans from peptides that now provide a shorter reaction time, a possible identification of O-linked sites, and a quantification of all reaction products. The release was initiated by a mild base, dimethylamine, and accelerated by microwave radiation. Differential analysis using standard glycoproteins has shown improved release efficiency concurrent with facile incorporation of dimethylamine into the former O-linked sites. In situ glycan reduction insures protection against peeling and is synchronous with subsequent studies by high performance MS(n) sequencing. The protocols were established with a synthetic O-GlcNAc peptide that would mimic the linkage chemistry and applied to a well characterized glycoprotein bovine fetuin with both N- and O-linked glycans and a highly glycosylated swine mucin.
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Affiliation(s)
- Stephanie Maniatis
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, USA
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Abstract
The O-glycosylation of Ser and Thr by N-acetylgalactosamine-linked (mucin-type) oligosaccharides is often overlooked in protein analysis. Three characteristics make O-linked glycosylation more difficult to analyse than N-linked glycosylation, namely: (a) no amino acid consensus sequence is known; (b) there is no universal enzyme for the release of O-glycans from the protein backbone; and (c) the density and number of occupied sites may be very high. For significant biological conclusions to be drawn, the complete picture of O-linked glycosylation on a protein needs to be determined. This review specifically addresses the analytical approaches that have been used, and the challenges remaining, in the characterization of both the composition and structure of mucin-type O-glycans, and the determination of the occupancy and heterogeneity at each amino acid attachment site.
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Affiliation(s)
- Pia H Jensen
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia
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10
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Zheng Y, Li H, Guo Z, Lin JM, Cai Z. Chip-based CE coupled to a quadrupole TOF mass spectrometer for the analysis of a glycopeptide. Electrophoresis 2007; 28:1305-11. [PMID: 17377943 DOI: 10.1002/elps.200600527] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A novel approach using sheath flow chip-based CE coupled to a quadrupole TOF mass spectrometer was developed and applied to the analysis of an O-glycopeptide. The method provided good separation and sensitive analysis of the glycopeptide and its beta-elimination product. The beta-elimination reaction of the glycopeptide with ammonia or dimethylamine was adapted for changing the glycopeptide into deglycosylated form and for specifying the site of glycosylation. MS/MS analysis of the native peptide, glycopeptide and beta-elimination product enabled the identification of the glycosylation site through the comparison of the fragmentations and peptide sequence analysis.
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Affiliation(s)
- Yufang Zheng
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China
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12
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Targeted glycoproteomics: serial lectin affinity chromatography in the selection of O-glycosylation sites on proteins from the human blood proteome. J Chromatogr A 2006; 1132:165-73. [PMID: 16919642 DOI: 10.1016/j.chroma.2006.07.070] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Revised: 04/17/2006] [Accepted: 07/28/2006] [Indexed: 10/24/2022]
Abstract
Although lectin selection is gaining increasing acceptance as a tool for targeting glycosylation in glycoproteomics, most of the work has been directed at N-glycosylation. The work reported here focuses on the use of lectins in the study of O-glycosylation. The problem with using lectins for studying O-glycosylation is that they are not sufficiently specific. This paper reports that through the use of serial lectin affinity chromatography (SLAC) it is possible to select predominantly O-glycosylated peptides from tryptic digests of human serum. Jacalin is relatively specific for O-glycosylation but has the problem that it also selects high mannose N-type glycans. This problem was addressed by using a concanavalin A affinity column to first remove high mannose, hybrid-type and biantennary complex-type N-type glycans before application of the Jacalin columns. When used in a serial format, concanavalin A and Jacalin together provide essentially O-glycosylated peptides. The glycoprotein parents of glycopeptides were identified by deglycosylating the selected O-glycopeptides by oxidative elimination. These peptides were then separated by RPC and further analyzed using ESI-MS/MS and MALDI-MS/MS. Using this approach all the O-glycosylated sites in a model protein (fetuin) and over thirty glycoprotein parents from human serum were identified. It is concluded that a serial combination of Con A and Jacalin can be of utility in the study of O-glycosylation in glycoproteomics.
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13
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Taylor AM, Holst O, Thomas-Oates J. Mass spectrometric profiling ofO-linked glycans released directly from glycoproteins in gels using in-gel reductive β-elimination. Proteomics 2006; 6:2936-46. [PMID: 16586430 DOI: 10.1002/pmic.200500331] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Glycosylation is a widespread PTM of proteins; the carbohydrate moieties provide various functional, immunological and structural aspects of both eukaryotic and prokaryotic glycoproteins. Traditional strategies used to analyse glycoprotein O-glycans involve glycoprotein isolation, followed by glycan release using solution-phase base-catalysed beta-elimination. However, in a proteomics context, mixtures of proteins and glycoproteins are routinely separated using SDS-PAGE. We have therefore developed a method to enable the profiling of O-linked glycans directly from glycoproteins on gels. This is achieved using in-gel reductive beta-elimination followed by mass spectrometric analysis of the released glycans. Here we describe our demonstration of the feasibility of this approach, our development and optimisation of the procedure using bovine submaxillary gland glycoproteins as a standard, and then show its usefulness by applying the developed procedure to the analysis of the O-glycans from a glycoprotein band from a Coomassie-stained SDS-PAGE separation of a mixture of Mycobacterium avium capsular proteins and glycoproteins. The procedure has been shown to be applicable to both CBB- and silver-stained gels. The method offers a quick and easy way to identify the O-glycans from gel-separated glycoproteins within gel-based proteomics workflows.
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Affiliation(s)
- Adrian M Taylor
- Department of Chemistry, University of York, Heslington, York, UK
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14
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Czeszak X, Morelle W, Ricart G, Tétaert D, Lemoine J. Localization of the O-Glycosylated Sites in Peptides by Fixed-Charge Derivatization with a Phosphonium Group. Anal Chem 2004; 76:4320-4. [PMID: 15283567 DOI: 10.1021/ac049767q] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present study demonstrates that matrix-assisted laser desorption ionization/postsource decay (MALDI/PSD) analysis of the molecular cation of glycopeptides derivatized at their amino terminus with a phosphonium group cleaves peptide backbone without removing the glycan. The predictable a-type fragment ions retain the glycan moiety, enabling unambiguous localization of O-glycans on the peptide chain. In contrast, collision-activated dissociation tandem mass spectrometry analysis carried out on the doubly charged protonated phosphonium cation results in the predominant loss of the sugar moiety from the peptide. This result supports the previously proposed charge-induced fragmentation mechanism of the sugar-peptide bond. MALDI/PSD analysis of glycopeptides converted to their acetyl phosphonium derivatives is an effective alternative to electron capture dissociation, as illustrated by the positioning of up to three GalNac residues along the full tandem repeat peptide sequence derived from the MUC 5AC mucin.
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Affiliation(s)
- Xavier Czeszak
- UMR 8576 CNRS, Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France
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15
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Czeszak X, Ricart G, Tetaert D, Michalski JC, Lemoine J. Identification of substituted sites on MUC5AC mucin motif peptides after enzymatic O-glycosylation combining beta-elimination and fixed-charge derivatization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2002; 16:27-34. [PMID: 11754244 DOI: 10.1002/rcm.532] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A strategy for determination of O-glycosylation site(s) in glycopeptides has been developed using model compounds obtained by enzymatic glycosylation (by human GaNTase-T2 isoform) on peptides derived from the human MUC5AC mucin tandem repeat motif. The beta-elimination-addition reaction (using dimethylamine and concomitantly ethanethiol) on the formerly glycosylated sites through a Michael-type condensation produced efficient deglycosylation with appropriate chemical modification. After N-terminal derivatization by a phosphonium group, peptide sequencing was then carried out by nanospray tandem mass spectrometry experiments. The highly predictable fragmentation pathways of these fixed-charge phosphonium derivatives enable straightforward recognition of glycosylation site(s) based on the mass increment of +44 Da for originally glycosylated threonine compared to the mass of fragments containing nonglycosylated residues.
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Affiliation(s)
- X Czeszak
- Laboratoire de Chimie Biologique, UMR 8576 CNRS, Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cédex, France
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16
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Sequence analysis of peptides with biological activities using electrospray-Fourier trans form ion cyclotron resonance mass spectrometry. CHINESE SCIENCE BULLETIN-CHINESE 2001. [DOI: 10.1007/bf03184325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Mirgorodskaya E, Hassan H, Clausen H, Roepstorff P. Mass spectrometric determination of O-glycosylation sites using beta-elimination and partial acid hydrolysis. Anal Chem 2001; 73:1263-9. [PMID: 11305661 DOI: 10.1021/ac001288d] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The present study demonstrates that treating O-glycosylated peptides with methylamine vapor followed by partial acid hydrolysis is an effective means for locating O-glycosylation site(s). The reaction with methylamine transforms the glycosylated Ser and Thr residues into stable methylamine derivatives with a mass increment of +13 Da relative to nonglycosylated Ser and Thr residues. Peptide sequencing based on partial acid hydrolysis followed by mass spectrometric analysis or in favorable cases by CID-MS/MS enables the determination of the formerly O-glycosylated sites.
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Affiliation(s)
- E Mirgorodskaya
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense University
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Mirgorodskaya E, Hassan H, Wandall HH, Clausen H, Roepstorff P. Partial vapor-phase hydrolysis of peptide bonds: A method for mass spectrometric determination of O-glycosylated sites in glycopeptides. Anal Biochem 1999; 269:54-65. [PMID: 10094775 DOI: 10.1006/abio.1998.3089] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study we present a method for determination of O-glycosylation sites in glycopeptides, based on partial vapor-phase acid hydrolysis in combination with mass spectrometric analysis. Pentafluoropropionic acid and hydrochloric acid were used for the hydrolysis of glycosylated peptides. The reaction conditions were optimized for efficient polypeptide backbone cleavages with minimal cleavage of glycosidic bonds. The glycosylated residues were identified by mass spectrometric analysis of the hydrolytic cleavage products. Although glycosidic bonds are partially cleaved under acid hydrolysis, the resulting mass spectra allowed unambiguous determination of the glycosylation sites. Examples are shown with mannosyl- and mucin-type glycopeptides. Performing the hydrolysis in vapor eliminates the risk for contamination of the sample with impurities from the reagents, thus allowing analysis of the reaction products without further purification both by matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry.
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Affiliation(s)
- E Mirgorodskaya
- Department of Molecular Biology, Odense University, Odense M, DK-5230, Denmark
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Rademaker GJ, Pergantis SA, Blok-Tip L, Langridge JI, Kleen A, Thomas-Oates JE. Mass spectrometric determination of the sites of O-glycan attachment with low picomolar sensitivity. Anal Biochem 1998; 257:149-60. [PMID: 9514784 DOI: 10.1006/abio.1997.2548] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A sensitive protocol for unambiguously and positively identifying O-glycosylation sites in glycopeptides is described, based on beta-elimination of the glycan chain(s) using NH4OH. On glycan elimination, NH3 is incorporated into the amino acid residue(s) to which the glycan(s) had been attached, to yield a modified amino acid residue having a distinct mass. Electrospray ionization collision-induced dissociation tandem mass spectrometry allows the released, modified peptide to be sequenced and the site(s) of the modified amino acid residue(s) to be identified. The protocol has been optimized using a series of structurally related O-glycopeptides, and standard conditions are recommended for handling unknowns. We demonstrate that site determination can be achieved using as little as 1 pmol of starting material.
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Affiliation(s)
- G J Rademaker
- Department of Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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