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Glycomics-Assisted Glycoproteomics Enables Deep and Unbiased N-Glycoproteome Profiling of Complex Biological Specimens

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Serum/Plasma Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2628))

Abstract

Mass spectrometry-driven glycomics and glycoproteomics, the system-wide profiling of detached glycans and intact glycopeptides from biological samples, respectively, are powerful approaches to interrogate the heterogenous glycoproteome. Efforts to develop integrated workflows employing both glycomics and glycoproteomics have been invested since the concerted application of these complementary approaches enables a deeper exploration of the glycoproteome. This protocol paper outlines, step-by-step, an integrated -omics technology, the “glycomics-assisted glycoproteomics” method, that first establishes the N-glycan fine structures and their quantitative distribution pattern of protein extracts via porous graphitized carbon-LC-MS/MS. The N-glycome information is then used to augment and guide the challenging reversed-phase LC-MS/MS-based profiling of intact N-glycopeptides from the same protein samples. Experimental details and considerations relating to the sample preparation and the N-glycomics and N-glycoproteomics data collection, analysis, and integration are discussed. Benefits of the glycomics-assisted glycoproteomics method, which can be readily applied to both simple and complex biological specimens such as protein extracts from cells, tissues, and bodily fluids (e.g., serum), include quantitative information of the protein carriers and site(s) of glycosylation, site occupancy, and the site-specific glycan structures directly from biological samples. The glycomics-assisted glycoproteomics method therefore facilitates a comprehensive view of the complexity and dynamics of the heterogenous glycoproteome.

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Acknowledgments

Prof. Giuseppe Palmisano is thanked for intellectual contributions to the protocol. T.H.C. was supported by an International Macquarie Research Excellence Scholarship (20224231). A.C. was supported by an Australian Government Research Training Program Scholarship. J.U. was supported by a Macquarie University Research Excellence Scholarship. B.L.P. was supported by a University of Melbourne Driving Research Momentum Fellowship. R.K. was supported by a Cancer Institute of New South Wales Fellowship (ECF181259). M.T.-A. was supported by an Australian Research Council Future Fellowship (FT210100455) and a Macquarie University Enterprise Partnership Scheme (175232162).

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Authors and Affiliations

  1. School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia

    The Huong Chau, Anastasia Chernykh, Julian Ugonotti, Rebeca Kawahara & Morten Thaysen-Andersen

  2. Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia

    The Huong Chau, Anastasia Chernykh, Julian Ugonotti, Rebeca Kawahara & Morten Thaysen-Andersen

  3. Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia

    Benjamin L. Parker

  4. Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan

    Morten Thaysen-Andersen

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Correspondence to Morten Thaysen-Andersen .

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  1. Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia

    David W. Greening

  2. Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, Melbourne, VIC, Australia

    Richard J. Simpson

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Chau, T.H., Chernykh, A., Ugonotti, J., Parker, B.L., Kawahara, R., Thaysen-Andersen, M. (2023). Glycomics-Assisted Glycoproteomics Enables Deep and Unbiased N-Glycoproteome Profiling of Complex Biological Specimens. In: Greening, D.W., Simpson, R.J. (eds) Serum/Plasma Proteomics. Methods in Molecular Biology, vol 2628. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2978-9_16

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  • DOI: https://doi.org/10.1007/978-1-0716-2978-9_16

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