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GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination

Gotz, Lou ; Abrahams, Jodie L. ; Mariethoz, Julien ; Rudd, Pauline M. ; Karlsson, Niclas G. ; Packer, Nicolle H. ; Campbell, Matthew P. ; Lisacek, Frederique

In: Bioinformatics, 2014, vol. 30, no. 21, p. 3131-3133

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    Titre
    • GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination
    Auteur
    • Gotz, Lou. Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
    • Abrahams, Jodie L.. Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
    • Mariethoz, Julien. Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
    • Rudd, Pauline M.. Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
    • Karlsson, Niclas G.. Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
    • Packer, Nicolle H.. Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
    • Campbell, Matthew P.. Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
    • Lisacek, Frederique. Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
    Type de document
    • Postprint
    Identifiant OAI-PMH
    • oai:doc.rero.ch:296502
    Summary
    Summary: Sequencing oligosaccharides by exoglycosidases, either sequentially or in an array format, is a powerful tool to unambiguously determine the structure of complex N- and O-link glycans. Here, we introduce GlycoDigest, a tool that simulates exoglycosidase digestion, based on controlled rules acquired from expert knowledge and experimental evidence available in GlycoBase. The tool allows the targeted design of glycosidase enzyme mixtures by allowing researchers to model the action of exoglycosidases, thereby validating and improving the efficiency and accuracy of glycan analysis. Availability and implementation: http://www.glycodigest.org. Contact: matthew.campbell@mq.edu.au or frederique.lisacek@isb-sib.ch