Literature DB >> 25015990

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

Lou Gotz1, Jodie L Abrahams1, Julien Mariethoz1, Pauline M Rudd1, Niclas G Karlsson1, Nicolle H Packer1, Matthew P Campbell1, Frederique Lisacek2.   

Abstract

UNLABELLED: 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.
© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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Year:  2014        PMID： 25015990      PMCID： PMC4609004          DOI： 10.1093/bioinformatics/btu425

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  10 in total

Review 1.  Use of endo- and exoglycosidases for structural studies of glycoconjugates.

Authors:  A Kobata
Journal:  Anal Biochem       Date:  1979-11-15       Impact factor: 3.365

2.  Exoglycosidase sequencing of N-linked glycans by the reagent array analysis method (RAAM).

Authors:  S Prime; T Merry
Journal:  Methods Mol Biol       Date:  1998

3.  UniCarb-DB: a database resource for glycomic discovery.

Authors:  Catherine A Hayes; Niclas G Karlsson; Weston B Struwe; Frederique Lisacek; Pauline M Rudd; Nicolle H Packer; Matthew P Campbell
Journal:  Bioinformatics       Date:  2011-03-12       Impact factor: 6.937

4.  Toolboxes for a standardised and systematic study of glycans.

Authors:  Matthew P Campbell; René Ranzinger; Thomas Lütteke; Julien Mariethoz; Catherine A Hayes; Jingyu Zhang; Yukie Akune; Kiyoko F Aoki-Kinoshita; David Damerell; Giorgio Carta; Will S York; Stuart M Haslam; Hisashi Narimatsu; Pauline M Rudd; Niclas G Karlsson; Nicolle H Packer; Frédérique Lisacek
Journal:  BMC Bioinformatics       Date:  2014-01-10       Impact factor: 3.169

5.  Detailed structural analysis of N-glycans released from glycoproteins in SDS-PAGE gel bands using HPLC combined with exoglycosidase array digestions.

Authors:  Louise Royle; Catherine M Radcliffe; Raymond A Dwek; Pauline M Rudd
Journal:  Methods Mol Biol       Date:  2006

6.  A rapid high-resolution high-performance liquid chromatographic method for separating glycan mixtures and analyzing oligosaccharide profiles.

Authors:  G R Guile; P M Rudd; D R Wing; S B Prime; R A Dwek
Journal:  Anal Biochem       Date:  1996-09-05       Impact factor: 3.365

7.  GlycoBase and autoGU: tools for HPLC-based glycan analysis.

Authors:  Matthew P Campbell; Louise Royle; Catherine M Radcliffe; Raymond A Dwek; Pauline M Rudd
Journal:  Bioinformatics       Date:  2008-03-14       Impact factor: 6.937

8.  The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments.

Authors:  David Damerell; Alessio Ceroni; Kai Maass; Rene Ranzinger; Anne Dell; Stuart M Haslam
Journal:  Biol Chem       Date:  2012-11       Impact factor: 3.915

9.  Structural Identification of O-Linked Oligosaccharides Using Exoglycosidases and MSn Together with UniCarb-DB Fragment Spectra Comparison.

Authors:  Liaqat Ali; Diarmuid T Kenny; Catherine A Hayes; Niclas G Karlsson
Journal:  Metabolites       Date:  2012-10-08

10.  UniCarbKB: building a knowledge platform for glycoproteomics.

Authors:  Matthew P Campbell; Robyn Peterson; Julien Mariethoz; Elisabeth Gasteiger; Yukie Akune; Kiyoko F Aoki-Kinoshita; Frederique Lisacek; Nicolle H Packer
Journal:  Nucleic Acids Res       Date:  2013-11-13       Impact factor: 16.971
  10 in total
  13 in total

1.  GlycoStore: A Platform for H/UPLC and Capillary Electrophoresis Glycan Data.

Authors:  Matthew P Campbell; Sophie Zhao; Jodie L Abrahams; Terry Nguyen-Khuong; Pauline M Rudd
Journal:  Methods Mol Biol       Date:  2022

2.  Building a PGC-LC-MS N-glycan retention library and elution mapping resource.

Authors:  Jodie L Abrahams; Matthew P Campbell; Nicolle H Packer
Journal:  Glycoconj J       Date:  2017-09-13       Impact factor: 2.916

Review 3.  Advancing Solutions to the Carbohydrate Sequencing Challenge.

Authors:  Christopher J Gray; Lukasz G Migas; Perdita E Barran; Kevin Pagel; Peter H Seeberger; Claire E Eyers; Geert-Jan Boons; Nicola L B Pohl; Isabelle Compagnon; Göran Widmalm; Sabine L Flitsch
Journal:  J Am Chem Soc       Date:  2019-08-21       Impact factor: 16.383

4.  HappyTools: A software for high-throughput HPLC data processing and quantitation.

Authors:  Bas Cornelis Jansen; Lise Hafkenscheid; Albert Bondt; Richard Andrew Gardner; Jenifer Lynn Hendel; Manfred Wuhrer; Daniel Ian Richard Spencer
Journal:  PLoS One       Date:  2018-07-06       Impact factor: 3.240

5.  Automated N-Glycosylation Sequencing Of Biopharmaceuticals By Capillary Electrophoresis.

Authors:  Marton Szigeti; Andras Guttman
Journal:  Sci Rep       Date:  2017-09-15       Impact factor: 4.379

6.  Glycomics@ExPASy: Bridging the Gap.

Authors:  Julien Mariethoz; Davide Alocci; Alessandra Gastaldello; Oliver Horlacher; Elisabeth Gasteiger; Miguel Rojas-Macias; Niclas G Karlsson; Nicolle H Packer; Frédérique Lisacek
Journal:  Mol Cell Proteomics       Date:  2018-08-10       Impact factor: 5.911

Review 7.  Early Stage Glycosylation Biomarkers in Alzheimer's Disease.

Authors:  Patricia Regan; Paula L McClean; Thomas Smyth; Margaret Doherty
Journal:  Medicines (Basel)       Date:  2019-09-03

8.  Mining High-Complexity Motifs in Glycans: A New Language To Uncover the Fine Specificities of Lectins and Glycosidases.

Authors:  Zachary Klamer; Ben Staal; Anthony R Prudden; Lin Liu; David F Smith; Geert-Jan Boons; Brian Haab
Journal:  Anal Chem       Date:  2017-11-03       Impact factor: 6.986

9.  GlycanAnalyzer: software for automated interpretation of N-glycan profiles after exoglycosidase digestions.

Authors:  Ian Walsh; Terry Nguyen-Khuong; Katherine Wongtrakul-Kish; Shi Jie Tay; Daniel Chew; Tasha José; Christopher H Taron; Pauline M Rudd
Journal:  Bioinformatics       Date:  2019-02-15       Impact factor: 6.937

Review 10.  Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics.

Authors:  Xing Li; Zhijue Xu; Xiaokun Hong; Yan Zhang; Xia Zou
Journal:  Int J Mol Sci       Date:  2020-09-14       Impact factor: 5.923
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