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

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.

[1]  Pauline M. Rudd,et al.  GlycoBase and autoGU: tools for HPLC-based glycan analysis , 2008, Bioinform..

[2]  Catherine A. Hayes,et al.  UniCarb-DB: a database resource for glycomic discovery , 2011, Bioinform..

[3]  Erik L. L. Sonnhammer,et al.  Predicting protein function from domain content , 2008, Bioinform..

[4]  Hisashi Narimatsu,et al.  Toolboxes for a standardised and systematic study of glycans , 2014, BMC Bioinformatics.

[5]  Rene Ranzinger,et al.  The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments , 2012, Biological chemistry.

[6]  Catherine A. Hayes,et al.  Structural Identification of O-Linked Oligosaccharides Using Exoglycosidases and MSn Together with UniCarb-DB Fragment Spectra Comparison. , 2012, Metabolites.

[7]  T. Merry,et al.  Exoglycosidase sequencing of N-linked glycans by the reagent array analysis method (RAAM). , 1998, Methods in molecular biology.

[8]  A. Kobata.  Use of endo- and exoglycosidases for structural studies of glycoconjugates. , 1979, Analytical biochemistry.

[9]  Pauline M Rudd,et al.  Detailed structural analysis of N-glycans released from glycoproteins in SDS-PAGE gel bands using HPLC combined with exoglycosidase array digestions. , 2006, Methods in molecular biology.

[10]  Kiyoko F. Aoki-Kinoshita,et al.  UniCarbKB: building a knowledge platform for glycoproteomics , 2013, Nucleic Acids Res..

[11]  R. Dwek,et al.  A rapid high-resolution high-performance liquid chromatographic method for separating glycan mixtures and analyzing oligosaccharide profiles. , 1996, Analytical biochemistry.