Volume 1, Issue 2 p. 340-349
Research Article

GlycoMod – A software tool for determining glycosylation compositions from mass spectrometric data

Catherine A. Cooper

Corresponding Author

Catherine A. Cooper

Proteome Systems Ltd, Sydney, Australia

Proteome Systems Ltd, Locked Bag 2073, North Ryde, Sydney, NSW 1670, Australia Fax: + 61-2-98891805===Search for more papers by this author
Elisabeth Gasteiger

Elisabeth Gasteiger

Swiss Institute of Bioinformatics, Geneve, Switzerland

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Nicolle H. Packer

Nicolle H. Packer

Macquarie University Center for Analytical Biotechnology, Sydney, Australia

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Abstract

GlycoMod (http://www.expasy.ch/tools/glycomod/) is a software tool designed to find all possible compositions of a glycan structure from its experimentally determined mass. The program can be used to predict the composition of any glycoprotein-derived oligosaccharide comprised of either underivatised, methylated or acetylated monosaccharides, or with a derivatised reducing terminus. The composition of a glycan attached to a peptide can be computed if the sequence or mass of the peptide is known. In addition, if the protein is known and is contained in the SWISS-PROT or TrEMBL databases, the program will match the experimentally determined masses against all the predicted protease-produced peptides (including any post-translational modifications annotated in these databases) which have the potential to be glycosylated with either N- or O-linked oligosaccharides. Since many possible glycan compositions can be generated from the same mass, the program can apply compositional constraints to the output if the user supplies either known or suspected monosaccharide constituents. Furthermore, known oligosaccharide structural constraints on monosaccharide composition are also incorporated into the program to limit the output.