Introduction

The GlycoWorkbench is a software tool designed for the glycomic experts that unite an intuitive visual editor for building glycan structures, a configurable mass calculator that can handle several type of ions and derivatizations, and a tool for the computation of structure fragments that can automatically annotate fragment peak lists.

The main component of the GlycoWorkbench is the structure building tool. The user can chose among a list of residues, markers and substituents that aim to be as complete as possible, in order to let every type of glycan structure to be drawn. The structures are displayed automatically in various notations using predefined rules so the user does not need to bother about residue placement. The simplest use of this tool is to draw glycan structures for presentation purposes. The drawn structures can be printed, exported into various graphical formats or simply copied into other documents and editors (like Word or PowerPoint).

The structure builder is coupled with a configurable mass calculator that automatically compute the mass of the glycan during the building process. Several types of ions and derivatizations can be selected and both monoisotopic or average mass can be computed. The structure builder and the mass calculator together form a valuable tool that can help during the annotation of mass spectra and can speed up the trial and error approach used to discover a structure with a certain mass.

Once a structure have been built, the fragmentation tool can be used to compute every type of fragment with every number of cleavages from the complete glycan. All the possible fragments can be generated or only a subset of them for selected residues. Each fragment is visualized with its mass and the structure can be copied in the structure builder tool for further processing. Additionally, a fragment peak list can be loaded and each peak can be automatically annotated with the computed fragments.