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Structural elucidation of glycosaminoglycans (GAGs) is one of the major challenges in biochemical analysis. This is mainly because of the diversity of GAG sulfation and N-acetylation patterns and variations in uronate isomers. ESI-MS and recently MALDI-MS methodologies are important strategies for investigating the molecular structure of GAGs. However, the interpretation of MS data produced by these strategies must take into account a large number of variables (including the number of monosaccharide residues, acetylations, sulfate groups, multiple charges, and exchanges between different cations). We have developed a bioinformatics tool to assist this complex interpretation task. The software is based on Glyco Workbench, a tool for semiautomatic interpretation of glycan MS data. The tool generates the sugar backbones in all their variants (GAG family, composition, acetylation positions, and number of sulfates) and automatically matches them with the selected MS peaks. The backbones corresponding to a given peak are validated against the selected MS/MS peaks by generating all possible fragmentations. Native chondroitin sulfate and heparin oligosaccharides as well as chemically modified heparin oligomers have been successfully analyzed by MALDI. and ESI-MS and MS/MS, and the results of the semiautomated annotation of these mass spectra are presented here. [ABSTRACT FROM AUTHOR]