Our group is involved in software and database development for the understanding of posttranslational modifications, especially glycosylation. In this context we have developed the following resources:
- PTM-oriented proteomics tools
Over the past few years we have implemented MzJava an open-source Java library for the analysis of mass spectrometry data from large-scale proteomics and glycomics experiments. Several ongoing research projects rely on the use and improvement of a PTM open search engine processing tandem mass spectrometry data (available on request).
- Glycomics databases and analysis software
A heterogeneous range of bioinformatics databases and tools is now available on the web for glycomics studies. We participate in an international consortium driven by glycobiologists with the prospect of creating a proteomics equivalent for the integration of glycomics knowledge. The consortium released UniCarbKB that collects annotated glycan structural data combined with protein and tissue information. The development of UniCarbKB is tightly bound to mass spectrometric data and structural assignment based on fragmentation data stored in UniCarb-DB, a repository also created by the consortium. Mass spectrometry analysis software supporting glycan structural assignment includes GlycoMod for MS data and soon GlycoForest (to be released in 2016) for MS/MS data. Other tools developed at PIG such as GlycoDigest simulate the exoglycosidase digestion of glycans.
Information on cellular interactions associated with changes in glycosylation structures is essential for the understanding of the functional role of sugars and needs to be collected in order to exploit the knowledge of these posttranslational additions to proteins. This task is undertaken with the expansion of SugarBindDB, which collates under expert supervision the known binding sites of pathogen adhesins/lectins to sugars. These structural glycan epitopes occur on both proteins and lipids and add to the knowledgebase of glycosylation function and refine the structural data contained in UniCarbKB. Both resources are curated and they are now sharing the knowledge of glyco-epitopes (glycan ligands) that are mapped in GlyDin', a network-based visualisation tool highlighting the shared monosaccharide composition of glyco-epitopes as well as their variety.
All our tools and databases are now grouped in the glycomics tab of the ExPASy server, along with a short selection of resources developed by partners. The focus of the most recently released PIG tools is on glycoproteomics. For example, GlycoSiteAlign aligns amino acid sequences surrounding glycosylation sites conditioned by the knowledge of the attached glycan structure(s), input as general or specific features (fucosylated vs. non-fucosylated, monosaccharide composition, etc).
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