What do we do?
At the Proteome Informatics Group (PIG) we are involved in software and database development for the benefit of the proteomics and the glycomics communities. These resources are made available through the ExPASy server. Software tools support experimental mass spectrometry data analysis, mainly for the detection of posttranslational modifications. Databases store knowledge of carbohydrates attached to proteins as well as protein-carbohydrate interactions.
In recent years, we have set out to collect and integrate information on glycans which role is increasingly described as key in many normal and pathological cellular processes. With the creation of a dedicated tab on the ExPASy server in 2015, we now centralise databases and tools useful for glycomics and glycoproteomics and gradually expand our range. In 2016, we introduced three new tools:
- GlycoSiteAlign that selectively aligns amino acid sequences surrounding glycosylation sites depending on structural properties of the glycan attached to the site. The tool previews and/or downloads alignments which may reveal amino acid patterns corresponding to selected features (e.g. fucosylated vs. non-fucosylated).
- PepSweetener that facilitates the manual annotation of intact glycopeptide spectra through the interactive inspection of theoretical glycopeptides matching queried molecular masses. It is currently focused on human glycoproteins.
- Glydin' that compiles knowledge on glyco-epitopes (glycan ligands) and displays their interrelations based on monosaccharide composition in an interactive network.
This tool collection is mainly designed to support scientists in shaping assumptions on glycan-binding properties and glycan attachment on proteins.
Main publications 2016
- Gastaldello A, Alocci D, Baeriswyl JL, Mariethoz J, Lisacek F, GlycoSiteAlign:
Glycosite Alignment Based on Glycan Structure, J Proteome Res 2016;15(10):3916-3928
- Horlacher O, Lisacek F, Müller, Mining Large Scale Tandem Mass Spectrometry
Data for Protein Modifications Using Spectral Libraries, J Proteome Res 2016;15(3):721-31
- Mariethoz J, Khatib K, Alocci D et al., SugarBindDB, a resource of glycan-mediated host-pathogen interactions. Nucleic Acids Res. 2016;44(D1):D1243-50