A proteome is the set of proteins expressed by a genome at a given time. Proteomics is the analysis of proteomes, and involves a range of experimental techniques. Experimental data is processed in order to identify and quantify proteins, determine their cellular location, modifications, interactions and function. Posttranslational modifications (PTMs) are chemical modifications of amino acids following protein synthesis, and form the repertoire of protein function modulators. Mass spectrometry is a technology of choice for the identification of PTMs and is often used in a high-throughput set-up. The subsequent analysis of data depends heavily on bioinformatics. For example, glycosylation is the most abundant and most structurally diverse PTM. Diversity arises from the many ways in which monosaccharides can be linked together. Glycosylation has crucial roles in most physiological processes and diseases.

Projects

Our research mainly concerns data analysis and data integration with a particular interest in semantic web technology – Resource Description Framework (RDF). We collaborate with mass spectrometry specialists and biologists on publicly funded projects. In mass spectrometry, we are involved in developing analytical tools needed for refining strategies, such as data-independent acquisition. We are also designing solutions for reducing the combinatorics in assigning spectra to glycan structures.
The current focus of biological applications is mostly on understanding host-pathogen interactions (HIV-dendritic cells, Helicobacter pylori in stomach cancer) and studying the effect of PTMs on proteins.

The Proteome Informatics Group co-authors eight to ten articles per year.

More information about two of our research projects in collaboration with SystemsX.ch and the Gastro Glyco Explorer