We develop targeted assays to monitor panels of proteins of high interest at VIB. These assays are based on the concept of sentinel proteins which are biological markers whose change in abundance or modification characterizes the activation state of a given cellular process. By Parallel Reaction Monitoring (PRM) on our orbitrap mass spectrometers we quantify hundreds of proteins in a single run and are able to provide fast and sensitive read-outs of the metabolic and inflammatory state of the cell.
We further focus on the analysis of ubiquitin-like protein modifications (UBLs), in particular ISG15. This UBL is only expressed upon cytokine induction in most cell types and is important to tackle microbial infections. In collaboration with the Gevaert and the Eyckerman labs we develop novel proteomics-based strategies to identify target proteins and conjugation sites of ISG15 that will help to further elucidate the role of ISGylation in the host defense against infection.
Finally, we focus on the analysis of antigenic peptides during infection. Although many aspects of the MHC presentation pathway are known in great detail, the rules for peptide selection remain largely unknown. In collaboration with the Callewaert and Saelens labs we develop robust pipelines for the LC-MS/MS identification of antigenic peptides presented on cells infected by Mycobacterium, influenza and RSV. Results from this research will lead to novel epitopes that can be used as vaccine candidates.