Research @ the Gevaert Group

“Our unique mass spectrometry-based proteomics approach, COFRADIC, enables us to shed light on biologically relevant protein modifications. This results in both fundamental insights and potential new applications.”

Contemporary proteomics for addressing the dynamics of proteomes

Our research focuses on the development and applications of contemporary mass spectrometry-driven proteomics techniques. We developed the COFRADIC portfolio of proteomics techniques by which a wide variety of peptide classes, each are readouts for a given protein modification, are chromatographically isolated prior to LC-MS/MS analysis.

The peptide classes that can be isolated by COFRADIC (and the proteomic features that are studied) include:

  • protein amino (N) terminal peptides: protease degradomics, protein N-alpha acetylation and N-terminal proteoforms (proteogenomics)
  • protein carboxy (C) terminal peptides: processing by carboxypeptidases
  • methionine-sulfoxide containing peptides: oxidative stress
  • ubiquitinylated peptides: protein degradation and functional modulation

A very successful COFRADIC application is the isolation of N-terminal peptides. Such peptides are amongst the most suitable proteotypic peptide candidates for quantification of proteins by targeted proteomics approaches. Neo-N- and neo-C-terminal peptides directly point to protein processing events as these are created upon protein cleavage by proteases. Ongoing research in the protein processing field focusses on both endogenous (e.g. inflammatory caspases and plant metacaspases) and exogenous (e.g. viral) proteases. Further, our lab is actively involved in deciphering the co-translational modifications that occur on eukaryotic nascent polypeptides such as removal of the initiator methionine and acetylation of primary alpha-amines. We mapped the specificities of the enzymes involved and are currently successful in implementing ribosomal footprinting in this particular research line.

Together with the Eyckerman lab, we are developing novel methods for affinity purification mass spectrometry (AP-MS), including the Virotrap method. In addition, we introduced novel technologies to study protein conformational changes by limited proteolysis coupled to mass spectrometry and invested in setting up a chemical proteomics platform to identify targets of small bioactive molecules.

The Gevaert lab also houses the VIB Proteomics Expertise Center which opens the whole proteomics platform to researchers worldwide.