How can we use our mass spectrometers to characterize the dynamic proteome?

Our research focuses on the development and applications of proprietary peptide-centric and mass spectrometry-driven proteomics techniques. These are known under the COFRADIC acronym COFRADIC, which stands for COmbined FRActional DIagonal Chromatography. Using COFRADIC, a wide variety of peptide classes can be chromatographically isolated, and, following after mass spectrometric analysis, each peptide class monitors one aspect of dynamic and complex proteomes.

One of the most successful applications of COFRADIC is the isolation of N-terminal peptides. Such peptides are the best discriminators for homologous and orthologous proteins, and thus allow xenoproteomics (i.e. the simultaneous analysis of proteomes from different organisms); they and are further also amongst the most suitable proteotypic peptide candidates for targeted analysis and quantification of proteins. Next Alongside to these exciting new research fields, neo-N-terminal peptides directly point directly to protein processing events. Indeed, protein cleavage by proteases creates a protein fragment holding the original C-terminal protein part, but with a novel N-terminal part. Using N-terminal COFRADIC in a differential setup, such novel N-terminal peptides – and thus protein processing events –, are readily picked up and identified. Current research in the protein processing field concentrates on both endogenous (e.g. granzymes, cathepsins and calpains) and (viral)exogenous (viral) proteases. Recently, the introduction of a COFRADIC technology that isolates C-terminal peptides paved the way for routine characterization of the substrates of carboxypeptidases.

 

COFRADIC generates tons enormous volumes of peptide MS/MS spectra needing requiring interrogation, linking to protein sequences, and finally dissemination of proteomics results. To meet these needs, our research unit also develops several "’proteome informatics tools"’, amongst other things to reduce the number of false positive identifications, validate peptide and protein quantification results, and visualize consensus patterns in large-scale proteomic datasets.

The repertoire of COFRADIC techniques is patented and used by the VIB and UGent spin-off company Pronota NV (http://www.pronota.com) for their biomarker research. Furthermore, these COFRADIC techniques are opened up to other VIB scientists by the VIB Proteomics Expertise Centrer, which is part of our research unit.