The Research of our group primarily focuses on further development and biomedical application of proprietary peptide-centric (gel-free) proteomics techniques. This repertoire of techniques is known under the COFRADIC acronym, which stands for COmbined FRActional DIagonal Chromatography. Using COFRADIC a wide variety of peptide classes can be chromatographically isolated and, following mass spectrometric analysis, each peptide class monitors one aspect of dynamic and complex proteomes.
The following classes of peptides can be isolated using COFRADIC:
- methionyl peptides: differential proteomics and oxidative stress,
- cysteinyl peptides: differential proteomics and oxidative stress,
- amino (N) terminal peptides: protease degradomics and xenoproteomics,
- phosphorylated peptides: phosphoproteomics,
- N-glycosylated and sialylated N-glycopeptides,
- peptides containing parts of ATP-binding sites: chemical proteomics.
COFRADIC is highly versatile and ongoing efforts focus on the further development of procedures allowing the isolation of an increasing set of modified peptides including O-glycosylation, nitration of tyrosine, nitrosylation of cysteine, binding of GTP (and analogues) etc …
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).Next to this exciting new research field, neo-N-terminal peptides directly point 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.
CORDAFIC generates tons of peptide MS/MS spectra needing 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 others to reduce the number of false positive identifications.
The repertoire of COFRADIC techniques is patented and used by 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 Centre, which is part of our research unit.