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.
- 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 xenoproteomics
- protein carboxy (C) terminal peptides: processing by carboxypeptidases
- methionyl peptides: differential proteomics and oxidative stress
- cysteinyl peptides: oxidative stress
- 3-nitrotyrosine-containing peptides: nitrosative stress
- N-glycosylated and sialylated N-glycopeptides
- peptides containing parts of ATP-binding sites: chemical proteomics.
COFRADIC is clearly 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, 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); 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.
29/07/2016 - The labs of Jan Tavernier, Kris Gevaert and Sven Eyckerman from the VIB Medical Biotechnology Center, UGent tackle some of the most fundamental life sciences questions in their research into the detection and analysis of protein-protein interaction.
26/02/2016 - In 2001, the entire human genome was decoded in an ambitious, collaborative project called the Human Genome Project.
15/01/2016 - On 15 January 2016, VIB and the Institute for Agriculture and Fisheries Research (ILVO) signed a strategic collaboration agreement.
22/04/2010 - During an infection, pathogenic bacteria sabotage the machinery in the cells of patient. In this manner, they attempt to break down the resistance of the host.
15/10/2009 - Kris Gevaert and colleagues have achieved a breakthrough in protein research. Using yeast, they have succeeded in making virtually the complete inventory of all the proteins in the mitochondria.
08/03/2004 - Prof. Joël Vandekerckhove of Ghent University − a world authority in the field of protein research − has been awarded the prestigious Belgian Francqui Chair 2003 - 2004 by the University of Antwerp.