VIB Proteomics Expertise Center, UGent
The VIB Proteomics Expertise Center (PEC) performs proteome analysis using the COFRADIC procedure (e.g. Gevaert et al., Nat Biotech, 2003).
In contrast to traditional 2-dimensional gel- electrophoresis based proteomic methods, COFRADIC relies on the chromatographic properties of proteome-derived peptide mixtures. These highly complex peptide mixtures are here reduced in complexity, following selected chemical or enzymatic amino acid alterations, without compromising the representation of the parent proteins.
In theory, COFRADIC can be applied to the isolation of any type of peptide, provided that it can be specifically and quantitatively modified. So far, COFRADIC has been used to isolate methionyl, cysteinyl, amino terminal, N-glycosylated and phosphorylated peptides and peptides structurally involved in ATP/ADP binding from trypsin digests of a proteome. The N-terminal peptides are particularly useful because every protein is represented by only one peptide, thereby reducing a sample's complexity to the highest degree while monitoring in vivo protein processing events on a proteome-wide level (Van Damme et al., Nat Methods, 2005). In theory, all posttranslational modified peptides that can be altered specifically could be analyzed by COFRADIC.
Potential applications for COFRADIC include:
• Differential proteome analysis of whole cells, tissues and body fluids
• Identification of in vivo posttranslational modifications
• Characterization of in vivo protein processing and protease targets (degradomics)
Due to the experimental stage of the technology and based on an agreement with the PEC, the allocated capacity to VIB research groups for performing COFRADIC experiments is currently limited. Therefore, the PEC will select only a limited amount of applications for COFRADIC experiments. The selection will be based on project feasibility and deliverables.
Interested?
Contact Joël Vandekerckhove or Kris Gevaert
ADDRESS
Go to the Department's own website for more details.
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