Proteomics is the study of the subsets of protein present in different parts of an organism and how they change with time and varying conditions.

Two-dimensional electrophoresis (2DE) currently remains the most popular separation technique for soluble proteins, and allows proteome mapping and comparison of protein expression under various conditions. Gel-free proteomics techniques based on mono- or multidimensional liquid chromatography coupled with tandem mass spectrometry (MDLC-MSMS) complement our 2DE techniques. Two tandem mass spectrometers, the QSTAR XL, and the 4800 MALDI-TOF/TOF exist in the laboratory.

Numerous proteomics approaches were carried out in the laboratory. One main focus was the comparative analysis of relative protein expression under different growth conditions or of different strains of an organism. For this aim, comparative 2DE or stable isotope labelling of peptides (iTRAQ) followed by MDLC-ESI-MSMS were applied to Mycobacterium tuberculosis (collaboration with N Winter, Mycobacterial Genetics), to Photorhabdus luminescens (collaboration with JF Charles, Genetics of Bacterial Genomes).

"Targeted proteomics” involves initial protein enrichment by various methodologies. This approach was widely used for different projects, especially for protein-protein interactions and phosphoproteome analyses. For instance, affinity purifications of protein complexes using the TAP (Tandem Affinity Purification) approach resulted in the identification of partners involved in active protein complexes. Moreover, quantitative results obtained with iTRAQ labelling gave valuable information for the understanding of the protein order assembly within the pre-60s maturation process (collaboration with A Jacquier, Molecular Interaction Genetics). The TAP method is also applied to protein analyses of Helicobacter pylori (collaboration with H de Reuse, Pathogenesis of Mucosal Bacteria). After an enrichment step of phosphorylated proteins, a combination of 2DE and mass spectrometry analyses led to the identification of the Leishmania donovani phosphoproteome (collaboration with G Spaeth, Parasite Virulence).

In parallel to our scientific activity, which involves the Proteomics platform in many collaborative projects, we are also dedicated to service activities.

Keywords: Proteomics, electrophoresis, mass spectrometry, LC-MSMS, proteins, tuberculosis, malaria

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