The Plateforme Bordeaux Proteome offers expertise and equipment for the separation, identification and characterization of proteins, quantification and differential analysis or the search for protein partners.

Protein analysis is carried out by the so-called “bottom-up” methodology using equipment coupling liquid nano-chromatography with latest-generation mass spectrometers equipped with Orbitrap-type analyzers. These new generations of analyzers allow analysis at very high resolution and at very high scanning speed for optimal sensitivity, allowing the analysis of complex or even very complex samples.

Regarding quantitative/differential proteomics, Bordeaux Proteome offers the possibility of analyzing your samples using the label-free technique, which makes it possible to compare several samples without the labeling of proteins/peptides. The choice of experimental design (label-free, SILAC, TMT, etc.) is however guided by various factors, including the type of samples (cell cultures, tissues, etc.), their complexity, the quantity of material available, etc. Alternatively, the methods of isotopic labeling are also available and make it possible to envisage protein or peptide fractionation with a minimum of experimental bias in the analysis.

The analysis of intact proteins (purified or mixed) is possible by the so-called “top-down” approach, using methods implemented on the latest generations of instruments available within Bordeaux Proteome.

For the study of non-sequenced species, the Plateforme Bordeaux Proteome offers its expertise relating to the identification of proteins by de novo sequencing. Different software specific to this type of analysis are available.

Finally, Bordeaux Proteome offers different enrichment and/or bioinformatics analysis strategies for the characterization of co/post-translational modifications (i.e. phosphorylation, ubiquitination, glycosylation).

With regard to protein separation, Bordeaux Proteome offers mono- (SDS-PAGE, BN-PAGE, 16-BAC-PAGE, IEF) or two-dimensional (BN/SDS-PAGE, 16-BAC/SDS- PAGE, IEF/SDS-PAGE). Gels can be stained with various visible and fluorescent dyes (Coomassie Blue, Colloidal Blue, Silver (MS Compatible), Pro Q Diamond, Ruthenium II, Sypro, Deep Purple). Membrane transfer of gels is also possible

Proteins separation in liquid vein by iso electrofocusing (IEF) or according to their molecular mass can be carried out on available commercial systems, respectively OffGel, Rotofor or GelFree.

The Platform being associated with the Mass Spectrometry of Biological Macromolecules research team, UMR 5248 CBMN, collaborative projects can be carried out around the following themes. For all new projects on the following themes, please contact the research team leader Caroline Tokarski and the theme leaders.

• Structural analysis of proteins by isotopic exchange or cross-linking (responsible : Stéphane Chaignepain).

• Mass Spectrometry Imaging (responsible: Nicolas Desbenoit).

• Analysis of N- and O-glycoproteins / glycopeptides (responsible: Katell Bathany)

• Tandem mass spectrometry analysis of intact proteins – “top-down” type proteomics (responsible: Caroline Tokarski).

• Analysis of traces and ultra traces in the field of cultural heritage (responsible: Caroline Tokarski).