Systematic and integrative proteomics

Our work focuses on achieving high throughput analysis of cell extracts and biofluids (Lavigne et al., 2012). We are also interested in improving methods of analyses of the mass spectra and identification of proteins. Current approaches are based on Shotgun and Label-free mass spectrometry.
We have developed an approach to select proteins of interest through integrative proteomics which uses (at least) transcriptomic expression datasets for the search lists of proteins from systematic or differential analysis programs (Com et al., 2014). This approach is particularly relevant, for example, for highlighting biomarkers from biological fluids (Rolland et al., 2013), but equally for the selection of proteins involved in a biological phenomenon of interest (Chalmel/Com et al., 2014). A set of specific tools is being integrated into Galaxy.
Finally, we participate in the e-Biogenouest project. This project aims at integrating and at exploiting at best the data stemming from various technological platforms of Biogenouest with the aim of promoting a systematic approach of the biology.

Imaging mass spectrometry

Our work is focused on developing innovative solutions for toxicoproteomics. They are intended to aid in the understanding of the mechanisms underlying the toxicity of small molecules (environmental toxins, pharmaceutical molecules) within an organ. Our efforts are focused primarily on the co-localization of proteins and small molecules, their in situ quantification (ISAQTM) (Lagarrigue et al., 2014) and the demonstration of their interaction.
Our work also concerns improving the lateral resolution (Lagarrigue et al., 2011) and the development of statistical analysis algorithms for molecular images (Lagarrigue et al., 2012). Finally, Protim is a member of the European consortium 3D-Massomics whose objective is the development of three-dimensional MALDI imaging.
Developments, methodological optimizations and innovations in each of these programs are directly implemented as part of our collaborative activities