Équipe CSTB : Systèmes Complexes et Bioinformatique Translationnelle

Spectrométrie de Masse

De Équipe CSTB : Systèmes Complexes et Bioinformatique Translationnelle
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* Encadrants : Pierre Collet, Anne Jeannin, Christian Rolando
* Lieu du l'apprentissage : Laboratoire ICUBE, équipe CSTB, 3 rue Humann, 67000 Strasbourg
* Contrat d'apprentissage : du 1er septembre 2016 au 31 août 2018

Mass spectrometry of biological molecules is driving the progress of emerging fields such as proteomics, metabolomics and is fundamental for pharmacology, environment, and forensic sciences. MS provides two kinds of information: molecular mass and structure through fragmentation. Whereas masses of all molecules are obtained serially all at once, structures are painfully obtained one by one. Two-dimensional techniques allow simultaneous parallel acquisition of structural information whatever the number of molecules opening a new way to work on complex sample without prior separation by chromatography. 2D Fourier transform techniques have revolutionized nuclear magnetic resonance (NMR) since their introduction by R. Ernst in 1974 and have been recognized by two Nobel prizes. They paved the way for the analysis of complex samples such as isolated proteins but also blood or urine. Among the mass analyzers the Fourier-transform ion-cyclotron-resonance-spectrometer (FT-ICR) has the best capacity to separate individual masses by at least two orders of magnitude. The principle of 2D FT-ICR was established in the late eighties but did not follow the development of 2D NMR for reasons linked to poor control of ion motion and the lack of processing algorithms for the big data generated. Indeed the size of the data generated may be higher than the Terabyte for one square spectrum of 1 million point by 1 million point. Spectrum of higher sizes may be generated ! Actually the treatment of such spectra has to be performed on a cluster or a computing center.

The aim of the project is to transpose the existing algorithms base on Fast Fourier Transform on next generation GPU (for example Nvidia Pascal) very efficient in handling double precision float nunbers. The project will give the opportunity to collaborate with academic teams in France and in Europe of different fields from applied mathematics to biology and with the FT-ICR manufacturer. The candidate will have the opportunity to present her/his work in scientific meetings. The project will be realized in Strasbourg in the ICube laboratory under the supervision of Pr Pierre Collet Dr Anne Jeannin and in collaboration with Dr Christian Rolando, CNRS Senior Scientist (Lille).