Bioinformatics for spatial metabolomics

Charles Pineau and the Protim platform (Institute for Research in Health, Environment and Work) are involved in METASPACE, a European H2020 project, whose objective is to enable untargeted spatial metabolomics for translational research and clinical applications.
La bioinformatique au service de la métabolomique spatiale


The METASPACE consortium aims to develop new bioinformatics tools and to demonstrate their potential for various studies in personalised human medicine, precision medicine and quality of life monitoring in several chronic conditions. The project partners are developing an open-source online engine called METASPACE dedicated to spatial metabolomics using mass spectrometry imaging. METASPACE will be a support tool for basic and clinical research teams conducting three-dimensional metabolomics studies.

The Metaspace project is made possible by the data produced by the FT-ICR SolariX mass spectrometer installed on the Protim platform on the Beaulieu Campus.

Project issues

  1. To date, there is no algorithm for the automatic annotation of molecular images generated by mass spectrometry imaging;
  2. Only innovative algorithms based on Big Data management concepts will allow millions of ion images to be rapidly translated into hundreds of molecular images;
  3. It is essential to design a tool that is open source, freely available and can be deployed by users on a workstation, a cluster or in the Cloud.

The work is divided into three steps to deliver accurate molecular metabolomic annotations: calculation of the Metabolite-Signal-Match score, estimation of the false positive rate (FDR) and FDR controlled annotation.

International dimension

The project consortium includes partners from 5 countries and one intergovernmental organisation:

  • Theodore Alexandrov, EMBL
  • Lennart Martens, VIB
  • Chris Steinbeck, EMBL-EBI
  • Zoltan Takats et Kirill Veselkov, ICL
  • Pieter Dorrestein, UCSD
  • Charles Pineau, UR1
  • Dennis Trede, SCILS
  • Oliver Panzer, ERS

Identity card

European project METASPACE - HORIZON 2020 Programme

Name of the Scientific Leader: Charles PINEAU
Laboratory / UMR: Protim - Institute for Research in Health, Environment and Work -
Project duration: From 01/07/15 to 30/06/18 (3 years)