Section: Bilateral Contracts and Grants with Industry

Bilateral Contracts with Industry

In this section, we describe the collaboration between ABS and MS Vision (http://msvision.eu/), a company based in the Netherlands. MSVision was created in 2004 and currently involves 20 employees; it is a worldwide leader in delivering tailored hardware solutions to the mass spectrometry community. As detailed below, the collaboration aims at strengthening the offer of the company on the algorithmic and software sides.

This collaboration is funded by the Instituts Carnots (http://www.instituts-carnot.eu/en).

Context

Protein complexes underlie most biological functions, so that studying such complexes in native conditions (intact molecular species taken in solution) is of paramount importance in biology and medicine. Unfortunately, the two leading experimental techniques to date, X ray crystallography and cryo electron microscopy, involve aggressive sample reparation (sample crystallization and sample freezing in amorphous ice, respectively) which may damage the structures and/or create artifacts. These experimental constraints legitimate the use of mass spectrometry (MS) to study biomolecules and their complexes under native conditions, using electrospray ionization (ESI), a soft ionization technique developed by John Fenn (Nobel prize in chemistry, 2002). MS actually delivers information on the masses of the molecular species studied, from which further information on the stoichiometry, topology and contacts between subunits can be inferred. Thanks to ESI, MS is expected to play a pivotal role in biology to unravel the structure of macromolecular complexes underlying all major biological processes, in medicine and biotechnology to understand the complex patterns of molecules involved in pathways, and also in biotechnologies for quality checks.

Specific goals

A mass spectrometer delivers a mass spectrum, i.e. an histogram representing the relative abundance of the ions (ionized proteins or protein complexes in our case), as a function of their mass-to-charge (m/z) ratio. Deconvoluting a mass spectrum means transforming it into a human readable mass histogram. Due to the nature of the ESI process (i.e. the inclusion of solvent and various other molecules) and the intrinsic variability of the studied biomolecules in native conditions, the interpretation of such spectra is delicate. Methods currently used are of heuristic nature, failing to satisfactorily handle the aforementioned difficulties. The goal of this collaboration is to develop optimal algorithms and the associated software to fill the critical gap of mass spectra deconvolution. The benefits for the analyst will be twofold, namely time savings, and the identification of previously undetected components. Upon making progress on the deconvolution problem, the collaboration will be expanded on the geometric and topological modeling of large macro-molecular assemblies, a topic to which ABS recently made significant contributions [2], [3].