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	    Raweb 
	    2016</a> | <a href="http://www.inria.fr/en/teams/abs">Presentation of the Project-Team ABS</a> | <a href="http://team.inria.fr/abs/">ABS Web Site
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        <h2>Section: 
      Bilateral Contracts and Grants with Industry</h2>
        <h3 class="titre3">Bilateral contracts with industry</h3>
        <p>In this section, we describe the collaboration between ABS and MS Vision
(<a href="http://msvision.eu/">http://msvision.eu/</a>), and 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.</p>
        <p>This collaboration is funded by the Instituts Carnots
(<a href="http://www.instituts-carnot.eu/en">http://www.instituts-carnot.eu/en</a>).</p>
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        <h4 class="titre4">Context</h4>
        <p>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.</p>
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        <h4 class="titre4">Specific goals</h4>
        <p>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
<a href="./bibliography.html#abs-2016-bid41">[2]</a>, <a href="./bibliography.html#abs-2016-bid42">[3]</a>.
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