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Faculté des Sciences
Faculté des Sciences
MASTER THESIS
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Implémentation d'un programme permettant l'annotation des lipides provenant de données MSI dans le but de segmenter une coupe histologique en des régions métaboliquement différentes

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La Rocca, Raphaël ULiège
Promotor(s) : De Pauw, Edwin ULiège
Date of defense : 6-Sep-2018 • Permalink : http://hdl.handle.net/2268.2/5339
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Title : Implémentation d'un programme permettant l'annotation des lipides provenant de données MSI dans le but de segmenter une coupe histologique en des régions métaboliquement différentes
Author : La Rocca, Raphaël ULiège
Date of defense  : 6-Sep-2018
Advisor(s) : De Pauw, Edwin ULiège
Committee's member(s) : Meyer, Patrick ULiège
Baurain, Denis ULiège
Matagne, André ULiège
Quinton, Loïc ULiège
Language : English
Discipline(s) : Life sciences > Biochemistry, biophysics & molecular biology
Institution(s) : Université de Liège, Liège, Belgique
Degree: Master en biochimie et biologie moléculaire et cellulaire, à finalité spécialisée en bioinformatique et modélisation
Faculty: Master thesis of the Faculté des Sciences

Abstract

[en] Mass Spectrometry Imaging (MSI) is an analytical method employed to map the distribution
of molecules inside a sample based on their mass-to-charge ratio. When working with
biological sample, classical histology is often combined due to the complementarity of the
data.
Unfortunately, bioinformatic tools used to treat those data are not open source and are
often limited in terms of their analytic possibilities. The lack of means to analyse imagery
by mass spectrometry data forces scientists to build their own tools.
In this work, we have developed a tool from existing methods to process image by mass
spectrometry data in order to identify lipids in an image by MALDI FT-ICR mass spec-
trometry from a biological section. The different methods used to achieve this goal are peak
picking methods, to process the mass spectra signals, followed by a FDR controlled anno-
tion of lipids. The identifications are made by the LIPID MAPS database. Furthermore,
not recorded lipids are infered according to the lipids already identified.
Moreover, we used the identification process as a feature reduction method to allow efficient
segmentation of an image by mass spectrometry. Then, the regions of interest, discovered
by the segmentation , can be analyzed in term of their lipid composition.
The pipeline is implemented in R and is tested on 3 biological sections of zebrafish.


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Author

  • La Rocca, Raphaël ULiège Université de Liège > Master bioch. & biol. mol. & cel., à fin.

Promotor(s)

Committee's member(s)

  • Meyer, Patrick ULiège Université de Liège - ULiège > Département des sciences de la vie > Biologie des systèmes et bioinformatique
    ORBi View his publications on ORBi
  • Baurain, Denis ULiège Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes
    ORBi View his publications on ORBi
  • Matagne, André ULiège Université de Liège - ULiège > Département des sciences de la vie > Enzymologie et repliement des protéines
    ORBi View his publications on ORBi
  • Quinton, Loïc ULiège Université de Liège - ULiège > Département de chimie (sciences) > Chimie biologique
    ORBi View his publications on ORBi
  • Total number of views 75
  • Total number of downloads 7










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