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• Mass spectrometry lab
• Microscopy lab
• NMR lab
• Compositional and structural phenotyping lab
• Computational solutions

Mass spectrometry Lab

Fine structure of oligo/polysaccharides

Trappe Ionique Amazon SL (Bruker) (2018) (Technologie ESI-IT - couplé avec une UPLC)

• Modifiée pour une activation des ions par des cations d’hélium accélérés (fragmentation MS/MS à haute énergie par CTD, Charge Transfer Dissociation)

Select SERIES Cyclic IMS (Waters) (2019) (Technologie ESI-Q-IM-TOF - couplé avec une UPLC)

• Un appareil équipé d’une cellule de mobilité ionique haute résolution (mobilité ionique cyclique), pour la séparation d’isomères structuraux et leur détermination structurale par MS/MS

Proteomics

Q-Exactive HF (Thermo-Fisher) (2019) (Technologie ESI-Q-Orbitrap - couplé avec une nano-UPLC)

• Haute cadence de fragmentation des peptides dans une cellule HCD et haute précision de masse des parents et fragments

Mass spectrometry imaging

rapifleX Tissue typer (Bruker) (2018) (Technologie MALDI TOF)

• Un laser à 10 kHz pour une cadence de tir adaptée aux expériences d’imagerie moléculaire, et une résolution spatiale de l’ordre de 5-µm.

Microscopy Lab

Observation of structures and topography at the nanometer scale. Measurement of elastic modulus & localized chemical composition.

Microscope à force atomique (Bruker) couplé en Raman (Renishaw) (2013)

Observation of structures at the nanometer scale.

Microscope électronique à transmission (JEOL 1230) (2005)

• Fonctionnement en mode cryogénique et conventionnel.

Observation of structures at the mesoscopic level.

Microscope électronique à balayage Quattro S (Thermo-Fisher) (2019)

• Fonctionnement en mode environnemental, adapté aux échantillons mous et hydratés. Mode transmission (STEM). Analyseur élémentaire.

Observation at the micrometer scale.

Microscope confocal à balayage laser (NIKON A1R) (2009, jouvence partielle en 2019)

• Microscopie de fluorescence. Observation de molécules cibles (ex. protéines) après marquage.

NMR Lab

Measurement of biopolymers structures, polymorphism, and interactions. Water density and mobility. Micro-imaging.

Spectromètre RMN haut champ Avance III 9.4T WB (Bruker) (2002, jouvence électronique en 2009, nouvel aimant en 2018)

• Equipé de sondes CPMAS et HRMAS, statiques X et HX pour les échantillons solides à mous

Deux spectromètres RMN bas champ Minispec Mq20 0.47T (2009 et 2018) (Bruker) 

• Robot passeur d'échantillon. 

Compositional and structural phenotyping Lab

Middle-throughput automated extraction and preparation of polysaccharides (derivatization, hydrolysis).

Extracteurs ASE 350 (Thermo-Fisher, deux extracteurs 2010 et 2012) et plateforme de préparation automatisée (Swing SL robotic workflow station, Chemspeed, 2011)

• Egalement un ensemble d'équipements de pesée automatique, broyage à billes, lyophilisation, etc.

Composition analyses of monosaccharides, linkage determination.

TRACE GC Ultra et TRACE ISQ (Thermo-Fisher, 2011)

• GC et GC/MS

Structural analyses of mono/oligosaccharides. Quantification.

HPAEC, ICS 6000 (Thermo-Fisher) (2019)

• Séparation d’oligosaccharides par chromatographie d'échange anionique 

ACQUITY ELSD FLUO SQD2 (Waters) (2016 et 2020)

• Une chromatographie UPLC couplée à un détecteur Fluo et un spectromètre de masse

Computational solutions

The BIBS platform is developing some computational methods for data processing (spectra or images), with the aim of improving their use or their interpretation. The tools developed are made available to the community.

Esmraldi

• Software library for merging images obtained in MALDI mass spectrometry and MRI. The interest is to facilitate the joint exploitation of the - different - information provided by these two imaging modalities. The library includes methods adapted to the processing of each data (noise reduction, peak picking, normalization, etc.), segmentation methods, image registration, as well as spatial correlative analysis of images from the two modalities.
• Available at : https://github.com/fgrelard/Esmraldi

MorphoLibJ

• Library for processing 2D and 3D images, based on mathematical morphology tools: filtering, segmentation, region analysis, etc.
• Available at : https://github.com/ijpb/MorphoLibJ

SpecOMS

• Allows to interpret the thousands of experimental spectra obtained as part of a proteomic analysis, with the aim of identifying and characterizing proteins on a large scale by mass spectrometry. It is particularly well suited to the reputedly difficult interpretation of spectra from proteins carrying chemical modifications. Thus, the SpecOMS software is capable of comparing tens of thousands of experimental spectra to hundreds of thousands of modeled spectra without filtering on their mass from a protein bank to find similarities and identify the spectra, in a few minutes on a standard workstation.
• Available at : https ://github.com/dominique-tessier/SpecOMS

Oligator

• Graphical interface for drawing the structure of an oligosaccharide and producing the theoretical list of its fragments in MS/MS, based on the usual nomenclature. The tool offers the user great flexibility in the choice of oligosaccharide patterns as well as in the fragmentation parameters, to best approach the conditions of the experiment. To configure chemical substitutions independently of any repository, but also to keep the structure described or subsequently exploit the list of fragments with classic tools (R type), Oligator uses the SMILES (Simplified Molecular Input Line Entry System) notation system. , widespread in chemoinformatics.
• Available at : https://github.com/vlollier/oligator

MzLabelEditor

• Tool to help with the annotation of MS/MS type experimental spectra, with the idea of keeping the annotated spectrum in a library and capitalizing on the interpretation work. The interface makes it possible to preserve, associated with the annotated spectrum, the key information of the experiment (instrument, ionization mode, type of fragmentation, etc.). Annotation of the spectrum is done by placing labels on the peaks of interest. This process can be carried out by comparison to another spectrum, used as a reference (possibly a theoretical spectrum, such as generated by Oligator): the interface allows you to visualize the two spectra and see their peaks in common. It also offers classic spectrum manipulation functionalities (zoom, etc.).
• Available at : https://github.com/vlollier/mzLabelEditor