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Reference : UMR5248-CARTOK-002
Workplace : BORDEAUX
Date of publication : Thursday, September 26, 2019
Scientific Responsible name : Pr Caroline Tokarski
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 December 2019
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly
Description of the thesis topic
-Title: PhD fellowship in High Resolution Mass Spectrometry applied to Cultural Heritage
Tenure: Three years
Project running title: Methodological developments based on high resolution mass spectrometry for the analysis of intact proteins, their crosslinking and breakdown in cultural heritage samples
Keywords of the project: high resolution mass spectrometry, intact protein analysis and top-down proteomics, protein crosslinking, cultural heritage, museum collections – i.e. artworks, archeological objects.
The analysis of Cultural Heritage samples is crucial for the understanding of artists' technique, the conservation and the preservation of artworks. The studied artworks are priceless and the sample size available for analysis is extremely low, thus requiring the development of the most efficient, informative and robust analytical methodologies.
The PhD project proposes to decipher the complexity of Cultural Heritage organic materials using unexplored developments in both chemistry and high resolution mass spectrometry (e.g. top down proteomics) to achieve structural information on the biological compounds (i.e. proteins) in their environments and to map their degradation state. One of the challenges is linked to the chemical decoding of the organic molecular network. Applied to the study of artworks, this information will have a major impact on the understanding of artworks' construction, composition and degradation, and will aid in determining preservation conditions (conservation treatment and storage).
This proposed research will exploit the latest technical developments in high-resolution mass spectrometry as well as alternative fragmentation modes (ETD, UVPD) for the study of intact or transformed biomolecules found in cultural heritage material.
The major objectives of this PhD project are the development and optimization of: (i) fully-adapted and original sample preparations tailored to the study of very small sample amounts (trace analysis), to circumvent the complex inorganic/organic nature of the formulated materials of interest and (ii) top down methods to study proteins modifications, breakdowns, cross-linkings and their relationship to the surrounding matrix made of mixtures of organic and inorganic compounds. To help in this complex task, development of customized software solutions will be proposed in collaboration with bioinformatics experts (local and European collaborations).
This PhD project will address specific questions about material manufacture or origin (i.e. to gain knowledge on the formulations of the master artists or societal information) and its degradation state (i.e. effect of particular conservation treatments).
The candidate will have to interact with art conservators, historians and archaeologists from the partners' museums within an interdiciplinary research environment.
The project will require careful development of activities for public engagement as well as writing scientific articles, papers, reports or books, as appropriate.
Place of employment: The Institute of Chemistry and Biology of Membrane and NanoObjects (CBMN), UMR CNR 5248 (Director: S. Lecomte) and the Proteome Platform of Bordeaux (Director: C. Tokarski).
Environment: The project will benefit from the exceptional environment of the CNRS International Associated Laboratory ARCHE with The Metropolitan Museum of Art, New York, U.S.A. (Co-Directors: J. Arslanoglu, C. Tokarski, open in 2019).
Expertise of the laboratory team and platform: “Omics” developments based on high-end technologies applied to various fields (biology, chemistry, medicine, pharmaceutical science, plant science, environment, cultural heritage) from sample preparation (in-gel/ off-gel separation) to (bio)macromolecular identification, targeted/non-targeted quantitative analysis and intact protein characterization using top-down analysis. Website: https://proteome.cgfb.u-bordeaux.fr/en/proteome. Considering Cultural Heritage: head of cross-disciplinary projects (e.g. European JPI-JHEP LeadART 2014-2018), partner of European networks (ETN TEMPERA 2017-2021, ETN PUSHH 2020-2024, IPERION HS 2020-2023), organization of the 1st School and Symposium on Advanced Mass Spectrometry Applied to Cultural Heritage (17-21 June 2019, Palais de la Bourse, Bordeaux) involving a consortium of pioneer researchers in the field (https://www.hrms-heritage2019.org/; http://bss-appliedchemistry.u-bordeaux.fr/en/Bordeaux-Summer-Schools/r969.html).
Equipment available: For analysis: 2 x NanoLC-U3000 RSLC (peptides and proteins)-nanoESI-Orbitrap Fusion Lumos (1 million FWHM; FAIMS; UVPD, ETD, HCD, CID); NanoLC-U3000 RSLC nanoESI-Orbitrap Fusion Lumos (ETD, HCD, CID); MALDI (TRANSMIT AP SMALDI10)-Orbitrap QExactive; MALDI-TOF-TOF Ultraflex III equiped with high mass detector. For method optimization: NanoLC nanoESI-Orbitrap XL (HCD, CID); NanoLC Q-TOF Premier; NanoLC Q-TRAP 5500; Bioinformatic platform: Proteome Discoverer, PEAKS, ProSight PC, MaxQuant, ProteinScape, Byonics and home-made software developed with the Bioinformatic Platform; Equipments for dedicated sample preparation (extraction, purification, quantification).
e « home-made » développés avec l'équipe bioinformatique; Equipement pour la préparation d'échantillon (extraction, purification, quantification).
Constraints and risks
Essential Experience and Skills
Essential skills and experience include:
- Chemistry or biochemistry background
- Demonstrated knowledge of analytical chemistry, in particular, mass spectrometry techniques (theoretical and experimental).
- Demonstrated knowledge of protein (bio)chemistry and understanding of processes of protein degradation, both spontaneous and enzymatic.
- Knowledge of, and demonstrated experience in designing, implementing, and optimizing: (i) analytical methods for protein characterisation, (ii) biochemical methodologies for sample preparation for protein analysis.
- Demonstrated experience in tandem MS-based proteomics data generation and analysis is a valued plus.
- Demonstrated experience in interpretation and analysis of MS/MS data, protein sequence reconstruction and statistical validation of the results is a valued plus.
- Ability to comfortably work in a highly interdisciplinary environment with colleagues with different scientific and non-scientific backgrounds
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