Domain: Microfluidics, automation, image analysis, method development, MS-based proteomics

Keywords: Imaged-based single cell isolation, image analysis algorithms, acoustic-based microfluidics, software development, automation engineering, MS single cell proteome analysis

Promotor: Anjali Seth

Starting date: 1st of September 2024, for a period of 3 + 1 years

Location: Cellenion, Lyon, France ; LSMBO; IPHC; CNRS, Université de Strasbourg, Strasbourg, France.

Funding: HORIZON-MSCA-2022-DN project PROHITS

In this project, you will develop new tools to help improving technological tools such as imaged-based single cell isolation and associated sample preparation workflows. Single cell proteomics mass spectrometry (MS)-based analyses are becoming more and more popular and are considered as cutting-edge techniques in proteomics today. In the framework of this project, you will have to develop innovative solution to adapt the current tools to the analysis of single procaryotic cells. Working with these cells poses new challenges in term of sensitivity both of sample preparation in the frontend as well as the analysis in the backend. You will be in charge of improving the image-detection algorithms used to better detect bacteria (below 1µm in diameter) as well as developing and implementing any relevant microfluidic strategy to improve the isolation and sample preparation relevant for these cells prior to tandem mass spectrometry (LC-MS/MS) analyses.

Your goal will be to implement any relevant strategies to our liquid handler robotic system to facilitate the adoption of these new workflow by the community. You will at Cellenion set up and optimize cell isolation and sample preparation protocols for prokaryote cells, while testing existing Cellenion image processing algorithms, with the complete protocols evaluated by nano LC-MS/MS in Strasbourg.

Throughout the duration of this doctoral training, you will be working in close collaboration with two other DC (DC6 and DC7) based in Strasbourg, France and will have to travel to Strasbourg regularly to exchange with the two other DN. After optimising sample preparation protocols with DC6, you will work on LC-MS/MS acquisition method developments for the analysis of low amounts of material with DC7 on timsTOF instruments at CNRS. You will also participate in evaluating the data processing workflows from DC3, and the associated visualisations developed by DC4.

Finally, you will explore the feasibility of TPP experiments on single cells together with DC6 and DC7. Your secondment will be at VIB (Ghent, Belgium) to work with DC3 to discuss further perspectives for optimized data analysis for single cell proteomics, including image analysis (3 months, month 36).

The project is part of a computational/experimental EU MSCA-DN project with a total of 10 Ph.D. students and is highly interdisciplinary. Good knowledge, ideally with previous experience, in microfluidics, image analyses and engineering are essential. Background in acoustics, protein biochemistry and mass spectrometry will be a bonus. Candidates must be motivated to learn about all disciplines relevant to the project.

Applications must be submitted online in English following the instructions and respecting the conditions at https://bit.ly/prohits. The deadline for applications is 15/03/2024 at 23:59 (CET)

Further general information about the PROHITS project: http://prohits.eu