Domain: mass spectrometry-based proteomics; protein biochemistry; methods development

Keywords: quantitative mass spectrometry; multiplex TMT-labelling; thermal proteome profiling; thermophilic bacteria; protein stability

Promotor: Christine Carapito

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

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

Funding: HORIZON-MSCA-2022-DN project PROHITS

In this project, elucidating temperature-induced proteome changes in thermophiles will be instrumental to create efficient and green industrial processes. Mass spectrometry-driven thermal proteome profiling (TPP) is the method of choice to generate temperature-dependent proteome-wide information on protein stability. In collaboration with DC2 at VUB, who will cultivate thermophiles, and DC7, who will develop high performing MS methods, you will optimize methods to conduct TPP experiments on the selected thermophiles. Strain-specific temperature gradients and efficient lysis protocols will need to be developed prior to multiplexed, TMT-labelled MS analysis. You will also be involved, with DC4 at UiB, in subsequent TPP data interpretation, which revolves around the creation of melting curves with the highest possible resolution and proteome coverage. Moreover, you will be able to integrate the effect of post-translational modifications on TPP-derived protein stability thanks to the AI-based data interpretation tools developed at VIB (DC3).

After TPP bulk experiments on selected thermophiles, together with DC7 and DC9, you will explore the response to temperature changes at the single cell proteome level. This challenging exploration should enable a view on proteome variability in thermophiles in general, and will ultimately help tailor optimal factory cells.

Besides your work in Strasbourg, you will also have two secondments. The first is a one-month secondment to learn about the operation of the latest generation timsTOF instruments in-house at the Bruker Daltonics site in Bremen, Germany. The second secondment, of two months, will happen later in the project, once you will have acquired most of the TPP data, at VUB in Brussels, Belgium, to work closely with the microbiologists there on advanced data interpretation in biological context.

The project is part of a computational/experimental EU MSCA-DN project with a total of 10 Ph.D. students, and is highly interdisciplinary. Your role in the project will be pivotal, as you will have to learn and apply the best experimental and computational methods developed by DC2, DC7 and DC3, and provide DC4 with high quality data. Knowledge of protein biochemistry is essential, and a solid background in mass spectrometry and proteomics will be an asset. 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