PhD position in Mass Spectrometry-Based Antibody Analysis

You will join an expert team that pushes the boundaries of mass spectrometry-based technologies to investigate the human immune response. Our lab researches the repertoires of antibodies circulating in our body, aiming to identify antibodies of interests that target microbial antigens and/or represent auto-antibodies. You will focus on the identification of these antibodies by using mass spectrometry based de novo sequencing, machine learning and AI-tools to interpret the data.

Your job
The primary objective of the project is to further develop mass spectrometry-based techniques to sequence and identify circulating antibodies. Our lab introduced innovative methods to enrich antibodies of interest (e.g. anti-viral antibodies) from individual serum samples. You will further develop and optimize these methods, with as special aim to enrich for antigen-specific antibodies. A secondary key objective is to improve bioinformatic and AI tools to analyse the mass spectrometry data and improve the de novo sequencing workflows. Your work will lead to new antibody leads, that can be recombinantly produced and ultimately tested for efficacy and development into therapeutics.

Main responsibilities:

• Perform a combination of biochemistry, analytical chemistry and bioinformatic research to study the humoral immune response.
• Plan and perform experiments, followed by the analysis, interpretation and reporting of data and results.
• Communicate and interact with the research group, as well as with collaboration partners from academia and industry.
• Write scientific publications and present at national and/or international conferences.
• Operate and maintain LC-MS instruments (ZenoToF, TimsTOF and Orbitraps).
• Help the team in laboratory specific tasks whenever needed.

• a position for 18 months (1.0 FTE), with an extension to a total of four years upon successful assessment in the first 18 months;
• a gross monthly salary between € 3.059 and €3.881 in the case of full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU));
• 8% holiday pay and 8.3% year-end bonus;
• a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU.

In addition to the terms of employment laid down in the CAO NU, Utrecht University also offers a range of its own schemes for employees. This includes arrangements for professional development, various types of leave, and options for sports and cultural activities. You can also tailor your employment conditions through our Terms of Employment Options Model. In this way, we encourage you to keep investing in your personal and professional development. For more information, please visit Working at Utrecht University.

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The Utrecht Institute for Pharmaceutical Sciences (UIPS) is the research institute of the department of Pharmaceutical Sciences of Utrecht University. UIPS focuses on processes around discovery, development, and use of drugs and medical nutrition using molecular and technological principles from the Natural and Life Sciences. This research is well positioned in the Faculty of Science to work on basic scientific problems and to translate new findings into potential solutions to urgent societal medical needs, which are addressed in the Faculties of Medicine and Veterinary Medicine. Every year around 400 peer-reviewed articles are published and around 30 PhD candidates defend their thesis. UIPS is partner in several open-source innovation networks.

You will be embedded in the division of Biomolecular Mass Spectrometry and Proteomics. The research in this division focuses on the use of mass spectrometry based enabling technologies to deeply understand the inner workings of cells at the molecular level. Mass spectrometry enables the characterization of molecules that are present in cells and allows thereby the identification, quantification and characterization of proteins and other biomolecules that work together and are involved in all cellular processes. The group houses an excellent infrastructure that includes more than a dozen state-of-the-art mass spectrometers, combined with cell culture facilities and access to microscopes etc. The group is world-renown for mass spectrometry-based proteomics and structural biology, and applies these technologies to study amongst others cancer, auto-immune disorders, immunology, infections, and infectious diseases. Additionally, the group is on the forefront of developing new mass spectrometry based technologies in chemical proteomics, structural biology and the analysis of protein post-translational modifications.