Novel workflows for identification of intracellular biomarkers by shotgun proteomics

Advisor: Boris Macek

Location: University of Tübingen

Workflow in a typical proteomics experiment. Proteins are extracted from a tissue or cell line and digested by a protease into peptides. The resulting peptide mixtures are separated and analyzed by mass spectrometry; peptide masses are recorded in a "full scan" or "MS" spectrum; peptide ions are fragmented and the fragment ions are recorded in an "MS/MS" spectrum. Both levels of information are used in protein database search and peptide identification.

Workflow in a typical proteomics experiment. Proteins are extracted from a tissue or cell line and digested by a protease into peptides. The resulting peptide mixtures are separated and analyzed by mass spectrometry; peptide masses are recorded in a "full scan" or "MS" spectrum; peptide ions are fragmented and the fragment ions are recorded in an "MS/MS" spectrum. Both levels of information are used in protein database search and peptide identification.

Prof. Boris Macek advertises a PhD position in his group at University of Tübingen, Germany. This PhD position is a part of the BUG-ID Marie Skłodowska-Curie Doctoral Training Network (DN), funded by the European Commission. BUG-ID consortium has a mission to improve infection diagnostics. All BUG-ID PhD students will be trained in an interdisciplinary environment and experience a collaboration among academia, healthcare and the private sector.

The candidate hired for this position will work on development and application of novel workflows for MS-based identification of intracellular protein biomarkers in low abundance samples of bacterial pathogens and host cells. Graphene-based strategies will be developed to facilitate chemical rupture and homogenization of small numbers of bacterial and eukaryotic cells. This pipeline will be coupled to state-of-the-art mass spectrometry analyses of proteins and their post-translational modifications, including downstream bioinformatics. Biological applications will include work on bacterial communities (incl. metaproteomics), host cells and their signal transduction under various perturbations.

The specific tasks will include:

Studying the available literature in the field and formulating own scientific hypotheses and questions
Conducting scientific experiments and analysing data
Writing peer reviewed scientific publications
Actively interacting and collaborating with other partners in the consortium
Participating in consortium outreach activities
Completing courses and training required for being awarded the PhD degree

More information about the research of Boris Macek and a selection of recent publications can be found on his faculty page.

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Application deadline: 19 January 2026