Martin Pabst Group


The Microbial Proteomics Group develops novel mass spectrometric approaches and data processing pipelines to explore the remarkable diversity of microbes and their communities they live in.

Prokaryotes—the unseen majority on our planet—encompass an enormous metabolic and biochemical diversity. However, only a small fraction of this potential has been discovered and explored for their use in biotechnology to date (e.g., novel enzymes or valuable compounds).

Our laboratory is equipped with micro- and nano-flow chromatographic systems coupled to state-of-the-art high-resolution mass spectrometers (GC-MS and LC-Orbitrap-MS instruments).


Environmental proteomics

In nature, microbes live in diverse communities that fundamentally impact human health and are responsible for global processes, such as the biogeochemical cycles. METAPROTEOMICS—the large-scale identification and quantification of proteins from complete microbial communities—is a powerful technology for measuring the link between protein diversity, expressed metabolic pathways and ecological functions. We aim to advance metaproteomics approaches and expand this emerging technology into new fields of microbial ecologies.

If you want to find out more, please have a look at our recent Cell Systems paper Quantitative profiling of microbial communities by de novo metaproteomics

Prokaryotic protein glycosylation

Glycosylation—the covalent attachment of carbohydrate chains to proteins—is one of the most abundant but also most diverse protein post-translational modifications found in nature.

PROTEIN GLYCOSYLATION is fundamental to all domains of life, but the many biological roles protein glycosylation serves in bacteria and archaea have yet to be explored. Moreover, the large diversity of carbohydrate structures produced by prokaryotes offer significant opportunities for new applications in biotechnology and industry. Our focus lies on establishing new large-scale discovery approaches that tackle the large chemical diversity and strain variability expressed in prokaryotes.

Please check our recent paper in Chemical Science (HOT articles February) about the phylogenetic distribution of remarkable nine-carbon sugars (sialic acids) and our recent preprint featuring unique anammox surface layers!

Industrial proteomics

YEAST PROTEOMICS: Saccharomyces cerevisiae is one of the best-studied eukaryotic model cells and increasingly used as a cell factory in industry. We establish and apply new approaches to identify and quantify protein dynamics and covalent protein modifications in yeast. The proteome shows a vastly higher diversity compared to the genome, which is by a significant proportion due to covalent protein modifications (e.g., for fast regulation of intermolecular interactions) or by tuning of enzyme activities. Our yeast proteomics activities are in collaboration with the Daran-Lapujade Lab (yeast synthetic biology).

Please have a look to our recent FEMS yeast research review (articles making impact 2020): Shot-gun proteomics: why thousands of unidentified signals matter

HOST CELL PROTEOMICS: We establish novel mass spectrometric approaches for monitoring host cell protein removal, with the goal to accelerate downstream process development. This project is being performed in collaboration with the Ottens Lab.

Martin Pabst

Assistant Professor