What we do
Research
The Proteomics Technology Hub develops next-generation, mass spectrometry–based proteomics methods for the Vienna BioCenter campus and for the wider research community. Our current work spans single-cell and structural proteomics, and we are actively moving toward multiomic and spatial, deep visual omics analyses.
Our mission
We build, benchmark and improve proteomics workflows, and transfer mature methods into routine service on campus. Our aim is to develop robust, easy-to-use techniques that are of general value to the field — bridging cutting-edge method development with everyday application for research groups at the Vienna BioCenter and beyond.
Single-cell proteomics
Measuring proteins in individual cells reveals cellular heterogeneity that bulk measurements average away. We develop robust, easy-to-use sample-preparation workflows — from one-pot protocols to automated nanowell arrays — and push sensitivity on the latest instrumentation to quantify thousands of proteins per single cell.
These methods are now being applied to diverse biological questions, from immune and disease cell states to bacterial biology (Leodolter et al, Nature Commun., 2026; Bubis et al., Nature Methods 2025; Matzinger et al., Analytical Chemistry 2023; Ctortecka et al., Molecular & Cellular Proteomics 2023).
Structural proteomics (crosslinking MS)
Crosslinking mass spectrometry captures how proteins fold and interact within their native environment. We advance the throughput and sensitivity of these experiments and develop dedicated software for confident cross-link identification, enabling interactome and structural studies from purified complexes to whole cells (Müller et al., Nature Communications 2025; Bräuer et al., Communications Chemistry 2025; MS Annika: Birklbauer et al. Communications Chemistry 2024).
Future directions
We are extending our toolkit toward multiomics and spatial, deep visual omics — integrating proteomics with complementary molecular readouts and preserving spatial context to map biology at ever-finer resolution.
Open to collaboration
The hub is open to collaborations across the Vienna BioCenter and beyond. If you would like to apply or co-develop these technologies for your research, we would be glad to work with you to drive cutting-edge developments together.
![A typical single-cell proteomics workflow developed and applied at the hub: individual cells are isolated into nanowells, lysed and digested, optionally labeled, and analyzed by nano-LC–mass spectrometry to identify and quantify proteins for each cell. [image created with biorender.com, modified from Matzinger et al., Anal. Chem. 2023]](images/research/scp-workflow.png)
