One of the key challenges in proteomics is that it is far more complex and dynamic than genomics and requires a technology that is as high throughput as it is cost efficient. Recent advances in liquid chromatography and mass spectrometry have dramatically increased sample throughput and reduced costs, enabling the analysis of up to 100 samples per day at a fraction of previous costs. This progress has made mass-spec proteomics useful for routine analysis in drug development and clinical research.
Yuehan Feng, Senior Director of Application Sciences at Biognosys AG stated that his company has set up a mass spec-based platform as a CRO service provider to analyse tissue and plasma samples, mainly focusing on case studies in the field of immuno-oncology.
Feng presented two case studies. The first involves analysing FFPE tissue samples from endometrial cancer patients in an immuno-oncology trial. Using mass spec, the team identified upregulated extracellular matrix proteins, particularly collagen, in non-responders to therapy. This finding was validated with microscopy, suggesting that high collagen content may hinder immune cell infiltration and thus treatment efficacy.
The second case study focuses on plasma proteomics in a lung cancer trial. The team developed a platform to enrich low-abundance proteins, enabling the quantification of thousands of proteins and inflammatory markers. By summarising complex data into clinically relevant pathways, the approach supports biomarker discovery and clinical decision-making.
Overall, the presentation highlights how advances in mass spec technology are transforming proteomics into a routine, actionable tool for both research and clinical practice.
