The main mission of the Proteomics Core Facility is to empower the scientific community by providing innovative proteomics solutions. We aim to facilitate groundbreaking research by overcoming challenges such as limited cell quantities, contaminant removal, and sample loss—factors that have traditionally hindered protein quantification when working with small sample amounts.
Spatial proteomics, awarded as Method of the year 2024 by Nature¹, offers unique insights into the distribution of proteins within tissues, which is crucial for a deeper understanding of complex biological processes such as cellular and tissue development, disease progression mechanisms, and biomarker discovery.
We have developed a generalizable spatial proteomics pipeline based on the DVP strategy (Deep Visual Proteomics²). Recognized for its impact³, our approach addresses key challenges through:
- Laser-Cut Tissue Microdissection – A cost-effective alternative to automated methods, allowing precise selection of regions of interest at the cellular level.
- Bottom-Up Mass Spectrometry (MS) Analysis – Utilizing data-independent acquisition (DIA) with various optimized methods specifically designed for low-input samples.
- Optimized Sample Preparation – Minimizing sample loss and contaminant interference, enabling extended protein characterization from as little as a few dozen cells.
- Extended Protein Quantification – Effective and reliable quantification of up to 7,000 proteins from minimal starting sample quantities.
- Efficient Workflow – Optimized processes ensure timely data delivery while maintaining high-quality results.
- Versatility – Adaptable to various sample types, animal and human tissues, biopsies, organoids, and organs-on-chip.
- Fixation Compatibility – Supports various fixation methods, including FFPE blocks, fresh frozen, fixed frozen, and PFA/GA fixatives.
- Cost-Effective – An affordable analytical solution without compromising data quality.
Researchers are invited to utilize our affordable spatial proteomics pipeline for their projects. We offer:
- Consultation: Discuss your research goals and how our pipeline can assist,
- Assist you in your experimental design to meet the requirement for MS analysis,
- Customized Workflow: Adapt the pipeline to suit your specific samples and objectives,
- Expert Support: Guidance from our experienced team throughout the project
- Analysis Support: Assistance with data analysis and interpretation.
Interested in learning more or in embarking in Spatial Proteomics or Spatial Omics?
Reach out to our Spatial Team:
Spatial Proteomics:
- Email: Thibault Courtellemont (Project Leader Spatial Proteomics) ; Maria Pavlou (Head of PCF) ;
- Phone:+41 21 693 18 27
- Address: Plateformes Technologiques – SV, EPFL, Station 15, 1015 Lausanne, Switzerland
- Anjalie Schläppi (System Specialist Spatial Transcriptomics), Jessica Sordet-Dessimoz (Head of HCF), Bastien Mangeat (Head of GECF)
Literature:
1. Method of the Year 2024: spatial proteomics. Nat Methods 21, 2195–2196 (2024). https://doi.org/10.1038/s41592-024-02565-3
2. Mund, Andreas et al. “Deep Visual Proteomics defines single-cell identity and heterogeneity.” Nature biotechnology vol. 40,8 (2022): 1231-1240. doi:10.1038/s41587-022-01302-5
3. PCF development awarded as best oral presentation during LS2 Proteomics 2024