Protein and Cell Biology

Being integrated into the Proteomics and Mass Spectrometry Core Facility, our research focuses on the study of system-wide protein regulation using (mostly, but not exclusively) mass spectrometry-based technology. We have developed a LC-MS/MS based method for the protein profiling of circulating extracellular vesicles in blood plasma. On the same line, we have established an immunopeptidomics/proteogenomics pipeline in order to identify antigenic peptides presented on the cell surface by the MHC-I complex. Furthermore, we are able to analyse samples with low cell numbers, down to a single cell. The idea is to offer comprehensive diagnostic methods for biomedical research in the context of leukemia, cancer, cardiovascular and pneumological disease. Our laboratory is furthermore equipped with a 96-channel and a one-arm liquid handling robots on which phosphopeptide enrichment and magnetic bead-based methods are implemented.

Bioinformatics

Bioinformatics students possibly interested in joining our lab for a project should sent an email to anne-christine.uldry at unibe.ch and manfred.heller at unibe.ch, stating the following information:

*) Type of project: master thesis, research project…
*) Time frame for the project (start in Sept/January for 6 months, etc.)
*) Particular wishes, like skills to learn (neural networks? Single cell proteomics ? mass spec data validation?  downstream data analysis?  etc.)
*) Your programming skills

The poster shown at the genomics day is reproduced here below.

In a nutshell: as a core facility, most of the data we produced are not owned by us, but by our clients. Joining on a specific client project is possible, provided the clients give their consent and the project suits their time frame.

Some data however are owned by us, and were produced within the framework of our own particular research interests (phosphoproteomics, immunopeptidomics and extracellular vesicles).  Further data could be produced synthetically, and/or obtained from the public repositories.

We can make a short but concrete proposal once we have the information above, which can be in time further discussed.