External and internal signals are integrated in cells via signal transduction cascades of proteins that are regulated by various reversible protein modifications. Among the most important post-translational protein modifications are phosphorylation on serine, threonine and tyrosine residues, as well as (ε)-N-acetylation and ubiquitination on lysine residues. Enzymes catalyzing the reactions that add and remove these adducts play a central role in signaling networks and are targets of novel drug development efforts for a multitude of diseases such as cancer, immune disorders, psychiatric disease and diabetes.

In the Proteomics Platform we study the physiological function of these protein modifications together with our collaboration partners by means of quantitative mass spectrometry techniques that employ SILAC or iTRAQ labeling. Recent improvements in the resolution and sensitivity of mass spectrometers make these instruments ideally suited for quantitative discovery-type analyses of protein modifications. In a typical global phospho-proteome experiment that utilizes proteome-level fractionation and subsequent enrichment of phosphorylated peptides, more than 10,000 phosphorylation events can be quantified using the latest generation of instruments. In addition, affinity enrichment with antibodies directed against (ε)-N-acetyl lysine or ubiquitin-modified lysine yields quantitative information of several hundred of acetylation and ubiquitination sites, respectively. The interdisciplinary nature of the platform — we have scientists who specialize in computational techniques for proteomics — has allowed us to develop tools for confident peptide identification, modification-site localization and quantification.

Examples of collaborative projects include:

  • Analysis of phosphorylation and ubiquitination signalling in innate immune cells
  • Global phosphorylation analysis of k-Ras dependent cancer cells
  • Effects of kinase inhibitor treatment on phosphorylation signaling in various model systems such as neural progenitor cells, pancreatic alpha-cells and immune cells.