Biotechnology Programme

Proteomics Core Unit

Head of Unit:  Javier Muñoz
Research highlights

Throughout 2016, the Unit continued its mission of implementing and optimising quantitative proteomic strategies. More specifically, we have introduced a new fractionation method using high pH reverse phase micro columns, which minimises sample loss and thus is highly suitable for low amounts of material. We used this approach to post-fractionate samples enriched in phosphopeptides, substantially increasing the number of identifications. This workflow was used to determine phosphorylation dynamics upon activation of WT and kinase- mutant platelets (in collaboration with the Cell Division and Cancer Group), as well as to identify potential substrates of CDK8 involved in the establishment of ground state pluripotency (in collaboration with the CNIO Tumour Suppression Group). More recently, in collaboration with the Metabolism and Cell Signalling Group at the CNIO, we also used phosphoproteomics to better understand the molecular mechanism of the mTOR pathway. Together with the CNIO Genomic Instability Group, we are using a recent approach, named Thermal Proteome Profiling (Savitski et al., see FIGURE), to identify protein targets of certain inhibitors (e.g. target deconvolution). We have also performed several AP-MS/MS experiments for different proteins (STAG1, STAG2, PDS5A, PDS5B) belonging to the cohesion complex (with CNIO’s Chromosome Dynamics Group). Likewise, we have identified a large protein network (more than 300 proteins) that interacts with the RNA pol II complex (in collaboration with the Tumour Suppression Group). Over the last few years, the analysis of the protein content of exosomes has received great interest in the context of metastasis and the pre-metastatic niche. Along this line, we are conducting several proteomic analyses of exosomes from different origins in collaboration with CNIO’s Microenvironment and Metastasis Group, the Gastrointestinal Cancer Clinical Research Unit and the Melanoma Group.