Abstract

Mass spectrometry (MS)-based quantitative phosphoproteomics is a powerful technology for global analysis of cellular signaling networks. In particular, understanding the dynamics of tyrosine phosphorylation (pTyr) is of great importance in eukaryotic cells due to its crucial role in regulating intracellular signaling networks controlling cell fate decisions such as proliferation, migration, differentiation, cell cycle progression and apoptosis. I will present how we optimized and employed quantitative phosphoproteomics technologies to delineate receptor tyrosine kinase (RTK) signaling dynamics activated by different growth factor ligands leading to differential cellular outcome. Reproducible workflows based on phosphopeptide enrichment using TiO2 or pTyr-specific antibodies in combination with label-free quantitation and LC-MS/MS analysis on Q-Exactive Orbitrap type mass spectrometers allowed us to quantify thousands of phosphorylation sites and derive their kinetic profiles as a function of ligand and stimulation time. Using this strategy, we revealed RTK -specific phospho-regulation of key adaptor and signaling molecules, which fine-tune cell migration and proliferation. Based on a multidisciplinary approach, which combines quantitative phosphoproteomics and functional cell-based assays, we identified ligand-dependent mechanisms for the control of RTK signaling and for the specification of long-term cellular outcomes. Our findings underscore the importance of investigating receptor tyrosine kinase signaling networks in a ligand-dependent manner to identify the key regulatory phosphotyrosine sites, which can determine cell fate decisions.