Proteomics

Our research is centered around the systematic study of the biogenesis of the proteome of mitochondria and peroxisomes and the integration of these vital organelles into larger signaling networks in yeast and human cells. In a complementary line of research, we are systematically studying protein kinase- and protein phosphatase-dependent signalling networks in mammalian cells to decode intricate substrate-kinase/-phosphatase relationships on a system-wide level. We are here in particular interested in signalling processes involved in mechanical stress protection. To characterize these dynamic organellar and signalling systems in a cellular context, we design multi-faceted and integrative proteomics approaches that also allow for specifically addressing cross-scaling biological questions. We here build on our expertise in quantitative, functional, and structural proteomics methodologies including

• High-resolution organelle proteomics
  • subcellular and suborganellar protein profiling
  • membrane complexome and topology profiling
  • organellar proteome dynamics and ImportOmics
• Interaction and proximity proteomics
  • quantitative affinity purification-mass spectrometry (qAP-MS)
  • in vivo proximity labelling techniques (APEX, BioID)
• Structural proteomics
  • cross-linking mass spectrometry (XL-MS)
  • Native MS
• Signalling proteomics
  • global, quantitative and time-resolved phosphoproteomics
  • quantitative redox proteomics using thiol trapping technology
  • further PTM analysis (e.g. methylation, ubiquitination)
• Quantitative proteomics
  • targeted MS using parallel reaction monitoring (PRM)
  • stable isotope labelling techniques (SILAC, dimethyl, TMT, ICAT)
  • label-free and absolute quantification