Juri Rappsilber

About Juri Rappsilber

Juri Rappsilber studied chemistry at the Institute of Technology, Berlin (Germany), Strathclyde University, Glasgow (UK) and with Tom Rapoport, Harvard Medical School, Boston (USA). In 2001, he earned his Ph.D. jointly from EMBL Heidelberg and the Johann Wolfgang Goethe University, Frankfurt (Germany) working in the laboratory of Matthias Mann on the mass spectrometric analysis of protein complexes. He completed a postdoctoral fellowship at the University of Southern Denmark, Odense before starting his independent career as a group leader at IFOM, Milan (Italy) in 2003. In 2006, Juri Rappsilber joined the Wellcome Trust Centre for Cell Biology in the Institute of Cell Biology at the University of Edinburgh. In 2009, Juri Rappsilber became a Senior Research Fellow of the Wellcome Trust, in 2010 he was appointed Professor of Proteomics in Edinburgh and in 2011 Professor of Bioanalytics in Berlin.

Research Overview

Juri Rappsilber is a pioneer in developing methods for the qualitative and quantitative analysis of proteins in complex mixtures by mass spectrometry, with special emphasis on protein-nucleic acid (RNA and DNA) and protein-protein interactions. Proteins and their interactions are at the heart of most biological processes and if erroneous cause diseases such as cancer or neurodegenerative diseases.

Juri Rappsilber’s interests are focused on combining chemistry and informatics with biological mass spectrometry to expand the frontiers of our current knowledge on how cells work.

Juri Rappsilber’s lab is working on novel methods for identifying and quantifying the interactions and the accurate sites of interaction of proteins with other proteins, DNA and RNA. This makes use of chemical cross-linking to preserve non-covalent interactions for their analysis by mass spectrometry and novel computer algorithms to automatically interpret the mass spectrometric data.

Another goal of the lab’s research is the development and application of biochemical and computational methods in conjunction with mass spectrometry to study chromatin-associated processes in health and disease.

Key achievements
Chromatin proteomics

  • The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics. Cell 142, 810-821, 2010.[Press release]

Protein-protein interactions

  • Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J 29, 717-726, 2010.
  • Structural analysis of multiprotein complexes by cross-linking, mass spectrometry, and database searching. Mol Cell Proteomics 6, 2200-2211, 2007.
  • A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry. Anal Chem 72, 267-275, 2000.

Proteomics fundamentals: StageTips, Stoichiometry, SILAC in yeast

  • A genetic engineering solution to the “arginine conversion problem” in stable isotope labeling by amino acids in cell culture (SILAC).Mol Cell Proteomics 9, 1567-1577, 2010.
  • Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2, 1896-1906, 2007.
  • Modular stop and go extraction tips with stacked disks for parallel and multidimensional peptide fractionation in proteomics. J Proteome Res 5, 988-994, 2006.
  • Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 4, 1265-1272, 2005.
  • Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem 75, 663-670, 2003.
  • Large-scale proteomic analysis of the human spliceosome. Genome Res 12, 1231-1245, 2002.
  • What does it mean to identify a protein in proteomics? Trends Biochem Sci 27, 74-78, 2002.