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Juri Rappsilber  

Juri Rappsilber

My interest in proteomics and the structure of protein complexes dates from my work as a PhD student in the lab of Matthias Mann at EMBL from 1997-2001, externally supervised by Michael Karas. As one of the first, I combined cross-linking and mass spectrometry for the structural analysis of a protein complex [1]. The principle power of the approach was immediately clear. However, so where many technological limitations. It was to take me nearly ten years, three of which together with my own group, to solve one of the major limitations: the automated interpretation of the mass spectrometric data of cross-linked peptides. Before achieving this, I learned as a PhD student at EMBL and in collaboration with Angus Lamond about molecular biology. I conducted the bioinformatic analysis as part of the first proteomic analysis of the human spliceosome [2], the first analysis of a large protein complex by proteomics, and went on to characterize one of the identified factors, SPF30, in detail [3]. The similarity of SPF30 to SMN led to long term collaborations with Gideon Dreyfuss and Liveo Pellizzoni. Furthermore, I engaged into Sudoku for mass spectrometrists, the development of methods for the analysis of protein modifications [4, 5].

As a postdoc, in 2001-2003, still in the Mann lab but then at CEBI in Odense, Denmark, I revisited the spliceosome to find over 300 proteins, of which 100 were previously uncharacterized or entirely unknown [6]. This study doubled the number of proteins known to be involved in the processing of pre-mRNA. It superseded our previous study of the spliceosome by almost one order of magnitude in the number of identified proteins (312 instead of 42). Incidentally, this study addressed for the first time the question of stoichiometry in a complex protein mixture. To enable this work I set up and partially reinvented sample preparation and LC-MS/MS together with Yasushi Ishihama. This work also lead me to wonder, what it actually meant, to identify a protein in proteomics [7], a question that still is unsolved.

In 2003, I moved to IFOM, Milan, to start my own group. We succeeded with the proof-of-principle for the automated interpretation of the mass spectrometric data of small, cross-linked protein complexes [8]. In 2006, my lab relocated to the Wellcome Trust Centre for Cell Biology. We now focus on the work with large cross-link datasets and large databases. Our aim is to develop cross-linking, mass spectrometry and bioinformatics into a structure and network analysis tool to investigate a large and insoluble protein complex: chromatin. For this, also a number of principle questions need to be solved such as how to optimize the confidence in protein identifications, how to determine the stoichiometry of proteins in a complex mixture and how to determine the completeness of an analysis. Our interest in chromatin has also resulted in a long term collaboration with BRIC, Copenhagen.