Z03 - Proteomics platform for protein interaction mapping

Principal Investigators

Prof. Dr. Christian Freund, FU Berlin

Dr. Fan Liu, FMP

In the central project Z03 we have established a robust proteomics platform that allows us to combine specific purification approaches with quantitative proteomics in the coming funding period. Combining protein ligation techniques for immobilization of target proteins with 18O/16O-labelling will extend the interactome analysis in the coming funding period to primary cells and organotypic tissue cultures in several projects of the CRC. Detection of post-translational modifications such as palmitoylation or phosphorylation can be combined with the quantitative methods to yield compositional information on membrane scaffolds.


  • C. Barucker, A. Sommer, G. Beckmann, M. Eravci, A. Harmeier, C.G. Schipke, D. Brockschnieder, T. Dyrks, V. Althoff, P.E. Fraser, L.N. Hazrati, P.S. George-Hyslop, J.C. Breitner, O. Peters and G. Multhaup, J. Alzheimers Dis. 2015, 44, 613-24. 

  • Kuropka, B., Royla, N., Freund, C., Krause, E. (2015) Sortase A mediated site-specific immobilization for identification of protein interactions in affinity purification-mass spectrometry experiments. Proteomics. 15, 1230-1234.

  • Stephanowitz, H., Lange, S., Lang, D., Freund, C. & Krause, E. An improved two-dimensional reversed phase-reversed phase LC-MS/MS approach for identification of peptide-protein interactions. J. Proteome Res. 11, 1175-83 (2012)

  • Eravci, M., Sommer, C.& Selbach, M. IPG strip-based peptide fractionation for shotgun proteomics. Methods Mol. Biol. 1156, 67-77 (2014)

  • Lange, S., Sylvester, M., Schümann, M., Freund, C. & Krause, E. Identification of phosphorylation-dependent interaction partners of the adapter protein ADAP using quantitative mass spectrometry: SILAC vs (18)O-labeling. J. Proteome Res. 9, 4113-22 (2010)

  • Lehmann, R., Meyer, J., Schuemann, M., Krause, E. & Freund, C. A novel S3S-TAP-tag for the isolation of T-cell interaction partners of adhesion and degranulation promoting adaptor protein. Proteomics 9, 5288-5295 (2009)

  • Kofler, M., Schümann, M., Merz, C., Kosslick, D., Schlundt, A., Tannert, A. Schaefer, M., Lührmann, R., Krause, E. and Freund, C. (2009). Proline-rich sequence recognition I: Marking GYF and WW domain assembly sites in early spliceosomal complexes. Mol. Cell. Proteom. 8 2461-2473.

  • Schlundt A, Sticht J, Piotukh K, Kosslick D, Jahnke N, Keller S, Schuemann M, Krause E, Freund C. (2009). Proline-rich sequence recognition II: proteomic analysis of TSG101-UEV interactions. Mol. Cell. Proteom. 8, 2474-2486.