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Platform technologies for the analysis of glycosaminoglycans and mediator proteins

Prof. Martin von Bergen, Johannes Schmidt, Florent Jouy, Nagarajan Kumaran

Within the scope of subproject Z4, qualitative and quantitative protein analysis is carried out as a service for all Transregio 67 projects. For this purpose, the development of methods for the highly sensitive detection of low molecular weight proteins as well as highly modified proteins, including cytokines and growth factors, is being developed.

  • The identification and quantification of proteins extracted by microdialysis from injured tissue during the wound healing process by means of nano-HPLC / nano-ESI mass spectrometry
  • Protein expression analysis from cell models
  • Enrichment and determination of glycosylation
  • Protein separation by 1D / 2D-SDS-PAGE or HPLC (size exclusion chromatography, C4 reverse phase chromatography)
  • Implementation of trainings / introduction of TRR67 employees.

 

Project-related Publications
  1. Hofmann T, Fischer AW, Meiler J, Kalkhof S. Protein structure prediction guided by crosslinking restraints - A systematic evaluation of the impact of the crosslinking spacer length. Methods 2015 May 15. pii: S1046-2023(15)00207-8. doi: 10.1016/j.ymeth.2015.05.014. [Epub ahead of print]
  2. Hofmann T, Samsonov SA, Pichert A, Lemmnitzer K, Schiller J, Huster D, Pisabarro MT, von Bergen M, Kalkhof S. Structural analysis of the interleukin-8/glycosaminoglycan interactions by amide hydrogen/deuterium exchange mass spectrometry. Methods. 2015 Feb 26. pii: S1046-2023(15)00054-7. doi: 10.1016/j.ymeth.2015.02.011. [Epub ahead of print] PMID: 25726910
  3. Jouy F, Müller SA, Wagner J, Otto W, von Bergen M, Tomm JM. Integration of conventional quantitative and phospho-proteomics reveals new elements in activated Jurkat T-cell receptor pathway maintenance. Proteomics. 2015 Jan;15(1):25-33. doi: 10.1002/pmic.201400119. Epub 2014 Dec 10.
  4. Kalkhof S, Förster Y, Schmidt J, Schulz MC, Baumann S, Weißflog A, Gao W, Hempel U, Eckelt U, Rammelt S, von Bergen M. Proteomics and metabolomics for in situ monitoring of wound healing. Biomed Res Int. 2014;2014:934848. doi: 10.1155/2014/934848. Epub 2014 Aug 4. PMID:    25162036
  5. Blumert C, Kalkhof S, Brocke-Heidrich K, Kohajda T, von Bergen M, Horn F. Analysis of the STAT3 interactome using in-situ biotinylation and SILAC. J Proteomics. 2013 Dec 6;94:370-86. doi: 10.1016/j.jprot.2013.08.021. Epub 2013 Sep 4. PMID: 24013128
  6. Möbius K, Nordsieck K, Pichert A, Samsonsov SA, Thomas L, Schiller J, Kalkhof S, Pisabarro MT, Beck-Sickinger AG, Huster D. Investigation of lysine side chain interactions of interleukin-8 with heparin and other glycosaminoglycans studied by a methylation-NMR approach. Glycobiology. 2013;23:1260-9.
  7. Baumann S, Kalkhof S, Hackermüller J, Otto W, Tomm JM, Wissenbach DK, Rolle-Kampczyk U, von Bergen M. Requirements and perspectives for integrating Metabolomics with other omics data. Current Metabolomics. 2012; in press.
  8. Müller SA, van der Smissen A, von Feilitzsch M, Anderegg U, Kalkhof S, von Bergen M. Quantitative proteomics reveals altered expression of extracellular matrix related of proteins of human primary dermal fibroblasts in response to sulphated hyaluronan and collagen applied as artificial extracellular matrix. J Mater Sci Mater Med. 2012;23:3053-65.
  9. Salbach J, Kliemt S, Rauner M, Rachner TD, Goettsch C, Kalkhof S, von Bergen M, Möller S, Schnabelrauch M, Hintze V, Scharnweber D, Hofbauer LC. The effect of the degree of sulfation of glycosaminoglycans on osteoclast function and signaling pathways. Biomaterials. 2012;33:8418-29.
  10. Goettsch C, Kliemt S, Sinnigen K, von Bergen M, Hofbauer LC, Kalkhof S. Quantitative proteomics reveals novel functions of osteoclast-associated receptor in STAT signaling and cell adhesion in human endothelial cells. J Mol Cell Cardiol. 2012;53:829-37.
  11. Abburi R, Kalkhof S, Oehme R, Kiontke A, Birkemeyer C. Artificats in amine analsis from anodic oxidation of organic solvents upon electrospray ionization for mass spectrometry. Eur J Mass Spectrom. 2012;18:301-12.
  12. Dautel F, Kalkhof S, Trump S, Michaelson J, Beyer A, Lehmann I, von Bergen M. DIGE based protein expression analysis of B[a]P-exposed hepatoma cells reveals a complex stress response including alterations in oxidative stress, cell cycle control, and cytoskeleton motility at toxic and subacute concentrations. J Proteome Res. 2011;10:379-93.
  13. Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA. 2011;17:578-94.
  14. Rockstroh M, Müller SA, Jende C, Kerzhner A, von Bergen M, Tomm JM. Cell frationation – an important tool for compartment proteomics. J Integr OMICS. 2011;1:135-43.
  15. Müller SA, Kohajda T, Findeiß S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S. Optimization of parameters for coverage of low molecular weight proteins. Anal Bioanal Chem. 2010;398:2867-81.
  16. Mörbt N, Mögel I, Kalkhof S, Feltens R, Röder-Stolinski C, Zheng J, Vogt C, Lehmann I, von Bergen M. Proteome changes in human bronchoalveolar cells following styrene exposure indicate involvement of oxidative stress in the molecular-response mechanism. Proteomics. 2009;21:4920-4933.