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CECAD/CMMC Proteomics Facility

Proteins are essential building blocks of living organisms and main components of nearly all metabolic pathways. The Proteome of a cell is a highly dynamic entity and systematic protein profiling is important to study cellular regulations under regular and diseased conditions. The proteomics platform uses high performance liquid chromatography in combination with modern mass spectrometers (LC-MS) for an unbiased and comprehensive proteome analysis of complex biological systems.

Services: The CECAD/CMMC Proteomics Facility applies state-of-the-art methods of mass spectrometry to analyze the aging process on the protein level. The proteomics platform uses the shotgun proteomics approach. Here, sample processing starts with cell lysis, fractionation, and digestion of the proteins. The resulting peptide mixture is separated by reversed phase chromatography using nano-UHPLC system. As the peptides elute from the column they are ionized and detected by a Quadrupole Orbitrap hybrid mass spectrometer. In data-dependent acquisition mode masses of intact peptides are detected by MS scans which are followed by peptide fragmentation to determine the sequence and post-translational modifications of the peptides.

Scientific achievements: To profile the dynamics of protein expression and changes in protein modification with maximum sensitivity the CECAD/CMMC Proteomics Facility is equipped with latest generation liquid chromatography and mass spectrometers. In continuation of the successful Orbitrap technology, the proteomics platform is now equipped with two Q Exactive Plus LC-MS/MS systems (Thermo Scientific). These instruments combine quadruple precursor ion selection with high-resolution accurate-mass Orbitrap detection. The superior quality of these instruments enables the analysis of complex biological samples in depth and with great confidence.

Future plans: The proteomics platform will continue to develop and apply state of the art liquid chromatography and mass spectrometry. This includes high throughput proteomic analysis of biological samples, the discovery of protein-protein complexes via crosslinkers, and the global identification of post-translational modification (PTM), including phosphorylation and ubiquitination. The facility will develop analytical protocols to measure low-level protein concentrations and will continue its analytical efforts to use targeted proteomics for biomarker analysis.

Dr. Christian Frese
Head of Proteomics Facility CECAD
Tel.  +49 221 478 84013
cfrese[at]uni-koeln.de

CECAD Research Institute
Universität zu Köln
Joseph-Stelzmann-Str. 26
50931 Köln

Dr. Christian Frese

Team

Publications
  • Havarushka N, Fischer-Schrader K, Lamkemeyer T, Schwarz G. (2014) Structural basis of thermal stability of the tungsten cofactor synthesis protein MoaB from Pyrococcus furiosus. PLoS One. 9, e86030.
  • Kohli P, Bartram MP, Habbig S, Pahmeyer C, Lamkemeyer T, Benzing T, Schermer B, Rinschen MM. (2014) Label-free quantitative proteomic analysis of the YAP/TAZ interactome. Am. J. Physiol. Cell Physiol. 306, C805-18. Epub 2014 Feb 26.
  • Rinschen MM, Wu X, König T, Pisitkun T, Hagmann H, Pahmeyer C, Lamkemeyer T, Kohli P, Schnell N, Schermer B, Dryer S, Brooks BR, Beltrao P, Krueger M, Brinkkoetter PT, Benzing T. (2014) Phosphoproteomic Analysis Reveals Regulatory Mechanisms at the Kidney Filtration Barrier. J. Am. Soc. Nephrol. [Epub ahead of print].
  • Marcon C, Lamkemeyer T, Malik WA, Ungrue D, Piepho HP, Hochholdinger F. (2013) Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC-MS. J. Proteomics. 93, 295-302. Epub 2013 Apr 19.
  • Steinfeldt T, Könen-Waisman S, Tong L, Pawlowski N, Lamkemeyer T, Sibley LD, Hunn JP, Howard JC. (2010) Phosphorylation of mouse immunity-related GTPase (IRG) resistance proteins is an evasion strategy for virulent Toxoplasma gondii. PLoS Biol. 8:e1000576.