At IBC2, we established and maintain a MS-based proteomics platform that allows our researchers to quantitatively describe signaling networks and to determine how components of signaling complexes are modified in response to pathway perturbations. Our current instrumentation consists of three mass spectrometers – besides an Orbitrap Elite and a LTQ Velos, we are also hosting the instrument of the SFB 1177 (www.SFB1177.de) proteomics platform, a Q Exactive HF. All machines are coupled to nano HPLC systems to enable LC-MS/MS (liquid chromatography-tandem MS)-based proteomics for unbiased and comprehensive analysis of complex biological systems. To this end, we take advantage of various labelling techniques, such as Tandem Mass Tag (TMT) reagents or Stable Isotope Labelling Using Amino acids (SILAC) in cell culture. These methods enable us to compare various experimental conditions simultaneously and to quantify subtle differences in complex protein mixtures.
Using this platform, we perform complementary qualitative and quantitative MS approaches ranging from identification to quantitation of proteins and post-translational modifications (PTMs), Our expertise includes interactome studies as well as proteome-wide analyses. The resulting large proteomic datasets are analysed using several bioinformatics tools.
For the members of SFB 1177, the platform offers analytical and instructional expertise in mass spectrometry. We perform shotgun proteomic approaches for all research groups of the SFB1177 to analyze autophagy signaling networks, identify novel autophagy components, map global PTMs, and determine how signaling complexes are altered by perturbations of autophagy. Members of the SFB1177 with projects requiring MS analysis should contact Soraya Hölper, Florian Bonn or Meike Hoffmeister () for a first consultation. Afterwards, please register to ms.submission and fill out the sample submission form.
For external researchers, use of the MS platform is possible on the basis of collaboration. Please contact first the IBC2 group leaders with whom you wish to collaborate to discuss the options.