CP02: Quantitative Proteomics

In recent years mass spectrometry-based proteomics has been successfully used for the analysis of complex biological samples and the technique can be applied to analyze the whole proteome and its posttranslational modifications (PTMs) in an unbiased and systematic manner. In addition, quantitative proteomics based on stable isotope labelling, chemical peptide labelling or label free protein quantification (LFQ) has been applied to large-scale mapping of a tremendous number of PTMs which helped to decipher dynamic protein networks and activated signaling pathways in response to a given stimulus. A central task of this project will be to establish limited proteolysis-coupled mass spectrometry (LiP-MS) for the CRC. LiP-MS enables the identification of structural changes in proteins and protein complexes on a proteome-wide scale. The CECAD/CMMC mass spectrometry core facility will assure that all groups of the CRC have access to state-of-the-art bioanalytical tools and quantitative mass spectrometry. The platform will provide a broad spectrum of proteomics methods, including protein-protein interaction studies, global protein quantification, and the enrichment of post-translational modifications. The service project will advise scientists of the CRC in the experimental design, will perform standardized statistical analysis, and help to interpret the resulting proteomics data. The unit is equipped with modern quadrupole-orbitrap and ion mobility mass spectrometers. All instruments are coupled online to fast liquid chromatography systems, allowing short LC-MS gradients and analysis of large-scale projects. Overall, the major focus is the development and application of quantitative proteomics and LiP-MS technologies, to increase the sensitivity of mass spectrometry measurements, which ultimately serves to quantify the consequences of fidelity changes for the proteome.