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 disease conditions. The CECAD Proteomics Core 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 an 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.

The Proteomics Core 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. 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.

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 equipped with three Q-Exactive LC-MS/MS systems (Thermo Scientific). These instruments combine quadruple precursor ion selection with high-resolution accurate-mass Orbitrap detection, enabling 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, acetylation 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.