Services
Proteome Profiling - Quantification of global proteome changes between cell states or conditions
Total proteomes or subproteomes can be analyzed efficiently and deeply with modern mass spectrometry (MS). Depending on the exact nature of the biological material and the questions to be answered, different relative quantification strategies can be applied, including (i) label-free relative quantification from data-dependent acquisition MS, (ii) label-free relative quantification from data-independent acquisition MS or (iii) label-based quantification using SILAC or isobaric mass labeling (TMT). To decrease complexity and expand the number of identifications per MS run, fractionation of peptides is usually performed.
Complexome Profiling
Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient ultracentrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance and arrangement of multiprotein complexes in a biological sample.
Extraction and separation of proteins under native conditions
Our Core Facility offers service for protein extraction under native conditions and further separation by native polyacrylamide electrophoresis methods, such as Blue Native (BN)-PAGE and high-resolution Clear Native (hrCN)-PAGE.
Identification of proteins from gel spots
Either bands from purified or complex mixture of proteins separated by denaturing (SDS-) or native (BN-, hrCN-) PAGE can be excised and analyzed by LC-MS/MS.
Identification of proteins from the extracellular matrix and secretome
Cells that form tissues commonly secrete and accumulate proteins within the extracellular matrix. We have recently established several complementary strategies to identify these proteins, ranging from standard proteomic profiling to SILAC-based quantitative analysis of secreted protein fractions.