Mass Spec

Mass Spectrometry

 

General

 At IBC2, we maintain a proteomics platform allowing our researchers to quantitatively describe signaling networks and to determine how components of signaling complexes are modified in response to pathway perturbations. We perform complementary qualitative and quantitative MS approaches for identification and quantitation of proteins and their post-translational modifications (PTMs, e.g. phosphorylation and ubiquitination), both at small (e.g. interactomes) and large (whole cell- or subcellular proteome) scale.

In general, we follow the so-called bottom-up approach: protein samples are first treated with proteases (e.g. Trypsin and/or LysC) and then analyzed by LC-MS/MS for identification and quantification of the resulting peptides and thus the underlying proteins. Besides label-free protein quantitation based on summed peak intensities of identified peptides, we take advantage of various labelling techniques, such as Tandem Mass Tag (TMT) reagents or Stable Isotope Labelling using Amino acids in Cell culture (SILAC), providing higher throughput and/or more accurate quantification. The generated spectral data is mostly analyzed using MaxQuant (MPI Martinsried) and Proteome Discoverer (Thermo Scientific) in order to obtain the list of identified proteins and their abundances in the samples.