Proteomic analysis of mouse DC subsetsproteomics dataset
We have established an in-depth proteomic map of murine dendritic cell subsets. We have been working in the attempt to overcome the limits in sample availability, exploiting the recent significant improvements of proteomic technology. The results allowed to lower the required sample amount significantly, an essential feature to analyze limited cell populations like dendritic cells. The group completed the measurements of murine dendritic cell subsets and established an in-depth proteomic map of them. These preliminary results show more than 4500 identified proteins in each subset. All of the known markers like CD11c, CD11b, DEC-205, Langerin, etc. were found according to their differential expression pattern. Due to recent major developments in analysis software it is now possible to compare these subsets quantitatively based on the extracted ion current (XIC) and without any need of stable isotope labels. This software is still in development, but preliminary results show a high similarity of all there subsets in the steady state.
Experiments have been performed to verify these differences in a biological point of view and analysis of the proteomic data itself using novel label-free software has also been completed. In 2008 our group showed the most comprehensive overview of molecular components in yeast (deGodoy et al.). However this study so far required SILAC (stable isotope labelling with amino acids in cell culture) labelling leaving rare cell populations, like in vivo DC subsets, out of reach. In this work package we introduced a robust and generally applicable quantification technology, which allowed us to quantify the dendritic cell subset proteomes to a depth of more than 5000 proteins. Additionally, we were able to make functional predictions about closely related cell types using our large-scale proteomic data set. Biological follow up experiments fully confirmed our proteomic findings. Currently we are wrapping up our data for publication of the DC subset proteome and the quantitation software. All our data can be accessed and analyzed through the MAPU database (Gnad et al.)
After finishing our proteomic study of steady-state dendritic cell we will now start to analyze proteomic changes of DC subsets after different stimuli.
- organism type
- Mus musculus
- cell type
- dendritic cell
- experimental design type
- cell type comparison experiment