SPATIAL TARGETED PROTEOMICS USING PASEF-PRM

The fast scanning abilities of modern mass spectrometers allow the parallel identification of more than 700 proteins in targeted mode9. The sensitivity of this method reaches mid attomolar ranges for the detection in serum5. Applied to a histological slice, the amount of protein material contained in an FFPE slice is sufficient for several proteomics analyses. Therefore, we will cut an FFPE slice into a raster of smaller pieces. Each of the smaller pieces will be analyzed separately by targeted mass spectrometry. For the targeted analysis, we will develop in close collaboration with the group of Michel Mittelbronn a specific panel of proteins, which will be quantified in each of the pieces. The approach will allow the parallel measurement and quantification of about one hundred markers for each slice. The collected data will be visualized in collaboration with Petr Nazarovs group at LIH.
The method will be developed in close collaboration with Bruker Daltonics, who will co-fund the bridges application. Here we will be able to access prototype machines or machines with different modes of ionization, which will allow us to develop this cutting-edge technology, which is necessary to identify the targeted number of biomarker proteins.