A Mass Spectrometry-Based Approach for Mapping Protein Subcellular Localization Reveals the Spatial Proteome of Mouse Primary Neurons

We previously developed a mass spectrometry-based method, Dynamic Organellar Maps, for the determination of protein subcellular localisation, and the identification of translocation events in comparative experiments. The use of metabolic labelling for quantification (SILAC) renders the method best suited to cells grown in culture. Here we have adapted the workflow to both label-free quantification (LFQ) and chemical labelling/multiplexing strategies (Tandem Mass Tagging, TMT). Both new methods are highly effective for generation of organellar maps and capture of protein translocations. Furthermore, application of label-free organellar mapping to acutely isolated mouse primary neurons provided subcellular localisation and copy number information for over 8,000 proteins, allowing a detailed analysis of organellar organisation. Our study extends the scope of Dynamic Organellar Maps to any cell type or tissue, and also to high throughput screening.This work was funded by the German Research Foundation (DFG/Gottfried Wilhelm Leibniz Prize MA 1764/2-1), the Louis-Jeantet Foundation, the Max Planck Society for the Advancement of Science, a Wellcome Trust Senior Clinical Research Fellowship 108070/Z/15/Z (to M.P.W.), and a strategic award to Cambridge Institute for Medical Research from the Wellcome Trust (100140)