SIMPLEX enriches hydrophobic and lipidated proteins in membrane proteomics experiments

Synaptosome (Syn) and synaptic junctions (SJ) are widely used in omics experiments to investigate protein content and networks of synapses. Synapses are a neuronal compartment wit a high lipid content. Liquid-liquid extraction (LLE), typically used in lipidomics, shows great potential for multiomics experiments, where data is generated from the same sample, due to its ability to integrate different molecule classes in one extraction. However, the influence of liquid-liquid extraction on protein and phospho-proteins analysis of membrane-enriched samples has not been investigated nor compared to one-phase extraction. In this study, we compared the suitability of SIMPLEX (Simultaneous Metabolite, Protein, Lipid Extraction)- an example of LLE- for mass-spectrometry based protein identification to a commonly used acetone protein precipitation.