The identification of membrane proteins in mass spectrometry (MS) analyses requires the attention of researchers as pathophysiological regulators of signaling pathways or inter/extracellular exchanges, as pathological markers or as potential mediators of pharmacological vectorisation. However, conventional methods of sample preparation do not provide access to the full pattern of membrane proteins and in particular transmembrane proteins due to their low abundance, hydrophobic nature, and limited enzyme accessibility. Based on the use of the iST kit for the preparation of LC-MS samples, the study aims to investigate the potential of the BeatBoxÒ homogenizer to improve the identification of membrane and transmembrane proteins from whole cell lysates or cellular fractions enriched for cell membranes by ultracentrifugation, using brain pericytes as the study cell type. By using BeatBox for protein extraction and solubilization in conjunction with iST sample preparation, we observed an improvement in the identification of membrane and transmembrane proteins compared to the iST kit alone. Better peptide alignment scores further highlight that the BeatBox improves the detection of such proteins in a state-of-the-art manner.

Further investigations are focusing on strategies to further increase the extraction and digestion efficiency of transmembrane proteins, for example through detergent-mediated destabilization of lipid bilayers.