As a central platform for exchange of signaling communication and substance between cells and within cells, mapping of membrane proteome can provide new insights into the pathophysiology of cancer and other diseases, explore potential drug targets and biomarkers for prognosis or diagnosis, and ultimately contribute to the development of precision medicine. However, mass spectrometry-based identification of membrane proteins poses many challenges due to the intrinsic properties of membrane proteins, especially high hydrophobicity and low abundance. Herein, we described a metal organic layers (MOL)-based sample preparation method for membrane proteome analysis in living cells, involving the cell surface engineering process through the exquisite interaction between MOL and phospholipid bilayers on the membrane and the following biomembrane fusion process, providing a simple and robust tool for dissection of membrane proteome with high specificity. This chapter details the preparation of such metal organic layers and enrichment workflow of HeLa membrane proteins.