A Peptidisc-Based Survey of the Plasma Membrane Proteome of a Mammalian Cell

Membrane proteins play critical roles at the cell surface, and their misfunction is a hallmark of many human diseases. A precise evaluation of the plasma membrane proteome is, therefore, essential for cell biology and for discovering novel biomarkers and therapeutic targets. However, the low abundance of this proteome relative to soluble proteins makes it difficult to characterize, even with the most advanced proteomics technologies. Here, we apply the peptidisc membrane mimetic to purify the cell membrane proteome. Using the HeLa cell line as a reference, we capture 500 different integral membrane proteins, with half annotated to the plasma membrane. Notably, the peptidisc library is enriched with several medically relevant ABC, SLC, GPCR, CD, and cell adhesion molecules that generally exist at low to very low copy numbers in the cell. We extend the method to compare two pancreatic cell lines, Panc-1 and hPSC. Consistent with other studies, we observe a striking difference in the relative abundance of the cancer markers L1CAM, ANPEP, ITGB4, and CD70. We also identify two novel SLC transporters, SLC30A1 and SLC12A7, that are highly present in the Panc-1 cell only. The peptidisc workflow thus emerges as an effective way to survey and compare the membrane protein system of mammalian cells. Furthermore, since the method stabilizes proteins in a water-soluble state, members of the library can be isolated, here SLC12A7. [Display omitted] •Peptidisc stabilizes membrane proteins in a water-soluble library.•The membrane protein library is amenable to protein purification and proteomic analysis.•The library comprehensively reflects the membrane proteome.•The method facilitates the identification of cell surface markers. Membrane proteins are difficult to detect in bottom-up proteomics due to their hydrophobicity and low abundance compared to soluble proteins. We apply here the peptidisc membrane-mimetic to isolate the plasma membrane proteome. The method captures membrane proteins in a water-soluble state that is amenable to mass spectrometry analysis and protein purification. The technique is promising in identifying naturally low abundant plasma membrane proteins. It is also applicable to compare the panels of cell surface markers.