Improved plasma membrane proteome coverage with a label-free non-affinity-purified workflow

The proteins of the cellular plasma membrane perform important functions relating to homeostasis and intercellular communication. Due to its overall low cellular abundance, amphipathic character, and low membrane-to-cytoplasm ratio, the plasma membrane proteome has been challenging to isolate and characterize, and is poorly represented in standard liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. In this study, we employ a label-free, non-affinity-purified workflow for the enrichment of the plasma membrane proteome and use subsequent bioinformatics tools to select plasma membrane proteins, herein referred to as the surfaceome. Using this methodology, we identified over 2500 cell surface-associated proteins in a human acute myeloid leukemia (AML) cell line. These surface proteins comprised 60% of all detected cellular proteins, a number that substantially exceeds the depth of coverage in previously published studies describing the leukemia surfaceome.