Protocol for plasma membrane enrichment by ultracentrifugation for mass spectrometry of cell lines, xenografts, and patient tumors

The success of immunotherapies hinges on identifying targetable cell surface proteins expressed in the cancer of interest. Here, we present a protocol for enriching plasma membrane proteins for mass spectrometry analysis using a density gradient ultracentrifugation approach. We describe steps for cell lysis, membrane isolation, and preparation for downstream analysis. This protocol is applicable to cell lines, cell-/patient-derived xenografts (CDX/PDX), and primary tissues. For complete details on the use and execution of this protocol, please refer to Glisovic-Aplenc et al., 1 Hamilton et al., 2 and Mooney et al. 3 • Instructions for isolating membrane proteins • Steps for plasma membrane protein enrichment • Procedure for samples with limited input • Guidance on sample preparation for downstream applications Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. The success of immunotherapies hinges on identifying targetable cell surface proteins expressed in the cancer of interest. Here, we present a protocol for enriching plasma membrane proteins for mass spectrometry analysis using a density gradient ultracentrifugation approach. We describe steps for cell lysis, membrane isolation, and preparation for downstream analysis. This protocol is applicable to cell lines, cell-/patient-derived xenografts (CDX/PDX), and primary tissues.