Protocol for eukaryotic plasma membrane isolation using superparamagnetic nanoparticles

•Phospholipid functionalized Fe3O4 SPMNPs are synthesized for subcellular fractionation.•We report a simplified protocol for SPMNP based Plasma membrane fractionation.•Cationic silica beads with SPMNPs can contribute for plasma membrane fractionation. Superparamagnetic nanoparticles (SPMNP) are used in cell biology for various applications such as subcellular fractionation and for high pure organelle isolation. We simplified previously established methodology with the use of SPMNP for isolation of high pure and high yield plasma membrane from adherent eukaryotic cell line (Thimiri Govinda Raj et al., 2011, 2012, 2016; Tharkeshwar et al., 2014). Here, we show a step by step protocol for SPMNP based plasma membrane fractionation. Our research thus could be used as an alternative method to isolate plasma membrane fraction for cell biology, system biology and immunology research.