Identification of Lipid Droplet Proteomes by Proximity Labeling Proteomics Using APEX2

Methods Mol Biol. 2019:2008:57-72. doi: 10.1007/978-1-4939-9537-0_5.


Lipid droplets (LDs) are ubiquitous lipid storage organelles composed of a neutral lipid core surrounded by a phospholipid monolayer that is decorated with integral and peripheral proteins. Accurate identification of LD proteins using biochemical fractionation methods has been challenging due to the presence of contaminant proteins from co-fractionating organelles. Here, we describe a method to identify high-confidence LD proteomes that employs an engineered ascorbate peroxidase (APEX2) to induce spatially and temporally restricted biotinylation of LD proteins. This proximity labeling method can be broadly applied to define the composition of the LD proteome in any cultured cell line and can be utilized to examine LD proteome dynamics.

Keywords: APEX; APEX2; Biotinylation; Lipid droplet; Organelle; Proteome; Proximity labeling.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Ascorbate Peroxidases / chemistry
  • Biotinylation
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Lipid Droplets / chemistry*
  • Lipid Droplets / metabolism
  • Mice
  • Proteomics / methods*
  • Staining and Labeling / methods*


  • Ascorbate Peroxidases