Biotin Proximity Labeling for Protein-Protein Interaction Discovery: The BioID Method

Methods Mol Biol. 2021:2261:357-379. doi: 10.1007/978-1-0716-1186-9_22.


Biotinylation identification (BioID) is a method designed to provide new cellular location and functional knowledge of the protein of interest through the identification of those proteins surrounding and in direct contact. A biotin ligase is fused onto the protein of interest and expressed in cells where it can biotinylate even short-lived transient protein complexes. In addition, due to the proximity labeling nature of the experiment, cellular localization and functional enrichment information can also be obtained. Since labeling occurs only after the addition of biotin, temporal relationships and localization changes (e.g., cytoplasmic to nuclear) can also be identified. Labeled proteins are easily purified, and contaminants minimized, using the strong interaction between biotin and streptavidin. Mass spectrometry analysis of the purified proteins allows for the identification of potential interactors for further validation and characterization.

Keywords: BioID; Biotinylation; Protein–protein interaction; Proximity labeling.

MeSH terms

  • Analytic Sample Preparation Methods
  • Animals
  • Biotinylation
  • Carbon-Nitrogen Ligases / genetics
  • Carbon-Nitrogen Ligases / metabolism*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • HEK293 Cells
  • Humans
  • Mass Spectrometry*
  • Protein Binding
  • Protein Interaction Maps*
  • Protein Transport
  • Proteomics*
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism*
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*
  • Time Factors


  • Escherichia coli Proteins
  • Recombinant Fusion Proteins
  • Repressor Proteins
  • Carbon-Nitrogen Ligases
  • birA protein, E coli