Fig. 2.

The PDB-MS workflow. In PDB, a biotin ligase (BioID), a horseradish peroxidase (HRP) or a peroxidase (APEX) is genetically fused to a selected bait protein and expressed in a chosen cell line. In vivo labelling is achieved by adding biotins (BioID) or biotin phenols (APEX) to the cells, whereby these molecules are converted to reactive biotin intermediates. These reactive intermediates then diffuse away from the enzyme in a distance-dependent manner to covalently modify lysine (BioID) or tyrosine (APEX) residues located in close proximity. After performing cell lysis in harsh, denaturing conditions, biotinylated proteins are enriched using resin conjugated with streptavidin or neutravidin for subsequent quantitative proteomics analysis