To discover novel factors that modulate S. flexneri infection, we developed a proteomic-based approach based on the biotin ligation enzyme APEX2. To target the host-Shigella interface, we coated bacteria in vitro prior to infection using anti-GFP nanobody-expressing shigella and recombinant GFP-APEX2. Upon infection in HeLa cells, biotinylated proteins from both host and pathogen were enriched by streptavidin pulldown and identified by mass spectrometry. Here, we analyzed two biological groups where cells were infected with either wild-type Shigella flexneri (S. flexneri) or delta-mixE Shigella flexneri mutant. In each group, four petri dishes were infected to generate four replicates.