Three AIEC strains were isolated from CD patients. We analyzed three types of cell: before adhesion and adhesion-invasion(control), after adhesion-invasion and after invasion. Proteins were assessed in an untargeted label-free bottom-up proteomic experiment using IDA approach (i.e. Information Dependent Acquisition) on Sciex TripleTOF 6600 Q-TOF mass-spectrometer couplet with LFQ (label-free quantification) by MaxQuant software. Dataset covers 54 samples (three biological replicates and two technical).