FLAG-tagged VafA and VafB were expressed in E. coli BL21(DE3) cells, and VafA/VafB-associated proteins were immunoprecipitated from cell lysates using anti-DYKDDDDK magnetic beads. Bead-bound proteins were digested on beads with trypsin/Lys-C mix, and the resulting peptides were desalted and analyzed by LC-MS/MS using an EASY-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer. Raw data were searched against the SwissProt E. coli database supplemented with VafA and VafB sequences using Proteome Discoverer 2.5. Peptides were filtered at a 1% false discovery rate using the Percolator node, and label-free precursor ion quantification was performed.