Data-dependent and independent acquisition of Salmonella in epithelial cells throughout the infection process

Viewing the scarce amount of protein material coming from the bacterial pathogen in infection models and despite the availability of contemporary, highly sensitive and fast scanning mass spectrometers, the power requirement still not suffices to study the host and pathogen proteomes simultaneously. In the present work we aimed to establish a DIA mass spectrometry workflow for improving the protein identification and quantification of LC-MS/MS, in Salmonella infected epithelial cells, therefore enabling simultaneous host and pathogen protein expression profiling at different time post infection.