Analysis of Salmonella PhoP/PhoQ regulation by dimethyl-SRM-based quantitative proteomics

• Established a dimethyl-SRM method for Salmonella protein analysis
• Analyzed activation dynamics of Salmonella PhoP/PhoQ network
• Discovered distinct patterns in PhoP/PhoQ activation
• Found new protein groups and pathways regulated by PhoP/PhoQ

SRM (selected reaction monitoring), a tandem mass spectrometry-based method characterized by high repeatability and accuracy, is an effective tool for the quantification of predetermined proteins. In this study, we built a time-scheduled dimethyl-SRM method that can provide the precise relative quantification of 92 proteins in one run. By applying this method to the Salmonella PhoP/PhoQ two-component system, we found that the expression of selected PhoP/PhoQ-activated proteins in response to Mg2 + concentrations could be divided into two distinct patterns. For the time-course SRM experiment, we found that the dynamics of the selected PhoP/PhoQ-activated proteins could be divided into three distinct patterns, providing a new clue regarding PhoP/PhoQ activation and regulation. Moreover, the results for iron homeostasis proteins in response to Mg2 + concentrations revealed that the PhoP/PhoQ two-component system may serve as a repressor for iron uptake proteins. And ribosomal protein levels clearly showed a response to different Mg2 + concentrations and to time.