Genome-wide analytical approaches using semi-quantitative expression proteomics for aromatic hydrocarbon metabolism in Pseudomonas putida F1

► The genome-wide proteome analysis was performed using 1-D PAGE and nanoLCMS/MS. ► For semi-quantitative proteomics, protein content calculated from emPAI is used. ► We identified all key enzymes in the degradation pathway of aromatic hydrocarbons. ► An ideal primary analysis of physiological processes of bacterial cells is proposed.