The goals of this study are to use SWATH-MS to detect bacterial proteomic profiles of E. coli K-12 LE392 with conjugative RP4 plasmid, P. putida KT2440, and their protein response under the exposure of six kinds of non-antibiotic pharmaceuticals, i.e., ibuprofen (ibu), naproxen (nap), gemfibrozil (gem), iopromide (iop), diclofenac (dic), propanolol (pro). Each treatment condition was conducted in triplicate. By comparing the proteomic profiles of experimental groups and control group, the effects of these non-antibiotic pharmaceuticals on translational levels can be revealed.