This protocol desribes the bacterial proteomic workflow used in the article: "The use of SWATH to analyse the dynamic changes of bacterial proteome of carbapenemase-producing Escherichia coli under antibiotic pressure" published in Scientific Reports.

The workflow begins with growing the bacterial strains, isolating the bacterial proteins, processing the samples for submission to LCMS (protein quantitation, digestion, clean up, desalting). Then, once the samples are being processed on LCMS, the data analysis requires high performance computers.