In this study, we used liquid chromatography–tandem mass spectrometry to quantify protein abundance in the exponential and stationary phases of BLR (DE3) cells, an Escherichia coli B strain. Our findings are consistent with previous studies, which showed that metabolic processes such as translation and ribosome biogenesis decrease during the stationary phase compared to the fast-growing exponential phase, whereas tricarboxylic acid cycle activity increases. Importantly, our data reveal that distinct antibiotic resistance pathways are activated during the exponential and stationary phases, underscoring the potential for developing phase-specific antibiotic therapies.