Triplicate bioreactor samples were acquired using the developed MRM method. Higher variation in protein abundances was observed within the MRM assay examining each bioreactor separately (Figure ) than with global untargeted methods (Figure ). In our discovery proteomics workflow such variation is reduced during data normalization steps. Despite this, observed trends in protein abundance were consistent between bioreactors (Figure ), and the use of peptide standards mean that ratios of protein abundance within the bioreactor can be applied to identify the cellular phase.