Comparison of ratios of peptide from the target proteins from four different days during the bioreactor process allows us to normalize for the variation between bioreactors. This simple assay now provides clear evidence of the change in abundance (Figure ). From MRM measurements of each bioreactor these ratios of peptides can quantify expression changes in these key proteins. This approach, using data from 12 separate injections (total machine time ~3 hours), can be readily analyzed in minutes to provide robust quantification of pathways that are altered in the bioreactors.