Using microorganisms such as S. cerevisiae to produce materials has been applied across many industries such as fermented foods, chemicals, pharmaceuticals, and biofuels. These microbial cell factories are metabolically orchestrated by regulating expression levels of enzymatic proteins. To understand these metabolic pathways, it is important to monitor enzyme abundances. An analytical technique used for targeted proteomics utilizes LC-MS/MS to monitor pre-selected tryptic peptides generated from these proteins of interest. Multiple reaction monitoring (MRM) of these peptide transitions provides high sensitivity and specificity and is a powerful tool for quantification of proteins in biological samples. This LC-MS based approach does not require antibodies for each protein or peptide analyzed as ELISA does. On the other hand, to be effective, the mass spectrometer must be capable of high-speed scanning to monitor the many tryptic peptides derived from a complex mixture of proteins. The high scan speed capability of Shimadzu UFMS technologies can reveal the dynamic behavior of many proteins from these biological samples.