Mass spectrometry can be used to quantify proteins of interest by combining samples with a known concentration of stable isotope labeled amino acids (SILAC) proteins. These samples can then be digested into peptides and analyzed by mass spectrometry to determine the ratio of labeled to non-labeled peptides allowing the quantity of the protein of interest to be determined. The protein peptides produce a pattern of specific peaks depending on their composition. These peaks will be shifted when labeled. The relative size of the shifted and non-shifted (or labeled and non-labeled) can then be compared to determine a ratio. Since the quantity of labeled protein is known the quantity of the unlabeled protein can be determined.