Stable Isotope Labeling by Amino Acids in Cell Culture for Quantitative Proteomics

Mass spectrometry (MS)-based quantitative proteomics is an increasingly popular approach to study changes in protein abundances in biological samples. Stable isotope labeling by amino acids in cell culture (SILAC), one of the more widely used methods for quantitative proteomics, is a metabolic-labeling strategy that encodes whole cellular proteomes. Cells are grown in a culture medium where the natural form of an amino acid is replaced with a stable isotope form, such as arginine bearing six ¹³ C atoms. Incorporation of the “heavy” amino acid occurs through cell growth, protein synthesis, and turnover. SILAC allows “light” and “heavy” proteomes to be distinguished by MS while avoiding any chemical derivatization and associated purification. In this chapter, we provide detailed SILAC protocols and explain how to incorporate SILAC into any experiment.