Quantitative Proteomics by Mass Spectrometry

Volume 359 of the series Methods in Molecular Biology pp 37-52

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

  • Shao-En OngAffiliated withProteomics and Biomarker Discovery, The Broad Institute of MIT and Harvard
  • , Matthias MannAffiliated withDepartment of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry

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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 13C 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.

Key Words

SILAC stable isotope labeling mass spectrometry proteomics gene expression