Proteomic Profiling of Cell Death: Stable Isotope Labeling and Mass Spectrometry Analysis

Proteins directly control almost all cellular processes and researchers in many biological areas routinely use mass spectrometry for the characterization of proteins. Amongst a growing list of available quantitative proteomic techniques, Stable Isotope Labeling by Amino acids in Culture (SILAC) remains one of the most simple, accurate, and robust techniques for cultured cellular systems. SILAC enables strict quantitative peptide measurements, thus removing false positives and facilitates large-scale kinetics of entire proteomes. In this, chapter we describe an optimized labeling strategy and experimental design for SILAC workflows for characterizing the components downstream of cell death stimuli.