Quantitative proteomic approaches in mouse: stable isotope incorporation by metabolic (SILAC) or chemical labeling (reductive dimethylation) combined with high-resolution mass spectrometry.

Mass spectrometry-based quantitative proteomics is a powerful method for in-depth exploration of protein expression, allowing researchers to probe its regulation and study signal-transduction networks, protein turnover, secretion, and spatial distribution, as well as post-translational modification and protein-protein interaction, on a large scale. Precise protein quantitation may be achieved by incorporation of stable isotopes, which introduce a mass shift detectable by mass spectrometry, allowing multiplexing of several samples and therefore relative quantification. Stable isotope incorporation into proteins or peptides can be attained either by metabolic labeling (e.g., SILAC) or by chemical labeling (e.g., reductive dimethylation). Both labeling approaches are presented here. They are straightforward and robust and can be applied to murine samples. While both SILAC and reductive dimethylation offer similar multiplexing capabilities and quantitative accuracy, reductive dimethylation is more versatile and can be used with any sample type.