Stable isotope dimethyl labeling

The quantitative analysis of proteomes is an increasingly important aspect of mass spectrometry (MS)-based proteomics. The most commonly used methods for comparing and accurately quantifying protein levels rely on the use of differential isotopic labeling. Proteins or peptides from different samples are labeled using compounds with near identical chemical properties yet each containing a unique stable isotope composition resulting in different masses. This way, the different samples can be combined and still be distinguished in a single MS analysis. The stable isotopes can be introduced by chemical labeling at the protein or peptide level with isotopomeric tags. This method is particularly suited for tissue samples derived from animals or humans where metabolic incorporation is difficult.

In this example, cell lysate-level digest prior to labeling was performed, and then SCX fractionation followed by LCMS using both electron transfer dissociation (ETD) and collision induced dissociation (CID) for peptide sequencing was carried out.