Chapter 8: Quantitative LC-MS of Proteins

In this chapter we describe how mass spectrometry can be applied to analyse proteins quantitatively on a system-wide level, also referred to as quantitative proteomics. We focus on a popular and easy to use method for quantification of protein samples by introducing stable isotopes into the analytes. This method, stable isotope labelling with amino acids in cell culture (SILAC), makes use of the metabolic incorporation of isotopically labelled amino acids into the proteomes of cultured cells. SILAC-based quantitative proteomics is used today to study a wide range of biological phenomena such as protein dynamics and dynamics of post-translational protein modifications, as well as protein–protein and protein–ligand interactions, to name only a few examples.