Quantitative Proteomics for Differential Protein Expression Profiling

Mass spectrometry (MS)-based proteomics has become an integral analytical technology in life science research. Multiple quantification strategies for MS-based proteomics have been reported. They can be categorized into two main regimes: absolute and relative quantification. The basic principle of stable isotope-based labeling for peptide and protein quantification is that the physicochemical characteristics of the differentially labeled peptides are nearly identical. Labeling via stable isotopes by amino acids in cell culture (SILAC) is a strategy that facilitates complete and proteome-wide labeling. Label-free quantification strategies are based on either spectral counting or precursor ion signal intensity. Several studies have focused on head-to head comparisons between spectral counting-based label-free quantification and metabolic labeling. The chapter presents a systematic global comparison of SILAC, dimethyl labeling, and isobaric tagging (TMT). The ideal quantitative proteomics approach would enable reproducible, comprehensive, sensitive and unbiased analysis that provides accurate and precise quantitative data with a high dynamic range and within reasonable analysis time.