Mass spectrometry is an extremely versatile analytical technique that is capable of characterizing proteins at various levels of biochemical sophistication from recognition of protein components and their modifications to their quantification within a sample. With the development of electrospray ionization and matrix-assisted laser desorption ionization, the last decade of protein analysis using mass spectrometry has fully established the field of proteomics within the life sciences and a major player in the systems biology paradigm. The diversity of proteins and their multi-facetted functions are indicative of the numerous mass spectrometry methods that are used in quantitative proteomic analysis. In this review, the various techniques developed to quantify protein abundance by mass spectrometry are presented in terms of those associated with both stable isotope coding and label-free strategies. The implementation of these methods to the quantitative mass spectrometry analysis from “proof-of-concept” to those that tackle investigations of protein expression and those of protein function mediated by post-translation modifications are also discussed.