Proteomics is loosely defined as the description of sets of proteins from any biological source, which have in most cases been identified by using mass spectrometry. However, only the mere identity of proteins present in a certain sample does not give any information about the dynamics of the proteome, involving relevant cellular events such as protein synthesis and degradation, or the formation of protein assemblies. In order to retrieve information on proteome dynamics, relative protein abundances between different protein samples should be assessed. Comparative or differential proteomics aims to identify and quantify proteins in different samples, to study e.g. differences between healthy and diseased states, mutant and wildtype cell lines, undifferentiated and differentiated cells, etc. Since mass spectrometry is in itself only a qualitative technique, various methods to obtain quantitative information of the proteome have been developed over the past decade and will be described in this Chapter.