Proteomics is a fast and powerful discipline aimed at the study of the whole proteome or the sum of all proteins from an organism, tissue, cell or biofluid, or a subfraction thereof, resulting in an information-rich landscape of expressed proteins and their modulations under specific conditions. Most proteomic discoveries and efforts to date have been mainly directed towards the areas of cancer research, drug and drug target discovery and biomarker research. In this chapter, we will present the most common processes and workflows used in proteomic studies. To this end, we will summarize the main methodologies used for sample preparation and possible methods for the separation, detection, identification, and quantification of proteins/peptides. Key points for downstream processing, data analysis and evalution,[ also discussed. Finally, some relevant studies aimed at biomarker discovery or sub-cellular composition analysis that have been published using different proteomic workflows will be summarized.