Proteomics allows the simultaneous detection and identification of thousands of proteins within a sample. Here, we describe a quantitative method to compare protein expression and subcellular localization of different cell lines representative of different stages of colorectal cancer using stable isotope labeling with amino acids in culture, or SILAC. We also describe a biochemical fractionation approach to separate different cellular compartments and the necessary steps to obtain a specific proteomic profile of each cell line. This technique enables a comprehensive proteomic analysis of cancer cell lines and the identification of pathways that are deregulated in different cancer cell lines.
Keywords: Colorectal cancer; Mass spectrometry; Proteomics; SILAC; Subcellular fractionation.