Human genome sequencing has identified about 25,000 genes, most being of unknown function. Localization of the final gene products—that is, the proteins - in a specific organelle is a key to deciphering the proteins' roles within the cell. Over the past 20 years, proteomic analyses have progressively proved to be an invaluable tool to obtain high-throughput protein identification from low-abundance, complex biological samples. These analyses boomed thanks to dramatic technological progresses in mass spectrometry instrumentation, optimization of its coupling to capillary liquid chromatography, and the development of software enabling processing of the vast amount of generated data. In the context of organelle study, such analyses have allowed greater depth in the characterization of the proteins constitutive of, or transiently present in, these large functional modules...