We describe a proteomics method for determining the subcellular localization of membrane
proteins. Organelles are partially separated using centrifugation through self-generating
density gradients. Proteins from each organelle co-fractionate and therefore exhibit similar
distributions in the gradient. Protein distributions can be determined through a series of pair-
wise comparisons of gradient fractions, using cleavable ICAT to enable relative quantitation
of protein levels by MS. The localization of novel proteins is determined using multivariate …