EXPERIMENTAL FIGURE 3-48 Density-gradient centrifugation and LC-MS/MS can be used to identify many of the proteins in organelles. (a) The cells in liver tissue were mechanically broken to release the organelles, and the organelles were partially separated by density-gradient centrifugation. The locations of the organelles—which were spread out through the gradient and somewhat overlapped with one another—were determined using immunoblotting with antibodies that recognized previously identified, organelle-specific proteins. Fractions from the gradient were subjected to proteolysis and LC-MS/MS to identify the peptides, and hence the proteins, in each fraction. Comparisons with the locations of the organelles in the gradient (called protein correlation profiling) permitted assignment of many individual proteins to one or more organelles (organelle proteome identification). (b) The hierarchical breakdown of data derived from the procedures in part (a). Note that not all proteins identified could be assigned to organelles and that some proteins were assigned to more than one organelle.

[Data from L. J. Foster et al., 2006, Cell 125:187–199.]