PCA reveals clustering of CCV and non-CCV proteins into functional groups. The SILAC data were decorrelated by PCA. The figure shows the projections of the data on the first (x axis) and second (y axis) principal components (scores plot). Each scatter point represents a protein. Distance from the origin of the plot indicates how strongly a protein is affected under the experimental conditions. Close proximity of proteins indicates similar profiles. Only the 688 proteins common to all 10 SILAC sets were analyzed. Subunits of a known protein complex are shown in the same color. Clathrin heavy and light chains, AP-1, and AP-2 form distinct clusters that and are clearly separated from the bulk of the other proteins. Known CCV coat proteins are annotated as AF (accessory factors). Mannose 6-phopshate receptors (M6PR) and lysosomal enzymes (Lys) are established cargo molecules of intracellular CCVs. A fully annotated version of this plot is shown in Fig. S3. Retro, retromer; RPS and RPL, small and large ribosomal subunits; COPI, COPI coat; CCT, CCT chaperone; Sig, signalosome; BLOC, BLOC-1; EIF3, translation initiation factor 3; PHK, phosphorylase kinase. P19, P20, PA: 19S, 20S, and 11S subcomplexes of the proteasome.