Automated PCA of sample CCV proteins. Automated PCA was performed in the context of a reference set (85 proteins belonging to six protein complexes: AP-1, AP-2, AP-3, AP-4, retromer, and ribosomes; Table S1). For each candidate protein, PCA of the reference set was performed using only those datasets in which the candidate protein was represented. The candidate protein was then projected onto the corresponding PCA plot, and the nearest reference cluster was determined. The figure shows the projections on the first two principal components for six sample proteins. The relative positions of reference clusters change with different combinations of available data, but in each case, all reference proteins are correctly grouped into the expected complexes. Candidate proteins are shown in red and reference proteins in black.