Fig. 2

Assessment of protein half-lives in different cell types. a Scatter plots comparing protein half-lives determined in two experiments. On the diagonal the half-lives determined in biological replicate experiments in the same cell type are compared. Red dots indicate nuclear pore complex components. The plots below the diagonal compare the average protein half-lives determined in one cell type against other cell types as indicated. b, c, d Highly reproducible individual peptide fold changes from proteins with very-long half-lives determined from the B-cell experiment. The median protein fold changes are denoted by the slope of the line. The fold changes at the different time points are denoted by the different colors (red, 7 h; gray 11 h; green 24 h, and blue 34 h) with replicate one represented by a solid line and replicate two by a dashed line. The insets on each graph show the heavy and light SILAC intensities plotted on the same scale. b O75367 (Core histone macro-H2A.1, H2AFY) half-life from replicate one/two 945.9/995.9 h. c P16403 (Histone H1.2, gene HIST1H1C) half-life from replicate one/two: 2168.8/2315.5 h. d P20700 (Lamin-B1, gene LMNB1) half-life from replicate one/two: 1479.9/1623.5 h. The same is shown for three nuclear pore complex members (NUPs) as for (b, c, d). e Protein NUP205 has a half-life of 103.3 h in replicate one and 138.9 h in replicate two. f Protein NUP153 (P49790) has the shortest half-life of all the NUPs identified in B-cells with a half-life of 49.8 h in replicate one and 55.1 in replicate two. g Protein NUP107 (P57740) has a half-life of 91.2 h in replicate one and 104.5 h in replicate two