Figure 2 .

Comparison to antibody assay. A comparison between the antibody assay estimate of the protein level expression patterns for Apo B (panel A) and Apo E (panel B) (x-axes in both figures), and the LC-MS/MS estimates using the summation, top 3 and metaprotein methods for protein level expression. We note that the three algorithms are in agreement to a high degree. Correlations for Apo B are .55, .54 and .56 for Metaprotein, Summation and Top 3 models respectively and they are .31, .28 and .32 for respectively for Apo E. Note that there is an outlier in each of the top left and bottom right of the Apo E figure, and without these two outliers, correlations are just under .6 for all three methods. Antibody assay values, which measure protein per volume, were converted to protein per total protein using total protein levels from a Bradford assay. All measurements were standardized to mean zero and standard deviation 1.