Figure 4. Peptide and protein repeatability.

To assess repeatability, we evaluated the overlapping fraction of identified peptides in pairs of technical replicates. For example, if 2523 and 2663 peptides were identified in two different replicates and 1362 of those sequences were common to both lists, the overlap between these replicates was 35.6%. Shaded boxes represent peptide repeatability, and open boxes represent protein repeatability (where two distinct peptide sequences were required for protein to be detected). For Study 5, only peptide repeatability was characterized; the boxes represent the inter-quartile range, while the whiskers represent the full range of observed values (Panels A and B). The mid-line in each box is the median. The six replicates of yeast in Study 5 enabled fifteen pair-wise comparisons per instrument, while the five replicates of NCI-20 enabled ten comparisons for that sample. Studies 6 (Panels C and D) and 8 (Panels E and F) produced triplicates, enabling only three pair-wise comparisons for repeatability. These images show all three values.