Figure 4

Protein coverage plots. A) Protein coverage plot for the yeast study. The left vertical axis indicates MS experiment while the right vertical axis indicates the number of proteins observed in each MS experiment. The horizontal axis indicates the protein rank when sorted by average abundance. The dashed smoother indicates average number of MS experiments in which proteins in that region were detected. B) Protein coverage plot for the GCM study (Reprinted with permission from [9]. Copyright 2008 American Chemical Society.) The left vertical axis indicates rank average protein abundance while the right vertical axis indicates sort order of abundance. The bottom axis indicates MS experiment number. C) Protein coverage plot for the prostate cancer study. The left vertical axis indicates MS experiment while the right vertical axis indicates number of proteins observed in each experiment (experiments 1R and 13R are not included here). The bottom horizontal axis indicates rank of protein ID, where proteins are sorted by the number of experiments they were detected in. The stair-step line helps the eye to delineate which proteins were observed in 1 MS experiment (first step on the far left) up to all experiments (top step on the far right) while the top horizontal axis indicates the number of proteins represented by each step.