Fig. 5.

Sensitivity and specificity of ΔFit depends on threshold. A, The distribution of ΔFit scores from rabbit GAPDH peptides shown in Fig. 4B. In blue is a histogram of the 590 ΔFit scores from modified peptides. To match the size of the blue distribution, in red is a random sample of 590 out of the 4507 total ΔFit scores from unmodified peptides. At each ΔFit threshold, the specificity (B, red line) is the fraction of the isotope distributions from unmodified GAPDH peptides (red distribution) that lies to the left of the threshold. The sensitivity (C, blue line) is the fraction of the isotope distributions from GAPDH modified peptides (blue distribution) that lies to the right of the threshold. B and C also show sensitivity and specificity of ΔFit on E. coli proteomic preparations for comparison. In panel (B), the specificity shown by orange lines a-d is the fraction of the orange distribution from the same-lettered histogram in Fig. 6 that is less than the threshold. The specificity line labeled “e” shows the fraction of all summed features (using the orange distribution in Fig. 6D) eliminated by both the ΔFit threshold AND a fitHg threshold of 0.05 to produce the distribution in Fig. 6E. In panel (C) the letters on the purple sensitivity lines refer to the histograms in Fig. 6 that produce the sensitivity estimate.