Assigning Significance in Label-Free Quantitative Proteomics to Include Single-Peptide-Hit Proteins with Low Replicates
Figure 7
Receiver operating characteristic analysis of the PLGEM-STN approach with (red curve) or without (blue curve) the combination with MPSP. Positives are the differentially regulated proteins selected from the comparison of proteins abundances between samples and (see Table 1 and Figure 1 for definition). False positives are the differentially regulated proteins selected from the comparison of proteins abundances between samples c and c (see Table 1 for definition). True positives are estimated by subtracting false positives from the positives. For each approach that is, PLGEM-STN-MPSP or PLGEM-STN, 37 data points at different confidence levels (C.L.) are plotted in this figure, starting from C.L. = 0.0001 up to C.L. = 0.01. The relationship between STN thresholds and C.L. can be found in Figure S2. The increment is 0.001 between C.L. of 0.0001 and 0.003 (30 data points). Between C.L. of 0.0.003 and 0.01, the increment is 0.01 (7 data points). The use of PLGEM here is similar to that in Table 3.
