Assigning Significance in Label-Free Quantitative Proteomics to Include Single-Peptide-Hit Proteins with Low Replicates
Figure 8
Comparison of the 26 and 44 differentially regulated proteins respectively selected by the 4-fold-change-MPSP and PLGEM-STN-MPSP approaches at a 5% false discovery rate. (a) Overlap of the two sets of differentially regulated proteins. Panels (b–d) show the distributions of (b) the number of detected PCSs, (c) the fold changes, and (d) the abundances of the quantified proteins. The blue square, the purple diamond, and the tan triangle markers represent the differentially regulated proteins selected by 4-fold-change-MPSP only, by both, and by PLGEM-STN-MPSP respectively. The protein number was from 1 to 55 on the x-axis representing the 55 unique proteins ranked according to their in each of the three groups (blue, purple, or tan).
