Fig. 4.

Stable isotope-labeled peptide analysis validates MS1 intensity analysis. A, Observed intensity versus amount measured using ¹³C- and ¹⁵N-labeled internal standards, for 9 selected peptides (supplemental Table S13), each assayed in 3 replicate injections of a WT (blue) or DO-KO-1 (red) sample. Pearson correlation coefficient indicated. B, Observed DO-KO-1/WT abundance ratio for peptides selected from groups with intensity greater in WT than DO-KO (blue), approximately equal intensity in WT and DO-KO (green), or greater in DO-KO than WT (red). Mean ± S.D. shown (n = 3–10).