DataFilter_Script for experiment 2

To determine how DEX treatment in WT and MKO mice leads to muscle atrophy, we measured muscle protein fractional synthesis rates using shot-gun LC-MS/MS analysis after <i>in vivo</i> ²H₂O labeling . Mice were treated with PBS or DEX for 10 days. During the final 7 days, mice were also labeled with ²H₂O. The sample size for wild type controls treated with PBS (WT-PBS, n=6), wild type treated with DEX (WT-DEX, n=6), MKO treated with PBS (MKO-PBS, n=5) and MKO treated with DEX (MKO-DEX, n=5). The rational for biological replicates of n=5 -6 were used to ensure accurate comparison among each group. Biological replicates were chosen to asses biological variability rather than sole reliance on technical replicates. Controls included WT-PBS treated mice (n=6). Two separate dynamic proteomic experiments were completed and combined for final data analysis. This consisted of experiment 1 that included WT-PBS (n=4) and WT-DEX (n=4). Experiment 2 included the final biological replicates of WT-PBS (n=2), WT-DEX (n=2), MKO-PBS (n=5) and MKO-DEX (n=5). The data sets were combined and annotated as described by the following.<br>The data filter script contains the mass isotopomer distribution processed data that includes the peptide output, protein output, parameters, and project details for experiment 2.