DataFilter_Script for experiment 1

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 in vivo 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.The data filter script contains the mass isotopomer distribution processed data that includes the peptide output, protein output, parameters, and project details for experiment 1.