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.

为探究野生型（Wild Type, WT）与肌肉特异性敲除型（Muscle-specific Knockout, MKO）小鼠经地塞米松（Dexamethasone, DEX）处理后诱发肌肉萎缩的机制，本研究通过体内（in vivo）²H₂O标记后采用鸟枪法液相色谱-串联质谱（shot-gun LC-MS/MS）分析技术，测定了肌肉蛋白质的分数合成速率。实验小鼠经磷酸盐缓冲液（PBS）或地塞米松处理10天，在处理的最后7天，同时用²H₂O进行标记。本研究设置的各组样本量如下：PBS处理的野生型对照组（WT-PBS, n=6）、DEX处理的野生型组（WT-DEX, n=6）、PBS处理的MKO组（MKO-PBS, n=5）以及DEX处理的MKO组（MKO-DEX, n=5）。本研究采用n=5~6的生物学重复样本，旨在确保各组间的比较结果准确可靠。选择生物学重复是为了评估生物学变异，而非仅依赖技术重复。对照组为经PBS处理的WT-PBS组小鼠（n=6）。本研究共完成两项独立的动态蛋白质组学实验，并将两组数据合并用于最终的数据分析。其中第一项实验包含WT-PBS组（n=4）与WT-DEX组（n=4）；第二项实验则包含剩余生物学重复样本：WT-PBS组（n=2）、WT-DEX组（n=2）、MKO-PBS组（n=5）以及MKO-DEX组（n=5）。合并后的数据集将按照下述方式进行注释。本研究的数据过滤脚本包含经质量同位素分布处理后的实验2数据，其中涵盖肽段输出结果、蛋白质输出结果、分析参数以及项目相关细节。