Additional file 1 of Many kinds of oxidized proteins are present more in the urine of the elderly

Additional file 1. Table S1. Detailed information of individuals. Table S2. The proportion of modifications occurring at each amino acid. Table S3. Differences and statistics of oxidations and AA modifications between different groups. Table S4. ROC performance parameters and Delong test in the discovery cohort. Table S5. Random grouping calculation results in 14 modifications. Table S6. ROC performance parameters and Delong test in validation cohort. Table S7. The urine sample processing methods of the published studies in the literature, and the comparison with this method. Table S8. The urine sample data collection methods of published studies in the literature and compares them with our method. Fig. S1. Oxidative proteins PPI analysis and gene functional analysis using STRING. Fig. S2. Functional profiling of each protein set was conducted using the GO, KEGG and WikiPathways databases. Fig. S3. The differentially expressed proteins overlap between each group. Fig. S4. O-Y-David. BF, MF, CC, and KEGG by David and gene functional analysis by g:Profiler. Fig. S5. O-M-David. BF,MF,CC, and KEGG by David and gene functional analysis by g:Profiler. Fig. S6. PFind parameters setting (Open-search). Fig. S7. a. A illustration of the definition of Species and Sites. As for any modification, “sites” means the quantity of all sites where modifications occur, “species” refers to the type of peptide that is modified. b. Schematic representation of the comparison between the significant modifications via “sites” and “species” aging urinary proteomes. Supplementary site calculate method code: The program codes to extract this information from the “pd.all_result” document.

附加文件1。
表S1 研究个体详细信息。
表S2 各氨基酸（amino acid, AA）位点上发生修饰的占比。
表S3 不同组别间氧化修饰与氨基酸修饰的差异及统计结果。
表S4 发现队列中的受试者工作特征曲线（Receiver Operating Characteristic，ROC）性能参数与德龙（Delong）检验结果。
表S5 14种修饰的随机分组计算结果。
表S6 验证队列中的ROC性能参数与德龙检验结果。
表S7 已发表文献中尿液样本处理方法及其与本研究方法的对比。
表S8 已发表文献中尿液样本数据采集方法及其与本研究方法的对比。
图S1 基于STRING数据库的氧化修饰蛋白质蛋白质相互作用（Protein-Protein Interaction，PPI）分析与基因功能富集分析。
图S2 基于基因本体（Gene Ontology，GO）、京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）以及WikiPathways数据库对各蛋白质组进行功能注释分析。
图S3 各组间差异表达蛋白质的重叠情况。
图S4 基于David工具完成O-Y组的BF、MF、CC及KEGG功能富集分析，并通过g:Profiler进行基因功能注释分析。
图S5 基于David工具完成O-M组的BF、MF、CC及KEGG功能富集分析，并通过g:Profiler进行基因功能注释分析。
图S6 PFind（开放搜索模式）参数设置。
图S7 a. 物种（Species）与位点（Sites）的定义示意图。对于任意修饰而言，“位点”指所有发生修饰的位点数量，“物种”指发生修饰的肽段类型。b. 基于“位点”与“物种”维度对衰老尿液蛋白质组中显著修饰进行对比的示意图。
补充位点计算方法代码：用于从“pd.all_result”文件中提取上述信息的程序代码。