E human orthologs approximately represents their abundance in human urine under physiological conditions. The 981 human orthologs were LED 209 paired to rat proteins that were identified in both 10781694 isolated rat kidney perfusion-driven urine samples. The rat proteins corresponding to human orthologs had an emPAI value when they were identified in the perfusiondriven urine, which can be used to approximately estimate the absolute Mirin protein content in the perfusion-driven urine. The rat proteins corresponding to the human orthologs were sorted according to their emPAI values in the two perfusion-driven samples from most to least abundant in the perfusion-driven urine. Due to the correspondence between rat proteins and their human orthologs, this resulted in the re-ordering of the 981 human orthologs. We assume that the abundances of orthologous proteins in the human and rat samples have a certain correlation. The new order of the 981 human orthologs sorted by the abundance of their paired rat proteins in the perfusion-driven urine might approximately represent the anundance order in the pathological condition. For a given protein, if the abundance ranking increased significantly from the normal urine to the perfusion-driven urine, expression of that protein might increase under pathological conditions compared to other proteins. The ranks 16985061 of the corresponding rat proteins in the two perfusion-driven urine samples were compared first. The vast majority, 922 proteins (94 ), had ranking changes of less than 300. Therefore, a ranking change of 300 was considered to be significant. In total, 75 of the 981 human orthologs increased in rank by 300 from the normal human urine to the two perfusion-driven urine samples (Table S2). The emPAI value is only an approximate estimation of the absolute protein content in a protein mixture [29]. The degree of correlation between orthologous protein abundance was not investigated. Here, we only observed that, for the 75 human orthologs, the rank of their corresponding rat proteins increased significantly in the perfusion-driven urine compared to their rank in the normal urine. We expect the large difference in the abundance ranking of these proteins will indicate their potential to be kidney disease biomarkers. These 75 proteins were compared with the pooled human urine and urinary exosome proteome and the human plasma proteome. Of these proteins, 35 had been identified both in the urine (including urinary exosome) proteome and the plasma proteome; 15 proteins had only been identified in the urine (including urinary exosome) proteome but not in the plasma proteome; 13 proteins had only been identified in the plasma proteome but not in the urine (including urinary exosome) proteome; and 12 proteins had not been identified in either the urine (including urinary exosome) proteome or the plasma proteome.the other two rats were profiled with the TripleTOF 5600 platform, which identified 474 and 466 proteins during perfusion with oxygen supplementation and 511 and 527 proteins during perfusion without oxygen supplementation. The expression of the proteins present during perfusion with oxygen-supplemented medium was compared with expression during perfusion without oxygen supplementation using the labelfree quantitative method provided by the SCAFFOLD program. The expression of 39 proteins was significantly increased in all four perfusion-driven urine samples when the kidneys were perfused without oxygen supplementation (p,0.05.E human orthologs approximately represents their abundance in human urine under physiological conditions. The 981 human orthologs were paired to rat proteins that were identified in both 10781694 isolated rat kidney perfusion-driven urine samples. The rat proteins corresponding to human orthologs had an emPAI value when they were identified in the perfusiondriven urine, which can be used to approximately estimate the absolute protein content in the perfusion-driven urine. The rat proteins corresponding to the human orthologs were sorted according to their emPAI values in the two perfusion-driven samples from most to least abundant in the perfusion-driven urine. Due to the correspondence between rat proteins and their human orthologs, this resulted in the re-ordering of the 981 human orthologs. We assume that the abundances of orthologous proteins in the human and rat samples have a certain correlation. The new order of the 981 human orthologs sorted by the abundance of their paired rat proteins in the perfusion-driven urine might approximately represent the anundance order in the pathological condition. For a given protein, if the abundance ranking increased significantly from the normal urine to the perfusion-driven urine, expression of that protein might increase under pathological conditions compared to other proteins. The ranks 16985061 of the corresponding rat proteins in the two perfusion-driven urine samples were compared first. The vast majority, 922 proteins (94 ), had ranking changes of less than 300. Therefore, a ranking change of 300 was considered to be significant. In total, 75 of the 981 human orthologs increased in rank by 300 from the normal human urine to the two perfusion-driven urine samples (Table S2). The emPAI value is only an approximate estimation of the absolute protein content in a protein mixture [29]. The degree of correlation between orthologous protein abundance was not investigated. Here, we only observed that, for the 75 human orthologs, the rank of their corresponding rat proteins increased significantly in the perfusion-driven urine compared to their rank in the normal urine. We expect the large difference in the abundance ranking of these proteins will indicate their potential to be kidney disease biomarkers. These 75 proteins were compared with the pooled human urine and urinary exosome proteome and the human plasma proteome. Of these proteins, 35 had been identified both in the urine (including urinary exosome) proteome and the plasma proteome; 15 proteins had only been identified in the urine (including urinary exosome) proteome but not in the plasma proteome; 13 proteins had only been identified in the plasma proteome but not in the urine (including urinary exosome) proteome; and 12 proteins had not been identified in either the urine (including urinary exosome) proteome or the plasma proteome.the other two rats were profiled with the TripleTOF 5600 platform, which identified 474 and 466 proteins during perfusion with oxygen supplementation and 511 and 527 proteins during perfusion without oxygen supplementation. The expression of the proteins present during perfusion with oxygen-supplemented medium was compared with expression during perfusion without oxygen supplementation using the labelfree quantitative method provided by the SCAFFOLD program. The expression of 39 proteins was significantly increased in all four perfusion-driven urine samples when the kidneys were perfused without oxygen supplementation (p,0.05.
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Cathepsins
