Abstract
BackgroundWith the help of proteomics technology, the human plasma and urine proteomes, which closely represent the protein compositions of the input and output of the kidney, respectively, have been profiled in much greater detail by different research teams. Many datasets have been accumulated to form “reference profiles” of the plasma and urine proteomes. Comparing these two proteomes may help us understand the protein handling aspect of kidney function in a way, however, which has been unavailable until the recent advances in proteomics technology.Methodology/Principal FindingsAfter removing secreted proteins downstream of the kidney, 2611 proteins in plasma and 1522 in urine were identified with high confidence and compared based on available proteomic data to generate three subproteomes, the plasma-only subproteome, the plasma-and-urine subproteome, and the urine-only subproteome, and they correspond to three groups of proteins that are handled in three different ways by the kidney. The available experimental molecular weights of the proteins in the three subproteomes were collected and analyzed. Since the functions of the overrepresented proteins in the plasma-and-urine subproteome are probably the major functions that can be routinely regulated by excretion from the kidney in physiological conditions, Gene Ontology term enrichment in the plasma-and-urine subproteome versus the whole plasma proteome was analyzed. Protease activity, calcium and growth factor binding proteins, and coagulation and immune response-related proteins were found to be enriched.Conclusion/SignificanceThe comparison method described in this paper provides an illustration of a new approach for studying organ functions with a proteomics methodology. Because of its distinctive input (plasma) and output (urine), it is reasonable to predict that the kidney will be the first organ whose functions are further elucidated by proteomic methods in the near future. It can also be anticipated that there will be more applications for proteomics in organ function research.
Highlights
A large volume of plasma (350–400 mL/100 g of tissue per min) is filtered by the kidney to generate about 150–180 L/per day ultrafiltrate, and most components in the ultrafiltrate are selectively reabsorbed until less than 1% of the ultrafiltrating volume is excreted as urine [1]
A total of 292 proteins in plasma were identified by Jin Young Kim et al using both SEQUEST searching[24] and a protein data filtration method based on correlation (MWcorr) between the experimental (1-DE) and the theoretical molecular weights (MWs)[17], more than half of the assignments were based on single peptide identification
184 proteins were acquired as the plasma proteins with experimental MW information [17]
Summary
A large volume of plasma (350–400 mL/100 g of tissue per min) is filtered by the kidney to generate about 150–180 L/per day ultrafiltrate, and most components in the ultrafiltrate are selectively reabsorbed until less than 1% of the ultrafiltrating volume is excreted as urine [1]. With the help of proteomics technology, it can be studied with the black box method by comparing the input and output proteomes, which are well represented by the plasma and urine proteomes. With the help of proteomics technology, the human plasma and urine proteomes, which closely represent the protein compositions of the input and output of the kidney, respectively, have been profiled in much greater detail by different research teams. Many datasets have been accumulated to form ‘‘reference profiles’’ of the plasma and urine proteomes. Comparing these two proteomes may help us understand the protein handling aspect of kidney function in a way, which has been unavailable until the recent advances in proteomics technology
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