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Ubiquitin ligases (E3s) confer specificity to ubiquitination by recognizing target substrates. However, the substrates of most E3s have not been extensively discovered, and new methods are needed to efficiently and comprehensively identify these substrates. Mostly, E3s specifically recognize substrates via their protein interaction domains. We developed a(More)
Urine is an important source of biomarkers. A single proteomics assay can identify hundreds of differentially expressed proteins between disease and control samples; however, the ability to select biomarker candidates with the most promise for further validation study remains difficult. A bioinformatics tool that allows accurate and convenient comparison of(More)
By nature, biomarker is the measurable change associated with a physiological or pathophysiological process. Unlike blood which has mechanisms to minimize changes and to keep the internal environment homeostatic, urine is more likely to reflect changes of the body and is a better biomarker source. Because of its potential in biomarker discovery, urinary(More)
The use of targeted proteomics to identify urinary biomarkers of kidney disease in urine can avoid the interference of serum proteins. It may provide better sample throughput, higher sensitivity, and specificity. Knowing which urinary proteins to target is essential. By analyzing the urine from perfused isolated rat kidneys, 990 kidney origin proteins with(More)
BACKGROUND 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(More)
Biomarker is the measurable change associated with a physiological or pathophysiological process. Unlike blood which has mechanisms to keep the internal environment homeostatic, urine is more likely to reflect changes of the body. As a result, urine is likely to be a better biomarker source than blood. However, since the urinary proteome is affected by many(More)
Nitrocellulose membrane based urinary protein preservation method is simple, fast and economic, but its advantage over the traditionally used acetone precipitation method is still unclear. In this work, we prepared urinary proteins by the two methods by LC-MS/MS. Then we used protein spectra counts to assess the reproducibility of the two methods. Proteins(More)
Secretome study presents new possibilities for understanding liver secretory function in a comprehensive and exploratory way. Perfusates from isolated perfused rat liver are good targets for liver secretome study on the organ level. There are two major concerns in this type of study, cytosolic and blood contaminations in the perfusates. Therefore, the(More)
To compare two enrichment and preservation methods of urinary proteins, stored in polyvinylidene difluoride (PVDF) membrane (Urimem) or direct freezing, we examined the differences between the two methods in time, space, costs of supplies and electricity, degree of protein degradation and convenience of the sample handling. The urimem method is superior in(More)