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Src homology 2 (SH2) domains are the largest family of interaction modules encoded by the human genome to recognize tyrosine-phosphorylated sequences and thereby play pivotal roles in transducing and controlling cellular signals emanating from protein-tyrosine kinases. Different SH2 domains select for distinct phosphopeptides, and the function of a given(More)
Both the urinary proteome and its glycoproteome can reflect human health status, and more directly, functions of kidney and urinary tracts. Because the high abundance protein albumin is not N-glycosylated, the urine N-glycoprotein enrichment procedure could deplete it, and urine proteome could thus provide a more detailed protein profile in addition to(More)
The urinary proteome is known to be a valuable field of study related to organ functions. There have been several extensive urine proteome studies. However, the overlapping rate among different studies is relatively low. Whether the low overlapping rate was caused by different sample sources, preparation, separation and identification methods is unknown.(More)
The past decade witnessed a few biomarkers discovered and validated; however, biomarker research as a whole has not been fruitful as expected. A majority of our efforts has been focused on blood, the dynamic tissue directly connecting every part of the body. Nevertheless, despite all the interest and endeavor spent on it, the blood has failed to deliver(More)
The combinations of gel electrophoresis or LC and mass spectrometry are two popular approaches for large scale protein identification. However, the throughput of both approaches is limited by the speed of the protein digestion process. Present research into fast protein enzymatic digestion has been focused mainly on known proteins, and it is unclear whether(More)
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)
Immobilized-metal-ion affinity chromatography (IMAC) is used extensively for phosphopeptide enrichment in phosphoproteomics. However, the effect of nucleic acids in protein samples on phosphopeptide enrichment by IMAC has not yet been well clarified. In this study, we demonstrate that IMAC beads possess a strong adsorption of nucleic acids, especially(More)
Time-consuming and experience-dependent manual validations of tandem mass spectra are usually applied to SEQUEST results. This inefficient method has become a significant bottleneck for MS/MS data processing. Here we introduce a program AMASS (advanced mass spectrum screener), which can filter the tandem mass spectra of SEQUEST results by measuring the(More)
RScore, a new criterion of randomicity for evaluating tandem mass (MS/MS) spectra, is described. RScore is defined as the relative quality in cross-correlation and matched intensity percentage of a potentially positive peptide to those of other possible candidates for the same spectrum. By utilizing RScore combined with less stringent SEQUEST score filters,(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)