The laboratory studies the molecular mechanisms of water transport in the renal collecting duct and the pathophysiology of water balance disorders. Much of the data for tthese studies comes from protein mass spectrometry and next-generation sequencing. Mass spectrometers suitable for protein mass spectrometry are rapidly improving in performance capabilities, providing more and more data for systems biology-oriented studies. However, quite often data processing tasks are rate limiting for progress in proteomics-based studies. In this project, we are developing software tools need for interpretation of the large data sets obtained. They are developed initially for our own studies but we make these tools available to other investigators. To aid in dissemination of our software, the algorithms are coded in Java, which is platform-independent, allowing the code to run on a variety of machines. In addition, where possible, we are striving to make software available online (on the World Wide Web) for execution (see http://helixweb.nih.gov/ESBL/). In addition, proteomic investigation often requires the design and production of new antibodies. We have developed software to predict the optimal synthetic peptide sequences for production of antibodies (see http://helixweb.nih.gov/AbDesigner/). The advent of next-generation sequencing has created new computational challenges that are being addressed in the laboratory.
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