Computational Tools for Proteomics

National Heart, Lung, And Blood Institute

Investigators

Linked publications, trials & patents

Abstract

The Knepper laboratory studies the molecular mechanisms of water transport in the renal collecting duct and the pathophysiology of water balance disorders. The studies employ multi-omic methods including those involving protein mass spectrometry and various next generation sequencing (NGS) modalities. ----- Proteomics tools. 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 needed for interpretation of the large data sets obtained. These tools are developed initially for our own studies but we make them available to other investigators at https://esbl.nhlbi.nih.gov/Bioinformatic%20Tools.htm. ---- NGS data integration. The identification of putative enhancers involved in transcriptional regulation of Aqp2 gene transcription and other key genes important to kidney water transport is an important objective of the laboratory. They can be identified through a combination of ATAC-seq data, histone H3K27 acetylation ChIP-seq data, and RNA-polymerase II ChIP-seq data. To integrate such data sets to make the most precise identification of enhancers, we have developed NGS-Integrator, which employs Bayesian integration techniques. ---- Big Data integration of multi-omic data sets. To integrate multiple -omic data sets to addressed focused questions, we have developed Bayesian integration approaches. --- Systems biology based 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 https://esbl.nhlbi.nih.gov/AbDesigner/). ---- To aid in dissemination of our software, the algorithms are coded in Java or Python, which are platform-independent, allowing the code to run on a variety of machines. In addition, where possible, we are striving to make software available online for execution (see https://esbl.nhlbi.nih.gov/Bioinformatic%20Tools.htm). ---- <b><u>Data Resources</u></b>: <i>Genes Expression Atlases for Renal Epithelia</i>. The kidney is made up of a myriad of renal tubules, each consisting of 14 distinct segments arranged in series, made up of at least 17 cell types. Modeling the physiology and pathophysiology of the kidney requires knowledge of what genes are expressed in each of these cell types. The Epithelial Systems Biology Laboratory (ESBL) has used RNA-seq and protein mass spectrometry in microdissected renal tubule segments, as well as single-cell RNA-seq, to identify mRNA and protein abundances in each cell type. The data have been provided to kidney researchers worldwide in the form of curated online databases that can be searched, browsed or downloaded. These databases can be access through an index page at https://esbl.nhlbi.nih.gov/Databases/KSBP2/. ---- b><u>Data Resources</u></b>: <i>Phosphoproteomics Databases</i>. Regulation of transport in the nephron and collecting ducts of the kidney occurs in part through phosphorylation changes, for example in response to the hormone vasopressin, which regulates salt and water transport. Epithelial Systems Biology Laboratory members have generated extensive phosphoproteomic data in renal tubule epithelia and provided the data to kidney researchers worldwide in the form of curated online databases that can be searched, browsed or downloaded. These databases can be access through an index page at https://esbl.nhlbi.nih.gov/Databases/KSBP2/