TOPP goes Rapid The OpenMS Proteomics Pipeline in a Grid-Enabled Web Portal

Abstract

Proteomics, the study of all the proteins contained in a particular sample, e.g., a cell, is a key technology in current biomedical research. The complexity and volume of proteomics data sets produced by mass spectrometric methods clearly suggests the use of grid-based high-performance computing for analysis. TOPP and OpenMS are open-source packages for proteomics data analysis, however, they do not provide support for Grid computing. In this work we present a portal interface for high-throughput data analysis with TOPP. The portal is based on Rapid, a tool for efficiently generating standardized port lets for a wide range of applications. The web-based interface allows the creation and editing of user-defined pipelines and their execution and monitoring on a Grid infrastructure. The portal also supports several file transfer protocols for data staging. It thus provides a simple and complete solution to high-throughput proteomics data analysis for inexperienced users through a convenient portal interface.