The Computational Portal and Analysis System (CPAS) is an open-source, extensible infrastructure for evaluating and publishing data from high throughput biological experiments. CPAS is a three-tiered web application written with the Sun Microsystems Java Enterprise Edition. Currently CPAS’s most developed module is for MS/MS proteomics experiments.

The original installation of CPAS installed the X!Tandem search engine and the Institute for System Biology’s Trans-Proteomic Pipeline(TPP). From the CPAS user interface, data files from MS/MS analyses of complex protein samples can be automatically processed through a pipeline that searches MS spectra against protein databases, assigns peptide search hits to proteins, and performs relative quantitation of normal vs. other, isotope labeled samples. Simpler experiments are also possible.

X!Tandem is a powerful open-source search engine but there are several other search engines that are in common use; X!Tandem (www.thegpm.org), Sequest (Thermo Scientific), and Mascot (Matrix Science) are probably the most widely used. Each search engine has its own strengths and weaknesses; therefore their complementary results are a powerful tool for validation of identified peptides. The standard data formats implemented by the TPP (mzXML, pepXML) allow the direct comparison of results produced by different search engines and MS instrument manufacturers.

Because of licensing costs and limited IT resources implementing multiple search engines and an analysis pipeline is a serious endeavor. Through open-source development contributions - Mascot integration by the Bioinformatics Institute, Matrix, Singapore (CPAS version 1.7) and Sequest Cluster integration by the University of Kentucky, Lexington, Kentucky (CPAS version 2.0) - CPAS lessens the resources required to implement a complex data analysis pipeline and provides a mechanism for multiple labs to share a common resource.