GeneBio's Phenyx Integrated with Institute for System Biology's TPP

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Geneva, Switzerland, and Seattle, Washington, USA - September 13, 2007 -Geneva Bioinformatics (GeneBio) SA and the Institute for Systems Biology (ISB) today announced the successful integration of GeneBio's Phenyx MS data analysis platform into the ISB's Trans Proteomic Pipeline (TPP), an Open Source analysis platform for unified storage and analysis of tandem mass spectrometry data based on open XML file formats. This integration, that was rendered very straightforward thanks to Phenyx's increased flexibility and the wealth of import/export formats it accepts, brings TPP developers and users access to a powerful search engine while giving Phenyx users the freedom to automatically process results with a host of high-throughput proteomics analysis tools.

Developed in collaboration with the Swiss Institute of Bioinformatics (SIB), Phenyx is GeneBio's renowned software platform for the identification and characterization of proteins and peptides from mass spectrometry data, specifically designed to meet the concurrent demands of high-throughput MS data analysis and dynamic results assessment while offering a flexible user experience and an adaptable architecture to help instill confidence in results assessment. (http://phenyx.vital-it.ch/pwi)

ISB's TPP was one of the earliest comprehensive tools suites to address the requirements of the proteomics community for standardized MS/MS data analysis and validation. Using TPP tools, each putative identification is assigned a probability of being correct and robust; global false discovery rates (FDRs) are calculated both at the spectrum and peptide level with PeptideProphet and at the protein level with ProteinProphet.

"Phenyx is a major player in the mass spectrometry field; an increasing number of TPP users are requesting the ability to validate Phenyx search results using the TPP tools," said Dr. Eric Deutsch of the ISB. "Our goal is to make the TPP an invaluable part of the analysis process for as many users as possible by ensuring it works well with other industry tools; the integration of Phenyx fulfils user expectations and extends the functionality of the TPP. The integration of Phenyx will improve confidence levels in protein and peptide identifications for all its users."

"This integration brings Phenyx users a wealth of functionalities while also broadening our market penetration," said Nasri Nahas, CEO of GeneBio. "Phenyx users can now automatically process their results into the TPP statistical validation pipeline via PeptideProphet and ProteinProphet, while publishing results via PeptideAtlas. These are only a few examples of what this integration brings to Phenyx users; looking at it from a different angle, we look forward to a plethora of new Phenyx users from our exposure in the TPP. This fantastic opportunity is perfectly congruent with GeneBio's increased effort to integrate Phenyx in major proteomics platforms and software in order to facilitate its accessibility to our ever growing client-base."

For more information about Phenyx and its interaction with the TPP please go to www.phenyx-ms.com or contact us at phenyx@genebio.com. To download the new version of the TPP and start using it with Phenyx now, please visit the following link: http://tools.proteomecenter.org/software.php