September 13th, 2007

FOR IMMEDIATE RELEASE

 

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


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 GeneBios Phenyx MS data
analysis platform into the ISBs 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 Phenyxs 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 GeneBios 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)



ISBs 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 GeneBios
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