Beyond Phenyx

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Phenyx has been successfully integrated into Proteome Software's Scaffold proteomics meta-analysis software, thereby giving Scaffold and Phenyx users access to an even greater abundance of and confidence in available results as well as the opportunity to go beyond a certain level of analysis thanks to Phenyx's innovative features.

Proteome Software's Scaffold statistically validates peptides and proteins from tandem mass spectrometry results data. One of the many advantages of Scaffold is that it considers the results from multiple search engines amongst which are Phenyx, SEQUEST® or Mascot®, as well as optionally running X!Tandem on data files.

Phenyx has been successfully integrated 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.

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.

GeneBio and Bruker Daltonics are collaborating to enhance Phenyx's functionality and further optimize the platform for a diverse array of Bruker Daltonics' mass spectrometers and workflows. Bruker Daltonics offers Phenyx as an option in its ProteinScape software platform in order to help proteomics customers achieve an even greater level of accuracy and success.

GeneBio's Phenyx will be capable of seamless data integration with GenoLogics' Proteus, the industry's most advanced solution for proteomics purposed lab and scientific data management and analysis. This integration enables users to experience an optimized protein search and identificaion managed from a centralized data management platform and user interface, making the experience more efficient and by extension providing customers with more of what they want in a total lab and data management environment.

Insilicos LLC develops life science software for pharmaceutical development, biological research and clinical diagnostics. IPP is a high performance software system for the identification and analysis of proteomics data resulting from an open-source collaboration led by the ISB to further develop their TPP. IPP brings major advances in speed, usability and workflow efficiency to all users of TPP.

Insilicos is the exclusive global reseller of a bundled Phenyx/IPP offer, while GeneBio is the exclusive European reseller of this Phenyx/IPP bundle. In addition, GeneBio and Insilicos have acquired the right to non-exclusively sell each other's products in Europe and North America, respectively. The technical aspect of the partnership involves the inclusion of Phenyx within the IPP, thereby allowing both IPP and TPP users to seamlessly utilize Phenyx within their specific workflows.

Sage-N Research sells Phenyx worldwide as a pre-installed software option on its Sorcerer 2 IDA (Integrated Data Appliance), a compact system that allows researchers to submit analysis jobs for both Phenyx and the Sorcerer version of SEQUEST using a simple Web interface for complete support of mass spectrometry data from both ion traps and quadrupole time-of-flight (Q-TOF) instruments. The two companies plan to extend the integration of their technologies over time, including integrated workflows using multiple algorithms, and an accelerated version of Phenyx using Sorcerer's Pattern Match Accelerator (TM) technology.