Phenyx is a standalone platform, but we realize that it is used in conjunction with existing hardware, workflows and management systems that have been developed to fit complex laboratory requirements. In light of this, GeneBio has developed both business and marketing partnerships that see Phenyx integrated with third-party solutions. Phenyx can also be ordered from our business partners.
Bruker Daltonics : ProteinScapeTM
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.
Sage-N Research : SorcererTM
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.
Nonlinear Dynamics : Progenesis LC-MS
GeneBio and Nonlinear Dynamics are engaged in a distribution agreement whereby Nonlinear will distribute Phenyx both as a standalone software package and alongside the Progenesis LC-MS identification platform. This partnership exploits the complementary technology of Phenyx and the novel Progenesis LC-MS software for label-free quantitative analysis.
Proteome Software : Scaffold
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.
Institute for Systems Biology : TPP
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.
Integromics : OmicsHub Proteomics
Phenyx has been successfully integrated into Integromics' data analysis and management tool - OmicsHub Proteomics. OmicsHub Proteomics serve as an end-to-end proteomics data analysis and management system, from protein peak detection, multiple search engine support and pathways integration to generation of final reports. It has been developed in cooperation with ProteoRed, the Spanish National Proteomics Network in which Phenyx is a central solution for protein identification. This integration enables OmicsHub Proteomics users to take greater advantage of Phenyx in term of data automation, result comparison and reporting.
Proxeon : ProteinCenterTM
GeneBio and Proxeon are engaged in an integration and distribution agreement whereby Phenyx will be integrated with Proxeon's ProteinCenter to provide proteomics scientists with a professional bioinformatics solution to significantly enhance the efficiency and effectiveness of analyzing and interpreting mass spectrometry data. The integration will be through direct links from Phenyx identifications to ProteinCenter and specific Phenyx exports loaded into ProteinCenter. In addition, ProteinCenter will be distributed through Proxeon and GeneBio sales channels, while GeneBio will continue as the supplier of Phenyx.
Protagen : Modiro®
GeneBio and Protagen are engaged in a distribution agreement that allows GeneBio to distribute Protagen's Modiro, a novel software tool enabling rapid and automated detection of true post-translational modifications in MS/MS datasets. At the same time, GeneBio and Protagen will collaborate closely in order to seamlessly link the Modiro functionalities to GeneBio's Phenyx.
GenoLogics : ProteusTM
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 : Insilicos Proteomics Pipeline (IPP)
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.