Always at the top
Phenyx is a 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.
About Phenyx Documentation DownloadsPhenyx Pack Partner News Events Links Contact Us
Welcome to Phenyx, where you can find out more about our MS data analysis package
GeneBio and Genedata Integrate Computational Platforms to Support Large-Scale Proteomics Projects
26.10.2005
GeneBio Partners with Proteomic Solutions to Distribute Updated Phenyx Platform in France
21.09.2005
ABRF 2006
11.2 - 14.2, 2006 - Long Beach, CA (USA)
Exhibitor Presentation
5th International Bio Expo Japan
17.5 - 19.5, 2006 - Tokyo, Japan
3,000 proteins get discovered each year find an application
Join them and increase your chances to get hired.
Driven by Excellence
Teachers are selected among experts of For more information, please choose from the list below.
Manuals, Requirements & Instructions
Tutorials
Release Notes
FAQ
Troubleshooting
Example Files & Databases
Disclaimers
Posters & Brochures
Further Reading
Manuals, Requirements & Instructions
Information about how to get up and running with Phenyx. This documentation is also supplied in print form when Phenyx is purchased.
Phenyx Quick Start (PDF) (updated 24.02.2005)
Phenyx User Manual (PDF) (updated 24.02.2005)
System Requirements & Installation Instructions (updated 24.02.2005)
^ Top
Tutorials
Animated tutorials walk you through Phenyx and show you what it can do.
Phenyx Overview
^ Top
Release Notes
Find out exactly what has changed since the last release of Phenyx.
Release Notes
^ Top
FAQ
Frequently Asked Questions concerning Phenyx.
FAQ
^ Top
Troubleshooting
Having installation difficulties or other problems with Phenyx? This guide will point you in the right direction.
Troubleshooting
^ Top
Example Files & Databases
These files will let you test the Phenyx results using example data. You can also download pre-compiled databases which can then be used within Phenyx.
Phenyx Example Files
Phenyx Pre-compiled Databases
^ Top
Disclaimers
These disclaimers can also be found when either registering for the public Phenyx version or when download and installing the Phenyx platform.
Phenyx Virtual Desktop Disclaimer
Phenyx Calculation Engine Disclaimer
^ Top
Posters & Brochures
For more information about Phenyx, download the brochure or one of the Phenyx posters from previous conferences.
Phenyx poster from HUPO 2004 (PDF)
Phenyx poster from SPS 2004 (PDF)
Phenyx poster from ASMS 2005 (PDF)
Phenyx brochure (PDF) (updated 23.11.2004)
^ Top
Further Reading
These articles describing the technology behind Phenyx can all be found via PubMed, a service of the National Library of Medicine.
Colinge J, Magnin J, Dessingy T, Giron M and Masselot A. Improved peptide charge state assignment. Proteomics, 3:1434-1440, 2003.
Colinge J, Masselot A, Giron M, Dessingy T, Magnin J. "OLAV: towards high-throughput tandem mass spectrometry data identification," Proteomics, Vol. 3, No. 8, August 2003, pp. 1454-1463.
Colinge J, Magnin J, Masselot A. A systematic statistical analysis of ion trap tandem mass spectra in view of peptide scoring. In: Proceeding of the Workshop on Algorithms in Bioinformatics (WABI), R. Page and G. Benson (Eds), Budapest, September 2003, LNBI 2812, Springer, 25-38, 2003.
Colinge J, Masselot A. "Mass spectrometry has married statistics: uncle is functionality, children are selectivity and sensitivity," DDT: TARGETS, Vol. 3, No. 2 (Suppl.), 2004, pp. 50-55.
Colinge J, Masselot A, Cusin I, Mahé E, Niknejad A, Argoud-Puy G, Reffas S, Bederr N, Gleizes A, Rey P-A, Bougueleret L. "High performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics," Proteomics. 2004 Jul;4(7):1977-84.
Colinge J, Chiappe D, Lagache S, Moniatte M, Bougueleret L. "Differential Proteomics via probabilistic peptide identification scores." Anal Chem. 2005 Jan 15;77(2): 596-606.
developers, etc. working effectively in their fields of excellence.
Faculties
Nationalities
Libraries
Students
What makes us different?
We make sure that everyone assumes an element of our long-term growth strategy is to seek out strong partnerships with leading organisations that allow us, while concentrating on our core innovations, to provide more comprehensive value-added solutions to our customers.
Sage-N Research (May 2006)
Sage-N Research, Inc. is an industry leader in developing high-throughput, easy-to-use integrated data appliances, including the SEQUEST® Sorcerer protein identification system. The company has developed proprietary technology based on novel software methods and hardware-optimized pattern matching algorithms. Through strategic collaborations with leading scientists, Sage-N Research advances the state of the art in ease-of-use, applications, and technology to enable world-changing discoveries in biology and medicine. More info...
Sage-N
authorized_reseller
GenoLogics (May 2006)
GenoLogics is the leading provider of an open integrating platform and bioinformatics solutions that help life science and pharmaceutical laboratories, specializing in the field of proteomics ans systems biology research, to manage, integrate and analyze enormous volumes of scientific and lab data to advance health science research and drug discovery. The company's mission is to provide solutions to accelerate the prevention and cure of diseases such as cancer. More info... GenoLogics
Genedata (October 2005)
Genedata specializes in computational solutions for life science research, drug discovery, and drug development. The Company combines a comprehensive, scientifically validated computational platform with expert scientific consulting services to provide tailor-made solutions for specific applications and multiple therapeutic areas. Founded in 1997 as a spin-off from Novartis, the Company is privately held and has grown to an interdisciplinary, international team of dedicated experts. Genedata is headquartered in Basel (Switzerland) with subsidiaries and branch offices in Munich (Germany), San Francisco (USA), and Boston (USA). The Company is also represented by Infocom Corporation (Japan), DigiGenomics (Taiwan), and Research Instruments (Singapore, Malaysia). More info... genedata
Proteomic Solutions (September 2005)
Founded in 2001, Proteomic Solutions is a specialized protein lab service located between Paris and Rouen that conducts proteomic projects and practices recombinant protein technology, combined with experience in the field of bioinformatics. More info...
proteomic solutions
authorized_reseller
KOOPrime Pte Ltd (June 2005)
Since 1996, a group of scholars, researchers and IT professionals have been working with one of the largest pharmaceutical giants in the world to develop a system to enhance overall productivity in pharmaceutical laboratories. KOOPrime Pte Ltd was established in 2000 as a result of this endeavour. KOOPrime is the leading provider of IT products and solutions for the biomedical industry. This is made feasible via its workflow-agent platform (KOOPlatform) that integrates components dealing with Data Collection, Data Warehousing, Data Mining and Data Visualization. Systems delivered are Cross-Platform, Cross-Language and Cross-Domain. KOOPrime has operations in the US and also an established presence in Asia, in particular Singapore, Japan, Malaysia, Thailand, China and India. More info...
kooprime
authorized_reseller
Hitachi Software Engineering, Ltd. (June 2005)
Hitachi Software Engineering Co., Ltd. was established in 1970 as the first software development company in the Hitachi Group and we are now among the leading IT service companies in the industry. We mainly deal with basic software for mainframe computers and large-scale systems and networks for government agencies as well as the financial, insurance, and securities industries.
Over the past 30 years, we have enjoyed steadily increasing success, pursuing our goal of becoming the industry's leading company. We have also established international leadership in Multimedia Technology, GIS, Bio Informatics Products, and High Level Security Software both in the US and Europe. More info...
hitachisoft
authorized_reseller
Bruker Daltonics (September 2002)
Bruker Daltonics is a leading developer and provider of innovative life science tools based on mass spectrometry. Bruker Daltonics also offers a broad line of nuclear, biological and chemical (NBC) detection products for defense and homeland security. Our association with Bruker enables us to provide research scientists with continuous, efficient and up-to-date technology in proteomics. More info to benefit from individualised protein identification support.
Programmes
Are you searching for a school where cutting-edge programmes are taught, in a continually evolving environment and located in the heart of a dynamic city? You have just found it!
The campus
The small and modern campus is only a 10-minute walk away from the city centre and is easily accessible by car and public transport. It is also close to the train stations.