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Geneva Bioinformatics (GeneBio) S.A.. (5/31/07). "Press Release: GeneBio’s Phenyx Integrated with Proteome Software’s Scaffold". Geneva & Portland, OR.

Organisations Organisation Geneva Bioinformatics S.A. (GeneBio)
  Group GeneBio (Group)
  Organisation 2 Proteome Software Inc.
Products Product Phenyx proteomics MS data analysis s/w
  Product 2 Scaffold proteomics meta-analysis software
Persons Person Pitman, Mark (Premier Biosoft 201406– VP Sales + Marketing before Omixon + Nonlinear Dynamics + GeneBio)
  Person 2 Nahas, Nasri G. (Spinomix 201506 CEO before GeneBio CEO)

Geneva Bioinformatics (GeneBio) SA and Proteome Software today announced that GeneBio's Phenyx software platform for MS data analysis 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.

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 and offering a flexible user experience and an adaptable architecture to help instill confidence in results assessment. (

Proteome Software's Scaffold meta-analysis software 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. This combination of results from several applications yields numerous cross-validated protein identifications, after which Scaffold displays the results in multiple biologically relevant formats. (

"We strive to listen to our users to find out what tools they need us to support, and an ever-increasing number are asking that we incorporate results from Phenyx," said Mark Pitman of Proteome Software. "This makes perfect sense, as it adds yet another high quality search engine to the Scaffold platform. We are always excited when we can deliver more value to our users, and we consider Phenyx to be of high value to our users and our overall platform."

"We are very pleased to have Phenyx join the list of results users can validate using Scaffold," said Nasri Nahas, CEO of GeneBio. "We are assured that our innovative approach to data analysis used in conjunction with the other leaders in the field will give Scaffold's users a level of results integrity hard to find elsewhere; everybody is a winner in this situation."

GeneBio will be present at ASMS 2007 in Indianapolis, from June 3rd to June 6th at booth #90. Please stop by to know more about this collaboration, to receive a Phenyx demo or answers to your questions. For more information concerning Phenyx, please go to

Proteome Software will be present at ASMS 2007 in Indianapolis, from June 3rd to June 6th at booth #151. Please stop by to learn more about this collaboration, to receive a Scaffold demo or answers to any questions. For more information concerning Scaffold, please go to

About GeneBio

Geneva Bioinformatics (GeneBio) SA is a leading bioinformatics company providing the life science community with world-class proteomics software that bridges the gap between information gathering and knowledge generation. Established in 1997, we focus our expertise on protein identification and characterization as well as proteome imaging, offering clients and partners a high degree of specialization essential to proteomics research. Close ties to academic peers and a thorough network of distribution and strategic partners give us both unfettered access to scientific excellence and recognized market presence so that we may best serve the scientific community. For more information about GeneBio, please visit:

About Proteome Software

Proteome Software is a leading developer of proteomics software tools. Passionate about developing software that enables cutting edge proteomics research, Proteome Software's Scaffold is a powerful and easy to use MS/MS meta-analysis package. Scaffold is designed to help proteomics researchers validate, visualize, and share their data. Proteome Software's mission is to enable proteomics research that will foster science and medicine for this and future generations. More information is available at

GeneBio contact:
Andrew Smith
Tel. +41.22.702.99.00

Proteome Software contact:
Mark Pitman
Tel. +1 503.244.6027

Record changed: 2016-03-19


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