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Geneva Bioinformatics SA (GeneBio) And Utrecht University Announce Collaborative Partnership Around Phenyx

1/22/2009 11:35:31 AM

Geneva, Switzerland and Utrecht, The Netherlands – January 22, 2009 - Geneva Bioinformatics (GeneBio) SA and Utrecht University’s Biomolecular Mass Spectrometry and Proteomics Group today announced that the University’s Heck Laboratory will utilize GeneBio’s Phenyx software platform in order to get optimised scorings for its Lys-N protein digestion workflow in combination with Electron Transfer Dissociation (ETD) and Collision-Induced Dissociation (CID) data, an application developed by the Heck-group and which was recently published in amongst others Nature Methods (1-3). The Lys-N workflow provides a novel complementary tool for high-throughput proteomics analysis with a special focus on the analysis of post-translational modifications and de novo sequencing.

Under the terms of the agreement, GeneBio and the University’s Heck-group will consider each other as privileged partners in the Mass Spectrometry based Proteomics field endeavouring continuously to optimize their respective efforts in order to maximize the synergies between the two groups, beginning with a collaborative project for the Lys-N protein digestion proteomics workflow.

The core research themes of the Heck-group are in the development of mass spectrometric methods applicable to the structural characterization of biomolecular systems, in relation to their biological function. As a world-renowned laboratory in the Mass Spectrometry based Proteomics field, the Heck-group also plays a leading role in the Netherlands Proteomics Centre (NPC), which is dedicated to the development of innovative proteomics techniques and knowledge transfer, with a special focus on cancer proteomics, proteome biology of plants, micro-organisms, stem cells and autoimmune diseases.

Developed in collaboration with the Swiss Institute of Bioinformatics (SIB), Phenyx is GeneBio’s renowned software platform for the identification, quantitation and characterization of proteins and peptides from mass spectrometry data. The Phenyx platform is specifically designed to meet the concurrent demands of high-throughput MS data analysis and dynamic results assessment via a customizable architecture and an innovative user-friendly interface. (

“We are happy to be using Phenyx in the lab and look forward to both immediate and long term positive results,” said Prof. Dr. Albert J.R. Heck, Head of the Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University and scientific director of the NPC. “Collaborative partnerships such as this one are extremely important in our field – because they work. We believe our relationship with GeneBio will further add to this perception and look forward to making this happen.”

“We are excited about this partnership as it will further enhance the functionalities of Phenyx for ETD/CID data, in a Lys-N workflow in particular, while at the same time add to the body of knowledge in our field,” said Nasri Nahas, CEO of GeneBio. “Prof. Heck is a well known and highly respected member of the Proteomics research community; his use of Phenyx, in conjunction with his own work, further solidifies Phenyx as an essential tool for any laboratory which desires to go beyond a certain level of Mass Spectrometry based proteomics analysis. We look forward to this partnership and hope it yields many positive results.”

For more information about Phenyx, the Heck-group partnership as well as others, including product demonstrations, please visit GeneBio’s booth (#212) at ABRF 2009 in Memphis, Tennessee, USA, from February 7-10, 2009, and booth #19 at the 5th annual US HUPO conference in San Diego, California, USA, from February 22-25, 2009.


1. Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase.

Taouatas N, Drugan MM, Heck AJ, Mohammed S. Nat Methods. 2008 May;5(5):405-7. Epub 2008 Apr 20.

2. Strong Cation Exchange-based Fractionation of Lys-N-generated Peptides Facilitates the Targeted Analysis of Post-translational Modifications.

Taouatas N, Altelaar AF, Drugan MM, Helbig AO, Mohammed S, Heck AJ. Mol Cell Proteomics. 2009 Jan;8(1):190-200. Epub 2008 Sep 29.

3. Straightforward and de novo peptide sequencing by MALDI-MS/MS using a Lys-N metalloendopeptidase.

Boersema PJ, Taouatas N, Altelaar AF, Gouw JW, Ross PL, Pappin DJ, Heck AJ, Mohammed S. Mol Cell Proteomics. 2008 Nov 29. [Epub ahead of print]

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 the Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University

The Biomolecular Mass Spectrometry and Proteomics Group at Utrecht University aims at a detailed understanding of proteins, in relation to their physiological functioning in cells using mass spectrometry as the primary research tool. The Heck group has diverse research themes such as i. the development of novel application in proteomics, ii. proteomics and quantitative proteomics of complex samples, iii. the analysis of (large) protein complexes, and iv. the development of bioinformatics tools for proteomics research. The Biomolecular Mass Spectrometry and Proteomics Group forms the core of the Netherlands Proteomics Centre (NPC), which is dedicated to the development of innovative proteomics techniques and knowledge transfer, with a special focus on cancer proteomics, proteome biology of plants, micro-organisms, and stem cells.

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