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The Basel Biozentrum Taps Phenyx as Protein Identification Platform

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Geneva Bioinformatics (GeneBio) SA and the Biozentrum of the University of Basel have announced a collaboration that will integrate GeneBio’s Phenyx software platform for MS data analysis into the Biozentrum multi-tiered proteomics cluster.

The Biozentrum will use Phenyx as its primary search engine, thanks to dedicated scoring schemes that GeneBio will customize for its partner’s equipment.

GeneBio’s Phenyx is a software platform for the identification and characterization of proteins and peptides from mass spectrometry data. Developed by GeneBio in collaboration with the Swiss Institute of Bioinformatics (SIB) and incorporating a true probabilistic scoring model, Phenyx is specifically designed to meet the concurrent demands of high-throughput MS data analysis and dynamic results assessment.

"Using classical search software for many years in my lab, we were looking for something better and are happy with what we found in Phenyx,” said Paul Jenö head of mass spectrometry service at the Biozentrum.

“Besides the high quality of the scoring and the results rendered by the search engine, what we appreciate very much in Phenyx is the friendly interface and the multitude of possibilities it offers; a clear desktop to start from, a protein overview as the main gate to have a look at the actual search results that leads then further to the identified peptides and MS/MS spectra that can be accessed by the individual peptides, and last but not least a colour-coded display of the ions in the MS/MS spectrum allowing users to get a nice overall visual impression without looking at the actual spectrum,” said Jenö.

“What we particularly value in Phenyx is that it is entirely Web-based. One major problem core labs have is to distribute the results in a suitable manner; Phenyx offers this possibility so that each user can access the results individually and elaborate on them to their liking,” Jenö added.

“To have Phenyx be used by a prestigious center like the Biozentrum is indeed an honor for us and a testimony to the quality of our software and its congruence with big cluster requirements,” said Nasri Nahas, CEO of GeneBio.

“Since its inception, Phenyx was designed for industrial use and massive scalability, and thus can accommodate both small and large cluster environments,” he continued.

“The next version (2.3), to be communicated about at the upcoming ABRF conference, and from which the Biozentrum will be amongst the first clients to profit, goes perfectly in this direction offering enhanced server functionalities and user capabilities, making Phenyx a second-to-none solution for clients willing to use their platform as a core facility accessible to other colleagues.”