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Geneva Bioinformatics (GeneBio) S.A. 25 Avenue de Champel CH 1206 Geneva Switzerland |
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Mail:phenyx@genebio.com Tel : +41 22 702 99 00 Fax : +41 22 702 99 99 |
Product Brochure (PDF) (updated October 2007)
Phenyx User Manual (updated 8.09.2007) Phenyx User Manual (PDF) (updated 8.09.2007) System Requirements (updated 8.02.2006)
GeneBio posters: "Phenyx: Combining High-Throughput and Pertinence in Protein Identification" "Phenyx: Manage Protein Identification with Flexibility and Pertinence" "Phenyx: The innovative software platform for proteomics mass spectrometry data analysis" "A quantitation module for Phenyx: An implementation compliant with several labeling techniques and enabling the use of various statistics" "An open-source toolkit for quality assessment and filtering of peptide mass spectra" "How to choose and define a protein identification strategy adapted to an experimental workflow" "Phenyx: The proteomics software platform for mass spectrometry data analysis" Selected posters: "swissPIT - The Swiss Protein Identification Toolbox" "Two Dimensional Digest (Chemdigest/Trypsin)-LC-MS/MS Strategy Increased the Coverage of Proteins in Human Mitochondria Proteome." "Automated MS data processing pipeline in the Testis Proteome Pilot Project" "Increasing the number of identified peptides with high measured mass accuracy on CID fragments" "Accidental Data Independent Collision Induced Dissociation on the LTQ-FT" "Differential membrane proteomics of the bacterial predator: Bdellovibrio bacteriovorus." "Comparison of Three Software Packages for Identification of MF 7 Membrane Proteins Extracted with Trifluoroethanol" Manfred Heller, Mingliang Ye, Philippe E. Michel, Patrick Morier, Daniel Stalder, Martin A. Jünger, Ruedi Aebersold, Frédéric Reymond, and Joël S. Rossier. Added Value for Tandem Mass Spectrometry Shotgun Proteomics Data Validation through Isoelectric Focusing of Peptides. J. Proteome Res.; 2005; ASAP Web Release Date: 05-Oct-2005 Colinge J, Cusin I, Reffas S, Mahé E, Niknejad A, Rey PA, Mattou H, Moniatte M, Bougueleret L. "Experiments in searching small proteins in unannotated large eukaryotic genomes." J Proteome Res. 2005 Jan-Feb;4(1):167-74. 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. 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, 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, 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, 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, Dessingy T, Giron M and Masselot A. Improved peptide charge state assignment. Proteomics, 3:1434-1440, 2003.
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