Phenyx Documentation
Find out more with the product brochure, user manual and tutorial movies:
Testimonials
A sample of what users have to say about Phenyx:
Posters
Phenyx clients:
- "Automated MS data processing pipeline in the Testis Proteome Pilot Project"
Authors: Régis Lavigne, Djibril Ousmanou, Morgane Couvet, Nathalie Guitton, Katja Schuerer, Jörg Glandorf, Peter Hufnagel, Herbert Thiele, and Charles Pineau.
(HUPO 2007)
- "Differential membrane proteomics of the bacterial predator: Bdellovibrio bacteriovorus."
Authors: Pratik D. Jagtap, Angela K. Walker, John R. Strahler, Eric S. Simon, Maureen T. Kachman, Janine R. Maddock, Philip C. Andrews.
(ASMS)
- "Increasing the number of identified peptides with high measured mass accuracy on CID fragments"
Authors: Alexander Scherl, Manhong Wu, Scott Shaffer, Greg Taylor, Alexandre Masselot, Pierre-Alain Binz, Samuel I. Miller and David R. Goodlett.
(ASMS 2006)
- "Two Dimensional Digest (Chemdigest/Trypsin)-LC-MS/MS Strategy Increased the Coverage of Proteins in Human Mitochondria Proteome"
Authors: Chang-hee Lee, Younyoung You, Taehoon Lee, Byung Yong Ahn, Young Min Cho, Kyong Soo Park, Martin Bluggel, Gerhard Korting, Herbert Thiele.
(HUPO 2007)
- "Accidental Data Independent Collision Induced Dissociation on the LTQ-FT"
Authors: Shawna M. Hengel, Scott Shaffer, Gregory K. Taylor, Alex Scherl, Alexandre Masselot, Pierre-Alain Binz, David R. Goodlett.
(ASMS 2006)
- "Comparison of Three Software Packages for Identification of MCF 7 Membrane Proteins Extracted with Trifluoroethanol"
Authors: Cédric Pionneau, Ludovic Canele, Jordane Bousquet, Julie Hardouin, Michel Caron and Raymonde Joubert-Caron.
(Hellenic Proteomics Society 2005)
- "swissPIT - The Swiss Protein Identification Toolbox"
Authors: Andreas Quandt, Alexandre Masselot, Celine Hernandez, Nicolas Budin, Erik Ahrne, Patricia Hernandez, Patricia Palagi, Pierre-Alain Binz, and Ron D. Appel.
(HUPO 2007)
GeneBio staff:
Publications
A selection of publications from our Phenyx clients:
On the benefits of acquiring peptide fragment ions at high measured mass accuracy.
J Am Soc Mass Spectrom. 2008 Jun;19(6):891-901. Epub 2008 Mar 4.
Scherl A, Shaffer SA, Taylor GK, Hernandez P, Appel RD, Binz PA, Goodlett DR.
Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
Added Value for Tandem Mass Spectrometry Shotgun Proteomics Data Validation through Isoelectric Focusing of Peptides
J. Proteome Res.; (Article); 2005; 4(6); 2273-2282. DOI: 10.1021/pr050193v
Heller, M.; Ye, M.; Michel, P. E.; Morier, P.; Stalder, D.; Junger, M. A.; Aebersold, R.; Reymond, F.; Rossier, J. S.
DiagnoSwiss SA, Monthey, Switzerland, Department of Clinical Research, University Hospital, 3010 Bern, Switzerland, Institute for Systems Biology, Seattle, Washington 98103, and Institute for Molecular Systems Biology, Swiss Federal Institute of Technology (ETH), Zürich, Switzerland.
Nitric Oxide and Oxygen Radical Attack on GDP-Dissociation Inhibitor 2 (GDI-2) in Spinal Cord Injury of the Rat
J. Proteome Res.; (Article); 2007; 6(4); 1500-1509. DOI: 10.1021/pr060620k
John, J. P. P.; Pintsov, O.; Petter-Puchner, A.; Redl, H.; Pollak, A.; Chen, W.-Q.; Lubec, G.
Department of Pediatrics, Medical University of Vienna, Vienna, Austria, and Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Vienna, Austria
Comparative Urine Analysis by Liquid Chromatography-Mass Spectrometry and Multivariate Statistics: Method Development, Evaluation, and Application to Proteinuria
J. Proteome Res.; (Article); 2007; 6(1); 194-206. DOI: 10.1021/pr060362r
Kemperman, R. F. J.; Horvatovich, P. L.; Hoekman, B.; Reijmers, T. H.; Muskiet, F. A. J.; Bischoff, R.
Department of Analytical Biochemistry, University Centre for Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.
InSilicoSpectro: An Open-Source Proteomics Library
J. Proteome Res.; (Article); 2006; 5(3); 619-624. DOI: 10.1021/pr0504236
Colinge, J.; Masselot, A.; Carbonell, P.; Appel, R. D.
Upper Austria University of Applied Sciences at Hagenberg, Bioinformatics Department, Hauptstrasse 117, A-4232 Hagenberg, Austria.
Identification of Brain Cell Death Associated Proteins in Human Post-mortem Cerebrospinal Fluid
J. Proteome Res.; (Article); 2006; 5(7); 1674-1681. DOI: 10.1021/pr060160v
Burgess, J. A.; Lescuyer, P.; Hainard, A.; Burkhard, P. R.; Turck, N.; Michel, P.; Rossier, J. S.; Reymond, F.; Hochstrasser, D. F.; Sanchez, J.-C.
Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
Mass Spectrometric Studies on Mouse Hippocampal Synapsins Ia, IIa, and IIb and Identification of a Novel Phosphorylation Site at Serine-546
J. Proteome Res.; (Article); 2007; 6(7); 2695-2710. DOI: 10.1021/pr070157r
John, J. P. P.; Chen, W.-Q.; Pollak, A.; Lubec, G.
Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, 1090 Vienna, Austria.
Limitations and Pitfalls in Protein Identification by Mass Spectrometry
Chem. Rev.; (Review); 2007; 107(8); 3568-3584. DOI: 10.1021/cr068213f
Lubec, G.; Afjehi-Sadat, L.
Medical University of Vienna, Department of Pediatrics, Waehringer Guertel 18, A-1090 Vienna, Austria
Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers
BMC Genomics 2006, 7:296doi:10.1186/1471-2164-7-296
Alexander Scherl1, Patrice François2, Yvan Charbonnier2, Jacques M Deshusses1, Thibaud Koessler2, Antoine Huyghe2, Manuela Bento2, Jianru Stahl-Zeng3, Adrien Fischer2, Alexandre Masselot4, Alireza Vaezzadeh1, Francesca Gallé2, Adriana Renzoni2, Pierre Vaudaux2, Daniel Lew2, Catherine G Zimmermann-Ivol1,5, Pierre-Alain Binz4, Jean-Charles Sanchez1, Denis F Hochstrasser1,5,6 and Jacques Schrenzel2
1 Biomedical Proteomics Research Group, Geneva University, Geneva, Switzerland
2 Service of infectious diseases, University Hospitals of Geneva, Geneva, Switzerland
3 Applied Biosystems, Darmstadt, Germany
4 Geneva Bioinformatics SA, Geneva, Switzerland
5 Central Clinical Chemistry Laboratory, University Hospitals of Geneva, Geneva, Switzerland
6 Pharmacy section, Faculty of Sciences, Geneva University, Geneva, Switzerland
Compositional Protein Analysis of High Density Lipoproteins in Hypercholesterolemia by Shotgun LC-MS/MS and Probabilistic Peptide Scoring
Mol. Cell. Proteomics, Jun 2007; 6: 1059 - 1072.
Manfred Heller, Evelyn Schlappritzi, Daniel Stalder, Jean-Marc Nuoffer, and André Haeberli
From the Laboratory of Thrombosis Research, Department of Clinical Research, University of Bern, and The Institute of Clinical Chemistry, University Hospital and University Children's Hospital, 3010 Bern, Switzerland
Differential Expression Profiling of the Hepatic Proteome in a Rat Model of Dioxin Resistance: CORRELATION WITH GENOMIC AND TRANSCRIPTOMIC ANALYSES
Mol. Cell. Proteomics, May 2006; 5: 882 - 894.
Roberta Pastorelli, Donatella Carpi, Roberta Campagna, Luisa Airoldi, Raimo Pohjanvirta, Matti Viluksela, Helen Hakansson, Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, and Roberto Fanelli
From the Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche "Mario Negri," 20157 Milan, Italy
Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, University of Helsinki, FIN-00014 Helsinki, Finland
National Veterinary and Food Research Institute and Department of Environmental Health, National Public Health Institute, FIN-70701 Kuopio, Finland
Institute of Environmental Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden
Department of Pharmacology, University of Toronto, Toronto M5S 1A8, Canada
ISG20L2, a novel vertebrate nucleolar exoribonuclease involved in Ribosome biogenesis
Mol. Cell. Proteomics, Dec 2007; doi:10.1074/mcp.M700510-MCP200
Yohann Couté, Karine Kindbeiter, Stéphane Belin, Régis Dieckmann, Laurent Duret, Laurent Bezin, Jean-Charles Sanchez, and Jean-Jacques Diaz
Biomedical Proteomics Research Group, Département de Biologie Structurale et Bioinformatique, Centre Médical Universitaire, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland.
Proteomics Analysis of Insulin Secretory Granules
Mol. Cell. Proteomics, Jun 2007; 6: 1007 - 1017
Yannick Brunner, Yohann Couté, Mariella Iezzi, Michelangelo Foti, Mitsonuri Fukuda, Denis F. Hochstrasser, Claes B. Wollheim, and Jean-Charles Sanchez
Biomedical Proteomics Research Group, University Medical Center, 1211 Geneva 4, Switzerland
Proteomics Demonstration That Normal Breast Epithelial Cells Can Induce Apoptosis of Breast Cancer Cells through Insulin-like Growth Factor-binding Protein-3 and Maspin
Mol. Cell. Proteomics, Jul 2007; 6: 1239 - 1247.
Robert-Alain Toillon, Chann Lagadec, Adeline Page, Valérie Chopin, Pierre-Eric Sautière, Jean-Marc Ricort, Jérôme Lemoine, Ming Zhang, Hubert Hondermarck, and Xuefen Le Bourhis
INSERM ERI-8 (JE 2488) Signalisation des facteurs de croissance dans le cancer du sein. Protéomique fonctionnelle, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq, France
Nerve Growth Factor Receptor TrkA Signaling in Breast Cancer Cells Involves Ku70 to Prevent Apoptosis
Mol. Cell. Proteomics, Nov 2007; 6: 1842 - 1854.
Emmanuelle Com, Chann Lagadec, Adeline Page, Ikram El Yazidi-Belkoura, Christian Slomianny, Ambre Spencer, Djilali Hammache, Brian B. Rudkin, and Hubert Hondermarck
INSERM ERI-8 (JE-2488), Growth factor signaling in breast cancer. Functional proteomics, University of Sciences and Technologies Lille, 59655 Villeneuve d'Ascq, France
Phosphorylation of B14.5a Subunit from Bovine Heart Complex I Identified by Titanium Dioxide Selective Enrichment and Shotgun Proteomics
Mol. Cell. Proteomics, Feb 2007; 6: 231 - 237.
Gabriella Pocsfalvi, Manuela Cuccurullo, Gitta Schlosser, Salvatore Scacco, Sergio Papa, and Antonio Malorni
Proteomic and Biomolecular Mass Spectrometry Centre, Institute of Food Science and Technology, Consiglio Nazionale delle Ricerche, 83100 Avellino, Italy
Labeling of Bifidobacterium longum Cells with 13C-Substituted Leucine for Quantitative Proteomic Analyses
Appl Environ Microbiol. 2007 September; 73(17): 5653–5656. Published online 2007 June 29.
Yohann Couté, Céline Hernandez, Ron D. Appel, Jean-Charles Sanchez, and Abelardo Margolles
Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, University of Geneva, 1 Rue Michel Servet, 1211 Geneva 14, Switzerland
Introduction to Computational Proteomics
PLoS Comput Biol. 2007 July; 3(7): e114. Published online 2007 July 27.
Jacques Colinge and Keiryn L Bennett
Ce-M-M-, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
Proteome characterization of a human urothelial cell line resistant to the bladder carcinogen 4-aminobiphenyl
Proteome Sci. 2007; 5: 6. Published online 2007 May 3. doi: 10.1186/1477-5956-5-6.
Roberta Pastorelli, Federica Saletta, Donatella Carpi, Roberta Campagna, Carlo dell'Osta, Silvia Schiarea, Paolo Vineis, Luisa Airoldi, and Giuseppe Matullo
Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
Web-based MS/MS data analysis.
Proteomics. 2006 Sep;6 Suppl 2:22-32.
Lisacek F.
Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
The minimum information about a proteomics experiment (MIAPE)
Nature Biotechnology 25, 887 - 893 (2007)
Published online: 8 August 2007 | doi:10.1038/nbt1329
Chris F Taylor1,2, Norman W Paton1,3, Kathryn S Lilley1,4, Pierre-Alain Binz1,5,6, Randall K Julian, Jr1,7, Andrew R Jones1,3, Weimin Zhu1,2, Rolf Apweiler1,2, Ruedi Aebersold1,8, Eric W Deutsch1,9, Michael J Dunn10, Albert J R Heck11, Alexander Leitner12, Marcus Macht13, Matthias Mann14, Lennart Martens1,2, Thomas A Neubert15, Scott D Patterson16, Peipei Ping17, Sean L Seymour1,18, Puneet Souda19, Akira Tsugita20, Joel Vandekerckhove21, Thomas M Vondriska22, Julian P Whitelegge19, Marc R Wilkins23, Ioannnis Xenarios24, John R Yates, III25 & Henning Hermjakob1,2
1 The HUPO Proteomics Standards Initiative, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
2 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
3 School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK.
4 Cambridge Centre for Proteomics, University of Cambridge, Cambridge, Cambridgeshire CB2 1QW, UK.
5 Swiss Institute of Bioinformatics, Geneva, Switzerland.
6 Geneva Bioinformatics SA, Geneva, Switzerland.
7 Indigo BioSystems, Indianapolis, Indiana, USA.
8 Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland.
9 Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA.
10 Proteome Research Centre, Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
11 Utrecht University and Netherlands Proteomics Centre, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
12 Department of Analytical Chemistry and Food Chemistry, University of Vienna, 1090 Vienna, Austria.
13 Bruker Daltonik GmbH, Bremen, Germany.
14 Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, D-82152 Martinsried, Germany.
15 Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA.
16 Molecular Sciences, Amgen Inc., Thousand Oaks, California, USA.
17 Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California 90075, USA.
18 Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA.
19 The Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, and The Molecular Biology Institute, and The Brain Research Institute, University of California, Los Angeles, California 90095, USA.
20 Proteomics Research Laboratory, Tokyo Rikakikai Co., Tsukuba, Japan.
21 Department of Biochemistry, Ghent University and Department of Medical Protein Research, Flanders Institute for Biotechnology, B-9000 Ghent, Belgium.
22 Department of Medicine (Cardiology) and Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA.
23 School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia.
24 Serono Pharmaceutical Research Institute, 14, Chemin des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland.
25 The Scripps Research Institute, 10550 North Torrey Pines Road, SR11, La Jolla, California 92037, USA.
C-Npys (S-3-nitro-2-pyridinesulfenyl) and peptide derivatives can inhibit a serine-thiol proteinase activity from Paracoccidioides brasiliensis
Biochemical and Biophysical Research Communications 355 (2007) 1000 - 1005 (Elsevier)
Alisson L. Matsuo a, Adriana K. Carmona b, Luiz S. Silvaa, Carlos E.L. Cunhab, Ernesto S. Nakayasuc, Igor C. Almeidac, Maria A. Julianob, Rosana Pucciaa
a Department of Microbiology, Immunology and Parasitology, Cell Biology Division, Federal University of Sao Paulo, Sao Paulo, SP 04023-062, Brazil
b Department of Biophysics, Federal University of Sao Paulo, Sao Paulo, SP 04044-062, Brazil
c Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
Received 30 January 2007
Available online 23 February 2007
Characterization of hepatic glutathione S-transferasesin coho salmon (Oncorhynchus kisutch)
Aquatic Toxicology 81 (2007) 126 - 136
Mary Trutea, Byron Gallisb, Catalin Doneanub, Scott Shafferb, David Goodlettb, Evan Gallaghera
a Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105-6099, United States
b Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195, United States
Mapping of macrophage elastase cleavage sites in insoluble human skin elastin
Matrix Biology 27 (2008) 420 - 428 (Elsevier)
Samuel Taddesea, Anthony S. Weissb, Reinhard H.H. Neuberta, Christian E.H. Schmelzera,b
a Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
b School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia
Received 24 December 2007; received in revised form 3 February 2008; accepted 4 February 2008
Differential expression of TGFb-stimulated clone 22 in normal prostate and prostate cancer
Int. J. Cancer: 118, 899 - 906 (2006) ' 2005 Wiley-Liss, Inc.
Cyrill A. Rentsch1, Marco G. Cecchini1, Ruth Schwaninger1, Markus Germann1, Regula Markwalder2, Manfred Heller3,Gabri van der Pluijm4, George N. Thalmann1 and Antoinette Wetterwald11 Urology Research Laboratory, Departments of Urology and Clinical Research, University of Bern, Switzerland
2 Institute of Pathology, University of Bern, Switzerland
3 Laboratory for Thrombosis Research, Department of Clinical Research, University of Bern, Switzerland
4 Departments of Endocrinology and Urology, Leiden University Medical Center, Leiden, The Netherlands
Mass spectrometry-based analytical tools for the molecular protein characterization of human plasma lipoproteins
Proteomics 2005, 5, 2619 - 2630 2619 DOI 10.1002/pmic.200401233
Manfred Heller1, Daniel Stalder1, Evelyn Schlappritzi1, Gertraud Hayn2, Urs Matter2 and André Haeberli1
1 Department of Clinical Research, University Hospital, Bern, Switzerland
2 Comet AG, Analytics, Flamatt, Switzerland
Identification of specific reachable molecular targets in human breast cancer using a versatile ex vivo proteomic method
Proteomics 2007, 7, 1188 - 1196 DOI 10.1002/pmic.200600888
Vincent Castronovo1, Philippe Kischel1, François Guillonneau2, Laurence de Leval3, Thierry Deféchereux4, Edwin De Pauw2, Dario Neri5 and David Waltregny1
1 Metastasis Research Laboratory, Center for Experimental Cancer Research, University of Liège, Liège, Belgium
2 Laboratory of Mass Spectrometry, Department of Chemistry, University of Liège, Liège, Belgium
3 Department of Pathology, University Hospital of Liège, Liège, Belgium
4 Department of Abdominal Surgery and Transplantation, University Hospital of Liège, Liège, Belgium
5 Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology Zürich, Zürich, Switzerland
A selection of articles describing the technology behind Phenyx (OLAV):
Improved peptide charge state assignment
Proteomics, Vol. 3, No. 8, August 2003, pp. 1434-1440.
Jacques Colinge, Jerome Magnin, Thierry Dessingy, Marc Giron, Alexandre Masselot.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
PMID: 12923768
OLAV: towards high-throughput tandem mass spectrometry data identification
Proteomics, Vol. 3, No. 8, August 2003, pp. 1454-1463.
Jacques Colinge, Alexandre Masselot, Marc Giron, Thierry Dessingy, Jerome Magnin.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
PMID: 12923771
A systematic statistical analysis of ion trap tandem mass spectra in view of peptide scoring
In: Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), R. Page and G. Benson (Eds), Budapest, September 2003, LNBI 2812, Springer, 25.38, 2003.
Jacques Colinge, Jerome Magnin, Alexandre Masselot.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
Mass spectrometry has married statistics: uncle is functionality, children are selectivity and sensitivity
DDT: TARGETS, Vol 3, No. 2 (Suppl.), 2004, pp. 50-55.
Jacques Colinge, Alexandre Masselot.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
High performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics
Proteomics. 2004 Jul;4(7):1977-84
Jacques Colinge, Alexandre Masselot, Isabelle Cusin, Eve Mahé, Anne Niknejad, Guilaine Argoud-Puy, Samia Reffas, N Bederr, Anne Gleizes, Pierre-Andre Rey, Lydie Bougueleret.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
PMID: 15221758
Differential proteomics via probabilistic peptide identification scores
Anal Chem. 2005 Jan 15;77(2):596-606.
Colinge J, Chiappe D, Lagache S, Moniatte M., Bougueleret L.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
PMID: 15649059
Experiments in searching small proteins in unannotated large eukaryotic genomes
J Proteome Res. 2005 Jan-Feb;4(1):167-74.
Jacques Colinge, Isabelle Cusin, Samia Reffas, Eve Mahé, Anne Niknejad, Pierre-Andre Rey, H Mattou, M Moniatte, Lydie Bougueleret.
GeneProt Inc., Pré de la Fontaine , CH-1217 Meyrin, Switzerland.
PMID: 15707372
