Phenyx Posters

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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)
• "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)
• "Evaluation of Multiple Search Engines in the Analysis of Leptin-Induced Mitochondrial Protein Expression in Mouse Liver"
  Authors: John R. Strahler, Angela K. Walker, George Michailidis, Amandeep Singh, Jeffrey Friedman, Philip C. Andrews.
  (ASMS 2007)
• "Decoy Strategy applied to a multi Workflow Proteomic Approach"
  Authors: Ulrike Schweiger-Hufnagel, Peter Hufnagel, Christian Klein, Gerhard Körting, Stephanie Hahner, Markus Lubeck, Detlev Suchau.
  (ASMS 2007)
• "Structural Characterization of Macromolecular rotein Complexes Using Chemical Cross-linking and Mass Spectrometry"
  Authors: Pragya Singh, Richard A. Pfuetzner, Scott A. Shaffer, Alexandre Panchaud, Eri Nakatani, Carlos E. Catalano, Alexandre Masselot, Samuel I. Miller, and David R. Goodlett.
  (ASMS 2009)
• "Unraveling secrets of the secretome: Approaches to identifying secreted lung cancer proteins during epithelial to mesenchymal transition (EMT)"
  Authors: Pratik D. Jagtap, Jayson A. Falkner, George Michailidis, Angela K. Walker, Eric S. Simon, Gilbert S. Omenn, Venkateshwar Keshamouni, Philip C. Andrews.
  (ASMS 2008)
• "Mass Spectrometric Analysis of the GPCR AIDS Virus Coreceptor, CXCR4"
  Authors: Ting Liu, Joyce Brewer, Royce Wilkinson, John Mills, Martin Teintze, Edward Dratz.
  (ASMS 2009)
• "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)
• "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)
• "High Charge-State Data-Dependent Sequencing of Peptides Allows Selective Identification of Disulfide Bridges"
  Authors: Scott A. Shaffer, Alexander Scherl, Pragya Singh, Byron Gallis, Yihsuan Shannon Tsai, and David R. Goodlett.
  (ASMS 2008)
• "Exploring antibiotic resistance with isobaric tags"
  Authors: Alexander Scherl, Patrice Francois, Manuela Bento, Joel DiDio, Jacques M. Deshusses, Alexandre Masselot, Pierre-Alain Binz, Christine Hoogland, Ron D. Appel, Jean-Charles Sanchez, Catherine G. Zimmermann-Ivol, Jianru Stahl-Zeng, Jacques Schrenzel, and Denis F. Hochstrasser.
  (ASMS 2005)
• "Towards High-Throughput Shotgun IEF"
  Authors: Ali R. Vaezzadeh, Jacques M.P. Deshusses, Alexis Chauvet, Pierre Lescuyer, Catherine G. Zimmermann, Celine Hernandez, Daniel Walther, Ron D. Appel, Denis F. Hochstrasser.
  (ASMS 2007)
• "Automated reprocessing pipeline for analysing heterogeneouse data of the HUPO Brain Proteome Project pilot phase"
  Authors: Christian Stephan, Kai A. Reidegeld, Michael Hamacher, André van Hall, Katrin Marcus, Michael Müller, Philip Jones, Rolf Apweiler, Lennart Martens, Gerhard Körting, Herbert Thiele, Martin Blüggel, Helmut E. Meyers.
  (ASMS 2006)
• "High-Throughput data management of Shotgun IEF results by ProteinScape"
  Authors: Alexis Chauvet, Ali R. Vaezzadeh, Pierre-Alain Binz, Catherine G. Zimmermann-Ivol, Patricia M. Palagi, Ron D. Appel, Herbert Thiele, Denis F. Hochstrasser.
  (ASMS 2007)
• "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)
• "Recent Advances in Performance and Search Engine Compatibility in the Trans-Proteomic Pipeline: Combining Phenyx and the Proteomic Pipeline for Quantitation"
  Authors: Bryan J. Prazen, Alexandre Masselot, David Shteynber, Nicolas Budin, Brian S. Pratt, Eric W. Deutsch.
  (ASMS 2007)
• "New Developments for Open-Source Shotgun Proteomics Analysis with the Trans-Proteomic Pipeline"
  Authors: Joshua Tasman, Luis Mendoza, David Shteynberg, James Eddes, Ning Zhang, Nichole King, Chee-Hong Wong, Brian Pratt, Patrick Pedrioli, Henry Lam, Eric Deutsch, Jimmy Eng, Xiao-jun Li, Alexey Nesvizhskii, Andrew Keller, and Ruedi Aebersold.
  (ASMS 2008)
• "How Stable are Peptide Identifications with Regards to Variations in MS/MS Spectra?"
  Authors: Markus Mueller, David Bouyssie, Erik Ahrne, Pierre-Alain Binz, Frederique Lisacek.
  (ASMS 2008)
• "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)

GeneBio staff:

• "An opensource toolkit for quality assessment and filtering of peptide mass spectra"
  Authors: Roman Mylonas; Alexandre Masselot; Pierre-Alain Binz; Ron D. Appel.
  (HUPO 2006)
• "How to choose and define a protein identification strategy adapted to an experimental workflow"
  Authors: Pierre-Alain Binz; Nicolas Budin; Anne Niknejad; Olivier Evalet; Alexandre Masselot.
  (ABRF 2006)
• "Phenyx: The proteomics software platform for mass spectrometry data analysis"
  Authors: GeneBio staff.
  (ASMS 2006)