David Fenyo

Summary

Affiliation: The Rockefeller University
Country: USA

Publications

  1. ncbi request reprint Informatics development: challenges and solutions for MALDI mass spectrometry
    David Fenyo
    The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
    Mass Spectrom Rev 27:1-19. 2008
  2. pmc Mass spectrometric protein identification using the global proteome machine
    David Fenyo
    The Rockefeller University, New York, NY, USA
    Methods Mol Biol 673:189-202. 2010
  3. pmc Protein quantitation using mass spectrometry
    Guoan Zhang
    Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, NY, USA
    Methods Mol Biol 673:211-22. 2010
  4. pmc Screening for EphB signaling effectors using SILAC with a linear ion trap-orbitrap mass spectrometer
    Guoan Zhang
    Department of Pharmacology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
    J Proteome Res 7:4715-26. 2008
  5. ncbi request reprint Determining the overall merit of protein identification data sets: rho-diagrams and rho-scores
    David Fenyo
    Rockefeller University, New York, New York 10019, University of California Davis, Davis, California 95616, USA
    J Proteome Res 6:1997-2004. 2007
  6. ncbi request reprint Informatics and data management in proteomics
    David Fenyo
    Proteometrics LLC, PO Box 984, New York, NY 10014, USA
    Trends Biotechnol 20:S35-8. 2002
  7. ncbi request reprint RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database
    Helen I Field
    The Rockefeller University, New York, NY, USA
    Proteomics 2:36-47. 2002
  8. pmc Comparative proteomic analysis of the ATP-sensitive K+ channel complex in different tissue types
    Eirini Kefaloyianni
    Pediatrics, NYU School of Medicine, New York, NY 10016, USA
    Proteomics 13:368-78. 2013
  9. pmc Rapid sensitive analysis of cysteine rich peptide venom components
    Beatrix M Ueberheide
    Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
    Proc Natl Acad Sci U S A 106:6910-5. 2009
  10. pmc Strategy for identifying dendritic cell-processed CD4+ T cell epitopes from the HIV gag p24 protein
    Leonia Bozzacco
    Laboratory of Cellular Physiology and Immunology and Chris Browne Center, The Rockefeller University, New York, New York, United States of America
    PLoS ONE 7:e41897. 2012

Collaborators

Detail Information

Publications13

  1. ncbi request reprint Informatics development: challenges and solutions for MALDI mass spectrometry
    David Fenyo
    The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
    Mass Spectrom Rev 27:1-19. 2008
    ..This allows the determination of the identity (sequence and modifications) of the analytes. We show how this general data analysis workflow is applied to protein and nucleic acid chemistry as well as proteomics...
  2. pmc Mass spectrometric protein identification using the global proteome machine
    David Fenyo
    The Rockefeller University, New York, NY, USA
    Methods Mol Biol 673:189-202. 2010
    ..We cover identification by searching protein sequence collections and spectral libraries as well as validation of the results using expectation values, rho-diagrams, and spectrum databases...
  3. pmc Protein quantitation using mass spectrometry
    Guoan Zhang
    Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, NY, USA
    Methods Mol Biol 673:211-22. 2010
    ....
  4. pmc Screening for EphB signaling effectors using SILAC with a linear ion trap-orbitrap mass spectrometer
    Guoan Zhang
    Department of Pharmacology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
    J Proteome Res 7:4715-26. 2008
    ..More than half of all known effectors downstream of EphB receptors were identified in this study, as well as numerous novel candidates for EphB signaling...
  5. ncbi request reprint Determining the overall merit of protein identification data sets: rho-diagrams and rho-scores
    David Fenyo
    Rockefeller University, New York, New York 10019, University of California Davis, Davis, California 95616, USA
    J Proteome Res 6:1997-2004. 2007
    ..The rho-score can also be used as a parameter to evaluate the relative merit of protein identifications, such as those made across proteome species taxonomic categories...
  6. ncbi request reprint Informatics and data management in proteomics
    David Fenyo
    Proteometrics LLC, PO Box 984, New York, NY 10014, USA
    Trends Biotechnol 20:S35-8. 2002
    ....
  7. ncbi request reprint RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database
    Helen I Field
    The Rockefeller University, New York, NY, USA
    Proteomics 2:36-47. 2002
    ..Statistical scoring methods provide close-to-expert accuracy and brings robust data analysis to the non-expert user...
  8. pmc Comparative proteomic analysis of the ATP-sensitive K+ channel complex in different tissue types
    Eirini Kefaloyianni
    Pediatrics, NYU School of Medicine, New York, NY 10016, USA
    Proteomics 13:368-78. 2013
    ..Overall, our data demonstrate that K(ATP) channels in different tissues may assemble with proteins having common functions, but that tissue-specific complex organization also occurs...
  9. pmc Rapid sensitive analysis of cysteine rich peptide venom components
    Beatrix M Ueberheide
    Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
    Proc Natl Acad Sci U S A 106:6910-5. 2009
    ..Using this strategy, we obtained full sequences for 31 peptide toxins, using just 7% of the crude venom from the venom gland of a single cone snail (Conus textile)...
  10. pmc Strategy for identifying dendritic cell-processed CD4+ T cell epitopes from the HIV gag p24 protein
    Leonia Bozzacco
    Laboratory of Cellular Physiology and Immunology and Chris Browne Center, The Rockefeller University, New York, New York, United States of America
    PLoS ONE 7:e41897. 2012
    ..These results support the application of our strategy to identify and characterize peptide epitopes derived from vaccine proteins processed by DCs and thus has the potential to greatly accelerate DC-based vaccine development...
  11. pmc GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome
    Matthew D Sekedat
    Laboratory for Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
    Mol Syst Biol 6:353. 2010
    ..In particular, a parsimonious model allowed us to accurately simulate fork movement throughout the genome and also revealed a subtle phenomenon, which we interpret as arising from low-frequency fork arrest...
  12. doi request reprint Efficient identification of phosphorylation by mass spectrometric phosphopeptide fingerprinting
    Eileen M Woo
    The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Anal Chem 80:2419-25. 2008
    ..We have applied this method to identify eight known phosphorylation sites of Xenopus Aurora A kinase, as well as several novel sites in the Xenopus chromosome passenger complex (CPC)...
  13. pmc Evaluation of the variation in sample preparation for comparative proteomics using stable isotope labeling by amino acids in cell culture
    Guoan Zhang
    Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
    J Proteome Res 8:1285-92. 2009
    ..By using informed experimental design, we demonstrated that the error associated with multiple steps of sample preparation in a comparative experiment can be limited to a reasonably low level...