David Fenyo

Summary

Affiliation: The Rockefeller University
Country: USA

Publications

  1. pmc MALDI sample preparation: the ultra thin layer method
    David Fenyo
    Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, USA
    J Vis Exp . 2007
  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. 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
  4. 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
  5. 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
  6. 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
  7. pmc Optimizing selection of large animals for antibody production by screening immune response to standard vaccines
    Mary K Thompson
    Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
    J Immunol Methods 430:56-60. 2016
  8. 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
  9. 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
  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

  • Brian T Chait
  • Thomas A Neubert
  • Jan Eriksson
  • Tom W Muir
  • Stephen K Burley
  • Katsuhiko Kamada
  • Mario Delmar
  • Torben Heick Jensen
  • Marlene Oeffinger
  • Alan J Tackett
  • Hironori Funabiki
  • Helen I Field
  • Haiteng Deng
  • Jörn Dengjel
  • Sarah Keegan
  • Guoan Zhang
  • Michael P Rout
  • Beatrix M Ueberheide
  • Mary K Thompson
  • Peter C Fridy
  • Yang Luo
  • Alejandra Leo-Macias
  • Zhanna Hakhverdyan
  • Eirini Kefaloyianni
  • John D Aitchison
  • Leonia Bozzacco
  • Matthew D Sekedat
  • Eileen M Woo
  • Tatiana Arcos
  • Tommy Tong
  • - Feng-Xia-Liang
  • Ileana M Cristea
  • Xianming Lin
  • James M Binley
  • Todd M Greco
  • Michelle Trester-Zedlitz
  • Eli Rothenberg
  • Jose L Sanchez-Alonso
  • Esperanza Agullo-Pascual
  • Yuri E Korchev
  • Mark A Muesing
  • Kevin D Mohammed
  • Julia Gorelik
  • Erica Y Jacobs
  • John LaCava
  • Vadim Sherman
  • Kelly R Molloy
  • David J Dilworth
  • Loren E Hough
  • Michal Domanski
  • Anil R Oroskar
  • Asha A Oroskar
  • Michel C Nussenzweig
  • Johannes F Scheid
  • Ilona Nudelman
  • Yinyin Li
  • Miyoun Hong
  • John S Lyssand
  • Charles V Mobbs
  • César Moreno
  • William A Coetzee
  • Diane Delaroche
  • Victoria Kuttner
  • Henry A Zebroski
  • Christine Trumpfheller
  • Nawei Zhang
  • Ralph M Steinman
  • Haiqiang Yu
  • Svetlana Mojsov
  • Richard S Rogers
  • Sofia Waldemarson
  • Kelly Molloy
  • Sunnie Myung
  • Paul F Alewood
  • Benjamin H Kwok

Detail Information

Publications21

  1. pmc MALDI sample preparation: the ultra thin layer method
    David Fenyo
    Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, USA
    J Vis Exp . 2007
    ..It is currently our method of choice for the molecular mass analysis of all proteins. The described procedure consistently produces high-quality spectra, and it is sensitive, robust, and easy to implement...
  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. 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...
  4. 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
    ....
  5. 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...
  6. 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...
  7. pmc Optimizing selection of large animals for antibody production by screening immune response to standard vaccines
    Mary K Thompson
    Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
    J Immunol Methods 430:56-60. 2016
    ..Thus, time and money can be saved by reducing the chances of getting poor responding animals and minimizing the use of superfluous animals. ..
  8. 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
    ....
  9. 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...
  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 HIV-host interactome revealed directly from infected cells
    Yang Luo
    Aaron Diamond AIDS Research Center, 455 1st Avenue, New York, New York 10016, USA
    Nat Microbiol 1:16068. 2016
    ..Understanding the pathophysiological consequences of these associations is likely to provide strategic targets for antiviral intervention...
  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 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...
  14. 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)...
  15. ncbi request reprint A modular cross-linking approach for exploring protein interactions
    Michelle Trester-Zedlitz
    Laboratories of Synthetic Protein Chemistry, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    J Am Chem Soc 125:2416-25. 2003
    ..This integrated approach has been applied to the study of cross-linking between the components of the heterodimeric protein complex negative cofactor 2...
  16. pmc Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc
    Alejandra Leo-Macias
    The Leon H Charney Division of Cardiology, New York University School of Medicine NYU SoM, 522 First Avenue, Smilow 805, New York, New York 10016, USA
    Nat Commun 7:10342. 2016
    ....
  17. pmc Rapid, optimized interactomic screening
    Zhanna Hakhverdyan
    Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
    Nat Methods 12:553-60. 2015
    ..Our approach is robust, economical and automatable, providing inroads to the rigorous, systematic dissection of cellular interactomes. ..
  18. doi request reprint The GPMDB REST interface
    David Fenyo
    Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, NY, USA and Department of Biochemistry and Medical Genetics, The University of Manitoba, Winnipeg, MB, Canada
    Bioinformatics 31:2056-8. 2015
    ..Version 1 of this interface gives access to 25 methods for retrieving experimental information about protein post-translational modifications, amino acid variants, alternate splicing variants and protein cleavage patterns...
  19. pmc A robust pipeline for rapid production of versatile nanobody repertoires
    Peter C Fridy
    Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
    Nat Methods 11:1253-60. 2014
    ..The approach presented here is well suited for the routine production of high-affinity capture reagents for various biomedical applications. ..
  20. 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...
  21. 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...