David Fenyo

Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 31	2007

Other Publications

Article	Year
RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics\| PubMed ID: 11788990	2002
A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis. Proteomics\| PubMed ID: 11921442	2002
Informatics and data management in proteomics. Trends in biotechnology\| PubMed ID: 12570158	2002
A modular cross-linking approach for exploring protein interactions. Journal of the American Chemical Society\| PubMed ID: 12603129	2003
A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Analytical chemistry\| PubMed ID: 12622365	2003
Probity: a protein identification algorithm with accurate assignment of the statistical significance of the results. Journal of proteome research\| PubMed ID: 14998160	2004
The statistical significance of protein identification results as a function of the number of protein sequences searched. Journal of proteome research\| PubMed ID: 15473685	2004
A proteomics approach to the study of absorption, distribution, metabolism, excretion, and toxicity. Journal of biomolecular techniques : JBT\| PubMed ID: 15585823	2004
Phosphotyrosine signaling networks in epidermal growth factor receptor overexpressing squamous carcinoma cells. Molecular & cellular proteomics : MCP\| PubMed ID: 15657067	2005
Protein identification in complex mixtures. Journal of proteome research\| PubMed ID: 15822914	2005
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics\| PubMed ID: 16047398	2005
Optimizing search conditions for the mass fingerprint-based identification of proteins. Proteomics\| PubMed ID: 16485258	2006
SwePep, a database designed for endogenous peptides and mass spectrometry. Molecular & cellular proteomics : MCP\| PubMed ID: 16501280	2006
Reproducibility of LC-MS-based protein identification. Journal of experimental botany\| PubMed ID: 16551682	2006
Detection of artifacts and peptide modifications in liquid chromatography/mass spectrometry data using two-dimensional signal intensity map data visualization. Rapid communications in mass spectrometry : RCM\| PubMed ID: 16628601	2006
Determining the overall merit of protein identification data sets: rho-diagrams and rho-scores. Journal of proteome research\| PubMed ID: 17397212	2007
Neuropeptidomics strategies for specific and sensitive identification of endogenous peptides. Molecular & cellular proteomics : MCP\| PubMed ID: 17401030	2007
Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs. Nature biotechnology\| PubMed ID: 17557102	2007
An automated method for scanning LC-MS data sets for significant peptides and proteins, including quantitative profiling and interactive confirmation. Journal of proteome research\| PubMed ID: 17559249	2007
Informatics development: challenges and solutions for MALDI mass spectrometry. Mass spectrometry reviews\| PubMed ID: 17979143	2008
Use of DNA ladders for reproducible protein fractionation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for quantitative proteomics. Journal of proteome research\| PubMed ID: 18189343	2008
Rapid isolation and identification of bacteriophage T4-encoded modifications of Escherichia coli RNA polymerase: a generic method to study bacteriophage/host interactions. Journal of proteome research\| PubMed ID: 18271525	2008
Efficient identification of phosphorylation by mass spectrometric phosphopeptide fingerprinting. Analytical chemistry\| PubMed ID: 18321079	2008
Finding protein sequences using PROWL. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]\| PubMed ID: 18428719	2004
Validation of endogenous peptide identifications using a database of tandem mass spectra. Journal of proteome research\| PubMed ID: 18549260	2008
Screening for EphB signaling effectors using SILAC with a linear ion trap-orbitrap mass spectrometer. Journal of proteome research\| PubMed ID: 18816084	2008
Evaluation of the variation in sample preparation for comparative proteomics using stable isotope labeling by amino acids in cell culture. Journal of proteome research\| PubMed ID: 19140678	2009
Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei. Genes & development\| PubMed ID: 19369410	2009
Rapid sensitive analysis of cysteine rich peptide venom components. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 19380747	2009
Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Molecular & cellular proteomics : MCP\| PubMed ID: 19858499	2010
GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Molecular systems biology\| PubMed ID: 20212525	2010
The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate-washed membrane standard. Proteomics\| PubMed ID: 20486120	2010
Mass spectrometric protein identification using the global proteome machine. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 20835799	2010
Protein quantitation using mass spectrometry. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 20835801	2010
Modeling experimental design for proteomics. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 20835802	2010
Modeling mass spectrometry-based protein analysis. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 21082431	2011
High-Capacity Ion Trap Coupled to a Time-of-Flight Mass Spectrometer for Comprehensive Linked Scans with no Scanning Losses. International journal of mass spectrometry\| PubMed ID: 21516228	2011
Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. Science (New York, N.Y.)\| PubMed ID: 21764753	2011
Strategy for identifying dendritic cell-processed CD4+ T cell epitopes from the HIV gag p24 protein. PloS one\| PubMed ID: 22860026	2012
Comparative proteomic analysis of the ATP-sensitive K+ channel complex in different tissue types. Proteomics\| PubMed ID: 23197389	2013
Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium. Journal of proteome research\| PubMed ID: 23249167	2013
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. Journal of proteome research\| PubMed ID: 23259914	2013
Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies. The Journal of experimental medicine\| PubMed ID: 23319701	2013
Developments in biobanking workflow standardization providing sample integrity and stability. Journal of proteomics\| PubMed ID: 23856607	2013
Super-resolution fluorescence microscopy of the cardiac connexome reveals plakophilin-2 inside the connexin43 plaque. Cardiovascular research\| PubMed ID: 23929525	2013
Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. Journal of proteome research\| PubMed ID: 24266786	2014
Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Molecular & cellular proteomics : MCP\| PubMed ID: 24719451	2014
Super-resolution imaging reveals that loss of the C-terminus of connexin43 limits microtubule plus-end capture and NaV1.5 localization at the intercalated disc. Cardiovascular research\| PubMed ID: 25139742	2014
A robust pipeline for rapid production of versatile nanobody repertoires. Nature methods\| PubMed ID: 25362362	2014
Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome. Journal of proteome research\| PubMed ID: 25369122	2015
Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study. BMC genomics\| PubMed ID: 25521637	2014
The GPMDB REST interface. Bioinformatics (Oxford, England)\| PubMed ID: 25697819	2015