Genomes and Genes
Affiliation: The Rockefeller University
- Informatics development: challenges and solutions for MALDI mass spectrometryDavid 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...
- Mass spectrometric protein identification using the global proteome machineDavid 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...
- Protein quantitation using mass spectrometryGuoan 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....
- Screening for EphB signaling effectors using SILAC with a linear ion trap-orbitrap mass spectrometerGuoan 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...
- Determining the overall merit of protein identification data sets: rho-diagrams and rho-scoresDavid 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...
- Informatics and data management in proteomicsDavid Fenyo
Proteometrics LLC, PO Box 984, New York, NY 10014, USA
Trends Biotechnol 20:S35-8. 2002....
- RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational databaseHelen 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...
- Comparative proteomic analysis of the ATP-sensitive K+ channel complex in different tissue typesEirini 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...
- Rapid sensitive analysis of cysteine rich peptide venom componentsBeatrix 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)...
- Strategy for identifying dendritic cell-processed CD4+ T cell epitopes from the HIV gag p24 proteinLeonia 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...
- GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genomeMatthew 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...
- Efficient identification of phosphorylation by mass spectrometric phosphopeptide fingerprintingEileen 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)...
- Evaluation of the variation in sample preparation for comparative proteomics using stable isotope labeling by amino acids in cell cultureGuoan 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...