R J Chalkley

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc The effect of using an inappropriate protein database for proteomic data analysis
    Giselle M Knudsen
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 6:e20873. 2011
  2. doi request reprint When target-decoy false discovery rate estimations are inaccurate and how to spot instances
    Robert J Chalkley
    Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, Genentech Hall Room N474A, San Francisco, California 94158, USA
    J Proteome Res 12:1062-4. 2013
  3. pmc Modification site localization scoring: strategies and performance
    Robert J Chalkley
    University of California San Francisco, 600 16th Street, Genentech Hall N 474A, San Francisco, California 94158, USA
    Mol Cell Proteomics 11:3-14. 2012
  4. ncbi request reprint Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry
    R J Chalkley
    Mass Spectrometry Faculty, University of California San Francisco, San Francisco, California 94143 0446, USA
    J Am Soc Mass Spectrom 17:1271-4. 2006
  5. pmc In-depth analysis of tandem mass spectrometry data from disparate instrument types
    Robert J Chalkley
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 2517, USA
    Mol Cell Proteomics 7:2386-98. 2008
  6. pmc Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry
    R J Chalkley
    Department of Pharmaceutical Chemistry, Mass Spectrometry Facility, University of California, San Francisco, California 94158, USA
    Anal Chem 82:579-84. 2010
  7. ncbi request reprint Characterization of Tetrahymena histone H2B variants and posttranslational populations by electron capture dissociation (ECD) Fourier transform ion cyclotron mass spectrometry (FT-ICR MS)
    K F Medzihradszky
    Department of Pharmaceutical Chemistry and Mass Spectrometry Facility, University of California, San Francisco, CA 94143 0446, USA
    Mol Cell Proteomics 3:872-86. 2004
  8. pmc Receptor tyrosine kinase signaling mechanisms: Devolving TrkA responses with phosphoproteomics
    R A Bradshaw
    Dept Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
    Adv Biol Regul 53:87-96. 2013
  9. pmc Rapid auxin-mediated changes in the proteome of the epidermal cells in rye coleoptiles: implications for the initiation of growth
    Z Deng
    Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
    Plant Biol (Stuttg) 14:420-7. 2012
  10. ncbi request reprint O-sulfonation of serine and threonine: mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes
    K F Medzihradszky
    Department of Pharmaceutical Chemistry and Mass Spectrometry Facility, University of California, San Francisco, CA 94143, USA
    Mol Cell Proteomics 3:429-40. 2004

Collaborators

Detail Information

Publications10

  1. pmc The effect of using an inappropriate protein database for proteomic data analysis
    Giselle M Knudsen
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 6:e20873. 2011
    ....
  2. doi request reprint When target-decoy false discovery rate estimations are inaccurate and how to spot instances
    Robert J Chalkley
    Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, Genentech Hall Room N474A, San Francisco, California 94158, USA
    J Proteome Res 12:1062-4. 2013
    ..This information will hopefully help researchers become more astute in their assessment of search results...
  3. pmc Modification site localization scoring: strategies and performance
    Robert J Chalkley
    University of California San Francisco, 600 16th Street, Genentech Hall N 474A, San Francisco, California 94158, USA
    Mol Cell Proteomics 11:3-14. 2012
    ..Methods for representing ambiguity are reviewed and a discussion of how the approaches transfer to different data types and modifications is presented...
  4. ncbi request reprint Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry
    R J Chalkley
    Mass Spectrometry Faculty, University of California San Francisco, San Francisco, California 94143 0446, USA
    J Am Soc Mass Spectrom 17:1271-4. 2006
    ..In this study, we report that electron capture on the sulfur of alkylated cysteine residues is also a dominant process, causing cysteine side-chain loss from z* ions...
  5. pmc In-depth analysis of tandem mass spectrometry data from disparate instrument types
    Robert J Chalkley
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 2517, USA
    Mol Cell Proteomics 7:2386-98. 2008
    ..Several modifications never previously reported in proteomics data were identified in these standard data sets using this mass modification searching approach...
  6. pmc Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry
    R J Chalkley
    Department of Pharmaceutical Chemistry, Mass Spectrometry Facility, University of California, San Francisco, California 94158, USA
    Anal Chem 82:579-84. 2010
    ....
  7. ncbi request reprint Characterization of Tetrahymena histone H2B variants and posttranslational populations by electron capture dissociation (ECD) Fourier transform ion cyclotron mass spectrometry (FT-ICR MS)
    K F Medzihradszky
    Department of Pharmaceutical Chemistry and Mass Spectrometry Facility, University of California, San Francisco, CA 94143 0446, USA
    Mol Cell Proteomics 3:872-86. 2004
    ..This study establishes that integration of the information from these two datasets provides a comprehensive map of posttranslational occupancy for each particular covalent assemblage selected for structural investigation...
  8. pmc Receptor tyrosine kinase signaling mechanisms: Devolving TrkA responses with phosphoproteomics
    R A Bradshaw
    Dept Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
    Adv Biol Regul 53:87-96. 2013
    ..A comparison with a similar set of data for EGFR indicates a considerable degree of similarity in the downstream signaling profile between these two RTKs...
  9. pmc Rapid auxin-mediated changes in the proteome of the epidermal cells in rye coleoptiles: implications for the initiation of growth
    Z Deng
    Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
    Plant Biol (Stuttg) 14:420-7. 2012
    ..The implications of these rapid auxin effects with respect to signal transduction and IAA-mediated secretion of glycoproteins (osmiophilic nano-particles) into the growth-controlling outer epidermal wall are discussed...
  10. ncbi request reprint O-sulfonation of serine and threonine: mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes
    K F Medzihradszky
    Department of Pharmaceutical Chemistry and Mass Spectrometry Facility, University of California, San Francisco, CA 94143, USA
    Mol Cell Proteomics 3:429-40. 2004
    ..These findings suggest that sulfonation of serine and threonine may be involved in multiple functions including protein assembly and signal transduction...