R J Chalkley
Affiliation: University of California
- When target-decoy false discovery rate estimations are inaccurate and how to spot instancesRobert 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...
- Modification site localization scoring: strategies and performanceRobert 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...
- Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometryR 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...
- In-depth analysis of tandem mass spectrometry data from disparate instrument typesRobert 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...
- Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometryR J Chalkley
Department of Pharmaceutical Chemistry, Mass Spectrometry Facility, University of California, San Francisco, California 94158, USA
Anal Chem 82:579-84. 2010....
- 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...
- Receptor tyrosine kinase signaling mechanisms: Devolving TrkA responses with phosphoproteomicsR 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...
- Rapid auxin-mediated changes in the proteome of the epidermal cells in rye coleoptiles: implications for the initiation of growthZ 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...
- O-sulfonation of serine and threonine: mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotesK 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...