Robert Chalkley
Position
Associate Adjunct Professor
Education
| Ph.D. | Biochemistry | 2001 | University College London, London, UK |
| B.Sc. | Biochemistry | 1997 | University of Sussex, Brighton, UK |
Work History
| 2010-present: | Associate Adjunct Professor, Dept of Pharmaceutical Chemistry, School of Pharmacy, UCSF, CA. |
| 2010-present: | Associate Research Biochemist, Dept of Pharmaceutical Chemistry, School of Pharmacy, UCSF, CA. |
| 2003-2010: | Assistant Adjunct Professor, Dept of Pharmaceutical Chemistry,School of Pharmacy, UCSF, CA. |
| 2003-2010: | Assistant Research Biochemist, Dept of Pharmaceutical Chemistry, School of Pharmacy, UCSF, CA. |
| 2001-2003: | Postdoctoral Fellow, Dept of Pharmaceutical Chemistry, School of Pharmacy, UCSF, CA. |
Research Interests
I have two major fields of research interest. I am heavily involved in the development and application of novel technologies for the study of protein post-translational modifications using mass spectrometry. Secondly, I am involved in the development of tools for reliable analysis of mass spectrometry data.
Mass spectrometry is probably the most powerful approach for the analysis of post-translational modifications (PTMs). However, modification analysis using mass spectrometry presents several challenges, both in terms of detecting generally low stoichiometry modifications and then reliably assigning the actual modified residues. I have been involved in the development of mass spectrometric methods for the study of a plethora of post-translational modifications including O-GlcNAcylation, phosphorylation, sulfation, methylation and acetylation. I have a particular emphasis in the development of improved methods for the enrichment and characterization of O-GlcNAc modification, and its interaction with other regulatory PTMs.
With the rapid development of robust and sensitive mass spectrometry platforms the analysis of complex mixtures using mass spectrometry has become a routine exercise in many laboratories. However, the software for the comprehensive and reliable analysis of this type of data is often lagging behind. I am a leading developer of a set of proteomics software tools named Protein Prospector. This software allows the searching and reliable summarizing of results from LC-MS data. It can also perform quantitative analysis using stable isotope labeling or label-free strategies. This software is freely available on the web for anyone to use. Video tutorials describing how to use this software can be found here: Protein Prospector Tutorial.
Select Publications
Baker, P.R., Medzihradszky, K.F., Chalkley, R.J., Improving software performance for peptide ETD data analysis by implementation of charge-state and sequence-dependent scoring Mol Cell Proteomics 9(9) 1795-803 (2010). [Pubmed]
Chalkley, R.J., Thalhammer, A., Schoepfer, R., and Burlingame, A.L., Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides, Proc Natl Acad Sci U S A (2009) 106(22) 8894-8899. [Pubmed]
Chalkley, R.J., Baker, P.R., Medzihradszky, K.F., Lynn, A.J., and Burlingame, A.L., In-depth analysis of tandem mass spectrometry data from disparate instrument types, Mol Cell Proteomics (2008) 7(12) 2386-2398. [Pubmed]
Vosseller, K., Trinidad, J.C., Chalkley, R.J., Specht, C.G., Thalhammer, A., Lynn, A.J., Snedecor, A.O., Guan, S., Medzihradszky, K.F., Maltby, D., Schoepfer, R., and Burlingame, A.L., O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry, Mol Cell Proteomics, 5(5), 923-934 (2006). [Pubmed]
Chalkley, R.J., Brinkworth, C.S., Burlingame, A.L. Side-Chain Fragmentation of Alkylated Cysteine Residues in Electron Capture Dissociation Mass Spectrometry J Am Soc Mass Spectrom, 17(9), 1271-1274 (2006). [Pubmed]
Chalkley, R.J., Hansen, K.C. and Baldwin, M.A., Bioinformatic methods to exploit mass spectrometric data for proteomics applications, Meth Enz, 402, 289-312 (2005). [Pubmed]
Burlingame, A.L., Zhang, X. and Chalkley, R.J., Mass spectrometric analysis of histone post-translational modifications, Methods, 36, 383-394 (2005). [Pubmed]