Robert Chalkley

Robert Chalkley


Associate Adjunct Professor



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

Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. The induction of serine/threonine protein phosphorylations by a PDGFR/TrkA chimera in stably transfected PC12 cells. Mol Cell Proteomics 11(5) 15–30. (2012) [Pubmed]

Baker PR, Trinidad JC, Chalkley RJ. /Modification site localization scoring integrated into a search engine. Mol Cell Proteomics 10(7) M111.008078 (2011) [Pubmed]

Chu F, Baker PR, Burlingame AL, Chalkley RJ. Finding Chimeras: A bioinformatic strategy for identification of cross-linked peptides. Mol Cell Proteomics 9(1), 25–31. (2010) [Pubmed]

Baker PR, Medzihradszky KF, Chalkley RJ. 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 RJ, Thalhammer A, Schoepfer R, Burlingame AL. 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 RJ, Baker PR, Medzihradszky KF, Lynn AJ, Burlingame AL. In-depth analysis of tandem mass spectrometry data from disparate instrument types. Mol Cell Proteomics (2008) 7(12) 2386–2398. [Pubmed]

Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor AO, Guan S, Medzihradszky KF, Maltby D, Schoepfer R, Burlingame AL. 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]

National Institute of General Medical Sciences Adelson Medical Research Foundation