Education
| Ph.D. | Biochemistry | 2001 | University College London, London, UK |
| B.Sc. | Biochemistry | 1997 | University of Sussex, Brighton, UK |
Work History
| 2017-present: | Adjunct Professor, Dept of Pharmaceutical Chemistry, School of Pharmacy, UCSF, CA. |
| 2017-present: | Research Biochemist, Dept of Pharmaceutical Chemistry, School of Pharmacy, UCSF, CA. |
| 2010-2017: | Associate Adjunct Professor, Dept of Pharmaceutical Chemistry, School of Pharmacy, UCSF, CA. |
| 2010-2017: | 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 protein glycosylation.
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. Recent development efforts have included improved software for analysis of intact glycopeptides and cross-linked peptides. 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
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]
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]
Baker PR, Trinidad JC, Chalkley RJ. Modification site localization scoring integrated into a search engine. Mol Cell Proteomics 10(7) M111.008078 (2011) [Pubmed]
Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ. Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics (2014) 13 (2) 420-34. [Pubmed]
Medzihradszky KF, Kaasik K, Chalkley RJ. Tissue-specific glycosylation at the glycopeptide level Mol Cell Proteomics (2015) 14 8 2103-10 [Pubmed]
Maynard JC, Chalkley RJ. Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites Mol Cell Proteomics (2021) 20 100031 [Pubmed]
