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Scientific Report 2007

Scripps Florida

Molecular Therapeutics

Mass Spectrometry for Analysis of Proteins

J.A. Caldwell Busby, V. Cavett

We work to develop methods compatible with mass spectrometry for the analysis of proteins. Our areas of interest are wide-ranging and include methods for subcellular compartmentalization for large-scale proteomics profiling and identification of proteins involved in gene regulation. Gene regulation, or epigenomics, is of particular interest. To date, the focus of epigenomics research has been patterns of DNA methylation and posttranslational modifications of the histone N termini. However, many other proteins are associated with chromatin, including transcription factors, enzymes, and scaffolding proteins. We are developing methods for isolating and analyzing the supermolecular structure of chromatin, particularly the regulatory protein machineries, and we are using cutting-edge mass spectrometric techniques to characterize the proteins involved in gene regulation.

Study of the interactions of proteins and DNA biopolymers is not new; much work has been done on transcription and gene regulation. However, most of this research has relied on the analysis of DNA methylation patterns and chromatin immunoprecipitation methods. Although informative, these studies ignore the extensive protein components of the system, potentially a rich source of information about how epigenetic patterns are established, maintained, and modified in healthy tissue. Such studies also cannot be used to assess how changes in these protein components contribute to disease states, aging, or cell death.

Mass spectrometry is a widely used technique in proteomics. Powerful, high-resolution instruments, coupled with new fragmentation methods, including electron capture dissociation, are driving the identification of novel proteins and new sites of protein identification. This identification is something for which neither traditional molecular biology nor modern RNA/DNA analysis is well suited. The development of a mass spectrometry–based process to identify components of the chromatin regulatory network will yield a broadly applicable method that will contribute to a wide range of biological investigations, including chromatin regulation of gene expression.


Godeny, M.D., Sayyah, J., VonDerLinden, D., Johns, M., Ostrov, D.A., Caldwell-Busby, J., Sayeski, P.P. The N-terminal SH2 domain of the tyrosine phosphatase, SHP-2, is essential for Jak2-dependent signaling via angiotensin II type AT1 receptor. Cell Signal. 19:600, 2007.

Sloley, S., Smith, S., Algeciras, M., Cavett, V., Caldwell Busby, J.A., London, S., Clayton, D.F., Bhattacharya, S.K. Proteomic analyses of songbird (zebra finch; Taeniopygia guttata) retina. J. Proteome Res. 6:1093, 2007.

Sloley, S., Smith, S., Gandhi, S., Caldwell Busby, J.A., London, S., Luksch, H., Clayton, D.F., Bhattacharya, S.K. Proteomic analyses of zebra finch optic tectum and comparative histochemistry. J. Proteome Res. 6:2341, 2007.


Jennifer C. Busby, Ph.D.
Assistant Professor

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