Scientific Report 2005

Molecular Biology

Mass Spectrometry

G. Siuzdak, J. Apon, E. Go, K. Harris, R. Lowe, A. Meyers, A. Nordstrom, Z. Shen, C. Smith, G. Tong, S. Trauger, W. Uritboonthai, E. Want, W. Webb, C. Wranik

Metabolite Profiling

Small molecules ubiquitous in biofluids are now widely used to predict disease states. The inherent advantage of monitoring small molecules rather than proteins is the relative ease of quantitative analysis with mass spectrometry. We are implementing novel mass spectrometry and bioinformatics techniques (Fig. 1) to investigate the metabolite profiles of small molecules as diagnostic indicators of disease.

Fig. 1. A novel nonlinear approach to analyzing mass spectrometry data for identification of metabolites.

The ultimate goal is to develop analytical and chemical technologies and a data management system to identify and structurally characterize metabolites of physiologic importance.

Viral Characterization

We have developed novel methods for characterizing viruses that have applications to whole viruses and viral proteins. Our results enabled us to examine both local and global viral structure, gaining insight into the dynamic changes of proteins on the viral surface.

Mass Spectrometry in Silico

We are also developing ultra-high-sensitivity approaches in mass spectrometry with a new strategy that involves pulsed laser desorption/ionization from a silylated silicon surface. In desorption/ionization on silicon, silicon is used to capture analytes, and laser radiation is used to vaporize and ionize these molecules. Using this technology, we can analyze a wide range of molecules with unprecedented sensitivity, in the yoctomole range (Fig. 2).

Fig. 2. Laser desorption/ionization mass spectrometry on structured silylated silicon has sensitivity rivaling that of fluorescence.

Publications

Bothner, B., Taylor, D., Jun, B., Lee, K.K., Siuzdak, G., Schultz, C.P., Johnson, J.E. Maturation of a tetravirus capsid alters the dynamic properties and creates a metastable complex. Virology 334:17, 2005.

Go, E.P., Apon, J.V., Luo, G., Saghatelian, A., Daniels, R.H., Sahi, V., Dubrow, R., Cravatt, B.F., Vertes, A., Siuzdak, G. Desorption/ionization on silicon nanowires. Anal. Chem. 77:1641, 2005.

Lacy, E.R., Wang, Y., Post, J., Nourse, A., Webb, W., Mapelli, M., Musacchio, A., Siuzdak, G., Kriwacki, R.W. Molecular basis for the specificity of p27 toward cyclin-dependent kinases that regulate cell division. J. Mol. Biol. 349:764, 2005.

Lowe, R., Go, E., Tong, G., Voelcker, N.H., Siuzdak, G. Monitoring EDTA and endogenous metabolite biomarkers from serum with mass spectrometry. Spectroscopy, in press.

Saghatelian, A., Trauger, S.A., Want, E., Hawkins, E.G., Siuzdak, G., Cravatt, B.F. Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry 43:14332, 2004.

Want, E., Cravatt, B.F., Siuzdak, G. The expanding role of mass spectrometry in metabolite profiling and characterization. Chembiochem, in press.