Scientific Report 2006

Molecular Biology

Mass Spectrometry

G. Siuzdak, J. Apon, H.P. Benton, E. Go, K. Harris, L. Hoang, R. Lowe, A. Meyers, H. Morita, A. Nordstrom, T. Northen, G. O’Maille, C. Qin, Z. Shen, C. Smith, M. Sonderegger, S. Trauger, W. Uritboonthai, E. Want, W. Webb, W. Wikoff, D. Wong

Metabolite Profiling

Endogenous small-molecule metabolites, ubiquitous in biofluids, are crucial elements in understanding living organisms whether in fundamental biochemistry, disease diagnosis, or drug toxicity. The inherent advantage of monitoring small molecules rather than proteins is the relative ease of quantitative analysis of the molecules with mass spectrometry. We are implementing novel mass spectrometry and bioinformatics techniques (Fig. 1) to investigate the profile of small-molecule metabolites. Our purposes are to correlate metabolite activity with protein regulation and to develop metabolite analysis as a diagnostic method. Our ultimate goal is to create analytical and chemical technologies and data management approaches to identify and structurally characterize metabolites of physiologic importance.

Fig. 1. A novel nonlinear approach for correcting and analyzing mass spectrometry data for characterization of metabolites.

Viral Characterization

We have developed novel methods for characterizing viruses that have applications to whole viruses, viral proteins, and viral metabolites. Our results have enabled us to examine both local and overall viral structure, gaining insight into the dynamic changes of proteins on the viral surface and the changes that occur during viral infection (Fig. 2).

Fig. 2. A comprehensive approach for studying viral infection by using a combination of mass spectrometry techniques. Three different aspects of viral infection within an infected cell—the expression kinetics of the viral proteins, changes in the expression levels of cellular proteins, and changes in cellular metabolites—were monitored. These analyses reveal the complexity of the protein and metabolite regulation involved in cellular transformations that occur during viral infection.

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.

Publications

Cohen, L., Go, E.P., Siuzdak, G. Small-molecule desorption/ionization mass analysis. In: A Practical Guide to MALDI MS: Instrumentation, Methods and Applications. Hillenkamp, F., Peter-Katalinic, J. (Eds.). Wiley & Sons, New York, in press.

Lee, J.-C.,Wu, C.-Y., Apon, J.V., Siuzdak, G., Wong, C.-H. Reactivity-based one-pot synthesis of tumor-associated antigen N3 minor octasaccharide for the development of a cleavable DIOS-MS sugar array. Angew. Chem. Int. Ed. 45:2753, 2006.

Lowe, R., Tong, G., Voelcker, N.H., Siuzdak, G. Monitoring EDTA and endogenous metabolite from serum with mass spectrometry. Spectroscopy 19:137, 2005.

Luo, G., Chen, Y., Siuzdak, G., Vertes, A. Surface modification and laser pulse length effects on internal energy transfer in DIOS. J. Phys. Chem. B. 109:24450, 2005.

Nordstrom, A., Apon, J.V., Uritboonthai, W., Go, E.P., Siuzdak, G. Surfactant enhanced desorption/ionization on silicon mass spectrometry. Anal. Chem. 78:272, 2006.

Nordstrom, A., He, L., Siuzdak, G. Desorption/ionization on silicon (DIOS). In: Hyphenation Methods. Niessen, W. (Ed.). Elsevier, St. Louis, in press. Encyclopedia of Mass Spectrometry, Vol 8. Gross, M.L., Caprioli, R.M. (Eds. in Chief).

Nordstrom, A., O’Maille, G., Qin, C., Siuzdak, G. Nonlinear data alignment for UPLC-MS and HPLC-MS based metabolomics: quantitative analysis of endogenous and exogenous metabolites in human serum. Anal. Chem. 78:3289, 2006.

Siuzdak, G. The Expanding Role of Mass Spectrometry in Biotechnology, 2nd ed. MCC Press, San Diego, CA, 2006.

Smith, C.A., O’Maille, G., Want, E.J., Qin, C., Trauger, S.A., Brandon, T.R., Custodio, D.E., Abagyan, R., Siuzdak, G. METLIN: a metabolite mass spectral database. Ther. Drug Monit. 27:747, 2005.

Smith, C.A., Want, E.J., O’Maille, G., Abagyan, R., Siuzdak, G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78:779, 2006.

Talkington, M.W., Siuzdak, G., Williamson, J.R. An assembly landscape for the 30S ribosomal subunit. Nature 438:628, 2005.

Want, E., Cravatt, B.F., Siuzdak, G. The expanding role of mass spectrometry in metabolite profiling and characterization. Chembiochem 6:1941, 2005.

Want, E.J., O’Maille, G., Smith, C.A., Brandon, T.R., Uritboonthai, W., Qin, C., Trauger, S.A., Siuzdak, G. Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry. Anal. Chem. 78:743, 2006.