Scripps Research Logo

Gary Siuzdak, Ph.D.

Sr. Director, Scripps Center For Metabolomics
Professor of Chemistry, Molecular and Computational Biology
Research Services
California Campus
Laboratory Website
siuzdak@scripps.edu
(858) 784-9415

Scripps Research Joint Appointments

Department of Chemistry
Department of Cell and Molecular Biology
Professor, Department of Integrative Structural and Computational Biology

Research Focus

Metabolomics and Mass Spectrometry

The Center for Metabolomics is developing mass spectrometry-based technologies for understanding metabolism. These developments include nanostructure-based imaging, cloud-based informatics, as well as a unique database to facilitate metabolite identification. Our XCMS Online informatic platform has thousands of users in over 100 different countries, and nanostructure-based mass spectrometry is a widely used matrix-free solution to tissue imaging, activity screening and analyzing nano-arrays.  The primary motivation driving these developments is the biological problems we are applying them to, examples from our lab include examining the fundamental biochemistry behind stem cell differentiation, understanding the role of the microbiome on cancer metabolism,and providing insight into pain pathology.  These studies have made me acutely aware of the power of this technology in understanding disease pathogenesis. 

Education

Ph.D., Physical Chemistry, Dartmouth, 1990

Selected References

Johnson C.H., Ivanisevic J., Siuzdak G.
Metabolomics: Beyond Biomarkers and Towards Mechanisms
Nature Reviews Molecular Cell Biology, 2016 17(7), 451-9

Kurczy M., Zhu Z.J., Ivanisevic J., Schuyler A., Lalwani K., Santidrian A., David J., Giddabasappa A.,  Roberts A., Olivos H., O'Brien P., Franco L., Fields M.,  Paris L., Friedlander M., Johnson C., Epstein A., Gendelman H., Wood, M., Felding B., Patti G., Spilker M., Siuzdak G.
Comprehensive bioimaging with fluorinated nanoparticles using breathing liquids
Nature Communications, 2015, 6, 5998.

Johnson C.H., Dejea C.H., Edler D., Hoang L.T., Santidrian A.F., Felding B.H., Ivanisevic J., Cho K., Wick E.C., Hechenbleikner E.M., Uritboonthai W., Goetz L., Casero R.A., Pardoll D.M., White J.R., Patti G.J., Sears C.L., Siuzdak G.
Metabolism Links Bacterial Biofilms and Colon Carcinogenesis
Cell Metabolism, 2015, 21(6), 891–897  

Rinehart D., Johnson C.H., Nguyen T., Ivanisevic J., Benton H.P., Lloyd J., Deutschbauer A., Arkin A., Patti G.J., Siuzdak G.
Metabolomic Data Streaming for Biology-Dependent Data Acquisition
Nature Biotechnology, 2014, 32, 524–527

Zhu Z-J., Schultz A.W., Wang J., Johnson C.H., Yannone S.M., Patti G.J., Siuzdak G.
Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database
Nature Protocols, 2013 8 451-460

Tautenhahn R., Cho K.Y., Uritboonthai W., Zhu Z., Patti G.J., Siuzdak G.
An accelerated workflow for untargeted metabolomics using the METLIN database
Nature Biotechnology, 2012, 30(9), 826-828

Patti G.J., Tautenhahn R., Siuzdak G.
Meta-Analysis of untargeted metabolomic data from multiple profiling experiments

Nature Protocols, 2012 7(3) 508-516

Patti G.J., Yanes O., Siuzdak G.
Metabolomics:  The Apogee of the Omic Trilogy
Nature Reviews, 2012, 13, 263-269

Patti G.J., Tautenhahn R., Siuzdak G.
Meta-Analysis of untargeted metabolomic data from multiple profiling experiments
Nature Protocols, 2012, 7(3), 508-516

Patti G.J., Yanes O., Shriver L., Courade J-P., Tautenhahn R., Manchester M., Siuzdak G.
Metabolomics Implicates Altered Sphingolipid Metabolites in Chronic Pain of Neuropathic Origin
Nature Chemical Biology, 2012, 8, 232-234

Yanes O., Hsu J., Wong D.M., Sanchez-Ruiz A., Benton H.P., Trauger S.A., Despont C., Ding S., Siuzdak G.
Metabolic oxidation regulates embryonic stem cell differentiation
Nature Chemical Biology2010, 6, 411-417.

Wikoff W.R., Anfora A.T., Liu J.W., Shultz P.G., Lesley S.A., Peters E.C., Siuzdak G.
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites
Proc Natl Sci USA, 2009 106(10) 3698-703

Woo H.K., Northen T.R., Yanes O., Siuzdak G.
Nanostructure-initiator mass spectrometry: a protocol for preparing and applying NIMS surfaces for high-sensitivity mass analysis
Nature Protocols, 2008, 3(8), 1341-1349

Northen T.R., Lee J-C, Hoang L., Raymond J., Hwang D-R, Yannone S.M., Wong C-H, Siuzdak G.
A Nanostructure-Initiator Mass Spectrometry-Based Enzyme Activity Assay

PNAS, 2008 105(10) 3678-3683

Northen T.R., Yanes O., Northen M.T., Marrinucci D., Uritboonthai W., Apon J., Golledge S.L., Nordstrom A., Siuzdak G.
Clathrate nanostructures for mass spectrometry
Nature2007, 449(7165), 1033-1037.

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
Analytical Chemistry2006, 78, 779-787  

Fuerstenau S.D., Benner W.H., Thomas J.J., Brugidou C., Bothner B., Siuzdak G
Mass Spectrometry of an Intact Virus
Angewandte Chemie, 2001 40 542-544

Wei J., Buriak J., Siuzdak G.
Desorption-ionization mass spectrometry on porous silicon
Nature1999, 399(6733), 243-246. 

Bothner B., Schneemann A., Marshall D., Reddy V., Johnson J.E., Siuzdak G.
Crystallographically Identical Virus Capsids Display Different Properties in Solution

Nature Structural Biology, 1999 6 114-116

Lewis J.K., Bothner B., Smith T.J., Siuzdak G.
Antiviral Agent Blocks Breathing of Common Cold Virus

Proceedings of the National Academy of Sciences, USA, 1998 95(12) 6774-6778  

Siuzdak G., Bothner B., Yeager M., Brugidou C., Fauquet C.M., Hoey K., Chang C.M.
Mass Spectrometry and Viral Analysis

Chemistry & Biology, 1996 3 45 

Links

Center for Metabolomics and Mass Spectrometry