Gary Siuzdak, PhD

Sr. Director, Scripps Center for Metabolomics
Professor of Chemistry, Molecular and Computational Biology
Research Services


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. 


Ph.D., Physical Chemistry, Dartmouth

Awards & Professional Activities

University of Umea Sweden, Honorary Doctorate for Metabolomics Research
Metabolomics Society Honorary Fellow
Lorne (Australian) Keynote Lecturer
Nordic Metabolomics Society Conference Keynote Lecturer
New Zealand Mass Spectrometry Keynote Lecturer
ASMS Asilomar Clinical Metabolomics Keynote Lecturer
Metabolomics Society Conference Keynote Lecturer
Experimental Biology Keynote Lecturer

Selected References

All Publications

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

Cognitive analysis of metabolomics data for systems biology
Erica L-W Majumder, Elizabeth M Billings, H Paul Benton, Richard L Martin, Amelia Palermo, Carlos Guijas, Markus M Rinschen, Xavier Domingo-Almenara, J Rafael Montenegro-Burke, Bradley A Tagtow, Robert S Plumb, Gary Siuzdak

Nature Protocols, 2021, 16, 3, 1376-1418

METLIN MS2 molecular standards database: a broad chemical and biological resource

J Xue, C Guijas, HP Benton, B Warth, G Siuzdak
Nature Methods 2020, 17, 953-954

Identification of bioactive metabolites using activity metabolomics

MM Rinschen, J Ivanisevic, M Giera, G Siuzdak
Nature Reviews Molecular Cell Biology 2019, 20, 353–367

XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules

Xavier Domingo-Almenaraa, J. Rafael Montenegro-Burkea, Julijana Ivanisevic, Aurelien Thomas, Jonathan Sidibé, Tony Teav, Carlos Guijas, Aries E. Aisporna, Duane Rinehart, Linh Hoang, Anders Nordström, Maríia Góomez-Romero, Luke Whiley, Matthew R. Lewis, Jeremy K. Nicholson, H. Paul Benton, Gary Siuzdak
Nature Methods 2018, 15, 681-684

Metabolomics Activity Screening for Identifying Metabolites that Modulate Phenotype

C Guijas, JR Montenegro-Burke, B Warth, ME Spilker, G Siuzdak
Nature Biotechnology 2018, 36 (4), 316-320

Systems Biology guided by XCMS Online Metabolomics

T Huan, EM Forsberg, D Rinehart, CH Johnson, J Ivanisevic, HP Benton, ...
Nature Methods 2017, 14 (5), 461-462


Center for Metabolomics and Mass Spectrometry