Gary Siuzdak, PhD
Scripps Research Joint Appointments
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, DartmouthAwards & Professional Activities
University of Umea Sweden, Honorary Doctorate for Metabolomics ResearchMetabolomics 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
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 Biology, 2010, 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
Nature, 2007, 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 Chemistry, 2006, 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
Nature, 1999, 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
https://doi.org/10.1038/s41596-020-00455-4
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
METLIN MS2 molecular standards database: a broad chemical and biological resource
Identification of bioactive metabolites using activity metabolomics
Nature Methods 2018, 15, 681-684
Metabolomics Activity Screening for Identifying Metabolites that Modulate Phenotype
Systems Biology guided by XCMS Online Metabolomics