Gary Siuzdak information

Gary Siuzdak
Gary Siuzdak
Born	December 29, 1961
	Scientific career
Fields	Analytical Chemistry, Metabolomics

Gary Siuzdak is an American chemist best known for his work in the field of metabolomics,^[1]^[2] activity metabolomics^[3]^[4]^[5]^[6]^[7] (a termed coined in 2019^[8]), and mass spectrometry.^[9]^[10]^[11]^[12]^[13]^[14] His lab discovered indole-3-propionic acid as a gut bacteria derived metabolite in 2009.^[15] He is currently the Professor and Director of The Center for Metabolomics and Mass Spectrometry at Scripps Research in La Jolla, California.^[16] Siuzdak has also made contributions to virus analysis,^[17]^[18] viral structural dynamics,^[19]^[20]^[21] as well as developing mass spectrometry imaging technology using nanostructured surfaces.^[11]^[22] The Siuzdak lab is also responsible for creating the research tools eXtensible Computational Mass Spectrometry (XCMS),^[9]^[23] METLIN,^[13] METLIN Neutral Loss^[24] and Q-MRM.^[25]^[26]^[27] As of January 2021,^[28] the XCMS/METLIN platform has over 50,000 registered users.

Siuzdak studied chemistry (B.S.) and applied mathematics (B.A.) at Rhode Island College. He then went to Dartmouth College for his graduate work where he built his first mass spectrometer^[29] to perform multi-photon ionization mass spectrometry experiments and occasionally competed in powerlifting.^[30] At Dartmouth he received his Ph.D. in Physical Chemistry (March 29, 1990) and on April 1, 1990, started at Scripps Research.^[16] In 2017 Siuzdak received an honorary doctorate (with Emmanuelle Charpentier) from Umeå University^[31] for his work in metabolomics. Siuzdak has hundreds of papers and has authored two books: Mass Spectrometry for Biotechnology (1996) and The Expanding Role of Mass Spectrometry in Biotechnology (2003) as well as The Expanding Role of Mass Spectrometry in Biotechnology 2nd Ed. (2006).^[32]

^ Guijas, Carlos; Montenegro-Burke, J. Rafael; Warth, Benedikt; Spilker, Mary E.; Siuzdak, Gary (April 2018). "Metabolomics activity screening for identifying metabolites that modulate phenotype". Nature Biotechnology. 36 (4): 316–320. doi:10.1038/nbt.4101. ISSN 1546-1696. PMC 5937131. PMID 29621222.
^ Johnson, Caroline H.; Ivanisevic, Julijana; Siuzdak, Gary (July 2016). "Metabolomics: beyond biomarkers and towards mechanisms". Nature Reviews Molecular Cell Biology. 17 (7): 451–459. doi:10.1038/nrm.2016.25. ISSN 1471-0080. PMC 5729912. PMID 26979502.
^ Rinschen, Markus M.; Ivanisevic, Julijana; Giera, Martin; Siuzdak, Gary (June 2019). "Identification of bioactive metabolites using activity metabolomics". Nature Reviews Molecular Cell Biology. 20 (6): 353–367. doi:10.1038/s41580-019-0108-4. ISSN 1471-0080. PMC 6613555. PMID 30814649.
^ Cite error: The named reference :5 was invoked but never defined (see the help page).
^ Yanes, Oscar; Clark, Julie; Wong, Diana M.; Patti, Gary J.; Sánchez-Ruiz, Antonio; Benton, H. Paul; Trauger, Sunia A.; Desponts, Caroline; Ding, Sheng; Siuzdak, Gary (June 2010). "Metabolic oxidation regulates embryonic stem cell differentiation". Nature Chemical Biology. 6 (6): 411–417. doi:10.1038/nchembio.364. ISSN 1552-4469. PMC 2873061. PMID 20436487.
^ Lerner, R. A.; Siuzdak, G.; Prospero-Garcia, O.; Henriksen, S. J.; Boger, D. L.; Cravatt, B. F. (1994-09-27). "Cerebrodiene: a brain lipid isolated from sleep-deprived cats". Proceedings of the National Academy of Sciences. 91 (20): 9505–9508. Bibcode:1994PNAS...91.9505L. doi:10.1073/pnas.91.20.9505. ISSN 0027-8424. PMC 44841. PMID 7937797.
^ Montenegro-Burke, J. Rafael; Kok, Bernard P.; Guijas, Carlos; Domingo-Almenara, Xavier; Moon, Clara; Galmozzi, Andrea; Kitamura, Seiya; Eckmann, Lars; Saez, Enrique; Siuzdak, Gary E.; Wolan, Dennis W. (2021-09-28). "Metabolomics activity screening of T cell–induced colitis reveals anti-inflammatory metabolites". Science Signaling. 14 (702): eabf6584. doi:10.1126/scisignal.abf6584. PMC 8757460. PMID 34582249.
^ Rinschen, Markus M.; Ivanisevic, Julijana; Giera, Martin; Siuzdak, Gary (June 2019). "Identification of bioactive metabolites using activity metabolomics". Nature Reviews Molecular Cell Biology. 20 (6): 353–367. doi:10.1038/s41580-019-0108-4. ISSN 1471-0080. PMC 6613555. PMID 30814649.
^ ^a ^b Smith, Colin A.; Want, Elizabeth J.; O'Maille, Grace; Abagyan, Ruben; Siuzdak, Gary (2006-02-01). "XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification". Analytical Chemistry. 78 (3): 779–787. doi:10.1021/ac051437y. ISSN 0003-2700. PMID 16448051.
^ Cite error: The named reference :3 was invoked but never defined (see the help page).
^ ^a ^b Cite error: The named reference :2 was invoked but never defined (see the help page).
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^ ^a ^b Xue, Jingchuan; Guijas, Carlos; Benton, H. Paul; Warth, Benedikt; Siuzdak, Gary (2020-08-24). "METLIN MS 2 molecular standards database: a broad chemical and biological resource". Nature Methods. 17 (10): 953–954. doi:10.1038/s41592-020-0942-5. ISSN 1548-7105. PMC 8802982. PMID 32839599.
^ Giera, Martin; Yanes, Oscar; Siuzdak, Gary (2022-01-04). "Metabolite discovery: Biochemistry's scientific driver". Cell Metabolism. 34 (1): 21–34. doi:10.1016/j.cmet.2021.11.005. ISSN 1550-4131. PMC 10131248. PMID 34986335. S2CID 245729571.
^ Cite error: The named reference :15 was invoked but never defined (see the help page).
^ ^a ^b "Faculty Page, Gary Siuzdak". scripps.edu. Retrieved 22 May 2019.
^ Cite error: The named reference :6 was invoked but never defined (see the help page).
^ Cite error: The named reference :7 was invoked but never defined (see the help page).
^ Bothner, Brian; Dong, X. Fan; Bibbs, Lisa; Johnson, John E.; Siuzdak, Gary (1998-01-09). "Evidence of Viral Capsid Dynamics Using Limited Proteolysis and Mass Spectrometry". Journal of Biological Chemistry. 273 (2): 673–676. doi:10.1074/jbc.273.2.673. ISSN 0021-9258. PMID 9422714.
^ Lewis, J. Kathleen; Bothner, Brian; Smith, Thomas J.; Siuzdak, Gary (1998-06-09). "Antiviral agent blocks breathing of the common cold virus". Proceedings of the National Academy of Sciences. 95 (12): 6774–6778. Bibcode:1998PNAS...95.6774L. doi:10.1073/pnas.95.12.6774. ISSN 0027-8424. PMC 22631. PMID 9618488.
^ Bothner, Brian; Schneemann, Anette; Marshall, Dawn; Reddy, Vijay; Johnson, John E.; Siuzdak, Gary (February 1999). "Crystallographically identical virus capsids display different properties in solution". Nature Structural Biology. 6 (2): 114–116. doi:10.1038/5799. ISSN 1545-9985. PMID 10048920. S2CID 1756648.
^ Cite error: The named reference :8 was invoked but never defined (see the help page).
^ Domingo-Almenara, Xavier; Siuzdak, Gary (2020), Li, Shuzhao (ed.), "Metabolomics Data Processing Using XCMS", Computational Methods and Data Analysis for Metabolomics, Methods in Molecular Biology, vol. 2104, New York, NY: Springer US, pp. 11–24, doi:10.1007/978-1-0716-0239-3_2, ISBN 978-1-0716-0239-3, PMID 31953810, S2CID 210709390, retrieved 2023-07-13
^ Aisporna, Aries; Benton, H. Paul; Galano, Jean Marie; Giera, Martin; Siuzdak, Gary (2021-04-04). "METLIN Neutral Loss Database Enhances Similarity Analysis": 2021.04.02.438066. doi:10.1101/2021.04.02.438066. S2CID 233175525. {{cite journal}}: Cite journal requires |journal= (help)
^ Cite error: The named reference :12 was invoked but never defined (see the help page).
^ Xue, Jingchuan; Derks, Rico J. E.; Webb, Bill; Billings, Elizabeth M.; Aisporna, Aries; Giera, Martin; Siuzdak, Gary (2021-08-10). "Single Quadrupole Multiple Fragment Ion Monitoring Quantitative Mass Spectrometry". Analytical Chemistry. 93 (31): 10879–10889. doi:10.1021/acs.analchem.1c01246. hdl:1887/3243130. ISSN 0003-2700. PMC 8762722. PMID 34313111.
^ Xue, Jingchuan; Derks, Rico J. E.; Hoang, Linh; Giera, Martin; Siuzdak, Gary (2021-10-11). "Proteomics with Enhanced In-Source Fragmentation/Annotation: Applying XCMS-EISA Informatics and Q-MRM High-Sensitivity Quantification". Journal of the American Society for Mass Spectrometry. 32 (11): 2644–2654. doi:10.1021/jasms.1c00188. ISSN 1044-0305. PMC 10245389. PMID 34633184. S2CID 238581609.
^ Majumder, Erica L.-W.; Billings, Elizabeth M.; Benton, H. Paul; Martin, Richard L.; Palermo, Amelia; Guijas, Carlos; Rinschen, Markus M.; Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Tagtow, Bradley A.; Plumb, Robert S. (2021-01-22). "Cognitive analysis of metabolomics data for systems biology". Nature Protocols. 16 (3): 1376–1418. doi:10.1038/s41596-020-00455-4. ISSN 1750-2799. OSTI 1774918. PMC 10357461. PMID 33483720. S2CID 231687415.
^ Siuzdak, Gary.; BelBruno, Joseph J. (May 1990). "Laser multiphoton dissociation/ionization of butylamines: competitive processes in radical cations". The Journal of Physical Chemistry. 94 (11): 4559–4565. doi:10.1021/j100374a038. ISSN 0022-3654.
^ Scandura, Mike (30 Dec 1987). "Weightlifting the right way good for Siuzdak". The Evening Times (Pawtucket, R.I.).
^ "Biochemist and metabolomics researcher take honorary roles at Umeå University". www.umu.se. Retrieved 2020-10-21.
^ "Interview with Dr. Gary Siuzdak". MetaboNews, Issue 13 - September 2012. Retrieved 22 May 2019.

[:9-1] Guijas, Carlos; Montenegro-Burke, J. Rafael; Warth, Benedikt; Spilker, Mary E.; Siuzdak, Gary (April 2018). "Metabolomics activity screening for identifying metabolites that modulate phenotype". Nature Biotechnology. 36 (4): 316–320. doi:10.1038/nbt.4101. ISSN 1546-1696. PMC 5937131. PMID 29621222.

[2] Johnson, Caroline H.; Ivanisevic, Julijana; Siuzdak, Gary (July 2016). "Metabolomics: beyond biomarkers and towards mechanisms". Nature Reviews Molecular Cell Biology. 17 (7): 451–459. doi:10.1038/nrm.2016.25. ISSN 1471-0080. PMC 5729912. PMID 26979502.

[:10-3] Rinschen, Markus M.; Ivanisevic, Julijana; Giera, Martin; Siuzdak, Gary (June 2019). "Identification of bioactive metabolites using activity metabolomics". Nature Reviews Molecular Cell Biology. 20 (6): 353–367. doi:10.1038/s41580-019-0108-4. ISSN 1471-0080. PMC 6613555. PMID 30814649.

[:5-4] Cite error: The named reference :5 was invoked but never defined (see the help page).

[:13-5] Yanes, Oscar; Clark, Julie; Wong, Diana M.; Patti, Gary J.; Sánchez-Ruiz, Antonio; Benton, H. Paul; Trauger, Sunia A.; Desponts, Caroline; Ding, Sheng; Siuzdak, Gary (June 2010). "Metabolic oxidation regulates embryonic stem cell differentiation". Nature Chemical Biology. 6 (6): 411–417. doi:10.1038/nchembio.364. ISSN 1552-4469. PMC 2873061. PMID 20436487.

[6] Lerner, R. A.; Siuzdak, G.; Prospero-Garcia, O.; Henriksen, S. J.; Boger, D. L.; Cravatt, B. F. (1994-09-27). "Cerebrodiene: a brain lipid isolated from sleep-deprived cats". Proceedings of the National Academy of Sciences. 91 (20): 9505–9508. Bibcode:1994PNAS...91.9505L. doi:10.1073/pnas.91.20.9505. ISSN 0027-8424. PMC 44841. PMID 7937797.

[7] Montenegro-Burke, J. Rafael; Kok, Bernard P.; Guijas, Carlos; Domingo-Almenara, Xavier; Moon, Clara; Galmozzi, Andrea; Kitamura, Seiya; Eckmann, Lars; Saez, Enrique; Siuzdak, Gary E.; Wolan, Dennis W. (2021-09-28). "Metabolomics activity screening of T cell–induced colitis reveals anti-inflammatory metabolites". Science Signaling. 14 (702): eabf6584. doi:10.1126/scisignal.abf6584. PMC 8757460. PMID 34582249.

[8] Rinschen, Markus M.; Ivanisevic, Julijana; Giera, Martin; Siuzdak, Gary (June 2019). "Identification of bioactive metabolites using activity metabolomics". Nature Reviews Molecular Cell Biology. 20 (6): 353–367. doi:10.1038/s41580-019-0108-4. ISSN 1471-0080. PMC 6613555. PMID 30814649.

[:0-9] Smith, Colin A.; Want, Elizabeth J.; O'Maille, Grace; Abagyan, Ruben; Siuzdak, Gary (2006-02-01). "XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification". Analytical Chemistry. 78 (3): 779–787. doi:10.1021/ac051437y. ISSN 0003-2700. PMID 16448051.

[:3-10] Cite error: The named reference :3 was invoked but never defined (see the help page).

[:2-11] Cite error: The named reference :2 was invoked but never defined (see the help page).

[:4-12] Cite error: The named reference :4 was invoked but never defined (see the help page).

[:1-13] Xue, Jingchuan; Guijas, Carlos; Benton, H. Paul; Warth, Benedikt; Siuzdak, Gary (2020-08-24). "METLIN MS 2 molecular standards database: a broad chemical and biological resource". Nature Methods. 17 (10): 953–954. doi:10.1038/s41592-020-0942-5. ISSN 1548-7105. PMC 8802982. PMID 32839599.

[:18-14] Giera, Martin; Yanes, Oscar; Siuzdak, Gary (2022-01-04). "Metabolite discovery: Biochemistry's scientific driver". Cell Metabolism. 34 (1): 21–34. doi:10.1016/j.cmet.2021.11.005. ISSN 1550-4131. PMC 10131248. PMID 34986335. S2CID 245729571.

[:15-15] Cite error: The named reference :15 was invoked but never defined (see the help page).

[scripps-16] "Faculty Page, Gary Siuzdak". scripps.edu. Retrieved 22 May 2019.

[:6-17] Cite error: The named reference :6 was invoked but never defined (see the help page).

[:7-18] Cite error: The named reference :7 was invoked but never defined (see the help page).

[19] Bothner, Brian; Dong, X. Fan; Bibbs, Lisa; Johnson, John E.; Siuzdak, Gary (1998-01-09). "Evidence of Viral Capsid Dynamics Using Limited Proteolysis and Mass Spectrometry". Journal of Biological Chemistry. 273 (2): 673–676. doi:10.1074/jbc.273.2.673. ISSN 0021-9258. PMID 9422714.

[20] Lewis, J. Kathleen; Bothner, Brian; Smith, Thomas J.; Siuzdak, Gary (1998-06-09). "Antiviral agent blocks breathing of the common cold virus". Proceedings of the National Academy of Sciences. 95 (12): 6774–6778. Bibcode:1998PNAS...95.6774L. doi:10.1073/pnas.95.12.6774. ISSN 0027-8424. PMC 22631. PMID 9618488.

[21] Bothner, Brian; Schneemann, Anette; Marshall, Dawn; Reddy, Vijay; Johnson, John E.; Siuzdak, Gary (February 1999). "Crystallographically identical virus capsids display different properties in solution". Nature Structural Biology. 6 (2): 114–116. doi:10.1038/5799. ISSN 1545-9985. PMID 10048920. S2CID 1756648.

[:8-22] Cite error: The named reference :8 was invoked but never defined (see the help page).

[23] Domingo-Almenara, Xavier; Siuzdak, Gary (2020), Li, Shuzhao (ed.), "Metabolomics Data Processing Using XCMS", Computational Methods and Data Analysis for Metabolomics, Methods in Molecular Biology, vol. 2104, New York, NY: Springer US, pp. 11–24, doi:10.1007/978-1-0716-0239-3_2, ISBN 978-1-0716-0239-3, PMID 31953810, S2CID 210709390, retrieved 2023-07-13

[24] Aisporna, Aries; Benton, H. Paul; Galano, Jean Marie; Giera, Martin; Siuzdak, Gary (2021-04-04). "METLIN Neutral Loss Database Enhances Similarity Analysis": 2021.04.02.438066. doi:10.1101/2021.04.02.438066. S2CID 233175525. {{cite journal}}: Cite journal requires |journal= (help)

[:12-25] Cite error: The named reference :12 was invoked but never defined (see the help page).

[doi.org-26] Xue, Jingchuan; Derks, Rico J. E.; Webb, Bill; Billings, Elizabeth M.; Aisporna, Aries; Giera, Martin; Siuzdak, Gary (2021-08-10). "Single Quadrupole Multiple Fragment Ion Monitoring Quantitative Mass Spectrometry". Analytical Chemistry. 93 (31): 10879–10889. doi:10.1021/acs.analchem.1c01246. hdl:1887/3243130. ISSN 0003-2700. PMC 8762722. PMID 34313111.

[27] Xue, Jingchuan; Derks, Rico J. E.; Hoang, Linh; Giera, Martin; Siuzdak, Gary (2021-10-11). "Proteomics with Enhanced In-Source Fragmentation/Annotation: Applying XCMS-EISA Informatics and Q-MRM High-Sensitivity Quantification". Journal of the American Society for Mass Spectrometry. 32 (11): 2644–2654. doi:10.1021/jasms.1c00188. ISSN 1044-0305. PMC 10245389. PMID 34633184. S2CID 238581609.

[28] Majumder, Erica L.-W.; Billings, Elizabeth M.; Benton, H. Paul; Martin, Richard L.; Palermo, Amelia; Guijas, Carlos; Rinschen, Markus M.; Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Tagtow, Bradley A.; Plumb, Robert S. (2021-01-22). "Cognitive analysis of metabolomics data for systems biology". Nature Protocols. 16 (3): 1376–1418. doi:10.1038/s41596-020-00455-4. ISSN 1750-2799. OSTI 1774918. PMC 10357461. PMID 33483720. S2CID 231687415.

[29] Siuzdak, Gary.; BelBruno, Joseph J. (May 1990). "Laser multiphoton dissociation/ionization of butylamines: competitive processes in radical cations". The Journal of Physical Chemistry. 94 (11): 4559–4565. doi:10.1021/j100374a038. ISSN 0022-3654.

[30] Scandura, Mike (30 Dec 1987). "Weightlifting the right way good for Siuzdak". The Evening Times (Pawtucket, R.I.).

[31] "Biochemist and metabolomics researcher take honorary roles at Umeå University". www.umu.se. Retrieved 2020-10-21.

[32] "Interview with Dr. Gary Siuzdak". MetaboNews, Issue 13 - September 2012. Retrieved 22 May 2019.

Gary Siuzdak information

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Gary Siuzdak

Scripps Research

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Richard Lerner

Gary Siuzdak

Born	December 29, 1961
Scientific career
Fields	Analytical Chemistry, Metabolomics