Metabolite discovery: Biochemistry’s scientific driver

Giera, Martin; Yanes, Oscar; Siuzdak, Gary

doi:10.1016/j.cmet.2021.11.005

Title: Metabolite discovery: Biochemistry’s scientific driver

Journal Article · 31 December 2021 · Cell Metabolism

DOI: https://doi.org/10.1016/j.cmet.2021.11.005 · OSTI ID:1908275

Giera, Martin; Yanes, Oscar; Siuzdak, Gary

Not Available

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1908275

Journal Information:: Cell Metabolism, Journal Name: Cell Metabolism Journal Issue: 1 Vol. 34; ISSN 1550-4131

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (132)

Ueber eine neue Art von Strahlen Röntgen, W. C. Annalen der Physik, Vol. 300, Issue 1 https://doi.org/10.1002/andp.18983000103	journal	January 1898
Neues Verfahren zur maßanalytischen Bestimmung des Wassergehaltes von Flüssigkeiten und festen Körpern Fischer, Karl Angewandte Chemie, Vol. 48, Issue 26 https://doi.org/10.1002/ange.19350482605	journal	June 1935
Zur Geschichte der Sterin- und Vitamin-Forschung. Adolf Windaus zum Gedächtnis Butenandt, A. Angewandte Chemie, Vol. 72, Issue 18 https://doi.org/10.1002/ange.19600721802	journal	September 1960
Liquid chromatography-mass spectrometry. II—continuous monitoring Arpino, Patrick; Baldwin, M. A.; McLafferty, F. W. Biological Mass Spectrometry, Vol. 1, Issue 1 https://doi.org/10.1002/bms.1200010117	journal	February 1974
Ueber ammon‐alkalische Silberlösung als Reagens auf Aldehyd Tollens, B. Berichte der deutschen chemischen Gesellschaft, Vol. 15, Issue 2 https://doi.org/10.1002/cber.18820150243	journal	July 1882
Alkoholische Gährung ohne Hefezellen Buchner, Eduard Berichte der deutschen chemischen Gesellschaft, Vol. 30, Issue 1 https://doi.org/10.1002/cber.18970300121	journal	January 1897
Ueber die Zuckersäure Thaulow, M. C. J. Annalen der Pharmacie, Vol. 27, Issue 2 https://doi.org/10.1002/jlac.18380270202	journal	January 1838
Special feature: Historical. Collision-induced dissociation: Readings and commentary Cooks, R. Graham Journal of Mass Spectrometry, Vol. 30, Issue 9 https://doi.org/10.1002/jms.1190300902	journal	September 1995
MassBank: a public repository for sharing mass spectral data for life sciences Horai, Hisayuki; Arita, Masanori; Kanaya, Shigehiko Journal of Mass Spectrometry, Vol. 45, Issue 7 https://doi.org/10.1002/jms.1777	journal	July 2010
Recent advances in liquid-phase separations for clinical metabolomics: Liquid Chromatography Kohler, Isabelle; Giera, Martin Journal of Separation Science, Vol. 40, Issue 1 https://doi.org/10.1002/jssc.201600981	journal	November 2016
NMR-Based Metabolomics Nagana Gowda, G. A.; Raftery, Daniel Advances in Experimental Medicine and Biology https://doi.org/10.1007/978-3-030-51652-9_2	book	January 2021
Beiträge zur Kenntniss des Cholesterins Reinitzer, Friedrich Monatshefte für Chemie - Chemical Monthly, Vol. 9, Issue 1 https://doi.org/10.1007/BF01516710	journal	December 1888
M. S. Tswett and the discovery of chromatography II: Completion of the development of chromatography (1903–1910) Ettre, L. S.; Sakodynskii, K. I. Chromatographia, Vol. 35, Issue 5-6 https://doi.org/10.1007/BF02277520	journal	March 1993
New software tools, databases, and resources in metabolomics: updates from 2020 Misra, Biswapriya B. Metabolomics, Vol. 17, Issue 5 https://doi.org/10.1007/s11306-021-01796-1	journal	May 2021
A Common Factor in the Enzymatic Acetylation of Sulfanilamide and of Choline Lipmann, Fritz; Kaplan, Nathan O. Journal of Biological Chemistry, Vol. 162, Issue 3 https://doi.org/10.1016/S0021-9258(17)41419-0	journal	March 1946
Deuterium as an Indicator in the Study of Intermediary Metabolism. i Schoenheimer, Rudolf; Rittenberg, D. Journal of Biological Chemistry, Vol. 111, Issue 1 https://doi.org/10.1016/S0021-9258(18)75075-8	journal	September 1935
Fritz Lipmann and the Discovery of Coenzyme A Kresge, Nicole; Simoni, Robert D.; Hill, Robert L. Journal of Biological Chemistry, Vol. 280, Issue 21 https://doi.org/10.1016/S0021-9258(20)64101-1	journal	May 2005
Otto Fritz Meyerhof and the Elucidation of the Glycolytic Pathway Kresge, Nicole; Simoni, Robert D.; Hill, Robert L. Journal of Biological Chemistry, Vol. 280, Issue 4 https://doi.org/10.1016/S0021-9258(20)76366-0	journal	January 2005
The Incidence of Alkaptonuria : a Study in Chemical Individuality. Garrod, ArchibaldE. The Lancet, Vol. 160, Issue 4137 https://doi.org/10.1016/S0140-6736(01)41972-6	journal	December 1902
Carl Djerassi Watts, Geoff The Lancet, Vol. 385, Issue 9968 https://doi.org/10.1016/S0140-6736(15)60225-2	journal	February 2015
Robinson, Woodward and the synthesis of cholesterol Mulheirn, Greg Endeavour, Vol. 24, Issue 3 https://doi.org/10.1016/S0160-9327(00)01310-7	journal	September 2000
Albert Szent-Györgyi and the unravelling of biological oxidation Manchester, Keith L. Trends in Biochemical Sciences, Vol. 23, Issue 1 https://doi.org/10.1016/S0968-0004(97)01167-5	journal	January 1998
Quantitative NMR analysis of intra- and extracellular metabolism of mammalian cells: A tutorial Kostidis, Sarantos; Addie, Ruben D.; Morreau, Hans Analytica Chimica Acta, Vol. 980 https://doi.org/10.1016/j.aca.2017.05.011	journal	August 2017
Regulated Accumulation of Desmosterol Integrates Macrophage Lipid Metabolism and Inflammatory Responses Spann, Nathanael J.; Garmire, Lana X.; McDonald, Jeffrey G. Cell, Vol. 151, Issue 1 https://doi.org/10.1016/j.cell.2012.06.054	journal	September 2012
A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics Donia, Mohamed S.; Cimermancic, Peter; Schulze, Christopher J. Cell, Vol. 158, Issue 6 https://doi.org/10.1016/j.cell.2014.08.032	journal	September 2014
Discovery of a Class of Endogenous Mammalian Lipids with Anti-Diabetic and Anti-inflammatory Effects Yore, Mark M.; Syed, Ismail; Moraes-Vieira, Pedro M. Cell, Vol. 159, Issue 2 https://doi.org/10.1016/j.cell.2014.09.035	journal	October 2014
Metabolomics and Isotope Tracing Jang, Cholsoon; Chen, Li; Rabinowitz, Joshua D. Cell, Vol. 173, Issue 4 https://doi.org/10.1016/j.cell.2018.03.055	journal	May 2018
Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application Scapin, Giovanna; Potter, Clinton S.; Carragher, Bridget Cell Chemical Biology, Vol. 25, Issue 11 https://doi.org/10.1016/j.chembiol.2018.07.006	journal	November 2018
Metabolite Exchange between Mammalian Organs Quantified in Pigs Jang, Cholsoon; Hui, Sheng; Zeng, Xianfeng Cell Metabolism, Vol. 30, Issue 3 https://doi.org/10.1016/j.cmet.2019.06.002	journal	September 2019
Quantitative Fluxomics of Circulating Metabolites Hui, Sheng; Cowan, Alexis J.; Zeng, Xianfeng Cell Metabolism, Vol. 32, Issue 4 https://doi.org/10.1016/j.cmet.2020.07.013	journal	October 2020
Advances in proteomic workflows for systems biology Malmström, Johan; Lee, Hookeun; Aebersold, Ruedi Current Opinion in Biotechnology, Vol. 18, Issue 4 https://doi.org/10.1016/j.copbio.2007.07.005	journal	August 2007
Proresolving Lipid Mediators and Mechanisms in the Resolution of Acute Inflammation Buckley, Christopher D.; Gilroy, Derek W.; Serhan, Charles N. Immunity, Vol. 40, Issue 3 https://doi.org/10.1016/j.immuni.2014.02.009	journal	March 2014
Dealing with the unknown: Metabolomics and Metabolite Atlases Bowen, Benjamin P.; Northen, Trent R. Journal of the American Society for Mass Spectrometry, Vol. 21, Issue 9 https://doi.org/10.1016/j.jasms.2010.04.003	journal	September 2010
OpenMS – A platform for reproducible analysis of mass spectrometry data Pfeuffer, Julianus; Sachsenberg, Timo; Alka, Oliver Journal of Biotechnology, Vol. 261 https://doi.org/10.1016/j.jbiotec.2017.05.016	journal	November 2017
Supercritical fluid chromatography – Mass spectrometry in metabolomics: Past, present, and future perspectives van de Velde, Bas; Guillarme, Davy; Kohler, Isabelle Journal of Chromatography B, Vol. 1161 https://doi.org/10.1016/j.jchromb.2020.122444	journal	December 2020
Can NMR solve some significant challenges in metabolomics? Nagana Gowda, G. A.; Raftery, Daniel Journal of Magnetic Resonance, Vol. 260 https://doi.org/10.1016/j.jmr.2015.07.014	journal	November 2015
Defining the Metabolome: Size, Flux, and Regulation Zamboni, Nicola; Saghatelian, Alan; Patti, Gary J. Molecular Cell, Vol. 58, Issue 4 https://doi.org/10.1016/j.molcel.2015.04.021	journal	May 2015
Role of plant alkaloids on human health: A review of biological activities Debnath, Bikash; Singh, Waikhom Somraj; Das, Manik Materials Today Chemistry, Vol. 9 https://doi.org/10.1016/j.mtchem.2018.05.001	journal	September 2018
Isoprostanes, neuroprostanes and phytoprostanes: An overview of 25 years of research in chemistry and biology Galano, Jean-Marie; Lee, Yiu Yiu; Oger, Camille Progress in Lipid Research, Vol. 68 https://doi.org/10.1016/j.plipres.2017.09.004	journal	October 2017
Analysis of biologically-active, endogenous carboxylic acids based on chromatography-mass spectrometry Kloos, D.; Lingeman, H.; Mayboroda, O. A. TrAC Trends in Analytical Chemistry, Vol. 61 https://doi.org/10.1016/j.trac.2014.05.008	journal	October 2014
Molecular fingerprint similarity search in virtual screening Cereto-Massagué, Adrià; Ojeda, María José; Valls, Cristina Methods, Vol. 71 https://doi.org/10.1016/j.ymeth.2014.08.005	journal	January 2015
XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification Smith, Colin A.; Want, Elizabeth J.; O'Maille, Grace Analytical Chemistry, Vol. 78, Issue 3 https://doi.org/10.1021/ac051437y	journal	February 2006
X ¹³ CMS: Global Tracking of Isotopic Labels in Untargeted Metabolomics Huang, Xiaojing; Chen, Ying-Jr; Cho, Kevin Analytical Chemistry, Vol. 86, Issue 3 https://doi.org/10.1021/ac403384n	journal	January 2014
Time-of-Flight Mass Spectrometry and Gas-Liquid Partition Chromatography Gohlke, R. S. Analytical Chemistry, Vol. 31, Issue 4 https://doi.org/10.1021/ac50164a024	journal	April 1959
isoMETLIN: A Database for Isotope-Based Metabolomics Cho, Kevin; Mahieu, Nathaniel; Ivanisevic, Julijana Analytical Chemistry, Vol. 86, Issue 19 https://doi.org/10.1021/ac5029177	journal	September 2014
Credentialing Features: A Platform to Benchmark and Optimize Untargeted Metabolomic Methods Mahieu, Nathaniel Guy; Huang, Xiaojing; Chen, Ying-Jr Analytical Chemistry, Vol. 86, Issue 19 https://doi.org/10.1021/ac503092d	journal	September 2014
Gas chromatography of volatiles from breath and urine Teranishi, Roy.; Mon, T. R.; Robinson, Arthur B. Analytical Chemistry, Vol. 44, Issue 1 https://doi.org/10.1021/ac60309a012	journal	January 1972
Ozone-Induced Dissociation: Elucidation of Double Bond Position within Mass-Selected Lipid Ions Thomas, Michael C.; Mitchell, Todd W.; Harman, David G. Analytical Chemistry, Vol. 80, Issue 1 https://doi.org/10.1021/ac7017684	journal	January 2008
FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry Kind, Tobias; Wohlgemuth, Gert; Lee, Do Yup Analytical Chemistry, Vol. 81, Issue 24 https://doi.org/10.1021/ac9019522	journal	December 2009
Effective Chiral Discrimination of Amino Acids through Oligosaccharide Incorporation by Trapped Ion Mobility Spectrometry Xie, Chengyi; Gu, Liancheng; Wu, Qidi Analytical Chemistry, Vol. 93, Issue 2 https://doi.org/10.1021/acs.analchem.0c03461	journal	November 2020
High-Throughput UHPLC/MS/MS-Based Metabolic Profiling Using a Vacuum Jacketed Column Plumb, Robert S.; McDonald, Thomas; Rainville, Paul D. Analytical Chemistry, Vol. 93, Issue 30 https://doi.org/10.1021/acs.analchem.1c01982	journal	July 2021
Differential Mobility Separation of Leukotrienes and Protectins Jónasdóttir, Hulda S.; Papan, Cyrus; Fabritz, Sebastian Analytical Chemistry, Vol. 87, Issue 10 https://doi.org/10.1021/acs.analchem.5b00786	journal	April 2015
Accelerated Isotope Fine Structure Calculation Using Pruned Transition Trees Loos, Martin; Gerber, Christian; Corona, Francesco Analytical Chemistry, Vol. 87, Issue 11 https://doi.org/10.1021/acs.analchem.5b00941	journal	May 2015
geoRge: A Computational Tool To Detect the Presence of Stable Isotope Labeling in LC/MS-Based Untargeted Metabolomics Capellades, Jordi; Navarro, Miriam; Samino, Sara Analytical Chemistry, Vol. 88, Issue 1 https://doi.org/10.1021/acs.analchem.5b03628	journal	December 2015
eRah: A Computational Tool Integrating Spectral Deconvolution and Alignment with Quantification and Identification of Metabolites in GC/MS-Based Metabolomics Domingo-Almenara, Xavier; Brezmes, Jesus; Vinaixa, Maria Analytical Chemistry, Vol. 88, Issue 19 https://doi.org/10.1021/acs.analchem.6b02927	journal	September 2016
iMet: A Network-Based Computational Tool To Assist in the Annotation of Metabolites from Tandem Mass Spectra Aguilar-Mogas, Antoni; Sales-Pardo, Marta; Navarro, Miriam Analytical Chemistry, Vol. 89, Issue 6 https://doi.org/10.1021/acs.analchem.6b04512	journal	March 2017
Exposome-Scale Investigations Guided by Global Metabolomics, Pathway Analysis, and Cognitive Computing Warth, Benedikt; Spangler, Scott; Fang, Mingliang Analytical Chemistry, Vol. 89, Issue 21 https://doi.org/10.1021/acs.analchem.7b02759	journal	October 2017
METLIN: A Technology Platform for Identifying Knowns and Unknowns Guijas, Carlos; Montenegro-Burke, J. Rafael; Domingo-Almenara, Xavier Analytical Chemistry, Vol. 90, Issue 5 https://doi.org/10.1021/acs.analchem.7b04424	journal	January 2018
ADAP-GC 4.0: Application of Clustering-Assisted Multivariate Curve Resolution to Spectral Deconvolution of Gas Chromatography–Mass Spectrometry Metabolomics Data Smirnov, Aleksandr; Qiu, Yunping; Jia, Wei Analytical Chemistry, Vol. 91, Issue 14 https://doi.org/10.1021/acs.analchem.9b01424	journal	June 2019
Low Volume in Vitro Diagnostic Proton NMR Spectroscopy of Human Blood Plasma for Lipoprotein and Metabolite Analysis: Application to SARS-CoV-2 Biomarkers Lodge, Samantha; Nitschke, Philipp; Loo, Ruey Leng Journal of Proteome Research, Vol. 20, Issue 2 https://doi.org/10.1021/acs.jproteome.0c00815	journal	January 2021
The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination Jones, Christopher G.; Martynowycz, Michael W.; Hattne, Johan ACS Central Science, Vol. 4, Issue 11 https://doi.org/10.1021/acscentsci.8b00760	journal	November 2018
Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation Kurczy, Michael E.; Forsberg, Erica M.; Thorgersen, Michael P. ACS Chemical Biology, Vol. 11, Issue 6 https://doi.org/10.1021/acschembio.6b00082	journal	April 2016
Model Colibactins Exhibit Human Cell Genotoxicity in the Absence of Host Bacteria Shine, Emilee E.; Xue, Mengzhao; Patel, Jaymin R. ACS Chemical Biology, Vol. 13, Issue 12 https://doi.org/10.1021/acschembio.8b00714	journal	November 2018
Metastable ion characteristics. VII. Collision-induced metastables Haddon, W. F.; McLafferty, F. W. Journal of the American Chemical Society, Vol. 90, Issue 17 https://doi.org/10.1021/ja01019a053	journal	August 1968
The Total Synthesis of Cholesterol Woodward, R. B.; Sondheimer, Franz; Taub, David Journal of the American Chemical Society, Vol. 73, Issue 7 https://doi.org/10.1021/ja01151a556	journal	July 1951
Lipid Metabolite Profiling Identifies Desmosterol Metabolism as a New Antiviral Target for Hepatitis C Virus Rodgers, Mary A.; Villareal, Valerie A.; Schaefer, Esperance A. Journal of the American Chemical Society, Vol. 134, Issue 16 https://doi.org/10.1021/ja207391q	journal	April 2012
Comparative Metabolomics and Structural Characterizations Illuminate Colibactin Pathway-Dependent Small Molecules Vizcaino, Maria I.; Engel, Philipp; Trautman, Eric Journal of the American Chemical Society, Vol. 136, Issue 26 https://doi.org/10.1021/ja503450q	journal	June 2014
Identification of a New Endogenous Metabolite and the Characterization of Its Protein Interactions through an Immobilization Approach Kalisiak, Jarosław; Trauger, Sunia A.; Kalisiak, Ewa Journal of the American Chemical Society, Vol. 131, Issue 1 https://doi.org/10.1021/ja808172n	journal	December 2008
Dissociation of Biomolecules by an Intense Low-Energy Electron Beam in a High Sensitivity Time-of-Flight Mass Spectrometer Baba, Takashi; Ryumin, Pavel; Duchoslav, Eva Journal of the American Society for Mass Spectrometry, Vol. 32, Issue 8 https://doi.org/10.1021/jasms.0c00425	journal	June 2021
Radioactive Indicators in the Study of Phosphorus Metabolism in Rats Chiewitz, O.; Hevesy, G. Nature, Vol. 136, Issue 3445 https://doi.org/10.1038/136754a0	journal	November 1935
A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis Kendrew, J. C.; Bodo, G.; Dintzis, H. M. Nature, Vol. 181, Issue 4610, p. 662-666 https://doi.org/10.1038/181662a0	journal	March 1958
Observation of tissue metabolites using 31P nuclear magnetic resonance Hoult, D. I.; Busby, S. J. W.; Gadian, D. G. Nature, Vol. 252, Issue 5481 https://doi.org/10.1038/252285a0	journal	November 1974
A new antibiotic kills pathogens without detectable resistance Ling, Losee L.; Schneider, Tanja; Peoples, Aaron J. Nature, Vol. 517, Issue 7535 https://doi.org/10.1038/nature14098	journal	January 2015
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking Wang, Mingxun; Carver, Jeremy J.; Phelan, Vanessa V. Nature Biotechnology, Vol. 34, Issue 8 https://doi.org/10.1038/nbt.3597	journal	August 2016
The colibactin warhead crosslinks DNA Vizcaino, Maria I.; Crawford, Jason M. Nature Chemistry, Vol. 7, Issue 5 https://doi.org/10.1038/nchem.2221	journal	April 2015
An atlas of genetic influences on human blood metabolites Shin, So-Youn; Fauman, Eric B.; Petersen, Ann-Kristin Nature Genetics, Vol. 46, Issue 6 https://doi.org/10.1038/ng.2982	journal	May 2014
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis Tsugawa, Hiroshi; Cajka, Tomas; Kind, Tobias Nature Methods, Vol. 12, Issue 6 https://doi.org/10.1038/nmeth.3393	journal	May 2015
OpenMS: a flexible open-source software platform for mass spectrometry data analysis Röst, Hannes L.; Sachsenberg, Timo; Aiche, Stephan Nature Methods, Vol. 13, Issue 9 https://doi.org/10.1038/nmeth.3959	journal	August 2016
Deciphering lipid structures based on platform-independent decision rules Hartler, Jürgen; Triebl, Alexander; Ziegl, Andreas Nature Methods, Vol. 14, Issue 12 https://doi.org/10.1038/nmeth.4470	journal	October 2017
Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics Lai, Zijuan; Tsugawa, Hiroshi; Wohlgemuth, Gert Nature Methods, Vol. 15, Issue 1 https://doi.org/10.1038/nmeth.4512	journal	November 2017
Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts Beckonert, Olaf; Keun, Hector C.; Ebbels, Timothy M. D. Nature Protocols, Vol. 2, Issue 11 https://doi.org/10.1038/nprot.2007.376	journal	October 2007
Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online Forsberg, Erica M.; Huan, Tao; Rinehart, Duane Nature Protocols, Vol. 13, Issue 4 https://doi.org/10.1038/nprot.2017.151	journal	March 2018
Emerging applications of metabolomics in drug discovery and precision medicine Wishart, David S. Nature Reviews Drug Discovery, Vol. 15, Issue 7 https://doi.org/10.1038/nrd.2016.32	journal	March 2016
The mysteries of macrocyclic colibactins Carlson, Erik S.; Balskus, Emily P. Nature Chemistry, Vol. 11, Issue 10 https://doi.org/10.1038/s41557-019-0339-1	journal	September 2019
Macrocyclic colibactins Herzon, Seth B. Nature Chemistry, Vol. 12, Issue 11 https://doi.org/10.1038/s41557-020-00551-8	journal	September 2020
Identification of bioactive metabolites using activity metabolomics Rinschen, Markus M.; Ivanisevic, Julijana; Giera, Martin Nature Reviews Molecular Cell Biology, Vol. 20, Issue 6 https://doi.org/10.1038/s41580-019-0108-4	journal	February 2019
A metabolomics pipeline for the mechanistic interrogation of the gut microbiome Han, Shuo; Van Treuren, Will; Fischer, Curt R. Nature, Vol. 595, Issue 7867 https://doi.org/10.1038/s41586-021-03707-9	journal	July 2021
A lipidome atlas in MS-DIAL 4 Tsugawa, Hiroshi; Ikeda, Kazutaka; Takahashi, Mikiko Nature Biotechnology, Vol. 38, Issue 10 https://doi.org/10.1038/s41587-020-0531-2	journal	June 2020
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra Dührkop, Kai; Nothias, Louis-Félix; Fleischauer, Markus Nature Biotechnology, Vol. 39, Issue 4 https://doi.org/10.1038/s41587-020-0740-8	journal	November 2020
Suppression of antitumor T cell immunity by the oncometabolite (R)-2-hydroxyglutarate Bunse, Lukas; Pusch, Stefan; Bunse, Theresa Nature Medicine, Vol. 24, Issue 8 https://doi.org/10.1038/s41591-018-0095-6	journal	July 2018
METLIN MS2 molecular standards database: a broad chemical and biological resource Xue, Jingchuan; Guijas, Carlos; Benton, H. Paul Nature Methods, Vol. 17, Issue 10 https://doi.org/10.1038/s41592-020-0942-5	journal	August 2020
Cognitive analysis of metabolomics data for systems biology Majumder, Erica L. -W.; Billings, Elizabeth M.; Benton, H. Paul Nature Protocols, Vol. 16, Issue 3 https://doi.org/10.1038/s41596-020-00455-4	journal	January 2021
Reproducible molecular networking of untargeted mass spectrometry data using GNPS Aron, Allegra T.; Gentry, Emily C.; McPhail, Kerry L. Nature Protocols, Vol. 15, Issue 6 https://doi.org/10.1038/s41596-020-0317-5	journal	May 2020
Linking in silico MS/MS spectra with chemistry data to improve identification of unknowns McEachran, Andrew D.; Balabin, Ilya; Cathey, Tommy Scientific Data, Vol. 6, Issue 1 https://doi.org/10.1038/s41597-019-0145-z	journal	August 2019
Scientific workflow managers in metabolomics: an overview Verhoeven, Aswin; Giera, Martin; Mayboroda, Oleg A. The Analyst, Vol. 145, Issue 11 https://doi.org/10.1039/D0AN00272K	journal	January 2020
The citric acid cycle and the Szent-Györgyi cycle in pigeon breast muscle Krebs, Hans Adolf Biochemical Journal, Vol. 34, Issue 5 https://doi.org/10.1042/bj0340775	journal	May 1940
A new form of chromatogram employing two liquid phases Martin, A. J. P.; Synge, R. L. M. Biochemical Journal, Vol. 35, Issue 12 https://doi.org/10.1042/bj0351358	journal	December 1941
A gas-liquid-chromatographic procedure for separating a wide range of metabolites occurring in urine or tissue extracts Dalgliesh, Ce; Horning, Ec; Horning, Mg Biochemical Journal, Vol. 101, Issue 3 https://doi.org/10.1042/bj1010792	journal	December 1966
Searching molecular structure databases with tandem mass spectra using CSI:FingerID Dührkop, Kai; Shen, Huibin; Meusel, Marvin Proceedings of the National Academy of Sciences, Vol. 112, Issue 41 https://doi.org/10.1073/pnas.1509788112	journal	September 2015
Topic modeling for untargeted substructure exploration in metabolomics van der Hooft, Justin Johan Jozias; Wandy, Joe; Barrett, Michael P. Proceedings of the National Academy of Sciences, Vol. 113, Issue 48 https://doi.org/10.1073/pnas.1608041113	journal	November 2016
Schema learning for the cocktail party problem Woods, Kevin J. P.; McDermott, Josh H. Proceedings of the National Academy of Sciences, Vol. 115, Issue 14 https://doi.org/10.1073/pnas.1801614115	journal	March 2018
Genetic Control of Biochemical Reactions in Neurospora Beadle, G. W.; Tatum, E. L. Proceedings of the National Academy of Sciences, Vol. 27, Issue 11 https://doi.org/10.1073/pnas.27.11.499	journal	November 1941
Cerebrodiene: a brain lipid isolated from sleep-deprived cats. Lerner, R. A.; Siuzdak, G.; Prospero-Garcia, O. Proceedings of the National Academy of Sciences, Vol. 91, Issue 20 https://doi.org/10.1073/pnas.91.20.9505	journal	September 1994
Biochemistry during the Life and Times of Hans Krebs and Fritz Lipmann Buchanan, John M. Journal of Biological Chemistry, Vol. 277, Issue 37 https://doi.org/10.1074/jbc.R200019200	journal	September 2002
Contributions to the knowledge of cholesterol Reinitzer, Friedrich Liquid Crystals, Vol. 5, Issue 1 https://doi.org/10.1080/02678298908026349	journal	July 1989
Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches Nguyen, Dai Hai; Nguyen, Canh Hao; Mamitsuka, Hiroshi Briefings in Bioinformatics, Vol. 20, Issue 6 https://doi.org/10.1093/bib/bby066	journal	August 2018
GMD@CSB.DB: the Golm Metabolome Database Kopka, J.; Schauer, N.; Krueger, S. Bioinformatics, Vol. 21, Issue 8 https://doi.org/10.1093/bioinformatics/bti236	journal	December 2004
Quantitative metabolic profiling based on gas chromatography. Gates, S. C.; Sweeley, C. C. Clinical Chemistry, Vol. 24, Issue 10 https://doi.org/10.1093/clinchem/24.10.1663	journal	October 1978
LMSD: LIPID MAPS structure database Sud, M.; Fahy, E.; Cotter, D. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl838	journal	January 2007
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models King, Zachary A.; Lu, Justin; Dräger, Andreas Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1049	journal	October 2015
HMDB 4.0: the human metabolome database for 2018 Wishart, David S.; Feunang, Yannick Djoumbou; Marcu, Ana Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1089	journal	November 2017
METLIN: A Metabolite Mass Spectral Database Smith, Colin A.; Maille, Grace O??; Want, Elizabeth J. Therapeutic Drug Monitoring, Vol. 27, Issue 6 https://doi.org/10.1097/01.ftd.0000179845.53213.39	journal	January 2005
A New Method of Measuring Nuclear Magnetic Moment Rabi, I. I.; Zacharias, J. R.; Millman, S. Physical Review, Vol. 53, Issue 4 https://doi.org/10.1103/PhysRev.53.318	journal	February 1938
Resonance Absorption by Nuclear Magnetic Moments in a Solid Purcell, E. M.; Torrey, H. C.; Pound, R. V. Physical Review, Vol. 69, Issue 1-2, p. 37-38 https://doi.org/10.1103/PhysRev.69.37	journal	January 1946
Host-Gut Microbiota Metabolic Interactions Nicholson, J. K.; Holmes, E.; Kinross, J. Science, Vol. 336, Issue 6086 https://doi.org/10.1126/science.1223813	journal	June 2012
Antimetabolites: They help in discovery of metabolic pathways and in the understanding and treatment of some diseases Woolley, D. W. Science, Vol. 129, Issue 3349 https://doi.org/10.1126/science.129.3349.615	journal	March 1959
Electrospray ionization for mass spectrometry of large biomolecules Fenn, J.; Mann, M.; Meng, C. Science, Vol. 246, Issue 4926, p. 64-71 https://doi.org/10.1126/science.2675315	journal	October 1989
Chemical characterization of a family of brain lipids that induce sleep Cravatt, B.; Prospero-Garcia, O.; Siuzdak, G. Science, Vol. 268, Issue 5216 https://doi.org/10.1126/science.7770779	journal	June 1995
Inhibition of the prostaglandin-degrading enzyme 15-PGDH potentiates tissue regeneration Zhang, Yongyou; Desai, Amar; Yang, Sung Yeun Science, Vol. 348, Issue 6240 https://doi.org/10.1126/science.aaa2340	journal	June 2015
The human gut bacterial genotoxin colibactin alkylates DNA Wilson, Matthew R.; Jiang, Yindi; Villalta, Peter W. Science, Vol. 363, Issue 6428 https://doi.org/10.1126/science.aar7785	journal	February 2019
Structure elucidation of colibactin and its DNA cross-links Xue, Mengzhao; Kim, Chung Sub; Healy, Alan R. Science, Vol. 365, Issue 6457 https://doi.org/10.1126/science.aax2685	journal	August 2019
Prostaglandins Bergstrom, S.; Samuelsson, B. Annual Review of Biochemistry, Vol. 34, Issue 1 https://doi.org/10.1146/annurev.bi.34.070165.000533	journal	June 1965
Oncometabolites: linking altered metabolism with cancer Yang, Ming; Soga, Tomoyoshi; Pollard, Patrick J. Journal of Clinical Investigation, Vol. 123, Issue 9 https://doi.org/10.1172/JCI67228	journal	September 2013
MetaboLab - advanced NMR data processing and analysis for metabolomics Ludwig, Christian; Günther, Ulrich L. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-366	journal	September 2011
The role of reporting standards for metabolite annotation and identification in metabolomic studies Salek, Reza M.; Steinbeck, Christoph; Viant, Mark R. GigaScience, Vol. 2, Issue 1 https://doi.org/10.1186/2047-217X-2-13	journal	October 2013
Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data Loos, Martin; Singer, Heinz Journal of Cheminformatics, Vol. 9, Issue 1 https://doi.org/10.1186/s13321-017-0197-z	journal	February 2017
Quantitative structural multiclass lipidomics using differential mobility: electron impact excitation of ions from organics (EIEIO) mass spectrometry Baba, Takashi; Campbell, J. Larry; Le Blanc, J. C. Yves Journal of Lipid Research, Vol. 59, Issue 5 https://doi.org/10.1194/jlr.D083261	journal	January 2018
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships Huber, Florian; Ridder, Lars; Verhoeven, Stefan PLOS Computational Biology, Vol. 17, Issue 2 https://doi.org/10.1371/journal.pcbi.1008724	journal	February 2021
Über die Konstitution des Cholesterins und der Gallensäuren. Windaus, A. Hoppe-Seyler´s Zeitschrift für physiologische Chemie, Vol. 213, Issue 3-4 https://doi.org/10.1515/bchm2.1932.213.3-4.147	journal	January 1932
A historical perspective on the discovery of statins Endo, Akira Proceedings of the Japan Academy, Series B, Vol. 86, Issue 5 https://doi.org/10.2183/pjab.86.484	journal	January 2010
Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas Frainay, Clément; Schymanski, Emma; Neumann, Steffen Metabolites, Vol. 8, Issue 3 https://doi.org/10.3390/metabo8030051	journal	September 2018
NMR Spectroscopy for Metabolomics Research Emwas, Abdul-Hamid; Roy, Raja; McKay, Ryan T. Metabolites, Vol. 9, Issue 7 https://doi.org/10.3390/metabo9070123	journal	June 2019

Similar Records

Quantum Computer Systems for Scientific Discovery

Journal Article · 2021 · PRX Quantum · OSTI ID:1767313

Alexeev, Yuri; Bacon, Dave; Brown, Kenneth R.; +21 more

A Global Hydrologic Framework to Accelerate Scientific Discovery

Journal Article · 2018 · Journal of Open Research Software · OSTI ID:1489899

Vernon, Chris R.; Hejazi, Mohamad I.; Turner, Sean W. D.; +4 more

An update on oxysterol biochemistry: New discoveries in lipidomics

Journal Article · 2018 · Biochemical and Biophysical Research Communications · OSTI ID:23134193

Wang, Yuqin

Title: Metabolite discovery: Biochemistry’s scientific driver

Citation Formats

References (132)

Similar Records

Related Subjects