Metabolomics: A Primer

A SIMPLE METHOD FOR THE ISOLATION AND PURIFICATION OF TOTAL LIPIDES FROM ANIMAL TISSUES

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Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

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Cytoscape: A software Environment for integrated models of biomolecular interaction networks

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Comprehensive genomic characterization defines human glioblastoma genes and core pathways

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Regulation of cancer cell metabolism

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Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

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DrugBank: a comprehensive resource for in silico drug discovery and exploration

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MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

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A branched-chain amino acid-related metabolic signature that differentiates obese and lean humans and contributes to insulin resistance

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Metabolite profiles and the risk of developing diabetes

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Data, information, knowledge and principle: back to metabolism in KEGG

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Personalized nutrition by prediction of glycemic responses

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HMDB 3.0—The Human Metabolome Database in 2013

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Metabolomics: beyond biomarkers and towards mechanisms

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Metabolomics: the apogee of the omics trilogy

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MassBank: a public repository for sharing mass spectral data for life sciences

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METLIN—a metabolite mass spectral database

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Gas chromatography mass spectrometry–based metabolite profiling in plants

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Organoid models of human and mouse ductal pancreatic cancer

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Network Integration of Parallel Metabolic and Transcriptional Data Reveals Metabolic Modules that Regulate Macrophage Polarization

Jha, A. K., Huang, S. C.-C., Sergushichev, A., Lampropoulou, V., Ivanova, Y., Loginicheva, E., Chmielewski, K., Stewart, K. M., Ashall, J., Everts, B., et al. (2015) · Immunity · doi:10.1016/j.immuni.2015.02.005 · Cited by 2,066 · see citing works

IDH mutation impairs histone demethylation and results in a block to cell differentiation

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Variations in the Prevalence of Obesity Among European Countries, and a Consideration of Possible Causes

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Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia

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Update of the LIPID MAPS comprehensive classification system for lipids

Fahy, E., Subramaniam, S., Murphy, R. C., Nishijima, M., Raetz, C. R. H., Shimizu, T., Spener, F., Gerrit van, M. E. E. R., Wakelam, M. J. O., & Dennis, E. A. (2008) · Journal of Lipid Research · doi:10.1194/jlr.r800095-jlr200 · Cited by 1,766 · see citing works

The Human Serum Metabolome

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Ion Suppression in Mass Spectrometry

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An atlas of genetic influences on human blood metabolites

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Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap

Olsen, J. V., de Godoy, L. M. F., Li, G., Maček, B., Mortensen, P., Pesch, R., Makarov, A., Lange, O., Horning, S. R., & Mann, M. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t500030-mcp200 · Cited by 1,513 · see citing works

Emerging applications of metabolomics in drug discovery and precision medicine

Wishart, D. S. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.32 · Cited by 1,499 · see citing works

Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation

Jain, M., Nilsson, R., Sharma, S., Madhusudhan, N., Kitami, T., Souza, A. L., Kafri, R., Kirschner, M. W., Clish, C. B., & Mootha, V. K. (2012) · Science · doi:10.1126/science.1218595 · Cited by 1,403 · see citing works

Reductive carboxylation supports growth in tumour cells with defective mitochondria

Mullen, A. R., Wheaton, W. W., Jin, E. S., Chen, P.-H., Sullivan, L. B., Cheng, T., Yang, Y., Linehan, W. M., Chandel, N. S., & DeBerardinis, R. J. (2012) · Nature · doi:10.1038/nature10642 · Cited by 1,328 · see citing works

Metabolic heterogeneity in human lung tumors

Hensley, C. T., Faubert, B., Yuan, Q., Lev-Cohain, N., Jin, E., Kim, J., Jiang, L., Ko, B., Skelton, R., Loudat, L., et al. (2016) · Cell · doi:10.1016/j.cell.2015.12.034 · Cited by 1,138 · see citing works

A positive/negative ion–switching, targeted mass spectrometry–based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue

Yuan, M., Breitkopf, S. B., Yang, X., & Asara, J. M. (2012) · Nature Protocols · doi:10.1038/nprot.2012.024 · Cited by 1,122 · see citing works

Quantitative flux analysis reveals folate-dependent NADPH production

Fan, J., Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., & Rabinowitz, J. D. (2014) · Nature · doi:10.1038/nature13236 · Cited by 1,114 · see citing works

Human metabolic individuality in biomedical and pharmaceutical research

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Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

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Quantitative Metabolome Profiling of Colon and Stomach Cancer Microenvironment by Capillary Electrophoresis Time-of-Flight Mass Spectrometry

Hirayama, A., Kami, K., Sugimoto, M., Sugawara, M., Toki, N., Onozuka, H., Kinoshitá, T., Saito, N., Ochiai, A., Tomita, M., et al. (2009) · Cancer Research · doi:10.1158/0008-5472.can-08-4806 · Cited by 959 · see citing works

Vitamin C selectively kills <i>KRAS</i> and <i>BRAF</i> mutant colorectal cancer cells by targeting GAPDH

Yun, J., Mullarky, E., Lu, C., Bosch, K. N., Kavalier, A., Rivera, K., Roper, J., Chio, I. I. C., Giannopoulou, E. G., Rago, C., et al. (2015) · Science · doi:10.1126/science.aaa5004 · Cited by 913 · see citing works

Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy

Dunn, W. B., Broadhurst, D., Atherton, H. J., Goodacre, R., & Griffin, J. L. (2010) · Chemical Society Reviews · doi:10.1039/b906712b · Cited by 870 · see citing works

Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics

Čajka, T., & Fiehn, O. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04491 · Cited by 839 · see citing works

Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer

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Acetyl-CoA synthetase 2 promotes acetate utilization and maintains cancer cell growth under metabolic stress

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Acetate is a bioenergetic substrate for human glioblastoma and brain metastases

Mashimo, T., Pichumani, K., Vemireddy, V., Hatanpaa, K. J., Singh, D. K., Sirasanagandla, S., Nannepaga, S., Piccirillo, S. G., Kovacs, Z., Foong, C., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.025 · Cited by 760 · see citing works

Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism

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Acetate dependence of tumors

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Metabolomics: A Global Biochemical Approach to Drug Response and Disease

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Single-Cell Metabolomics: Analytical and Biological Perspectives

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Elevation of circulating branched-chain amino acids is an early event in human pancreatic adenocarcinoma development

Mayers, J. R., Wu, C. H., Clish, C. B., Kraft, P., Torrence, M. E., Fiske, B. P., Yuan, C., Bao, Y., Townsend, M. K., Tworoger, S. S., et al. (2014) · Nature Medicine · doi:10.1038/nm.3686 · Cited by 652 · see citing works

Network-based prediction of human tissue-specific metabolism

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A roadmap for interpreting 13C metabolite labeling patterns from cells

Buescher, J. M., Antoniewicz, M. R., Boros, L. G., Burgess, S. C., Brunengraber, H., Clish, C. B., DeBerardinis, R. J., Féron, O., Frezza, C., Ghesquière, B., et al. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2015.02.003 · Cited by 623 · see citing works

A branched-chain amino acid metabolite drives vascular fatty acid transport and causes insulin resistance

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Solvent-Dependent Metabolite Distribution, Clustering, and Protein Extraction for Serum Profiling with Mass Spectrometry

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Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells

Lewis, C. A., Parker, S. J., Fiske, B. P., McCloskey, D., Gui, D. Y., Green, C. R., Vokes, N. I., Feist, A. M., Vander Heiden, M. G., & Metallo, C. M. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.008 · Cited by 562 · see citing works

Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights

Wen, W., Li, D., Li, X., Gao, Y., Li, W., Li, H., Liu, J., Liu, H., Chen, W., Luo, J., et al. (2014) · Nature Communications · doi:10.1038/ncomms4438 · Cited by 512 · see citing works

Metabolomic Analysis via Reversed-Phase Ion-Pairing Liquid Chromatography Coupled to a Stand Alone Orbitrap Mass Spectrometer

Lu, W., Clasquin, M. F., Melamud, E., Amador‐Noguez, D., Caudy, A. A., & Rabinowitz, J. D. (2010) · Analytical Chemistry · doi:10.1021/ac902837x · Cited by 504 · see citing works

A roadmap for natural product discovery based on large-scale genomics and metabolomics

Doroghazi, J. R., Albright, J. C., Goering, A. W., Ju, K., Haines, R. R., Tchalukov, K., Labeda, D. P., Kelleher, N. L., & Metcalf, W. W. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1659 · Cited by 479 · see citing works

Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database

Zhu, Z., Schultz, A. W., Wang, J., Johnson, C. H., Yannone, S. M., Patti, G. J., & Siuzdak, G. E. (2013) · Nature Protocols · doi:10.1038/nprot.2013.004 · Cited by 477 · see citing works

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

Park, J. O., Rubin, S. A., Xu, Y.-F., Amador-Noguez, D., Fan, J., Shlomi, T., & Rabinowitz, J. D. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2077 · Cited by 453 · see citing works

Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements

Antoniewicz, M. R., Kelleher, J. K., & Stephanopoulos, G. N. (2006) · Metabolic Engineering · doi:10.1016/j.ymben.2006.01.004 · Cited by 451 · see citing works

Heterogeneity of tumor-induced gene expression changes in the human metabolic network

Hu, J., Locasale, J. W., Bielas, J. H., O'Sullivan, J., Sheahan, K., Cantley, L. C., Heiden, M. G. V., & Vitkup, D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2530 · Cited by 407 · see citing works

Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach

Bennett, B. D., Yuan, J., Kimball, E., & Rabinowitz, J. D. (2008) · Nature Protocols · doi:10.1038/nprot.2008.107 · Cited by 384 · see citing works

Metabolism Links Bacterial Biofilms and Colon Carcinogenesis

Johnson, C. H., Dejea, C. M., Edler, D., Hoang, L. T., Santidrián, A. F., Felding, B. H., Ivanišević, J., Cho, K., Wick, E. C., Hechenbleikner, E. M., et al. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.04.011 · Cited by 355 · see citing works

Profiling metabolites and peptides in single cells

Rubakhin, S. S., Romanova, E. V., Nemes, P., & Sweedler, J. V. (2011) · Nature Methods · doi:10.1038/nmeth.1549 · Cited by 346 · see citing works

Multiple reaction monitoring for quantitative biomarker analysis in proteomics and metabolomics☆

Kitteringham, N. R., Jenkins, R. E., Lane, C. S., Elliott, V. L., & Park, B. K. (2008) · Journal of Chromatography B · doi:10.1016/j.jchromb.2008.11.013 · Cited by 343 · see citing works

Ultra‐performance liquid chromatography coupled to quadrupole‐orthogonal time‐of‐flight mass spectrometry

Plumb, R. S., Castro‐Perez, J. M., Granger, J. H., et al. (2004) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.1627 · Cited by 343 · see citing works

Metabolomics Applied to Diabetes Research

Bain, J. R., Stevens, R. D., Wenner, B. R., Ilkayeva, O., Muoio, D. M., & Newgard, C. B. (2009) · Diabetes · doi:10.2337/db09-0580 · Cited by 330 · see citing works

Towards quantitative metabolomics of mammalian cells: Development of a metabolite extraction protocol

Dietmair, S., Timmins, N. E., Gray, P. P., Nielsen, L. K., & Krömer, J. O. (2010) · Analytical Biochemistry · doi:10.1016/j.ab.2010.04.031 · Cited by 322 · see citing works

Defining the Metabolome: Size, Flux, and Regulation

Zamboni, N., Saghatelian, A., & Patti, G. J. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.04.021 · Cited by 299 · see citing works

Metabolomics applications of FT‐ICR mass spectrometry

Brown, S. C., Kruppa, G. H., & Dasseux, J. (2004) · Mass Spectrometry Reviews · doi:10.1002/mas.20011 · Cited by 286 · see citing works

In Situ Metabolic Profiling of Single Cells by Laser Ablation Electrospray Ionization Mass Spectrometry

Shrestha, B., & Vértes, Á. (2009) · Analytical Chemistry · doi:10.1021/ac901525g · Cited by 273 · see citing works

Optimized Preprocessing of Ultra-Performance Liquid Chromatography/Mass Spectrometry Urinary Metabolic Profiles for Improved Information Recovery

Veselkov, K., Karstens, L., Masson, P., Robinette, S. L., Want, E. J., Li, J. V., Barton, R. H., Boursier-Neyret, C., Walther, B., Ebbels, T. M. D., et al. (2011) · Analytical Chemistry · doi:10.1021/ac201065j · Cited by 267 · see citing works

Real-time metabolome profiling of the metabolic switch between starvation and growth

Link, H., Fuhrer, T., Gerosa, L., Zamboni, N., & Sauer, U. (2015) · Nature Methods · doi:10.1038/nmeth.3584 · Cited by 248 · see citing works

Use of a Novel 3D Culture Model to Elucidate the Role of Mesothelial Cells, Fibroblasts and Extra-cellular Matrices on Adhesion and Invasion of Ovarian Cancer Cells to the Omentum

Kenny, H. A., Krausz, T., Yamada, S. D., & Lengyel, E. (2007) · International Journal of Cancer · doi:10.1002/ijc.22874 · Cited by 243 · see citing works

A comparison of five lipid extraction solvent systems for lipidomic studies of human LDL

Reis, A., Rudnitskaya, A. M., Blackburn, G. J., Fauzi, N. M., Pitt, A. R., & Spickett, C. M. (2013) · Journal of Lipid Research · doi:10.1194/jlr.m034330 · Cited by 242 · see citing works

Improved batch correction in untargeted MS-based metabolomics

Wehrens, R., Hageman, J. A., van Eeuwijk, F., Kooke, R., Flood, P. J., Wijnker, T. G., Keurentjes, J. J. B., Lommen, A., van Eekelen, H. D. L. M., Hall, R. D., et al. (2016) · Metabolomics · doi:10.1007/s11306-016-1015-8 · Cited by 242 · see citing works

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

Gao, J., Tarcea, V. G., Karnovsky, A., Mirel, B. R., Weymouth, T. E., Beecher, C., Cavalcoli, J. D., Athey, B. D., Omenn, G. S., Burant, C., et al. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq048 · Cited by 231 · see citing works

Direct metabolomics for plant cells by live single-cell mass spectrometry

Fujii, T., Matsuda, S., Tejedor, M. L., Esaki, T., Sakane, I., Mizuno, H., Tsuyama, N., & Masujima, T. (2015) · Nature Protocols · doi:10.1038/nprot.2015.084 · Cited by 221 · see citing works

Hexosamine Pathway Metabolites Enhance Protein Quality Control and Prolong Life

Denzel, M. S., Storm, N. J., Gutschmidt, A., Baddi, R., Hinze, Y., Jarosch, E., Sommer, T., Hoppe, T., & Antebi, A. (2014) · Cell · doi:10.1016/j.cell.2014.01.061 · Cited by 219 · see citing works

Single Cell Analysis with Probe ESI-Mass Spectrometry: Detection of Metabolites at Cellular and Subcellular Levels

Gong, X., Zhao, Y., Cai, S., et al. (2014) · Analytical Chemistry · doi:10.1021/ac500882e · Cited by 218 · see citing works

13CFLUX2—high-performance software suite for 13C-metabolic flux analysis

Weitzel, M., Nöh, K., Dalman, T., Niedenführ, S., Stute, B., & Wiechert, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts646 · Cited by 202 · see citing works

Avoiding Misannotation of In-Source Fragmentation Products as Cellular Metabolites in Liquid Chromatography–Mass Spectrometry-Based Metabolomics

Xu, Y., Lu, W., & Rabinowitz, J. D. (2015) · Analytical Chemistry · doi:10.1021/ac504118y · Cited by 202 · see citing works

Analysis of Cell Metabolism Using LC-MS and Isotope Tracers

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Maximal Oxidative Capacity during Exercise Is Associated with Skeletal Muscle Fuel Selection and Dynamic Changes in Mitochondrial Protein Acetylation

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