The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
Metabolomic Analysis via Reversed-Phase Ion-Pairing Liquid Chromatography Coupled to a Stand Alone Orbitrap Mass Spectrometer
Open accessAbstract
We present a liquid chromatography-mass spectrometry (LC-MS) method that capitalizes on the mass-resolving power of the orbitrap to enable sensitive and specific measurement of known and unanticipated metabolites in parallel, with a focus on water-soluble species involved in core metabolism. The reversed phase LC method, with a cycle time 25 min, involves a water-methanol gradient on a C18 column with tributylamine as the ion pairing agent. The MS portion involves full scans from 85 to 1000 m/z at 1 Hz and 100,000 resolution in negative ion mode on a stand alone orbitrap ("Exactive"). The median limit of detection, across 80 metabolite standards, was 5 ng/mL with the linear range typically >or=100-fold. For both standards and a cellular extract from Saccharomyces cerevisiae (Baker's yeast), the median inter-run relative standard deviation in peak intensity was 8%. In yeast exact, we detected 137 known compounds, whose (13)C-labeling patterns could also be tracked to probe metabolic flux. In yeast engineered to lack a gene of unknown function (YKL215C), we observed accumulation of an ion of m/z 128.0351, which we subsequently confirmed to be oxoproline, resulting in annotation of YKL215C as an oxoprolinase. These examples demonstrate the suitability of the present method for quantitative metabolomics, fluxomics, and discovery metabolite profiling.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Breiman, L. (2001) · Machine Learning · doi:10.1023/a:1010933404324 · Cited by 133,538
KEGG for linking genomes to life and the environment
Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm882 · Cited by 6,782
Smith, C. A., Want, E. J., O'Maille, G., Abagyan, R., & Siuzdak, G. (2006) · Analytical Chemistry · doi:10.1021/ac051437y · Cited by 5,262
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395
HMDB: the Human Metabolome Database
Wishart, D. S., Tzur, D., Knox, C., Eisner, R., Guo, A. C., Young, N., Cheng, D., Jewell, K., Arndt, D., Sawhney, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl923 · Cited by 3,231
HMDB: a knowledgebase for the human metabolome
Wishart, D. S., Knox, C., Guo, A. C., Eisner, R., Young, N., Gautam, B., Hau, D. D., Psychogios, N., Dong, E., Bouatra, S., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn810 · Cited by 1,873
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., & Rabinowitz, J. D. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.186 · Cited by 1,830
Self-citationThe Orbitrap: a new mass spectrometer
Hu, Q., Noll, R. J., Li, H., Makarov, A., Hardman, M., & Graham Cooks, R. (2005) · Journal of Mass Spectrometry · doi:10.1002/jms.856 · Cited by 1,333
Electrostatic Axially Harmonic Orbital Trapping: A High-Performance Technique of Mass Analysis
Makarov, A. (2000) · Analytical Chemistry · doi:10.1021/ac991131p · Cited by 1,009
Construction of a set of convenient saccharomyces cerevisiae strains that are isogenic to S288C
Winston, F., Dollard, C., & Ricupero‐Hovasse, S. L. (1995) · Yeast · doi:10.1002/yea.320110107 · Cited by 941
Cited by
The return of metabolism: biochemistry and physiology of the pentose phosphate pathway
Stincone, A., Prigione, A., Cramer, T., Wamelink, M. M. C., Campbell, K., Cheung, E., Olin‐Sandoval, V., Grüning, N., Krüger, A., Tauqeer Alam, M., et al. (2015) · Biological Reviews · doi:10.1111/brv.12140 · Cited by 1,576
Self-citationQuantitative 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
Self-citationYuan, M., Breitkopf, S. B., Yang, X., & Asara, J. M. (2012) · Nature Protocols · doi:10.1038/nprot.2012.024 · Cited by 1,117
Kamphorst, J. J., Nofal, M., Commisso, C., Hackett, S. R., Lu, W., Grabocka, E., Vander Heiden, M. G., Miller, G., Drebin, J. A., Bar-Sagi, D., et al. (2015) · Cancer Research · doi:10.1158/0008-5472.can-14-2211 · Cited by 893
Self-citationKamphorst, J. J., Cross, J. R., Fan, J., de Stanchina, E., Mathew, R., White, E. P., Thompson, C. B., & Rabinowitz, J. D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1307237110 · Cited by 726
Self-citationElectrophilic properties of itaconate and derivatives regulate the IκBζ–ATF3 inflammatory axis
Bambouskova, M., Gorvel, L., Lampropoulou, V., Sergushichev, A., Loginicheva, E., Johnson, K., Korenfeld, D., Mathyer, M. E., Kim, H., Huang, L.-H., et al. (2018) · Nature · doi:10.1038/s41586-018-0052-z · Cited by 713
The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids
Jang, C., Hui, S., Lu, W., Cowan, A. J., Morscher, R. J., Lee, G., Liu, W., Tesz, G. J., Birnbaum, M. J., & Rabinowitz, J. D. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2017.12.016 · Cited by 639
Self-citationZhang, Y., Kurupati, R., Liu, L., Zhou, X. Y., Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.08.004 · Cited by 616
Self-citationGuo, J. Y., Karsli-Uzunbas, G., Mathew, R., Aisner, S. C., Kamphorst, J. J., Strohecker, A. M., Chen, G., Price, S., Lu, W., Teng, X., et al. (2013) · Genes & Development · doi:10.1101/gad.219642.113 · Cited by 589
Self-citationDietary fructose feeds hepatic lipogenesis via microbiota-derived acetate
Zhao, S., Jang, C., Liu, J., Uehara, K., Gilbert, M., Izzo, L., Zeng, X., Trefely, S., Fernandez, S., Carrer, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2101-7 · Cited by 553
Self-citationMetabolite Measurement: Pitfalls to Avoid and Practices to Follow
Lu, W., Su, X., Klein, M. S., Lewis, I. A., Fiehn, O., & Rabinowitz, J. D. (2017) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061516-044952 · Cited by 462
Self-citationAsparagine Plays a Critical Role in Regulating Cellular Adaptation to Glutamine Depletion
Zhang, J., Fan, J., Venneti, S., Cross, J. R., Takagi, T., Bhinder, B., Djaballah, H., Kanai, M., Cheng, E. H., Judkins, A. R., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.018 · Cited by 439
Self-citationMetabolite 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
Liu, X., & Locasale, J. W. (2017) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2017.01.004 · Cited by 453
Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia
Ye, J., Fan, J., Venneti, S., Wan, Y.-W., Pawel, B. R., Zhang, J., Finley, L. W. S., Lu, C., Lindsten, T., Cross, J. R., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-14-0250 · Cited by 452
“The LC-MS method involved reversed-phase ion-pairing chromatography coupled by negative mode electrospray ionization to a stand-alone orbitrap mass spectrometer (Thermo Scientific) scanning from m/z 85-1000 at 1 Hz at 100,000 resolution (42-44) with LC separation on a Synergy Hydro-RP column (100 mm × 2 mm, 2.”
MethodSelf-citationReversal of cytosolic one-carbon flux compensates for loss of the mitochondrial folate pathway
Ducker, G. S., Chen, L., Morscher, R. J., Ghergurovich, J. M., Esposito, M., Teng, X., Kang, Y., & Rabinowitz, J. D. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.04.016 · Cited by 419
“Samples were analyzed by reversed-phase ion-pairing chromatography coupled with negative-mode electrospray-ionization high-resolutionMS on a stand-alone orbitrap (ThermoFisher Exactive) (Lu et al., 2010).”
Self-citationFan, J., Kamphorst, J. J., Mathew, R., Chung, M. K., White, E., Shlomi, T., & Rabinowitz, J. D. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.65 · Cited by 428
Self-citationItaconic acid is a mammalian metabolite induced during macrophage activation
Strelko, C. L., Lu, W., Dufort, F. J., Seyfried, T. N., Chiles, T. C., Rabinowitz, J. D., & Roberts, M. F. (2011) · Journal of the American Chemical Society · doi:10.1021/ja2070889 · Cited by 391
Self-citationAs Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid
Pavlova, N. N., Hui, S., Ghergurovich, J. M., Fan, J., Intlekofer, A. M., White, R. M., Rabinowitz, J. D., Thompson, C. B., & Zhang, J. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2017.12.006 · Cited by 341
Self-citationJašarević, E., Howerton, C. L., Howard, C. D., & Bale, T. L. (2015) · Endocrinology · doi:10.1210/en.2015-1177 · Cited by 329
The gut microbiota regulates white adipose tissue inflammation and obesity via a family of microRNAs
Virtue, A. T., McCright, S. J., Wright, J. M., Jimenez, M. T., Mowel, W. K., Kotzin, J. J., Joannas, L., Basavappa, M. G., Spencer, S. P., Clark, M. L., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aav1892 · Cited by 317
Metabolite Spectral Accuracy on Orbitraps
Su, X., Lu, W., & Rabinowitz, J. D. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b00396 · Cited by 285
Self-citationDucker, G. S., Ghergurovich, J. M., Mainolfi, N., Suri, V., Jeong, S. K., Hsin-Jung Li, S., Friedman, A., Manfredi, M. G., Gitai, Z., Kim, H., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706617114 · Cited by 261
Kamphorst, J. J., Chung, M. K., Fan, J., & Rabinowitz, J. D. (2014) · Cancer & Metabolism · doi:10.1186/2049-3002-2-23 · Cited by 227
Self-citationStoichiometry of site-specific lysine acetylation in an entire proteome
Baeza, J., Dowell, J. A., Smallegan, M. J., Fan, J., Amador-Noguez, D., Khan, Z., & Denu, J. M. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.581843 · Cited by 154
Self-citationNicotinamide adenine dinucleotide is transported into mammalian mitochondria
Davila, A., Liu, L., Chellappa, K., Redpath, P., Nakamaru-Ogiso, E., Paolella, L. M., Zhang, Z., Migaud, M. E., Rabinowitz, J. D., & Baur, J. A. (2018) · eLife · doi:10.7554/elife.33246 · Cited by 142
Self-citationAbsence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells
Reaves, M. L., Sinha, S., Rabinowitz, J. D., Kruglyak, L., & Redfield, R. J. (2012) · Science · doi:10.1126/science.1219861 · Cited by 125
Self-citationKoyuncu, E., Purdy, J. G., Rabinowitz, J. D., & Shenk, T. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003333 · Cited by 114
Self-citationGuo, B., Chen, B., Liu, A., Zhu, W., & Yao, S. (2012) · Current Drug Metabolism · doi:10.2174/138920012803341401 · Cited by 80
DeBruyn, J. M., Hoeland, K. M., Taylor, L. S., Stevens, J. D., Moats, M. A., Bandopadhyay, S., Dearth, S. P., Castro, H. F., Hewitt, K. K., Campagna, S. R., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.608856 · Cited by 50
Metadata
- Authors
- Lu, W., Clasquin, M. F., Melamud, E., Amador-Noguez, D., Caudy, A. A., & Rabinowitz, J. D.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2010-03-29
- Volume
- 82
- Issue
- 8
- Pages
- 3212-3221
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W1994124478
- Cited by
- 502
- References
- 37
- FWCI
- 11.11
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
