The DOI matches its Crossref record; 18 of the 18 references it cites were found in a registry or an index.
Acidic Acetonitrile for Cellular Metabolome Extraction from Escherichia coli
Abstract
Cellular metabolome analysis by chromatography-mass spectrometry (MS) requires prior metabolite extraction. We examined a diversity of solvent systems for extraction of water-soluble metabolites from Escherichia coli. Quantitative yields of approximately 100 different metabolites were measured by liquid chromatography-tandem MS and displayed in clustered heat map format. Many metabolites, including most amino acids and components of central carbon metabolism, were adequately extracted by a broad spectrum of solvent mixtures. For nucleotide triphosphates, however, mixtures of acidic (0.1 M formic acid-containing) acetonitrile/water (80:20) or acetonitrile/methanol/water (40:40:20) gave superior triphosphate yields. Experiments involving isotopic tracers revealed that the improved triphosphate yields in the acidic acetonitrile were in part due to reduced triphosphate decomposition, which is a major problem when extracting with other solvent systems such as methanol/water. We recommend acidic solvent mixtures containing acetonitrile for extraction of the E. coli metabolome.
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
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 16,184
Metabolomics—the link between genotypes and phenotypes
Fiehn, O. (2002) · Plant Molecular Biology · doi:10.1023/a:1013713905833 · Cited by 3,445
Metabolomics — the link between genotypes and phenotypes
Fiehn, O. (2002) · Functional Genomics · doi:10.1007/978-94-010-0448-0_11 · Cited by 3,167
Bajad, S. U., Lu, W., Kimball, E. H., Yuan, J., Peterson, C., & Rabinowitz, J. D. (2006) · Journal of Chromatography A · doi:10.1016/j.chroma.2006.05.019 · Cited by 592
Self-citationGullberg, J., Jonsson, P., Nordström, A., Sjöström, M., & Moritz, T. (2004) · Analytical Biochemistry · doi:10.1016/j.ab.2004.04.037 · Cited by 503
Sampling for Metabolome Analysis of Microorganisms
Bolten, C. J., Kiefer, P., Letisse, F., Portais, J.-C., & Wittmann, C. (2007) · Analytical Chemistry · doi:10.1021/ac0623888 · Cited by 376
Lowry, O. H., Carter, J., Ward, J. B., & Glaser, L. (1971) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)34144-4 · Cited by 350
Conservation of the metabolomic response to starvation across two divergent microbes
Brauer, M. J., Yuan, J., Bennett, B. D., Lu, W., Kimball, E., Botstein, D., & Rabinowitz, J. D. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609508103 · Cited by 272
Self-citationMashego, M. R., Wu, L., Van Dam, J. C., Ras, C., Vinke, J. L., Van Winden, W. A., Van Gulik, W. M., & Heijnen, J. J. (2004) · Biotechnology and Bioengineering · doi:10.1002/bit.10907 · Cited by 258
Compounds Which Serve as the Sole Source of Carbon or Nitrogen for Salmonella typhimurium LT-2
Gutnick, D., Calvo, J. M., Klopotowski, T., & Ames, B. N. (1969) · Journal of Bacteriology · doi:10.1128/jb.100.1.215-219.1969 · Cited by 251
Cited by
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-citationZhou, B., Xiao, J. F., Tuli, L., & Ressom, H. W. (2011) · Molecular BioSystems · doi:10.1039/c1mb05350g · Cited by 639
Analytical strategies for LC–MS-based targeted metabolomics
Lu, W., Bennett, B. D., & Rabinowitz, J. D. (2008) · Journal of Chromatography B · doi:10.1016/j.jchromb.2008.04.031 · Cited by 481
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-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
Waters, C. M., Lu, W., Rabinowitz, J. D., & Bassler, B. L. (2008) · Journal of Bacteriology · doi:10.1128/jb.01756-07 · Cited by 425
Self-citationReductive glutamine metabolism is a function of the α-ketoglutarate to citrate ratio in cells
Fendt, S.-M., Bell, E. L., Keibler, M. A., Olenchock, B. A., Mayers, J. R., Wasylenko, T. M., Vokes, N. I., Guarente, L., Heiden, M. G. V., & Stephanopoulos, G. (2013) · Nature Communications · doi:10.1038/ncomms3236 · Cited by 364
Gorrochategui, E., Jaumot, J., Lacorte, S., & Tauler, R. (2016) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2016.07.004 · Cited by 352
Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli
Yuan, J., Doucette, C. D., Fowler, W. U., Feng, X., Piazza, M., Rabitz, H. A., Wingreen, N. S., & Rabinowitz, J. D. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.60 · Cited by 178
Self-citationPicone, G., Laghi, L., Gardini, F., Lanciotti, R., Siroli, L., & Capozzi, F. (2013) · Food Chemistry · doi:10.1016/j.foodchem.2013.07.004 · Cited by 65
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
Rivera Vazquez, J., Trujillo, E., Williams, J., She, F., Getahun, F., Callaghan, M. M., Coon, J. J., & Amador-Noguez, D. (2024) · Biotechnology for Biofuels and Bioproducts · doi:10.1186/s13068-023-02450-9 · Cited by 13
Metadata
- Authors
- Rabinowitz, J. D., & Kimball, E.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2007-07-14
- Volume
- 79
- Issue
- 16
- Pages
- 6167-6173
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2092504964
- Cited by
- 342
- References
- 18
- FWCI
- 5.63
- Type
- journal article
- Language
- en
- Open access
- closed
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.
