Repository » Data AccessID 63

Detail View - Data AccessID 63

Backimage Back

General Information info

Manuscript title Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.
PubMed ID 19690571
Journal Molecular Systems Biology
Year 2009
Authors Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz
Affiliations Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA
Keywords E. coli, ammonia assimilation, nitrogen upshift
Full text article Downloadarticle Yuan_2009.pdf
Project name not specified

Experiment Description info

Organism Escherichia coli
Strain NCM 3722 and mutants
Data type time-series data of metabolites
Data units mM
Execution date not specified

Experimental Details info

Temperature (0C) 37.0
pH ≈ 7.0
Carbon source glucose,
Culture mode batch
Process condition anaerobic
Dilution rate (h-1)
Working volume (L) not specified
Biomass concentration (g/L) not specified
Medium composition

Minimal salts media with 10 mM NH4Cl and 0.4 % glucose.

General protocol information Sampling method: filter cultures were prepared by passing 5 ml of exponentially growing liquid batch culture through membrane filters.

Quenching procedure: filters were submerged directly into -75 ºC methanol or -20 ºC 40:40:20 acetonitrile:methanol:water with 0.1 % formic acid.

Extraction technique: methanol

Sample analyzing method: LC-ESI-MS

Methods description - Notes

Detailed protocols for preparing filter cultures and extracting metabolites have been published [1,2].
Metabolite measurement - Cell extracts were analyzed by LC-electrospray ionization (ESI)-MS/MS on a Thermo Quantum triple quadrupole mass spectrometer operating in selected reaction monitoring (SRM) mode. All samples were analyzed within 24 h of their preparation. Separate LC runs were conducted for positive and negative ionization modes, using hydrophilic interaction chromatography and ion-pairing reversed phase chromatography, respectively [3].
Amino acids were derivatized before their quantitation by LC-ESIMS/MS. Cell extract (200 µl) was mixed with triethylamine (5 µl) and benzyl chloral formate (1 µl) to convert amines to N-benzylcarbamate (Cbz) derivatives [4].
As internal standard signals did not vary substantially or systematically between samples within a given time course, the reported metabolite concentration changes are between-sample ratios of the peak heights of the SRM chromatograms without correction for the internal standard response, except for glutamate and glutamine, in which correction for internal standards was performed to maximize quantitative accuracy.

-----------References-------------
[1] Bennett B, Yuan J, Kimball E, Rabinowitz J (2008) Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. Nat Protoc 3: 1299–1311. http://doi.org/dx4wxn
[2] Yuan J, Bennett B, Rabinowitz J (2008) Kinetic flux profiling for quantitation of cellular metabolic fluxes. Nature Protoc 3: 1328–1340. http://doi.org/cprs6m
[3] Lu W, Bennett BD, Rabinowitz JD (2008). Analytical strategies for LC-MS-based targeted metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 871: 236–242. http://doi.org/bc7n2m
[4] Kraml CM, Zhou D, Byrne N, McConnell O (2005) Enhanced chromatographic resolution of amine enantiomers as carbobenzyloxy derivatives in high-performance liquid chromatography and supercritical fluid chromatography. J Chromatogr A 1100: 108–115. http://doi.org/fwnt9q

Data file
Downloadmetabolites KIMODATAID63_v0.xlsx
Alternative format(s)
KIMODATAID63_trainingSet_WT_timeseries.csv
KIMODATAID63_trainingSet_GOGAT_timeseries.csv
KIMODATAID63_trainingSet_GDH_timeseries.csv
KIMODATAID63_additPerturb_WT_up_timeseries.csv
KIMODATAID63_additPerturb_WT_down_timeseries.csv
KIMODATAID63_additPerturb_GOGAT_up_timeseries.csv
KIMODATAID63_additPerturb_GOGAT_down_timeseries.csv
KIMODATAID63_additPerturb_ATAR_up_timeseries.csv
Cite|Share

Organism


Related Data: AccessID 30 | AccessID 35 | AccessID 41 | AccessID 44 | AccessID 51 | AccessID 54 | AccessID 64 | AccessID 65 | AccessID 67 | AccessID 68 | AccessID 74 | AccessID 75 | AccessID 78 | AccessID 79 | AccessID 80 | AccessID 86 | AccessID 87 | AccessID 92 | AccessID 96 | AccessID 101 | AccessID 102 | AccessID 103 | AccessID 104 | AccessID 105 | AccessID 106 | AccessID 107 | AccessID 108 | AccessID 109 | AccessID 110 | AccessID 112 | AccessID 116 | AccessID 118 | AccessID 119 | AccessID 125 | AccessID 126


Submission and curation info

Entered by Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Homepage: http://kdbio.inesc-id.pt/kimosys
Interests: mathematical modeling, accessible data, use of data

Created 2013-06-12 13:00:46 UTC

Updated 2014-06-12 23:22:03 UTC

Version 0

Status (reviewed) 2013-12-06 17:17:38 UTC




Associated Models


Here we can find relevant models associated with Data EntryID 63:

Model
EntryID
Model name Category Model Type Data used for Access Json
25
Authors: Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz

Original paper: Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.

Nitrogen assimilation model Metabolism ordinary differential equations Model building and Model validation Visto4 {"affiliation":"Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA","article_file_name":null,"authors":"Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz","biomodels_id":"","category":"Metabolism","combine_archive_content_type":"application/omex+xml","combine_archive_file_name":"COMBINE_KIMOMODELID25.omex","combine_archive_file_size":645413,"combine_archive_updated_at":"2014-06-30T17:56:44Z","comments":"","control":"2014-04-11T17:38:32Z","dilution_rate":"\u2014","id":25,"journal":"Molecular Systems Biology","keywords":"E. coli, ammonia assimilation, nitrogen upshift, differential equations, sensitivity analysis","main_organism":"Escherichia coli","manuscript_title":"Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.","model_name":"Nitrogen assimilation model","model_type":"ordinary differential equations","organism_id":63,"project_name":"","pubmed_id":"19690571","review_journal_id":null,"sbml_file_name":"Yuan_2009.pdf","software":"written in C++","used_for":"---\n- Model building\n- Model validation\n","year":2009} Administrator KiMoSys



Associate models to data

- Several models can be associated.

Add New Model



Backimage Back | Top