I have targeted tracer metabolomic data of a mammalian cell culture in 3 biological replicates, and 3 time-points (0, 10 and 60 minutes). Cultures were fed with 13C6-glucose. After manual curation I have reliable isotopologue measures for 7 metabolites in glycolysis, 5 metabolites in the tricarboxylic acid cycle and 7 aminoacids. Is my dataset suitable for performing 13C-MFA or FBA?

The metabolites in question:

  • Hexose
  • Hexose-P
  • Hexose-BP
  • 3PG
  • DHAP
  • PEP
  • Pyruvate
  • Citrate
  • cis-Aconitate
  • Oxoglutarate
  • Malate
  • Fumarate
  • Glutamate
  • Glutamine
  • Aspartate
  • Asparagine
  • Arginine
  • Serine
  • Glycine
  • 1
    $\begingroup$ It would help to include which metabolites you have. $\endgroup$
    – Michael_A
    May 17 at 4:04
  • $\begingroup$ Thank you @David and Michael_A for your remarks and corrections. Here the metabolites I have : Hexose, Hexose-P, Hexose-BP, 3PG, DHAP, PEP, Pyruvate; Citrate, cis-Aconitate, Oxoglutarate, Malate, Fumarate; Glutamate, Glutamine, Aspartate, Asparagine, Arginine, Serine, Glycine. $\endgroup$ May 22 at 9:33
  • $\begingroup$ The data are probably sufficient for something, but it's hard to evaluate without more details. What exactly are you trying to learn from this experiment? $\endgroup$ May 22 at 19:27
  • $\begingroup$ thank you @MaximilianPress, indeed we would like to estimate metabolic fluxes in a similar manner as these researchers : researchgate.net/publication/… . But we have mammalian tissue instead. I have some knowledge of python, but I have never used cobrapy $\endgroup$ May 23 at 14:22
  • 1
    $\begingroup$ I believe no one can answer your question entirely, except you set up a model in question. You need some metabolic network based on which you would formulate, for further computations, your balance equations (flux equations). If those equations with their boundary selected well, you may have a network where you could compute then with your observations (known fluxes) the unknown fluxes. $\endgroup$ May 24 at 10:46


You must log in to answer this question.

Browse other questions tagged .