FluxFix: automatic isotopologue normalization for metabolic tracer analysis

BMC Bioinformatics. 2016 Nov 25;17(1):485. doi: 10.1186/s12859-016-1360-7.


Background: Isotopic tracer analysis by mass spectrometry is a core technique for the study of metabolism. Isotopically labeled atoms from substrates, such as [13C]-labeled glucose, can be traced by their incorporation over time into specific metabolic products. Mass spectrometry is often used for the detection and differentiation of the isotopologues of each metabolite of interest. For meaningful interpretation, mass spectrometry data from metabolic tracer experiments must be corrected to account for the naturally occurring isotopologue distribution. The calculations required for this correction are time consuming and error prone and existing programs are often platform specific, non-intuitive, commercially licensed and/or limited in accuracy by using theoretical isotopologue distributions, which are prone to artifacts from noise or unresolved interfering signals.

Results: Here we present FluxFix ( http://fluxfix.science ), an application freely available on the internet that quickly and reliably transforms signal intensity values into percent mole enrichment for each isotopologue measured. 'Unlabeled' data, representing the measured natural isotopologue distribution for a chosen analyte, is entered by the user. This data is used to generate a correction matrix according to a well-established algorithm. The correction matrix is applied to labeled data, also entered by the user, thus generating the corrected output data. FluxFix is compatible with direct copy and paste from spreadsheet applications including Excel (Microsoft) and Google sheets and automatically adjusts to account for input data dimensions. The program is simple, easy to use, agnostic to the mass spectrometry platform, generalizable to known or unknown metabolites, and can take input data from either a theoretical natural isotopologue distribution or an experimentally measured one.

Conclusions: Our freely available web-based calculator, FluxFix ( http://fluxfix.science ), quickly and reliably corrects metabolic tracer data for natural isotopologue abundance enabling faster, more robust and easily accessible data analysis.

Keywords: Correction; Enrichment; Flux; Isotopologue; Metabolite; Normalization; Tracer.

MeSH terms

  • Algorithms*
  • Biomarkers, Tumor / metabolism*
  • Carbon Isotopes / analysis*
  • HeLa Cells
  • Hep G2 Cells
  • Humans
  • Isotope Labeling
  • Mass Spectrometry / methods*
  • Metabolomics / methods*
  • Software*


  • Biomarkers, Tumor
  • Carbon Isotopes