Quantification of Stable Isotope Label in Metabolites via Mass Spectrometry

Part of the Methods in Molecular Biology book series (MIMB, volume 1056)


Isotope labelling experiments with stable or radioactive isotopes have long been an integral part of biological and medical research. Labelling experiments led to the discovery of new metabolic pathways and made it possible to calculate the fluxes responsible for a metabolic phenotype, i.e., the qualitative and quantitative composition of metabolites in a biological system. Prerequisite for efficient isotope labelling experiments is a reliable and precise method to analyze the redistribution of isotope label in a metabolic network. Here we describe the use of the CORRECTOR program, which utilizes matrix calculations to correct mass spectral data from stable isotope labelling experiments for the distorting effect of naturally occurring stable isotopes (NOIs). CORRECTOR facilitates and speeds up the routine quantification of experimentally introduced isotope label from multiple mass spectral readouts, which are generated by routine metabolite profiling when combined with stable isotope labelling experiments.

Key words

Stable isotope labelling Stable isotope tracing Flux CORRECTOR software Metabolite profiling 



This work was supported by the Max Planck society and a grant from the DFG (Deutsche Forschungsgemeinschaft) to JK. The CORRECTOR software tool was supported in part by the European META-PHOR project, FOOD-CT-2006-036220, and the GoFORSYS project ( funded by the Bundesministerium für Bildung und Forschung (BMBF). JH and BH were supported by BMBF grants 0315295 and 0315426A.


  1. 1.
    Roessner U et al (2000) Simultaneous analysis of metabolites in potato tuber by gas chromatography–mass spectrometry. Plant J 23: 131–142PubMedCrossRefGoogle Scholar
  2. 2.
    Fiehn O et al (2000) Metabolite profiling for plant functional genomics. Nat Biotechnol 18:1157–1161PubMedCrossRefGoogle Scholar
  3. 3.
    Lisec J et al (2006) Gas chromatography mass spectrometry-based metabolite profiling in plants. Nat Protoc 1:387–396PubMedCrossRefGoogle Scholar
  4. 4.
    Erban A et al (2007) Non-supervised construction and application of mass spectral and retention time index libraries from time-of-flight GC-MS metabolite profiles. In: Weckwerth W (ed) Metabolomics: methods and protocols. Humana Press, New York, pp 19–38Google Scholar
  5. 5.
    Luedemann A et al (2008) TagFinder for the quantitative analysis of gas chromatography–mass spectrometry (GC-MS) based metabolite profiling experiments. Bioinformatics 24: 732–737PubMedCrossRefGoogle Scholar
  6. 6.
    Lee WNP, Byerley LO, Gergner EA (1991) Mass isotopomer analysis: theoretical and practical considerations. J Mass Spectrom 30: 451–458Google Scholar
  7. 7.
    Fernandez CA et al (1996) Correction of 13C mass isotopomer distributions for natural stable isotope abundance. J Mass Spectrom 31:255–262PubMedCrossRefGoogle Scholar
  8. 8.
    Wittmann C, Heinzle E (1999) Mass spectrometry for metabolic flux analysis. Biotechnol Bioeng 62:739–750PubMedCrossRefGoogle Scholar
  9. 9.
    van Winden WA et al (2002) Correcting mass isotopomer distributions for naturally occurring isotopes. Biotechnol Bioeng 80:477–479PubMedCrossRefGoogle Scholar
  10. 10.
    Wahl AS, Dauner M, Wiechert W (2003) New tools for mass isotopomer data evaluation in 13C flux analysis: mass isotope correction, data consistency checking, and precursor relationships. Biotechnol Bioeng 85:259–268CrossRefGoogle Scholar
  11. 11.
    Huege J et al (2011) Modulation of the major paths of carbon in photorespiratory mutants of synechocystis. PLoS One 6(1):e16278. doi: 10.1371/journal.pone.0016278 PubMedCrossRefGoogle Scholar
  12. 12.
    Rosman KJR, Taylor PDP (1998) Isotopic compositions of the elements 1997. Pure Appl Chem 70:217–235CrossRefGoogle Scholar
  13. 13.
    Huege J et al (2007) GC-EI-TOF-MS analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after (13CO2)-labelling. Phytochemistry 68:2258–2272PubMedCrossRefGoogle Scholar
  14. 14.
    Allen DK, Shachar-Hill Y, Ohlrogge JB (2007) Compartment-specific labelling information in metabolic flux analysis of plants. Phytochemistry 68:2197–2210PubMedCrossRefGoogle Scholar
  15. 15.
    Allen DK, Ratcliffe RG (2009) Quantification of isotope label. In: Schwender J (ed) Plant metabolic networks. Springer, New York, pp 105–149CrossRefGoogle Scholar
  16. 16.
    Leimer KR, Rice RH, Gehrke CW (1977) Complete mass spectra of the per-trimethylsilylated amino acids. J Chromatogr 141:355–375CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  1. 1.Systems Biology Research Group, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  2. 2.Department of Theory, Max-Planck-Institute of Coal ResearchMülheim an der RuhrRuhrGermany
  3. 3.Department of Molecular PhysiologyMax-Planck-Institute of Molecular Plant Physiology (MPIMP)Potsdam-GolmGermany

Personalised recommendations