title: Natural isotope correction of MS/MS measurements for metabolomics and (13)C fluxomics.
abstract: Fluxomics and metabolomics are crucial tools for metabolic engineering and biomedical analysis to determine the in vivo cellular state. Especially, the application of (13)C isotopes allows comprehensive insights into the functional operation of cellular metabolism. Compared to single MS, tandem mass spectrometry (MS/MS) provides more detailed and accurate measurements of the metabolite enrichment patterns (tandem mass isotopomers), increasing the accuracy of metabolite concentration measurements and metabolic flux estimation. MS-type data from isotope labeling experiments is biased by naturally occurring stable isotopes (C, H, N, O, etc.). In particular, GC-MS(/MS) requires derivatization for the usually non-volatile intracellular metabolites introducing additional natural isotopes leading to measurements that do not directly represent the carbon labeling distribution. To make full use of LC- and GC-MS/MS mass isotopomer measurements, the influence of natural isotopes has to be eliminated (corrected). Our correction approach is analyzed for the two most common applications; (13)C fluxomics and isotope dilution mass spectrometry (IDMS) based metabolomics. Natural isotopes can have an impact on the calculated flux distribution which strongly depends on the substrate labeling and the actual flux distribution. Second, we show that in IDMS based metabolomics natural isotopes lead to underestimated concentrations that can and should be corrected with a nonlinear calibration. Our simulations indicate that the correction for natural abundance in isotope based fluxomics and quantitative metabolomics is essential for correct data interpretation.
authors.affiliation: Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Niedenführ
authors.affiliation: Department of Biotechnology, Delft University of Technology, 2628BC Delft, The Netherlands.
authors.forename: Angela
authors.initials: A
authors.lastname: ten Pierick
authors.affiliation: Department of Biotechnology, Delft University of Technology, 2628BC Delft, The Netherlands.
authors.forename: Patricia T N
authors.initials: PT
authors.lastname: van Dam
authors.affiliation: Department of Biotechnology, Delft University of Technology, 2628BC Delft, The Netherlands. casuarezmendez@unal.edu.co.|Departamento de Procesos y Energia, Universidad Nacional de Colombia, Carrera 80 No. 65-223, Blq. M3, Medellin, Colombia. casuarezmendez@unal.edu.co.
authors.forename: Camilo A
authors.initials: CA
authors.lastname: Suarez-Mendez
authors.affiliation: Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany. k.noeh@fz-juelich.de.
authors.forename: Katharina
authors.initials: K
authors.lastname: Nöh
authors.affiliation: Department of Biotechnology, Delft University of Technology, 2628BC Delft, The Netherlands. s.a.wahl@tudelft.nl.
authors.forename: S Aljoscha
authors.initials: SA
authors.lastname: Wahl
mesh_terms: D002247:Carbon Isotopes / Q000032:analysis / Q000378:metabolism; D008401:Gas Chromatography-Mass Spectrometry; D007553:Isotope Labeling / Q000379:methods; D055432:Metabolomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D002247:Carbon Isotopes
keywords: 13C fluxomics; MS/MS; carbon labeling experiments; mass spectrometry; metabolic flux ratio analysis; metabolomics