Dataset Information

The importance of accurately correcting for the natural abundance of stable isotopes.

ABSTRACT: The use of isotopically labeled tracer substrates is an experimental approach for measuring in vivo and in vitro intracellular metabolic dynamics. Stable isotopes that alter the mass but not the chemical behavior of a molecule are commonly used in isotope tracer studies. Because stable isotopes of some atoms naturally occur at non-negligible abundances, it is important to account for the natural abundance of these isotopes when analyzing data from isotope labeling experiments. Specifically, a distinction must be made between isotopes introduced experimentally via an isotopically labeled tracer and the isotopes naturally present at the start of an experiment. In this tutorial review, we explain the underlying theory of natural abundance correction of stable isotopes, a concept not always understood by metabolic researchers. We also provide a comparison of distinct methods for performing this correction and discuss natural abundance correction in the context of steady state 13C metabolic flux, a method increasingly used to infer intracellular metabolic flux from isotope experiments.

SUBMITTER: Midani FS

PROVIDER: S-EPMC5343595 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The importance of accurately correcting for the natural abundance of stable isotopes.

Midani Firas S FS Wynn Michelle L ML Schnell Santiago S

Analytical biochemistry 20170111

The use of isotopically labeled tracer substrates is an experimental approach for measuring in vivo and in vitro intracellular metabolic dynamics. Stable isotopes that alter the mass but not the chemical behavior of a molecule are commonly used in isotope tracer studies. Because stable isotopes of some atoms naturally occur at non-negligible abundances, it is important to account for the natural abundance of these isotopes when analyzing data from isotope labeling experiments. Specifically, a di ...[more]

PMID: 27989585

Similar Datasets

Project description:BackgroundStable isotope tracing with ultra-high resolution Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS) can provide simultaneous determination of hundreds to thousands of metabolite isotopologue species without the need for chromatographic separation. Therefore, this experimental metabolomics methodology may allow the tracing of metabolic pathways starting from stable-isotope-enriched precursors, which can improve our mechanistic understanding of cellular metabolism. However, contributions to the observed intensities arising from the stable isotope's natural abundance must be subtracted (deisotoped) from the raw isotopologue peaks before interpretation. Previously posed deisotoping problems are sidestepped due to the isotopic resolution and identification of individual isotopologue peaks. This peak resolution and identification come from the very high mass resolution and accuracy of FT-ICR-MS and present an analytically solvable deisotoping problem, even in the context of stable-isotope enrichment.ResultsWe present both a computationally feasible analytical solution and an algorithm to this newly posed deisotoping problem, which both work with any amount of 13C or 15N stable-isotope enrichment. We demonstrate this algorithm and correct for the effects of 13C natural abundance on a set of raw isotopologue intensities for a specific phosphatidylcholine lipid metabolite derived from a 13C-tracing experiment.ConclusionsCorrection for the effects of 13C natural abundance on a set of raw isotopologue intensities is computationally feasible when the raw isotopologues are isotopically resolved and identified. Such correction makes qualitative interpretation of stable isotope tracing easier and is required before attempting a more rigorous quantitative interpretation of the isotopologue data. The presented implementation is very robust with increasing metabolite size. Error analysis of the algorithm will be straightforward due to low relative error from the implementation itself. Furthermore, the algorithm may serve as an independent quality control measure for a set of observed isotopologue intensities.

Project description:Stable potassium isotopes are one of the emerging non-traditional isotope systems enabled in recent years by the advance of Multi-Collector Inductively-Coupled-Plasma Mass-Spectrometry (MC-ICP-MS). In this review, we first summarize the geochemical and cosmochemical properties of K, its major reservoirs, and the analytical methods of K isotopes. Following this, we review recent literature on K isotope applications in the fields of geochemistry and cosmochemistry. Geochemically, K is a highly incompatible lithophile element, and a highly soluble, biophile element. The isotopic fractionation of K is relatively small during magmatic processes such as partial melting and fractional crystallization, whereas during low-temperature and biological processes fractionation is considerably larger. This resolvable fractionation has made K isotopes promising tracers for a variety of Earth and environmental processes, including chemical weathering, low-temperature alteration of igneous rocks, reverse weathering, and the recycling of sediments into the mantle during subduction. Sorption and interactions of aqueous K with different clay minerals during cation exchange and clay formation are likely to be of fundamental significance in generating much of the K isotope variability seen in samples from the Earth surface and samples carrying recycled surface materials from the deep Earth. The magnitude of this fractionation is process- and mineral-dependent. Comprehensive quantification of pertinent K isotope fractionation factors is currently lacking and urgently needed. Significant fractionation during biological activities, such as plant uptake, demonstrates the potential utility of K isotopes in the study of the nutrient cycle and its relation to the climate and various ecosystems, enabling new and largely unexplored avenues for future research. Of significant importance to the cosmochemistry community, K is a moderately volatile element with large variations in K/U ratio observed among chondrites and planetary materials. As this indicates different degrees of volatile depletion, it has become a fundamental chemical signature of both chondritic and planetary bodies. This volatile depletion has been attributed to various processes such as solar nebula condensation, mixing of volatile-rich and -poor reservoirs, planetary accretional volatilization via impacts, and/or magma ocean degassing. While K isotopes have the potential to distinguish these different processes, the current results are still highly debated. A good correlation between the K isotope compositions of four differentiated bodies (Earth, Mars, Moon, and Vesta) and their masses suggests a ubiquitous volatile depletion mechanism during the formation of the terrestrial planets. It is still unknown whether any of the K isotopic variation among chondrites and differentiated bodies can be attributed to inherited signatures of mass-independent isotopic anomalies.

Dataset Information

The importance of accurately correcting for the natural abundance of stable isotopes.

Publications

The importance of accurately correcting for the natural abundance of stable isotopes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure