Isotopologue ratio normalization for non-targeted metabolomics

Daniel Weindl,André Wegner,Christian Jäger,Karsten Hiller

doi:10.1016/j.chroma.2015.02.025

Abstract

Robust quantification of analytes is a prerequisite for meaningful metabolomics experiments. In non-targeted metabolomics it is still hard to compare measurements across multiple batches or instruments. For targeted analyses isotope dilution mass spectrometry is used to provide a robust normalization reference.Here, we present an approach that allows for the automated semi-quantification of metabolites relative to a fully stable isotope-labeled metabolite extract. Unlike many previous approaches, we include both identified and unidentified compounds in the data analysis. The internal standards are detected in an automated manner using the non-targeted tracer fate detection algorithm. The ratios of the light and heavy form of these compounds serve as a robust measure to compare metabolite levels across different mass spectrometric platforms. As opposed to other methods which require high resolution mass spectrometers, our methodology works with low resolution mass spectrometers as commonly used in gas chromatography electron impact mass spectrometry (GC–EI-MS)-based metabolomics.We demonstrate the validity of our method by analyzing compound levels in different samples and show that it outperforms conventional normalization approaches in terms of intra- and inter-instrument reproducibility. We show that a labeled yeast metabolite extract can also serve as a reference for mammalian metabolite extracts where complete stable isotope labeling is hard to achieve.

Highlights

Metabolomics, the attempt to measure the levels of all metabolites of a given system under the given conditions, has become increasingly important in biomedical research [1,2]
We present an approach for GC–EI-MS metabolomics that allows for the robust normalization or semi-quantification of both identified and unidentified metabolites relative to a spiked-in stable isotope-labeled metabolite extract
Our non-targeted isotope dilution mass spectrometry (IDMS) normalization approach is based on a complex stable isotope labeled metabolite mixture as internal standard and involves the following steps (Fig. 1):

Summary

Introduction

Metabolomics, the attempt to measure the levels of all metabolites of a given system under the given conditions, has become increasingly important in biomedical research [1,2]. Analytical variance poses problems to the comparison of measurements from different runs or instruments, especially in non-targeted metabolomics. Common data treatments like total ion current normalization cannot be used for cross-platform comparisons and only account for certain types of errors like fluctuations in overall sensitivity. Often these techniques are limited to a set of very similar metabolite profiles. Normalization on pool samples can be performed, but this does not take into account the potentially different metabolite profiles with different matrix effects

Methods

Results

Conclusion