MetExtract II: A Software Suite for Stable Isotope-Assisted Untargeted Metabolomics

Abstract

Stable isotope labeling (SIL) techniques have the potential to enhance different aspects of liquid chromatography–high-resolution mass spectrometry (LC-HRMS)-based untargeted metabolomics methods including metabolite detection, annotation of unknown metabolites, and comparative quantification. In this work, we present MetExtract II, a software toolbox for detection of biologically derived compounds. It exploits SIL-specific isotope patterns and elution profiles in LC-HRMS(/MS) data. The toolbox consists of three complementary modules: M1 (AllExtract) uses mixtures of uniformly highly isotope-enriched and native biological samples for selective detection of the entire accessible metabolome. M2 (TracExtract) is particularly suited to probe the metabolism of endogenous or exogenous secondary metabolites and facilitates the untargeted screening of tracer derivatives from concurrently metabolized native and uniformly labeled tracer substances. With M3 (FragExtract), tandem mass spectrometry (MS/MS) fragments of corresponding native and uniformly labeled ions are evaluated and automatically assigned with putative sum formulas. Generated results can be graphically illustrated and exported as a comprehensive data matrix that contains all detected pairs of native and labeled metabolite ions that can be used for database queries, metabolome-wide internal standardization, and statistical analysis. The software, associated documentation, and sample data sets are freely available for noncommercial use at .

Stable Isotope-Assisted Metabolomics for Deciphering Xenobiotic Metabolism in Mammalian Cell Culture

“…The MetExtract II workflow (Bueschl et al 2017) was successfully adapted to cell culture experiments employing human cell models. The workflow provides an efficient way to detect novel biotransformation products of any xenobiotic with the only requirement that isotopically labeled substances need to be available.…”

“…In order to capture all detectable biotransformation products of DON, the TracExtract approach, a modul of MetExtract II, (Bueschl et al 2017) was utilized. As the exogenous DON was applied as a mixture of both native and uniformly 13 C15-labeled toxin and similar metabolization of both forms can be assumed, all biotransformation products of DON formed in the cell cultures would also be present as a native and 13 Clabeled form, while any other metabolite in the cell culture sample itself would only be present as a purely native form but not as a 13 C-labeled form.…”

“…Advanced bioinformatics tools for the extraction of the desired information from generated data frequently represent a major bottle neck (Gertsman and Barshop 2018). A powerful tool for the elucidation of novel metabolic pathways and respective data analysis is the recently developed MetExtract II algorithm (Bueschl et al 2017). Concurrent analysis of stable isotopically labeled and native sample material allows the automated and comprehensive extraction of metabolic features relevant for the metabolism of practically any investigated small molecule.…”

“…Concurrent analysis of stable isotopically labeled and native sample material allows the automated and comprehensive extraction of metabolic features relevant for the metabolism of practically any investigated small molecule. The practicability and power of this approach has already been proven in a number of plantbased experiments (Kluger et al 2013;Bueschl et al 2017;Meng-Reiterer et al 2015;Chassy et al 2015;Nathanail et al 2015).…”

New tools and resources in metabolomics: 2016–2017

“…MetExtract II is a software for detection of biologically derived compounds which exploits SIL‐specific isotope patterns and elution profiles in LC‐HRMS(/MS) data . It consists of three complementary modules: M1 (AllExtract), M2 (TracExtract), and M3 (FragExtract) aiding in identification of all labelled ions.…”