MetExtract II

MetExtract II 2.7.0


MetExtract II is a software tool for stable isotope labeling (SIL) assisted untargeted metabolomics research using liquid chromatography high resolution mass spectrometry (LC-HRMS). It comprises of 3 modules:

  • AllExtract
    This module requires LC-HRMS data obtained from samples containing both native and uniformly as well as highly (≥98%) isotopically enriched samples material. AllExtract detects metabolite ions using the mirror-symmetric isotopolog patterns. Any substances that do not show these charaterisitica are discarded as non-sample derived compounds. Thus, this module efficiently detects only metabolites of the studied biological system. Additionally, using experiment- and metabolome wide internal standardisation, the analytical precision of the measurements and consequently the subsequently performed statistical analysis of the experiment are improved.

  • TracExtract
    This module is designed to investigate the metabolic fate of precursor substances (tracers) and requires the tracer to be applied as both a native and a highly isotopically enriched form. It mainly supports biotransformation experiments using secondary metabolites or such compounds, which are not heavily fragmented in the biological system and incorporated as larger parts in downstream secondary metabolites. Other than the AllExtract module, it is not designed to detect all metabolites of the biological system but will only report the biotransformation products of the studied tracer.

  • FragExtract
    The last module of MetExtract II is designed for processing LC-HRMS/MS datasets derived from MS/MS experiments of native and highly isotopically enriched metabolite ions. Using the distinct characteristics of SIL, FragExtract is able to efficiently clean and annotate the fragmentation spectra of unknown metabolites therefor supporting metabolite annotation and identification.

The software, associated documentation and sample datasets are avaialble free of charge and warranty and have been tested with modern LC-HRMS instruments including Thermo Fisher Orbitrap and Agilent QToF instruments. The tools import LC-HRMS data using the mzXML of mzML data formats and report the processing results as TSV files.


Download & installation

Download for Windows 7 (version 2.7.0, discontinued)

Download and follow the instructions of the setup. It will also ask to install and configure R 3.2.2 automatically. Any existing R-installations will not be affected by this installation.

Download for Windows 10 (version 2.11.6)

Download and follow the instructions of the setup. It will also ask to install and configure R 3.3.2 automatically. Any existing R-installations will not be affected by this installation. Certain anti-virus software may cause a problem during the installation / after the first start of MetExtract II when it tries to install a couple of R-packages. Please deactivate your anti-virus software during the installation / the software's first start.

Documentation

Documentation of MetExtract II is part of the download.

R packages

Required R packages should install automatically. If not, please download them here and extract them to the folder.

OBO files

Depending on the used mzML converter, an additional obo file might be required. Please find these files at https://bioportal.bioontology.org/ontologies/MS.

Screenshots

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Sample dataset

Sample data from the publication of MetExtract II (DOI: 10.1021/acs.analchem.7b02518)

AE_Std
This dataset consists of one LC-HRMS measurement presented by Bueschl et al. 2012. It contains 15 native and uniformly 13C-labeled fungal substances in a complex non-labeled Fusarium graminearum extract, which is used as simulated contaminants
AE_Wheat
This datasets consits of five LC-HRMS measurments of native and uniformly 13C-labeled wheat ear samples.
TE_DiW
This dataset demonstrates the detection of biotransformation products of a studied tracer substance. It is taken from Kluger et al. 2012
ATE_Blanks
This datasets demonstrates the high specificity of the AllExtract and the TracExtract modules. The LC-HRMS samples only contain non-labeled, native wheat material. Thus, no metabolites or biotransformation products should be detected by AllExtract or TracExtract. The corresponding LC-HRMS samples are included in the AE_Wheat and TE_DiW datasets and have been processed with the datasets AE_Wheat and TE_DiW. The filenames of the corresponding blank samples have "12C" included.
FE_PPAs
This dataset demonstrates the spectral cleaning and fragment annotation of the FragExtract module using 3 phenylpropanoid amides.

Supported experiments

MetExtract II supports stable isotope labeling experiments with highly isotope enriched metabolite samples. In general several atoms of the labeling-element (e.g. carbon) must be labeled uniformly (i.e. all those atoms have the same chance to be the labeling-isotope (e.g. 13C)). This isotopic enrichment must also be very high (e.g. higher than 98%) to achieve a separate and distinct isotope pattern in the LC-HRMS data. Overlapping isotope patterns resulting from a low isotopic enrichment are not supported. Furthermore, unequal labeling degrees or scrambled isotope patterns are also not supported by MetExtract II.
In general, the two isotope patterns derived from native and labeled ions of the same metabolite must look like the ones on the left side (see documentation for further details)

Documentation

Documentation of the MetExtract II software and its three module (AllExtract, TracExtract and FragExtract) are available as a part of the software.

The source code of MetExtract II can be found on GitHub project MetExtract-II (https://github.com/chrboku/MetExtract-II).

References

Sample applications using MetExtract II are:

  • Stable isotopic labelling-assisted untargeted metabolic profiling reveals novel conjugates of the mycotoxin deoxynivalenol in wheat
    Kluger et al. (2013) Anal and Bioanal Chem. 405(15):5031-6. DOI:10.1007/s00216-012-6483-8

  • A novel stable isotope labelling assisted workflow for improved untargeted LC–HRMS based metabolomics research
    Bueschl, Kluger et al. (2014) Metabolomics. 10(4):754-69 DOI:10.1007/s11306-013-0611-0

  • Automated LC-HRMS(/MS) approach for the annotation of fragment ions derived from stable isotope labeling-assisted untargeted metabolomics
    Neumann et al. (2014) Analytical Chemistry. 86(15):7320-7 DOI: 10.1021/ac501358z

  • Untargeted profiling of tracer derived metabolites using stable isotopic labeling and fast polarity switching LC-ESI-HRMS
    Kluger, Bueschl et al. (2014) Analytical Chemistry. 86(23):11533-7 DOI: DOI: 10.1021/ac503290j

  • Metabolism of HT-2 Toxin and T-2 Toxin in Oats
    Meng-Reiterer et al. (2016) toxins. 8(12)) DOI: DOI: 10.3390/toxins8120364

  • Transcription factor Xpp1 is a switch between primary and secondary fungal metabolism
    Derntl et al. (2016) PNAS. 114(4):E560-E569 DOI: DOI: 10.1073/pnas.1609348114

  • MetExtract II: A software suite for stable isotope assisted untargeted metabolomics
    Bueschl et al. (2017) Analytical Chemistry. DOI: DOI: 10.1021/acs.analchem.7b02518






Disclaimer
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
University of Natural Resources and Life Sciences, Vienna
Center for Analytical Chemistry, IFA-Tulln
Konrad-Lorenz-Straße 20
3430 Tulln, Austria
e-mail: rainer.schuhmacher@boku.ac.at