CPExtract

CPExtract


CPExtract is a software tool for stable isotope labeling (SIL) assisted untargeted metabolomics research using liquid chromatography high resolution mass spectrometry (LC-HRMS). It is designed to detect diagnostic isotopolog patterns that originate from labeling experiments and are characteristic for certain tracer compounds. These isotopolog patterns should be sufficiently different from the normal native isotopolog patterns in order to be a reliable criteria for metabolite annotation. Moreover, CPExtract is not intended for fluxomics applications.

The software, associated documentation and a sample dataset are avaialble free of charge and warranty and have been tested with modern LC-HRMS instruments. The tool imports LC-HRMS data using the mzXML of mzML data formats and report the processing results as TSV files.


Download & installation

Download for Windows 10

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 CPExtract 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 CPExtract is part of the download.

Screenshots

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Sample dataset

Fusarium graminearum with malonic acid tracer for the detection of polyketides (and similar compounds made from C2 units). From the publication of CPExtract (DOI: XXX)

Standard tracer approach
1,2,3-13C3-malonic acid diethyl ester in Fg cultures
Reversed tracer approach
Malonic acid monomethyl ester in U-13C-labeled Fg cultures

Trichoderma reesei with malonic acid tracer for the detection of polyketides (and similar compounds made from C2 units). From the publication of CPExtract (DOI: XXX)

Standard tracer approach
1,2,3-13C3-malonic acid diethyl ester in Tr cultures
Reversed tracer approach
Malonic acid monomethyl ester in U-13C-labeled Tr cultures

Supported experiments

CPExtract supports stable isotope labeling experiments with isotope enriched metabolite samples. In general several atoms of the labeling-element (e.g. carbon) must be labeled. The isotope patterns are can be specified via a set of user-defined rules. These rules check the presence or absence of certain isotopologs as well as ratios between them. In order to be even more versatile, the software also works with uniformly 13C-labeled samples that use native tracer compounds.
The image on the right side shows an isotope pattern, that can be detected with CPExtract. Using the generic rules, the software will also find similar isotopolog patterns that consist of at least three [13C]-2 isotopologs.

Documentation

Documentation of the CPExtract software is available as a part of the software.

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

References

Sample applications using CPExtract are:

  • TODO
    Seidl et al. (XXX) XXX







Disclaimer
All rights reserved
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.
Photo by Vojtěch Petr on Unsplash
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