MetMatch

MetMatch


MetMatch is a software tool for the semi-automated comparison of different LC-HRMS chromatograms of untargeted metabolomics experiments. It provides methods to correct the raw-LC-HRMS data for m/z and retention time shifts relative to one or several preprocessed reference chromatograms.


  • M/Z deviation correction
    MetMatch detects and corrects systematic bias in the m/z dimension of LC-HRMS data. For this step, search frames are used, which contain the likely chromatograpic peaks corresponding to a certain reference feature. Then, an overall m/z deviation is calculated using all signals from within the respective search frames.

  • Chromatographic and m/z alignment
    MetMatch uses a novel data alignment algorithm to correct retention time shifts using the local neighborhood of reference features. The iterative approach of MetMatch refines the alignment with each step and different alignment configurations can be easily tested with the comprehenise user interface and the animated illustration of the alignment process.

  • Flexibility
    MetMatch uses the open-data format mzXML to read and write LC-HRMS data. Thus, it is capable to work with virtually any LC-HRMS instrument. Moreover, MetMatch uses the TSV file format for the reference feature list, which can be generated with many of the currently avaialble software tools for untargeted data evaluation (e.g. XCMS). MetMatch then extends this feature matrix and also generated corrected mzXML files, which can be further processed.

MetMatch has been tested with modern LC-HRMS instruments including Thermo Fisher Orbitrap and Agilent QToF instruments. The software, associated documentation and sample datasets are avaialble free of charge and warranty.


Download & installation

Download for Windows 7

Download the file and double-click it to start the installation process.

R-Configuration

R will be automatically configurated upon installation of MetMatch. If not, please refer to the documentation for correctly configuring your system.

Documentation

Documentation of MetExtract is included with the download or available here.

Screenshots

Supported experiments

MetMatch is designed for the automated processing of LC-HRMS datasets. It calculates, aligns and corrects putative m/z and retention time deviation shifts between different measurement sequences or batches. Additionally, MetMatch is also capable of addressing the problem of different ion formation, which can be observed after a change of elution solvents.
MetMatch requires at least two experiments:
A reference dataset, which has to be processed with a software tool to detect the biologically relevant features, is used as a template.
One or more target datasets are then aligned to the reference dataset using the generated feature list.

MetMatch uses the open-data format mzXML to read and write LC-HRMS data. Thus, it virtually supports all different kinds of LC-HRMS instruments and vendors and has been tested with datasets obtained from an LTQ Orbitrap XL instrument (Thermo Fisher Scientific) and a 6550 QTOF instrument (Agilent technologies).

Sample dataset

Sample data from the publication used for the simulated datasets.

The provided dataset consists of the LC-HRMS sample used for creating the simulated datasets in the publication of the software. The following different files are required for reproducing these results:


Chromatogram (36 MB)
This file is the LC-HRMS sample used for generating the simulated reference list and alignment of the data to this lists. It was recorded on an LTQ Orbitrap XL instrument in the positive ESI mode.


Simulation 1
A constant Rt shift was assumed. See left figure for an illustration of the applied retention time shift.


Simulation 2
Monotonically increasing linear Rt shift. See left figure for an illustration of the applied retention time shift.


Simulation 3
Discontinuous Rt shift, as may e.g. happen by a defective LC-pump. See left figure for an illustration of the applied retention time shift.


Simulation 4
Non-linear Rt shift without inflection. See left figure for an illustration of the applied retention time shift.


Simulation 5
Non-linear Rt shift with inflection. See left figure for an illustration of the applied retention time shift.


Simulation 6
Complex non-linear Rt shift based on the type of Rt shift observed in the real-world wheat experiment. See left figure for an illustration of the applied retention time shift.


Documentation

Documentation of the MetMatch software is available as a part of the software or can be downloaded here

The source code of MetMatch is available on https://github.com/S-T-K/MetMatch



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.
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