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QCScreen: a software tool for data quality control in LC-HRMS based metabolomics.

Alexandra Maria Simader1, Bernhard Kluger2, Nora Katharina Nicole Neumann3

  • 1Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln, Austria. alexandra.simader@boku.ac.at.

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Summary

QCScreen software provides rapid quality control for liquid chromatography-high resolution mass spectrometry (LC-HRMS) metabolomics data. It quickly identifies potential errors, ensuring reliable results before extensive analysis.

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Area of Science:

  • Metabolomics
  • Analytical Chemistry
  • Biotechnology

Background:

  • Metabolomics experiments generate vast datasets requiring quality assessment.
  • Detecting errors like retention time or mass accuracy shifts is crucial for data reliability.
  • Liquid chromatography-high resolution mass spectrometry (LC-HRMS) demands rigorous quality control for comparable results.

Purpose of the Study:

  • To develop QCScreen, a software tool for efficient data quality checks in LC-HRMS metabolomics.
  • To enable flexible investigation and comparison of quality parameters across multiple samples and sequences.
  • To provide automated evaluation of quality control samples and experimental data.

Main Methods:

  • QCScreen software was developed for automated quality control of LC-HRMS data.
  • It analyzes user-defined target features and quality-related parameters.
  • The software processes data from multiple sample types across various measurement sequences.

Main Results:

  • QCScreen offers a user-friendly interface for easy parameter selection and processing.
  • Generated outputs include overview plots and detailed illustrations of chromatographic stability, mass accuracy, and detector sensitivity.
  • The software successfully identified problematic features, samples, and analytical parameters in experimental metabolomics data.

Conclusions:

  • QCScreen is an open-source tool for assessing LC-HRMS data suitability before detailed analysis.
  • It supports the generic mzXML format, compatible with diverse LC-HRMS platforms.
  • The software facilitates processing of both quality control and experimental samples across multiple sequences.