QCScreen: a software tool for data quality control in LC-HRMS based metabolomics.
BACKGROUND
Metabolomics experiments often comprise large numbers of biological samples resulting in huge amounts of data. This data needs to be inspected for plausibility before data evaluation to detect putative sources of error e.g. retention time or mass accuracy shifts. Especially in liquid chromatography-high resolution mass spectrometry (LC-HRMS) based metabolomics research, proper quality control checks (e.g. for precision, signal drifts or offsets) are crucial prerequisites to achieve reliable and comparable results within and across experimental measurement sequences. Software tools can support this process.


RESULTS
The software tool QCScreen was developed to offer a quick and easy data quality check of LC-HRMS derived data. It allows a flexible investigation and comparison of basic quality-related parameters within user-defined target features and the possibility to automatically evaluate multiple sample types within or across different measurement sequences in a short time. It offers a user-friendly interface that allows an easy selection of processing steps and parameter settings. The generated results include a coloured overview plot of data quality across all analysed samples and targets and, in addition, detailed illustrations of the stability and precision of the chromatographic separation, the mass accuracy and the detector sensitivity. The use of QCScreen is demonstrated with experimental data from metabolomics experiments using selected standard compounds in pure solvent. The application of the software identified problematic features, samples and analytical parameters and suggested which data files or compounds required closer manual inspection.


CONCLUSIONS
QCScreen is an open source software tool which provides a useful basis for assessing the suitability of LC-HRMS data prior to time consuming, detailed data processing and subsequent statistical analysis. It accepts the generic mzXML format and thus can be used with many different LC-HRMS platforms to process both multiple quality control sample types as well as experimental samples in one or more measurement sequences.
Center 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.
Alexandra Maria
AM
Simader
Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln, Austria. bernhard.kluger@boku.ac.at.
Bernhard
B
Kluger
Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln, Austria. nora.neumann@boku.ac.at.
Nora Katharina Nicole
NK
Neumann
Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln, Austria. christoph.bueschl@boku.ac.at.
Christoph
C
Bueschl
Institute for Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln, Austria. marc.lemmens@boku.ac.at.
Marc
M
Lemmens
University of Applied Sciences Upper Austria, School of Informatics, Communications and Media, Softwarepark 11, 4232, Hagenberg, Austria. gerald.lirk@fh-hagenberg.at.
Gerald
G
Lirk
Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln, Austria. rudolf.krska@boku.ac.at.
Rudolf
R
Krska
Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln, Austria. rainer.schuhmacher@boku.ac.at.
Rainer
R
Schuhmacher
D002851:Chromatography, High Pressure Liquid / Q000592:standards; D016247:Information Storage and Retrieval; D013058:Mass Spectrometry / Q000592:standards; D055432:Metabolomics / Q000592:standards; D011786:Quality Control; D012984:Software