Abstract
BackgroundMetabolomics 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.ResultsThe 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.ConclusionsQCScreen 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0783-x) contains supplementary material, which is available to authorized users.
Highlights
Metabolomics experiments often comprise large numbers of biological samples resulting in huge amounts of data
While some of the available comprehensive software programs for the processing of metabolomics data support different quality control (QC) checks [7, 13,14,15], to the best of the authors knowledge no free, standalone software tool is available that provides a quick and intuitive assessment of quality in liquid chromatography-high resolution mass spectrometry (LC-HRMS) raw data from several measurement sequences based on the inspection of basic quality-related parameters
For each evaluated parameter i.e. extracted ion chromatograms (EICs), Retention time (tR), mass accuracy and feature area, the results are plotted against the order of the data files
Summary
Biological experiments often include measurements over more than one measurement sequence. For time series experiments involving several biological replicates per time point, organism and condition, measurements can extend over several days or even weeks, as was the case for the presented biological experiment, which served as basis for the development of QCScreen In such cases, parameters like retention time, mass accuracy and feature area may drift or shift due to changes in MS instrument sensitivity or chromatographic separation. Verification of QCScreen results To verify that data processing by QCScreen yields consistent and valid results, automatically generated data were compared to manually derived EIC peak area, retention time as well as mass accuracy To this end, the LC-HRMS raw data of the above described QC standards were evaluated by the Thermo Xcalibur software. For a detailed comparison between QCScreen and manually derived results see Additional file 1
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