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Review
. 2018;14(6):72.
doi: 10.1007/s11306-018-1367-3. Epub 2018 May 18.

Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies

Affiliations
Review

Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies

David Broadhurst et al. Metabolomics. 2018.

Abstract

Background: Quality assurance (QA) and quality control (QC) are two quality management processes that are integral to the success of metabolomics including their application for the acquisition of high quality data in any high-throughput analytical chemistry laboratory. QA defines all the planned and systematic activities implemented before samples are collected, to provide confidence that a subsequent analytical process will fulfil predetermined requirements for quality. QC can be defined as the operational techniques and activities used to measure and report these quality requirements after data acquisition.

Aim of review: This tutorial review will guide the reader through the use of system suitability and QC samples, why these samples should be applied and how the quality of data can be reported.

Key scientific concepts of review: System suitability samples are applied to assess the operation and lack of contamination of the analytical platform prior to sample analysis. Isotopically-labelled internal standards are applied to assess system stability for each sample analysed. Pooled QC samples are applied to condition the analytical platform, perform intra-study reproducibility measurements (QC) and to correct mathematically for systematic errors. Standard reference materials and long-term reference QC samples are applied for inter-study and inter-laboratory assessment of data.

Keywords: Long-term reference (LTR) QC samples; Pooled QC samples; Quality assurance (QA); Quality control (QC); Standard reference materials (SRMs); System suitability samples.

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Conflict of interest statement

Compliance with ethical standardsThe authors have no disclosures of potential conflicts of interest related to the presented work.No research involving human or animal participants was performed in the construction of this manuscript.

Figures

Fig. 1
Fig. 1
Example of typical data acquired for a system suitability sample. Here, a seven component system suitability sample has been applied in a HILIC positive ion assay and includes an early elution metabolite (decanoic acid) and later elution metabolites. Leucine and isoleucine are included to assess chromatographic resolving power for isomers. The base peak chromatograms are shown for each metabolite to assess peak symmetry with retention time and m/z calculated to assess chromatographic stability and mass accuracy
Fig. 2
Fig. 2
Visualisation of how a pooled QC sample is prepared from aliquots of the study biological samples from which aliquots of the pooled QC sample are extracted for analysis in an identical manner as for the study biological samples
Fig. 3
Fig. 3
A typical PCA scores plot for a data set deemed of high quality, as the QC data points cluster tightly in comparison to the total variance in the projection
Fig. 4
Fig. 4
For a given metabolite peak, the measured response can be plotted against injection order (excluding conditioning samples and blanks) and the time varying systematic variation in metabolite response observed (a). The systematic variation can be modelled, in this case using a regularised cubic spline with a smoothing parameter. The optimal smoothing parameter value is the one with the lowest cross-validated error (b). The ‘correction curve’ can then be subtracted from the raw data (c). Accurate measures of precision after the correction can then be calculated (d). Red squares are QC samples, blue circles are study samples
Fig. 5
Fig. 5
When pooled QC samples drawn from an identical source are used across multiple analytical batches then it is also possible to correct for inter-batch systematic error. First, a grand mean is calculated across all batches, and then difference between each batch mean and the grand mean is subtracted from all the samples in that batch. Red squares are QC samples, blue, green and yellow circles are study samples from batches 1, 2, and 3, respectively
Fig. 6
Fig. 6
A typical analysis order applied for an untargeted metabolomics assay is composed of system suitability samples at the start and end of the analytical batch and pooled QC samples analysed at the start of the run (typically 10 injections with 8 system conditioning QC samples followed by 2 QC samples for QC processes and signal correction), at the end of the run (typically 2 injections) and periodically during the analysis of biological samples (typically every 5–10 biological samples). A system suitability blank sample is analysed at the start of the analytical batch, a blank extraction sample is typically analysed twice, and a standard reference material is analysed three times during an analytical run. If MS/MS data acquisition is not applied for each biological sample, then a set of pooled QC samples can be applied separately at the end of the run for MS/MS data acquisition

Comment in

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