Concepts and Software Package for Efficient Quality Control in Targeted Metabolomics Studies: MeTaQuaC

Targeted
quantitative mass spectrometry metabolite profiling is
the workhorse of metabolomics research. Robust and reproducible data
are essential for confidence in analytical results and are particularly
important with large-scale studies. Commercial kits are now available
which use carefully calibrated and validated internal and external
standards to provide such reliability. However, they are still subject
to processing and technical errors in their use and should be subject
to a laboratory’s routine quality assurance and quality control
measures to maintain confidence in the results. We discuss important
systematic and random measurement errors when using these kits and
suggest measures to detect and quantify them. We demonstrate how wider
analysis of the entire data set alongside standard analyses of quality
control samples can be used to identify outliers and quantify systematic
trends to improve downstream analysis. Finally, we present the MeTaQuaC
software which implements the above concepts and methods for Biocrates
kits and other target data sets and creates a comprehensive quality
control report containing rich visualization and informative scores
and summary statistics. Preliminary unsupervised multivariate analysis
methods are also included to provide rapid insight into study variables
and groups. MeTaQuaC is provided as an open source R package under
a permissive MIT license and includes detailed user documentation.