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Updated: Jul 14, 2025

Untargeted Metabolomics from Biological Sources Using Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry UPLC-HRMS
Published on: May 20, 2013
MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass
Thomas Naake1, Johannes Rainer2, Wolfgang Huber1
1Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
Motivation:
Multiple factors can impact accuracy and reproducibility of mass spectrometry data. There is a need to integrate quality assessment and control into data analytic workflows.
Results:
The MsQuality package calculates 43 low-level quality metrics based on the controlled mzQC vocabulary defined by the HUPO-PSI on a single mass spectrometry-based measurement of a sample. It helps to identify low-quality measurements and track data quality. Its use of community-standard quality metrics facilitates comparability of quality assessment and control (QA/QC) criteria across datasets.
Availability And Implementation:
The R package MsQuality is available through Bioconductor at https://bioconductor.org/packages/MsQuality.
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