The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.