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# MsQuality [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](]( ![R-CMD-check-bioc]( [![](]( [![license](]( Calculation of QC metrics from mass spectrometry data ## Description Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the `MsQuality` package, which 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 Proteome Organization-Proteomics Standards Intitiative (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): while it is easier to control for high-quality data acquisition in small-scale experiments, typically run in one or few batches, clinical data sets are often acquired over longer time frames and are prone to higher technical variation that is often unnoticed. `MsQuality` tries to address this problem by calculating metrics that can be stored along the spectral data sets (raw files or feature-extracted data sets). `MsQuality`, thus, facilitates the tracking of shifts in data quality and quantifies the quality using multiple metrics. It should be thus easier to identify samples that are of low quality (high-number of missing values, termination of chromatographic runs, low instrument sensitivity, etc.). 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. The list included in the `mzQC` framework is excessive, also including metrics that rely on more high-level information, that might not be readily accessible from .raw or .mzML files, e.g. pump pressure mean, or rely on alignment results, e.g. retention time mean shift, signal-to-noise ratio, precursor errors (ppm). The `MsQuality` package is built upon the `Spectra` and the `MsExperiment` package. Metrics will be calculated based on the information stored in a `Spectra` object, thus, the spectral data of each sample should be stored in one `Spectra` object. The `MsExperiment` serves as a container to store the mass spectral data of multiple samples. `MsQuality` enables the user to calculate quality metrics both on `Spectra` and `MsExperiment` objects. ## Contact You are welcome to * write a mail to <thomasnaake (at) googlemail (dot) com> * submit suggestions and issues: <> * send a pull request: <> ## Install `MsQuality` is available via Bioconductor. To install the package, users can either install from the [devel branch]( or from the current [RELEASE branch]( To install `MsQuality`, you have first to install the [`BiocManager`]( and [remotes]( package: ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") ``` Install the `MsQuality` package then via ```r ## to install from Bioconductor BiocManager::install("MsQuality") ## to install the development version from GitHub BiocManager::install("tnaake/MsQuality") ```