[](https://www.repostatus.org/#active) # The `hdxmsqc` package The [**hdxmsqc**] (Hydrogen-Deuterium Exchange Mass spectrometry quality control) package is an R/Bioconductor package for HDX-MS quality control. The package allows the enconding of experimental design, dedicated storage, quality control visualisation and metrics. Whilst many tools metrics are difficult to understand, unintpretable or rely on using a particular preprocessing software. `hdxmsqc` can examine any data that can be formatted correctly into a `QFeatures` object. # Installation requirements Users will require a working version of R, currently at least version >4. It is recommended to use [RStudio](https://www.rstudio.com). The package can then be installed using the `devtools` package. The package should take a few minutes to install on a regular desktop or laptop. The package will need to be loaded using `library(hdxmsqc)` # Basic ideas and concepts The [`hdxmsqc`] package implements quality control metrics for hdx-ms data. Data from form such experiments most commonly yield a matrix of measurements where we have peptides along the rows, and samples (timepoints/conditions) along the columns. Assessing the quality of `hdxmsqc` data can be challenging and laborious. This package seeks to streamline this analysis and provide a uniform way to present quality control of data. To use `hdxmsqc` the data must be stored as a `QFeatures`/`Spectra`, as implemented in the Bioconductor [`RForMassSpectrometry`](https://www.rformassspectrometry.org/) packages. There are functions within the package to coherse the data into the correct format. # Vignettes There is currently one vignette in the package which runs through the analysis. Analysis is designed to be quick. Though assessing the quality of Spectra can take longer. # Documentation Functions are documented and be founded in the `Help` # Contribution Contributions are welcome, please open an issue so ew can discuss any contribution in advance # Feature requests This package is actively being developed and maintained, please open Github issue if you would like to request or discuss a particular feature. # Licensing The package is free to use for academic and commerical users at no cost. Commerical users who need help installing on internal systems or more elaborate requests designed for their infrastructure may contact us.