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. 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 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.