Documentation

Documentation

Ample documentation is provided within each individual package. All package vignettes are also available Each package provides specific documentation.

In addition, a comprehensive book as well as tutorials and workshops are available showing how the functionality from different packages can be combined into specific analysis workflows.

R for Mass Spectrometry Book

The R for Mass Spectrometry book provides a good introduction into the ecosystem of the R for Mass Spectrometry packages. It is continuously expanded to include additional topics and example use cases.

Tutorials/workshops

Specific use cases and extended analysis workflows are also presented as workshops (tutorials). They usually come with a dedicated docker image that provides the workshop’s source code along with all data and an R installation which includes all required packages ensuring full reproducibility.

• Metabonaut: collection of tutorials and workflows for MS-based metabolomics data analysis including a complete end-to-end metabolomics data analysis workflow.
• SpectraTutorials: provides 3 tutorials explaining internals, properties and extensions of the Spectra package and the provided infrastructure to handle and process mass spectrometry data.
• xcms4gnps2: example workflow for an xcms-based preprocessing of an LC-MS/MS data set and export of the results in a format suitable for feature based molecular networking (FBMS) with GNPS.
• xcmsTutorials: explains general mass spectrometry data handling with Spectra and analysis of LC-MS data with the xcms package.
• MetaboAnnotationTutorials: use cases and examples for annotation of untargeted metabolomics data using the MetaboAnnotation package.