An Open Software Development-based Ecosystem of R Packages for Metabolomics Data Analysis
Creators: name: Rainer, Johannes
name: Louail, Philippine
name: Vicini, Andrea
name: Gine, Roger
name: Badia, Josep M
name: Stravs, Michele
name: Garcia-Aloy, Mar
name: Huber, Carolin
name: Salzer, Liesa
name: Stanstrup, Jan
name: Shahaf, Nir
name: Panse, Christian
name: Naake, Thomas
name: Kumler, William
name: Vangeenderhuysen, Pablo
name: Brunius, Carl
name: Hecht, Helge
name: Neumann, Steffen
name: Witting, Michael
name: Gibb, Sebastian
name: Gatto, Laurent
Publisher: name: Zenodo
Year: 2024
Subjects: Metabolomics
Mass Spectrometry
Open Software Development
Annotation

description: A frequent problem with scientific research software is the lack of support, maintenance and further development. In particular, development by a single researcher can easily result in orphaned software packages, especially if combined with poor documentation or lack of adherence to open software development standards.

The RforMassSpectrometry initiative aims to develop an efficient and stable infrastructure for mass spectrometry (MS) data analysis. As part of this initiative, a growing ecosystem of R software packages is being developed covering different aspects of metabolomics and proteomics data analysis.  To avoid the aforementioned problems, community contributions are fostered, and open development, documentation and long-term support emphasized.

At the heart of the package ecosystem is the Spectra package that provides the core infrastructure to handle and analyze MS data. Its design allows easy expansion to support additional file or data formats including data representations with minimal memory footprint or remote data access. The xcms package for LC-MS data preprocessing was updated to reuse this infrastructure, enabling now also the analysis of very large, or remote, data. This integration simplifies in addition complete analysis workflows which can include the MsFeatures package for compounding, and the MetaboAnnotation package for annotation of untargeted metabolomics experiments. Public annotation resources can be easily accessed through packages such as MsBackendMassbank, MsBackendMgf, MsBackendMsp or CompoundDb, the latter also allowing to create and manage lab-specific compound databases. Finally, the MsCoreUtils and MetaboCoreUtils packages provide efficient implementations of commonly used algorithms, designed to be re-used in other R packages. Ultimately, and in contrast to a monolithic software design, the package ecosystem enables to build customized, modular, and reproducible analysis workflows.

Future development will focus on improved data structures and analysis methods for chromatographic data, and better interoperability with other open source softwares including a direct integration with Python MS libraries.
description: contact: johannes.rainer@eurac.edu

 

R for Mass Spectrometry documentation and tutorials/workshops:



R for Mass Spectrometry book

Mass Spectrometry Data Analysis with Spectra

Exploring and Analyzing LC-MS data with Spectra and xcms

Streamlining LC-MS/MS data analysis in R with open-source xcms and RforMassSpectrometry: an end-to-end workflow