Use Cases and Examples for Annotation of Untargeted Metabolomics Data

This repository provides use cases and examples for the annotation of non-target metabolomics or small compound MS data using the MetaboAnnotation and MetaboCoreUtils R packages. Refer to the original article A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R to cite this package/repository or any functionality described here.

Installation

Requirements: R version >= 4.2 (and hence Bioconductor 3.15) is needed.

The R packages as well as the example files used in this document can be installed with the R code below:

install.packages("BiocManager")
BiocManager::install("jorainer/MetaboAnnotationTutorials",
    dependencies = TRUE, ask = FALSE, update = TRUE)

Alternatively, the packages can be installed individually with:

install.packages("BiocManager")
BiocManager::install("ProtGenerics")

## Packages with low-level core functionality
BiocManager::install("MsCoreUtils")
BiocManager::install("MetaboCoreUtils")

## Packages with high-level user functionality
BiocManager::install("Spectra")
BiocManager::install("MetaboAnnotation")
BiocManager::install("CompoundDb")

## Support for MGF files
BiocManager::install("MsBackendMgf")

## Support for MassBank
BiocManager::install("MsBackendMassbank")

## Support for MSP files
BiocManager::install("MsBackendMsp")

The source code for this document along with the test data can be downloaded from the github repository https://github.com/jorainer/MetaboAnnotationTutorials with the command (or alternatively downloading the zip archive directly from the github page).

git clone https://github.com/jorainer/MetaboAnnotationTutorials

Contribution

For contributions, see the RforMassSpectrometry contributions guideline.

Code of Conduct

See the RforMassSpectrometry Code of Conduct.

Additional documentation resources and tutorials

• Tutorial with additional examples and explanations for MS2-based annotations: https://jorainer.github.io/SpectraTutorials/
• Repository of the MsCoreUtils package: https://rformassspectrometry.github.io/MsCoreUtils/
• Repository of the MetaboCoreUtils package: https://rformassspectrometry.github.io/MetaboCoreUtils/
• Repository of the Spectra package: https://rformassspectrometry.github.io/Spectra/
• Repository of the MetaboAnnotation package: https://rformassspectrometry.github.io/MetaboAnnotation/
• Repository of the CompoundDb package: https://rformassspectrometry.github.io/CompoundDb/