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xcms-based LC-MS/MS data preprocessing for FBMN with GNPS2

License: CC BY-NC 4.0
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This repository contains an example workflow for preprocessing and preparation of an LC-MS/MS data set using xcms for feature-based molecular networking (FBMN) with GNPS2.

Analysis workflow

xcms-based preprocessing for FBMS with GNPS

This workflow explains preprocessing of a public LC-MS/MS data set with xcms and export of the results for feature-based molecular networking with GNPS.

🎥 a video recording of a presentation of this workshop is available at https://youtu.be/yc6fsegFg-k.

📌 Reproducibility & Usage

The current version of the workshop runs with packages from Bioconductor release 3.23 with the exception of the MsBackendMassIVE package that needs to be installed from GitHub as it currently only available in Bioconductor development branch.

There are 3 ways to use/read this workflow:

Reading

The workflow is available as pre-rendered web page xcms4gnps.

Interactive evaluation using Docker

In addition, a docker image is available allowing to run the workflow interactively:

  • If you don’t already have, install docker. Find installation information here.
  • Get the docker image of this tutorial e.g. from the command line with:
docker pull jorainer/xcms4gnps2:RELEASE_3_23

This installs a docker image with the correct R version, the required data files and Bioconductor packages to run this analysis.

  • Start the docker container, either through the Docker Desktop app, or on the command line with
docker run -e PASSWORD=bioc -p 8787:8787 jorainer/xcms4gnps2:RELEASE_3_23
  • Enter http://localhost:8787 in a web browser and log in with username rstudio and password bioc.
  • In the RStudio server version: open any of the Quarto files in the vignettes folder and evaluate the R code blocks in that document.

⚠️ Any changes to a file in the docker image are transient. To keep any changes to the document it is suggested to download the respective file before closing the session.

ℹ️ macOS users might need to emulate an AMD64 CPU to run the docker image:

docker pull --platform linux/amd64 jorainer/xcms4gnps2:latest
docker run --platform linux/amd64 -e PASSWORD=bioc -p 8787:8787 jorainer/xcms4gnps2:latest

Interactive evaluation using local installation

As an alternative to the docker-based workshop, it is also be possible to run and evaluate the workshop natively in a local R installation (R version >= 4.6):

#' install the workshop and all required dependencies
install.packages(c("BiocManager", "remotes"))
BiocManager::install("jorainer/xcms4gnps2", dependencies = TRUE)
BiocManager::install("RforMassSpectrometry/MsBackendMassIVE")

The vignettes/MSV000090156-preprocessing.qmd file could then be opened with any editor (after downloading locally) and the individual code lines evaluated in an R session.

🤝 Contribution

Interested in contributing? Please check out the RforMassSpectrometry Contributions Guide.

📜 Code of Conduct

We follow the RforMassSpectrometry Code of Conduct to maintain an inclusive and respectful community.

🙌 Acknowledgements

EU Logo
EU Logo

Part of this work is funded by the European Union under the HORIZON-MSCA-2021 project 101073062: HUMAN – Harmonising and Unifying Blood Metabolic Analysis Networks.

🔗 Learn more: HUMAN Project Website