MsExperimentStash

A safe way to store and preserve your MsExperiment objects in interoperable and portable formats.

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Overview

The MsStash Bioconductor package defines a framework for flexible, language-agnostic import and export formats for mass spectrometry (MS) data objects in R. The MsExperimentStash package extends this framework and implements the functionality to stash (and restore) MsExperiment objects. The goal of this stash format is support long term storage, interoperability and portability.

⤵️ Installation

To install the packages along with all its dependencies:

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

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Key Features

• 📦 Store/restore MsExperiment objects to/from portable, language agnostic storage formats (stash)
• 🧩 Modular design via S4 parameter classes and generic methods
• 🔄 Fully integrated with Bioconductor's alabaster.base package.

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Supported Formats

✅ Alabaster (AlabasterParam)

• Structured archival using HDF5 and JSON (via alabaster.base)

✅ Plain Text (PlainTextParam)

• Tab-delimited export/import for key objects.

⤵️ Retrieve data directly from MetaboLights (MetaboLightsParam)

• Load MS data and experimental metadata for metabolomics studies from the MetaboLights repository,

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Contributing

We appreciate contributions of all kinds — from bug fixes and tests to documentation and new format support.

If you're planning to contribute:

1. Read our contribution guidelines
2. Follow the RforMassSpectrometry style guide
3. Fork the repo, create a branch, implement your changes, and submit a pull request
4. For new formats, implement:
   • A *Param S4 class
   • A readMsObject() and/or saveMsObject() method
   • Tests in tests/testthat/

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License

This package is licensed under the GPL 3.0 License: 📄 https://opensource.org/license/gpl-3.0

Documentation (manuals, vignettes) is licensed under CC BY-NC-SA 4.0: 📄 https://creativecommons.org/licenses/by-nc-sa/4.0/

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Funding information

Part of this work was funded by the European Union under the HORIZON-MSCA-2021 project 101073062: HUMAN – Harmonising and Unifying Blood Metabolic Analysis Networks, by the Autonomous Province of Bolzano under the MetaRbolomics4Galaxy project (CUP: D53C25001030003) from the Joint Projects South Tyrol–Germany 2025 funding program and by the DFG grant no. 564004112.