SpectraStash

A safe way to store your Spectra objects in interoperable formats.

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Overview

MsStash defines a framework for flexible, language-agnostic import and export formats for mass spectrometry (MS) data objects in R. The SpectraStash package implements this framework for Spectra objects and its data backends.

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Key Features

• 📦 Export/import Spectra objects and related MsBackend implementations across interoperable file formats
• 🧩 Modular design via S4 parameter classes and generic methods
• 🔄 Fully integrated with Bioconductor's alabaster.base package.

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Supported Formats

✅ Plain Text (PlainTextParam)

• Tab-delimited export/import for key objects:

✅ Alabaster (AlabasterParam)

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

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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.