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MsIO

Project Status: Active
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Overview

MsIO provides flexible, language-agnostic import and export capabilities for mass spectrometry (MS) data objects in R. It facilitates interoperability by supporting various open file formats such as JSON, HDF5, plain text, and domain-specific standards like mzTab-M or MetaboLights archives.

While R’s native save()/load() functions allow object serialization, they rely on R-specific binary formats, making cross-platform data exchange difficult. MsIO addresses this by introducing standardized file formats and programmatic interfaces, simplifying integration between R-based tools and external software ecosystems.

Key Features

  • 📦 Export/import MS analysis results objects across interoperable file formats
  • 🧩 Modular design via S4 parameter classes and generic methods
  • 🔄 Integration with Bioconductor packages like Spectra, MsExperiment, xcms, and alabaster.base
  • 🔧 Support for plain text, JSON+HDF5, mzTab-M, and MetaboLights repository data

Package Architecture

Generic Methods

  • saveMsObject(object, param)
  • readMsObject(object, param)

These methods delegate the actual file handling based on the class of the supplied param object (e.g., PlainTextParam, AlabasterParam).

Parameter Classes

Each format is encapsulated in a dedicated S4 class:

Class Purpose
PlainTextParam Text-based tabular storage
AlabasterParam HDF5/JSON archival via alabaster
mzTabParam Export to mzTab-M (MS metabolomics)
MetaboLightsParam Import from MetaboLights repository

Corresponding logic is implemented in dedicated R/ files (e.g. XcmsExperiment.R, Spectra.R), with new formats expected to follow the same structure.

Supported Formats

✅ Plain Text (PlainTextParam)

  • Tab-delimited export/import for key objects:

✅ Alabaster (AlabasterParam)

  • Structured archival using HDF5 and JSON (via alabaster.base)
  • Compatible with MsExperiment, Spectra, XcmsExperiment, etc.

✅ mzTab-M Export (mzTabParam)

  • Export of XcmsExperiment preprocessing results to mzTab-M (HUPO PSI metabolomics standard)

✅ MetaboLights (MetaboLightsParam)

  • Import of complete experiments (including raw MS files) from MetaboLights

Planned Features & Contributions Welcome

Future development directions include:

  • 🔄 Import mzTab-M into SummarizedExperiment
  • 🔄 Import mzTab-M into QFeatures
  • 🔄 Generic ISA-tab import integration (if justified)

We welcome and encourage contributions — see below for how to get involved!

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:

License

This package is licensed under the Artistic 2.0 License:
📄 https://opensource.org/licenses/Artistic-2.0

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