MsIO

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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.

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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

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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.

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Supported Formats

✅ Plain Text (PlainTextParam)

• Tab-delimited export/import for key objects:
  • MsBackendMzR, Spectra (from Spectra)
  • MsExperiment (from MsExperiment)
  • XcmsExperiment (from xcms)

✅ 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

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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!

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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 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/