Sharing & Archiving Results

Sharing a complete, reproducible INTEGRATOR project as a single self-contained folder

Because INTEGRATOR and MRMhub-viz are portable executables that require no installation, a peak-integration analysis is already self-contained: the project folder holds the raw data, the input files with every parameter, the results, and the applications that produced them. The project folder is itself the shareable artefact: a recipient can inspect the outcome, or re-run and adjust the integration, from the folder alone, with no additional material to assemble.

A shareable project folder

A complete project combines the files documented on the Installation and Output Files pages. Kept together, they let a recipient do either of two things: re-run the processing (raw data + input files + applications) or inspect the result without re-running (result tables + misc/ + optional PDFs).

shared-project/
├── MRMhub.exe / .app      ┐
├── MRMhub-viz.exe / .app  ├ applications — re-run, or review in MRMhub-viz
├── MRMhub_plot.r          ┘ (no installation required)
├── param.txt          ┐
├── run_order.csv      ├  input files — every integration parameter
├── feature_list.csv   ┘
├── mzML/                  ← the converted raw data
├── long.csv           ┐
├── quant_raw.csv      ├  results — the peak tables (long.csv hands off to QUANT)
├── RT_matrix.csv      ┘  RT_matrix.csv carries the exact integration borders
├── misc/                 ← binary results read by MRMhub-viz
└── by_transition/ …      ← chromatogram PDFs (optional)

A complete project. See Output Files for the result formats and Installation for the applications and input files.

A short README may be added before sharing, recording the study, the INTEGRATOR version used, and any manual RT_matrix.csv adjustments; the release provides a readme.txt template as a starting point.

NoteKeep the applications in the project folder

Retaining one copy of the applications in each project folder is the recommended default. It makes the folder self-documenting and reproducible: the recipient opens MRMhub-viz to inspect every peak, or re-runs INTEGRATOR to reproduce or adjust the integration, without installing anything or matching software versions by hand.

Reproducibility and FAIR data

An INTEGRATOR project folder aligns with the FAIR principles for research data and is well suited to long-term archiving:

  • Interoperable — the raw data, results, and parameters are all in open, non-proprietary formats: mzML for the raw data, plain CSV for the result and configuration tables, and plain-text param.txt for the parameters, none of which require INTEGRATOR to be read. Only the auxiliary misc/ binaries are application-specific, and they are not needed to access the results.
  • Reusable — the bundled executables make the integration end-to-end reproducible with no external software: because INTEGRATOR is self-contained and no runtime, library, or vendor tool is involved, a recipient re-runs the entire integration from the folder alone (only the optional PDF plotting depends on an R installation). With the complete parameter record (param.txt plus the finalised RT_matrix.csv) travelling alongside the data, the result is reproduced exactly rather than approximately.
  • Findable & Accessible — because the folder consists only of standard files, it can be deposited as-is in a general-purpose research-data repository (for example Zenodo) to obtain a persistent, citable DOI alongside the associated publication.

See also