rformassspectrometry/Metabonaut: v1.6.2

Louail, Philippine; De Graeve, Marilyn; Mahmoud, Alexandru; Marques de Sá e Silva, Daniel; Nishida, Kozo; Suksi, Vilhelm; Tagliaferri, Anna; Tomè, Gabriele; Verri Hernandes, Vinicius; Rainer, Johannes

doi:10.5281/zenodo.22300919

Published September 4, 2026 | Version v1.6.2

Software Open

rformassspectrometry/Metabonaut: v1.6.2

1. Institute for Biomedicine, Eurac Research, Bolzano, Italy
2. Chair for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
3. Limerick Digital Cancer Research Centre, Health Research Institute, School of Medicine, University of Limerick, Limerick, Ireland
4. Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
5. Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
6. Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
7. Department of Computing, University of Turku, Turku, Finland
8. Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bolzano, Italy
9. Sensing Technologies Laboratory (STL), Faculty of Engineering, Free University of Bozen-Bolzano, Bolzano, Italy
10. Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria

First release since v1.5.0, collecting the work from 1.5.1 through 1.6.2. The main additions are a new vignette on the mzTab-M standard and the ability to run everything in the browser, alongside a substantial reproducibility overhaul of the container.

New

mzTab-M vignette. mzTab-M file format: import-export of mzTab-M 2.1 files from SummarizedExperiment covers writing a completed analysis to the HUPO-PSI standard reporting format and reading it back, so results leave the R session in a tool-agnostic form.
Run it in the browser. Metabonaut can now be run without any local installation on the Bioconductor Workshop platform (workshop.bioconductor.org).

Reproducibility

All packages installed from GitHub in the Docker image are locked to a specific commit: MsIO (0.0.17), RmzTabM (0.99.1), RuSirius (1.0.4).
The container is pinned to the Bioconductor 3.23 release (bioconductor/bioconductor_docker:RELEASE_3_23), and SpectriPy now comes from that release branch.
RmzTabM is installed in the image so the mzTab-M vignette runs.
The README points to the versioned image tag (rformassspectrometry/metabonaut:v1.6.2) rather than latest, matching the installation instructions.

An analysis run from this release can therefore be re-executed later in the same environment rather than against whatever the dependencies happen to be at the time.

Vignette updates

SpectriPy tutorial: updated to the current matchms API, where ModifiedCosine was renamed to ModifiedCosineGreedy (tested with matchms 0.33.1). This is a pure renaming, the implementation was already greedy; the vignette now also mentions the exact ModifiedCosineHungarian alternative.
Dataset Investigation and End-to-End: unfinished and placeholder sections removed, leftover comments cleared and partial sentences completed, so the published vignettes no longer announce content that is not there.
Using and Creating Metabolomics Data Annotation Resources, LC-MS/MS Data Annotation using R and Python, Normalization and feature selection with the notame package, and the mzTab-M vignette: typos and formatting fixed, several passages expanded or reformulated.

Documentation

Installation and usage descriptions updated, including the required R version (>= 4.6.0).
README wording on known issues clarified: all vignettes currently run without problems.

Using this release

docker pull rformassspectrometry/metabonaut:v1.6.2 docker run -e PASSWORD=bioc -p 8787:8787 rformassspectrometry/metabonaut:v1.6.2

Rendered vignettes: https://rformassspectrometry.github.io/Metabonaut/

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