Bioconductor

There is a newer version of the record available.

Published January 7, 2026 | Version v1.4.0
Software Open

rformassspectrometry/Metabonaut: v1.4.0

Authors/Creators

  • 1. Institute for Biomedicine, Eurac Research, 39100 Bolzano, Italy
  • 2. Chair for Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany
  • 3. Institute for Biomedicine, Eurac Research, Bolzano, Italy
  • 4. Sensing Technologies Laboratory (STL), Faculty of Engineering, Free University of Bozen-Bolzano, 39100, Bolzano, Italy
  • 5. Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100, Bolzano, Italy
  • 6. School of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
  • 7. Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 12 57001 Thessaloniki, Greece
  • 8. ROR icon University of Vienna
  • 9. ROR icon RIKEN Center for Integrative Medical Sciences
  • 10. ROR icon Tokyo University of Agriculture and Technology

Description

Metabonaut v1.4.0 🧑‍🚀

Welcome to the latest release of Metabonaut! This version introduces significant workflow expansions, including robust new tools for quality control and feature selection, and updates our core compatibility to the latest Bioconductor ecosystem.

🚀 What's New in v1.4.0?

🧪 New Vignettes & Workflow Enhancements

  • Quality Control and Feature Selection with notame: We've added a dedicated vignette for the notame package. This provides a powerful alternative for normalization and feature selection, ensuring your metabolomics data is clean and statistically sound.
  • GNPS Export & Peak-Picking: The main workflow now includes integrated steps for GNPS export and a comprehensive summary of peak-picking results.
  • Enhanced Dataset Investigation: New visual examples have been added to the "Dataset Investigation" vignette, including foreground/background comparisons and a visual guide to the effect of filterPeaksRanges.
  • Expanded Documentation: Added detailed descriptions for parameters like firstBaselineCheck to help users fine-tune their preprocessing.

⚙️ Technical Updates & Stability

  • Bioconductor 3.22: Metabonaut is now fully updated for BioC 3.22.
  • Bug Fixes: Fixed subsetting issues for Control samples during MS2 annotation.
  • Dependency Management: Improved workflow stability by resolving missing library dependencies (e.g., knitr).
  • Reference Updates: Updated the xcms references to reflect the latest standards in the field.

📚 Updated Vignette Overview

  1. Complete End-to-End LC-MS/MS Analysis: From raw data preprocessing to final metabolite annotation.
  2. Dataset Investigation: Critical first steps to examine your data and prevent downstream troubleshooting.
  3. Seamless Alignment: Integrating new datasets with existing preprocessed data using flexible alignment.
  4. QC & Feature Selection (Using notame) [NEW]: Robust normalization and cleaning of your metabolomics features.
  5. LC-MS/MS Data Annotation (R & Python): Leveraging the SpectriPy package to combine the best of both languages.
  6. Large Scale Processing: Practical guide to handling >4,000 files on a standard computer using xcms.

🤝 Community & Contributions

A huge thank you to our contributors for this release!

New Contributors:

  • @kozo2 made their first contribution in PR #37
  • @vsuksi made their first contribution in PR #57

Full Changelog: [v1.2.0...v1.4.0](https://github.com/rformassspectrometry/Metabonaut/compare/v1.2.0...v1.4.0)

Acknowledgment

Funded by the European Union under the HORIZON-MSCA-2021 project 101073062: HUMAN – Harmonising and unifying blood metabolic analysis networks.

Files

rformassspectrometry/Metabonaut-v1.4.0.zip

Files (10.0 MB)

Name Size Download all
md5:46df461dcb0b1d32f750a7d1d72e8e21
10.0 MB Preview Download

Additional details

Related works

Is supplement to
Software: https://github.com/rformassspectrometry/Metabonaut/tree/v1.4.0 (URL)

Software

Repository URL
https://github.com/rformassspectrometry/Metabonaut