IsoGroup - Isotopic Grouping for mass spectrometry labeling experiments

What is IsoGroup?

IsoGroup is a scientific software dedicated to the processing of isotopic data from untargeted mass spectrometry (MS) labeling experiments. It is suitable for diverse applications including annotation, isotopic profiling, quantification, and fluxomics experiments. IsoGroup supports two complementary modes of data processing:

• In targeted mode, IsoGroup performs annotation of isotopic clusters based on a user-provided database of compounds. Mass features (m/z, retention time, intensity) are matched to known metabolites and isotopologues according to their exact mass and retention time. A database of isotopologues specific to the selected tracer is generated and used for the annotation.
• In untargeted mode, IsoGroup performs clustering by grouping MS features identified as isotopologues into isotopic clusters without prior knowledge, based solely on the features mass differences induced by the tracer element and constrained by the user-defined retention time window.

IsoGroup generates an output file that catalogs all identified isotopic clusters, including the constituent features and their associated m/z values, retention times, intensities, and isotopologue information.

The code is open-source, and available under a GPLv3 license.

Detailed documentation can be found online at Read the Docs (https://isogroup.readthedocs.io/). Check out the Tutorials !

• Targeted mode: annotate isotopic clusters using a user-provided compound database,
• Targeted mode: generate a database with isotopologues for a given tracer element and use it for annotation,
• Targeted mode: calculate exact mass and retention time errors for annotated clusters,
• Untargeted mode: group MS features into isotopic clusters without prior knowledge,
• Untargeted mode: provide options to improve isotopologue annotation inside clusters,
• Untargeted mode: Untargeted mode: provides options to reduce redundancy at both cluster and feature levels, including filtering of features with identical isotopologue indices,
• Compatible with any tracer element,
• Handle multiple sample types (unlabeled, fully labeled, Pascal Triangle, etc)
• Open-source, free and easy to install everywhere where Python 3 and pip run.

Quick-start

IsoGroup requires Python 3.7 or higher and run on all platforms. Please check the documentation for complete installation and usage instructions.

Use pip to install IsoGroup from PyPi:

$ pip install isogroup

IsoGroup is also available directly from command-line and as a Python library.

Bug and feature requests

If you have an idea on how we could improve IsoGroup please submit a new issue to our GitHub issue tracker.

Developers guide

Contributions

Contributions are very welcome! :heart:

Please work on your own fork, follow PEP8 style guide, and make sure you pass all the tests before a pull request.

Local install with pip

In development mode, do a pip install -e /path/to/IsoGroup to install locally the development version.

Build the documentation locally

Build the HTML documentation with:

$ cd doc
$ make html

The PDF documentation can be built locally by replacing html by latexpdf in the command above. You will need a recent latex installation.

Authors

Noémie Butin, Loïc Le Grégam, Pierre Millard, Rochelle Kouakou

Contact

:email: noemie.butin@univ-perp.fr, loic.legregam@unige.ch, millard@insa-toulouse.fr, kouakou@insa-toulouse.fr