RECETOX / MSMetaEnhancer

Tool for mass spectra metadata annotation.

Home Page:https://msmetaenhancer.readthedocs.io/

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MSMetaEnhancer

install with bioconda docs Conda PyPI - Python Version DOI

MSMetaEnhancer is a tool used for .msp files annotation. It adds metadata like SMILES, InChI, and CAS number fetched from the following services: CIR, CTS, PubChem, IDSM, and BridgeDb. The app uses asynchronous implementation of annotation process allowing for optimal fetching speed.

If you use MSMetaEnhancer in your work, please cite the following publication:

Troják et al., (2022). MSMetaEnhancer: A Python package for mass spectra metadata annotation. Journal of Open Source Software, 7(79), 4494, https://doi.org/10.21105/joss.04494

Usage

import asyncio

from MSMetaEnhancer import Application

app = Application()

# import your .msp file
app.load_spectra('tests/test_data/sample.msp', file_format='msp')

# curate given metadata (e.g. fix CAS numbers)
app.curate_metadata()

# specify requested services (these are supported)
services = ['CTS', 'CIR', 'IDSM', 'PubChem', 'BridgeDb', 'RDKit']

# specify requested jobs
jobs = [('name', 'inchi', 'IDSM'), ('inchi', 'formula', 'IDSM'), ('inchi', 'inchikey', 'IDSM'),
        ('inchi', 'iupac_name', 'IDSM'), ('inchi', 'canonical_smiles', 'IDSM')]

# run asynchronous annotations of spectra data
asyncio.run(app.annotate_spectra(services, jobs))

# export .msp file 
app.save_spectra('tests/test_data/sample_out.msp', file_format='msp')

Installation

Prerequisites:

  • Python 3.9+
  • Anaconda

Install MSMetaEnhancer from Bioconda with:

# install MSMetaEnhancer in a new virtual environment to avoid dependency clashes
conda create --name MSMetaEnhancer python=3.9
conda activate MSMetaEnhancer
conda install --channel bioconda --channel conda-forge MSMetaEnhancer

Developer Documentation

Setup

Create your development environment using the provided script via conda to install all required dependencies.

Contributing

We appreciate contributions - feel free to open an issue on our repository, create your own fork, work on the problem and post a PR. Please add your contributions to the changelog and to adhere to the versioning. For more information see here.

Testing

All functionality is tested with the pytest framework.

About

Tool for mass spectra metadata annotation.

https://msmetaenhancer.readthedocs.io/

License:MIT License


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