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
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')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
Create your development environment using the provided script via conda to install all required dependencies.
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.
All functionality is tested with the pytest framework.