Weighting low-intensity MS/MS ions and m/z frequency for spectral library annotation

Table of Contents

• Citation
• General
• Datasets
• Reproducibility
• Code structure

Citation

If you have found our manuscript useful in your work, please consider citing:

Engler Hart, C., Kind, T., Dorrestein, P. D., Healey, D., and Domingo-Fernández, D. (2024). Weighting low-intensity MS/MS ions and m/z frequency for spectral library annotation. Journal of the American Society for Mass Spectrometry.

General

This repository contains code for evaluating weighting methods for spectral similarity metrics.

Datasets

• GNPS library
• NIST library

Links to the specific files are given in the notebooks The dump of the processed files are available at https://doi.org/10.5281/zenodo.8417612 and the zip files should be unzipped at placed ./data with the following structure:

-- data
    |-- modified_cosine_queries
    |-- network_method
    |-- nist
    |-- Wout_data

Reproducibility

To reproduce the results, run the notebooks in the given order.

1. The Python virtual environment can be installed using Poetry.
2. Install the spectral_entropy package from https://github.com/YuanyueLi/SpectralEntropy (this package is not available in PyPi).

Code

The project has the following structure:

-- notebooks
    |-- 1_spectral_aligment
        |-- 1_benchmark_other_similarity_metrics.ipynb
        |-- 1.1_benchmark_stats.ipynb
        |-- 2_weighted_modified_cosine.ipynb
        |-- 3_create_figures.ipynb
        |-- 4_compare_scores.ipynb
        |-- 5_some_weighted.ipynb
        |-- benchmark.py
    |-- 2_library_search
        |-- 1_gnps_ppm.ipynb
        |-- 2_query_library_example.ipynb
        |-- 3_results_benchmark.ipynb
        |-- 4_results_comparing_ppm_windows.ipynb
        |-- query_library.py

-- src
    |-- ms_similarity_metrics
        ├── __init__.py
        ├── create_spectrum.py
        ├── frequency.py
        ├── hash_utils.py
        ├── plot.py
        ├── query_pool.py
        ├── reformat_columns.py
        └── version.py