OPEs-ID

OPEs-ID is a user-friendly software based on fragments-dependent nontargeted screening and in silico fragmentation scoring (provided by Metfrag), aiming to provide a one-stop solution for the identification of OPEs based on LC-HRMS DDA data.

More refer to the paper "OPEs-ID: A software for non-targeted screening of organophosphate esters based on liquid chromatography-high-resolution mass spectrometry".

Requirements

• Python >= 3.11
• Java >= 11 (Optional, For running Metfrag)

Python dependencies

The list below is the version of Python dependencies used when developing the algorithm. Older versions might still work but are untested.

• joblib==1.3.2
• nest-asyncio==1.5.8
• numpy==1.26.2
• openpyxl==3.1.2
• pandas==2.1.4
• pymzml==2.5.2
• python-constraint==1.4.0
• rdkit==2023.9.3
• requests==2.31.0
• scipy==1.11.4
• tqdm==4.66.1
• Pyside6==6.6.1 (Optional for GUI)

Install

Either copy the OPEs_ID directory in the repository to your working directory or install using pip by runing following command

pip install git+https://github.com/speakinside/OPEs-ID.git

or

pip install "OPEs_ID[gui] @ git+https://github.com/speakinside/OPEs-ID.git"

to install the optional dependency for running the simple GUI script shipping with OPEs-ID.

There is also a ready-to-use GUI package for Windows which can be downloaded here.

Using

As a python lib

To use OPEs_ID in a script or a python notebook. Please refer to the python notebooks in example directory.

As a GUI application

Run OPEs_ID_gui.exe or python -m OPEs_ID.gui to launch a simple gui for OPEs_ID.

1. Input the MzML file in Box A.
2. Set parameters for computation in Box C.
   • MS2 ACC: Mass accuracy for MS2 feature search
   • ROI ACC: Mass accuracy for aggregating the precursors of the same chromatographic peak.
   • Cl range: The limit on the number of Cl atoms
   • Top n: The max number of peaks involved in chlorine isotope predictions
   • Mass acc: Mass accuracy for formula prediction
   • Formula Prediction: More detailed restriction on the elements for formula prediction
3. Click Calculate button to start searching and formula prediction

4. After the first calculation, results will be shown in box E without the Metfrag column.
5. (Optional) Click Metfrag Analysis button to config and run Metfrag Analysis. After the operation, Metfrag column will show on far right and the number shown in each row in this column represents how many candidate structures.
6. (Optional) Double-Clicking an item in Metfrag column, a popup would show the detailed Metfrag results as in box F.
7. Click Save button to save all the results.

Cite the paper

@article{XIONG2024133275,
    title = {OPEs-ID: A software for non-targeted screening of organophosphate esters based on liquid chromatography-high-resolution mass spectrometry},
    journal = {Journal of Hazardous Materials},
    volume = {465},
    pages = {133275},
    year = {2024},
    issn = {0304-3894},
    doi = {https://doi.org/10.1016/j.jhazmat.2023.133275},
    url = {https://www.sciencedirect.com/science/article/pii/S0304389423025591},
    author = {Yinran Xiong and Jinyue Liu and Jing Yu and Da Chen and Tiantian Li and Fengli Zhou and Ting Wu and Xiaotu Liu and Yiping Du},
    keywords = {Fragments-dependent screening, LC-HRMS, In silico fragmentation, Isotopic pattern matching, Organophosphate esters (OPEs)},
}

Future work

• Add more annotations and typing hints to the code
• Optimize the logics of the GUI script