Untargeted screening of environmental contaminants in human plasma using liquid chromatography high resolution mass spectrometry with negative ionization

In this paper, we developed a method to detect and identify both endogenous and exogenous compounds correlating with environmental contaminants in the body using mass-spectometry in untargeted mode.

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Setting up the environment

To create and activate the environment with necessary library and packages.

conda env create -f environment.yaml
conda activate envcon

To process the files nextflow workflow nf-core-metabolinden was used. Install the workflow in the newly created environment.

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File descriptions

The parameter files for the FeatureFinder is FF_param.ini and for FeatureLinker is FL_param.ini.
The command used for the nextflow workflow can be found here.
The data needed for identification using m/z is available at NORMAN database

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Data preprocessing

1. 0_tracefinder_analysis.ipynb
   
   • Plotting the correlation plot for result from TraceFinder.
     
     
2. 1_feature_linker_coverage_check.ipynb
   
   • Analysing and obtaining feature of native compounds from FeatureLinker
     
     
3. 2_correlation_analysis.ipynb
   
   • Plotting the correlation plot for result from FeatureFinder and FeatureLinker.
     
     
4. 3_clustering.ipynb
   
   • Clustering of features using coverage and correlation cutoff.
     
     
5. 4_Identification.ipynb
   
   • Identification of features using m/z using NORMAN database.
     
     
6. 5_ms2_extraction.ipynb
   
   • Extracting MS2 for the selected features and running CSI-FINGERID.
     
     
7. 6_post_CSI_consolidate_results.ipynb
   
   • Extracting and analysing CSI-FINGERID results.
     
     

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Acknowledgements and references

We thank everyone who helped us in the project.
Special thanks to nf-core-metabolinden for the workflow.

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Citation

Please cite:
Carlsson, Henrik & Sreenivasan, Akshai & Erngren, Ida & Larsson, Anders & Kultima, Kim. (2023). Combining targeted and untargeted screening of environmental contaminants reveals associations between PFAS exposure and vitamin D metabolism in human plasma. Environmental Science: Processes & Impacts. 25. 10.1039/D3EM00060E.