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Targeted_LCMS_QC_and_analysis

This repository contains scripts for quality control, processing, and normalization of targeted metabolomics data (LC-MS).

Please include this repository in your Code Availability section if you used scripts here.

Example Data

We included LC-MS measurement data from Blasche and Periwal et al. 2025 here as example.

Repository Structure

There are three folders in this repository:

  • input contains the following files:

    • MassHunter Workstation Quantitative Analysis for QQQ v10.1 (20231107_Blasche_S3_10xdil_AA_quant.csv)
    • Notes file (notes.csv)
    • Concentrations of standard used in the experiment (standard_concentrations_5xdil.csv)

  • scripts contains scripts for data processing and report generation. Please refer to the readme.md file inside this folder for details.

  • report contains the Rmarkdown report and data included in the report.

Publications

Benjamin J. Hershey et al., Clonal cooperation through soluble metabolite exchange facilitates metastatic outgrowth by modulating Allee effect. Sci. Adv. 9, eadh4184 (2023). DOI: 10.1126/sciadv.adh4184

Sonja Blanche and Vinita Periwal et al., Impact of low-calorie sweeteners on gut bacteria is modulated by common xenobiotics. bioRxiv (2025). DOI: https://doi.org/10.1101/2025.03.28.645995

Authors and Contributors

This repository is developed by Rui Guan and contributed by: Stephan Kamrad, Rebecca Boston, Rob Bradley, Sonja Blache, Francesca Eichacker and more.