LCMS analysis

Here we will provide a guide for the processing of raw LCMS output files from metabolomics and lipidomics runs, how to undertake curation and annotation, and approaches for their analysis downstream.

Overview

The MS-DIAL software we recommend provides a pipeline for untargeted metabolomics. Its outputs then require thorough quality control measures and additional annotation steps. Additional annotation with HMDB and/or LIPID MAPS supplements the annotations provided through standards and MS-DIAL to ensure we can retain and utilise the maximum number of features.

Citation

If you use this workflow and end up publishing something, please consider including a reference to our work! 😎🙏

Macowan, M., Pattaroni, C., Cardwell, B. A., Iacono, G., & Marsland, B. (2025). Mucosal Immunology Research Group - Processing metabolome and lipidome data with MS-DIAL. Zenodo. https://doi.org/10.5281/zenodo.15701971

Analysis workflow

1. Process raw LCMS data with MS-DIAL
2. Perform automated quality control with pmp
3. Secondary feature annotation with HMDB/LIPID MAPS
4. Manual curation of annotated spectra
5. Downstream analysis