metabolomics-msdial-preprocessing - Preprocess LC-MS metabolomics data using MS-DIAL
Processes LC-MS metabolomics data via MS-DIAL, covering peak detection, alignment, annotation, filtering, and export for R and Python analysis.
Tags
Updated: 2026-09-21Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Detect LC-MS chromatographic peaks
- Align peaks across samples
- Annotate metabolites using database
- Filter features by confidence
- Export results for analysis
- Run MS-DIAL console batch mode
- Normalize intensity matrix
Inputs
- LC-MS raw data files
- MS-DIAL alignment result CSV
- MS-DIAL parameter file
- Reference MSP database file
- Sample metadata file
Outputs
- Filtered feature intensity matrix
- Processed CSV data file
- SummarizedExperiment R object
- MetaboAnalyst compatible CSV file
Requirements
- MS-DIAL software or MsdialConsoleApp.exe
- Windows OS for console app
- Python (numpy 1.26+, pandas 2.2+)
- R (tidyverse, SummarizedExperiment)