bio-metabolomics-xcms-preprocessing - Preprocess untargeted LC-MS data with XCMS
Extract LC-MS features from mzML files in R using XCMS peak detection, retention-time alignment, correspondence, gap-filling, redundancy reduction, and QC filtering.
Tags
Updated: 2026-10-03Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Read mzML experiments
- Detect chromatographic peaks
- Align retention times
- Group corresponding peaks
- Fill missing peak areas
- Collapse feature redundancy
- Filter QC features
Inputs
- Centroided mzML files
- Sample metadata
- XCMS parameter objects
- Sample group labels
- QC and study indices
Outputs
- Feature-by-sample matrix
- Processed XcmsExperiment
- Feature definitions
- Retention-time alignment plots
- CAMERA peak list
- QC-filtered features
Requirements
- R environment
- xcms 4.x or later
- Spectra 1.12 or later
- CAMERA 1.58 or later
- Centroided LC-MS data for CentWave