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bio-metabolomics-xcms-preprocessing - Preprocess Untargeted LC-MS Data with XCMS

Extract LC-MS features in R with xcms 4.x, including peak detection, retention-time alignment, grouping, gap-filling, redundancy collapse, and QC filtering.

Tags

Updated: 2026-10-06
metabolomicsLC-MSRxcmsfeature extractionpreprocessing

Capabilities

Read centroided mzML filesDetect chromatographic peaksAlign retention timesGroup corresponding peaks

Typical Inputs

Centroided mzML filesSample metadataInstrument parameters

Typical Outputs

Feature-by-sample matrixProcessed XcmsExperiment objectRetention-time alignment results

What this skill does

  • Read centroided mzML files
  • Detect chromatographic peaks
  • Align retention times
  • Group corresponding peaks
  • Fill missing peak areas
  • Collapse feature redundancy
  • Apply QC feature filters

Inputs

  • Centroided mzML files
  • Sample metadata
  • Instrument parameters
  • Chromatography parameters
  • XCMS processing parameters

Outputs

  • Feature-by-sample matrix
  • Processed XcmsExperiment object
  • Retention-time alignment results
  • Feature definitions
  • Redundancy group annotations

Requirements

  • R environment
  • xcms 4.x or later
  • Spectra 1.12 or later
  • CAMERA 1.58 or later
  • Centroided LC-MS data

Source

  • Spec: SKILL.md

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