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metabolomics-xcms-preprocessing

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Load when running an XCMS-style preprocessing summary on LC-MS metabolomics raw / vendor-converted files — emits a peak table with m/z, retention time, and per-sample intensities. Skip when working with an already-built peak table (use `metabolomics-peak-detection`) or when only annotation is needed (use `metabolomics-annotation`).

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How to use this skill

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Source SKILL.md: https://github.com/TianGzlab/OmicsClaw/blob/HEAD/skills/metabolomics/metabolomics-xcms-preprocessing/SKILL.md

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metabolomics-xcms-preprocessing

When to use

The user has LC-MS / GC-MS metabolomics files (or a placeholder multi-file list) and wants the standard XCMS-style preprocessing output: peak table with mz, rt, and per-sample intensity columns. The skill mirrors the canonical CentWave + Obiwarp + correspondence + gap-fill workflow conceptually but is pure Python — there is no rcpp / xcms R bridge here.

For per-sample peak picking from a single intensity matrix use metabolomics-peak-detection. For metabolite annotation use metabolomics-annotation.

Inputs & Outputs

InputFormatRequired
Raw / converted MS files--input <file1> [<file2> ...] (multi-file via nargs="+")yes (unless --demo)
ppm--ppm <float> (default 25.0) — m/z toleranceno
Peak width--peakwidth-min / --peakwidth-max (default 10.0 / 60.0 sec)no
OutputPathNotes
Peak tabletables/peak_table.csvfeatures × (mz, rt, intensities…) — long form
Reportreport.md + result.jsonalways

Flow

  1. Load files (--input <files>) or generate a demo peak table (--demo).
  2. Apply CentWave-style peak detection at the configured --ppm and --peakwidth-* parameters.
  3. Write tables/peak_table.csv (metabolomics_xcms_preprocessing.py:211) + report.md + result.json.

Gotchas

  • Pure Python — NO real XCMS / CAMERA invocation. The script does not call R / rcpp / xcms / CAMERA. Demo and real-input runs both produce a synthetic-shaped peak table; for production XCMS workflows, run XCMS in R upstream and feed the resulting peak table into metabolomics-peak-detection or metabolomics-quantification.
  • --input accepts MULTIPLE files via nargs="+". metabolomics_xcms_preprocessing.py:186 declares nargs="+", so passing several files is the supported single-call shape. Demo ignores --input.
  • --input REQUIRED unless --demo. metabolomics_xcms_preprocessing.py:203 raises ValueError("--input required when not using --demo").
  • Peak-width units are SECONDS (chromatographic). --peakwidth-min 10.0 --peakwidth-max 60.0 defaults assume LC-MS scan timing. For UPLC narrow peaks consider --peakwidth-min 5 --peakwidth-max 20.
  • --ppm 25.0 default is broad. Suitable for low-resolution Orbitrap / Q-TOF; for high-resolution FTMS use --ppm 5.0. Wrong value silently yields false positive merges.

Key CLI

# Demo (synthetic peak table)
python omicsclaw.py run metabolomics-xcms-preprocessing --demo --output /tmp/xcms_demo

# Real LC-MS files
python omicsclaw.py run metabolomics-xcms-preprocessing \
  --input sample1.mzML sample2.mzML sample3.mzML --output results/ \
  --ppm 5.0 --peakwidth-min 5 --peakwidth-max 30

See also

  • references/parameters.md — every CLI flag
  • references/methodology.md — CentWave / Obiwarp conventions, ppm + peakwidth tuning
  • references/output_contract.md — tables/peak_table.csv schema
  • Adjacent skills: metabolomics-peak-detection (downstream — per-sample peak picking on a feature × intensity matrix), metabolomics-annotation (downstream — annotate features against HMDB / KEGG), metabolomics-quantification (downstream — impute + normalise), metabolomics-normalization (downstream — normalisation methods)