# Coeluting Ion Separation

> Use when raw GC-MS data (netCDF or mzML format) exhibits overlapping chromatographic peaks—i.e., when multiple analytes elute at similar retention times and produce composite mass spectra with ambiguous m/z signals.

- Skill: `holobiomicslab/coeluting-ion-separation` (Agent Skill)
- Install (CLI): `npx skillmds@latest add holobiomicslab/coeluting-ion-separation`
- Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/coeluting-ion-separation/raw
- Safety review: PASS (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- License: CC-BY-4.0
- Author: HolobiomicsLab (https://skillmd.com/u/holobiomicslab)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/holobiomicslab/coeluting-ion-separation

---


# coeluting-ion-separation

## Summary

Spectral deconvolution method that separates co-eluting ions in gas chromatography–mass spectrometry (GC-MS) data to resolve individual mass spectra from overlapping chromatographic peaks. This skill transforms composite signals into distinct component-level features suitable for molecular identification and networking.

## When to use

Apply this skill when raw GC-MS data (netCDF or mzML format) exhibits overlapping chromatographic peaks—i.e., when multiple analytes elute at similar retention times and produce composite mass spectra with ambiguous m/z signals. Use it as a preprocessing step before molecular networking, feature extraction, or metabolite annotation to increase peak count and spectral coherence.

## When NOT to use

- Input is already a feature table or pre-deconvolved peak list
- GC-MS data contains no overlapping peaks (baseline-resolved chromatography)
- Instrument produces high-resolution separations where co-elution is not a concern

## Inputs

- Raw GC-MS data in netCDF format
- Raw GC-MS data in mzML format
- Mass spectrometry data with overlapping chromatographic peaks

## Outputs

- Deconvolved peak table (tabular format, one row per component)
- Peak features (retention time, m/z values, intensity per component)
- Individual resolved mass spectra for each co-eluting component

## How to apply

Load raw GC-MS data in netCDF or mzML format containing overlapping peaks. Apply a spectral deconvolution algorithm that separates co-eluting ions by resolving individual mass spectra from composite signals. Extract deconvolved peak features (retention time, m/z values, intensity) for each resolved component and generate a peak table with one row per deconvolved component. Validate deconvolution quality by confirming an increase in peak count and verifying spectral coherence of separated components—components should have internally consistent m/z patterns consistent with single analytes.

## Related tools

- **GNPS_GC** (Implements auto-deconvolution algorithm and spectral separation workflow for GC-MS data) — https://github.com/bittremieux/GNPS_GC

## Evaluation signals

- Peak count increases after deconvolution compared to raw input (indicates successful component separation)
- Deconvolved peak table schema includes retention time, m/z, and intensity columns with valid numeric values
- Separated mass spectra exhibit internal coherence (m/z ratios consistent with single chemical compounds)
- Retention time ranges of separated components do not exceed instrument resolution limits
- Visual inspection confirms that previously overlapping signals are now resolved into distinct spectral patterns

## Limitations

- Deconvolution quality depends on peak overlap severity; heavily overlapped signals may not fully resolve
- Method assumes input data is in valid netCDF or mzML format; malformed files will fail
- No documented changelog or versioning in the repository limits reproducibility tracking across releases
- Spectral coherence validation requires manual expert review for complex or noisy data

## Evidence

- [other] Load raw GC-MS data (netCDF or mzML format) containing overlapping chromatographic peaks.: "Load raw GC-MS data (netCDF or mzML format) containing overlapping chromatographic peaks."
- [other] Apply spectral deconvolution algorithm to separate co-eluting ions and resolve individual mass spectra from composite signals.: "Apply spectral deconvolution algorithm to separate co-eluting ions and resolve individual mass spectra from composite signals."
- [other] Extract deconvolved peak features including retention time, m/z values, and intensity for each resolved component.: "Extract deconvolved peak features including retention time, m/z values, and intensity for each resolved component."
- [other] Generate output peak table in tabular format with one row per deconvolved component, including intensity, m/z, and retention time columns.: "Generate output peak table in tabular format with one row per deconvolved component, including intensity, m/z, and retention time columns."
- [other] Validate deconvolution quality by confirming peak count increase and verifying spectral coherence of separated components.: "Validate deconvolution quality by confirming peak count increase and verifying spectral coherence of separated components."
- [other] Auto-deconvolution as a processing method for gas chromatography–mass spectrometry data, implemented in the GNPS_GC companion repository.: "auto-deconvolution as a processing method for gas chromatography–mass spectrometry data, implemented in the GNPS_GC companion repository."