# Scan Window Routing Mass Spectrometry

> Use when when processing LC-MS data with multiple overlapping m/z scan windows and observing sawtooth-pattern distortions in EICs during tardisPeaks() execution.

- Skill: `holobiomicslab/scan-window-routing-mass-spectrometry` (Agent Skill)
- Install (CLI): `npx skillmds@latest add holobiomicslab/scan-window-routing-mass-spectrometry`
- Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/scan-window-routing-mass-spectrometry/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/scan-window-routing-mass-spectrometry

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# scan-window-routing-mass-spectrometry

## Summary

A quality-control technique for LC-MS targeted metabolomics that segregates overlapping m/z scan windows by mass range to eliminate sawtooth artefacts in extracted ion chromatograms (EICs). Proper routing ensures clean peak profiles during automated integration in TARDIS.

## When to use

When processing LC-MS data with multiple overlapping m/z scan windows and observing sawtooth-pattern distortions in EICs during tardisPeaks() execution. This artefact appears because empty spectra within TARDIS filtering cause discontinuities in the chromatographic signal across scan windows that share m/z ranges without separation logic.

## When NOT to use

- When LC-MS data contains only non-overlapping m/z scan windows (sawtooth artefact will not occur)
- When input files are already in processed feature-table format rather than raw mzML
- When peak integration is not the downstream goal; mass_range separation is not needed for screening-mode visibility checks alone

## Inputs

- centroided mzML files
- Spectra object loaded from mzML vignettes
- target list data.frame with columns: compound ID, compound name, m/z, RT (minutes), polarity

## Outputs

- EIC (Extracted Ion Chromatogram) plots without sawtooth artefacts
- clean chromatographic peak profiles suitable for automated integration
- results list containing data.frame with AUC per target per run

## How to apply

After loading centroided mzML data as Spectra objects and defining a target list with compound ID, name, m/z, RT, and polarity columns, execute tardisPeaks() with an explicitly configured mass_range argument that assigns each scan window to a distinct m/z range rather than allowing windows to overlap without separation. The mass_range parameter must route scan windows so that filtering of empty spectra does not create gaps in the EIC trace. Re-run tardisPeaks() with the corrected mass_range configuration and visually compare the resulting EIC plots against the original artefactual output to confirm elimination of sawtooth profiles and restoration of continuous peak shape.

## Related tools

- **TARDIS** (Executes tardisPeaks() function with mass_range routing to separate overlapping scan windows and generate EICs) — https://github.com/pablovgd/TARDIS
- **xcms** (Provides retention time correction algorithm used within TARDIS for peak detection)
- **Spectra** (R class for loading and managing MS data from mzML files prior to tardisPeaks() execution)
- **knitr** (Visualization and output of EIC plots for comparison of artefact presence/absence)

## Examples

```
tardisPeaks(file_paths = c('sample1.mzML', 'sample2.mzML'), target_list = targets_df, mass_range = list(c(100, 250), c(250, 400)), screening_mode = FALSE)
```

## Evaluation signals

- EIC plots show continuous, smooth chromatographic peak profiles without sawtooth discontinuities after mass_range segregation
- Comparison of before/after EIC outputs demonstrates visual elimination of the sawtooth pattern
- Peak quality metrics (AUC, max intensity, SNR, peak_cor) are stable and unaffected by scan-window filtering
- No gaps or missing data points appear in the extracted ion trace across the retention time window of interest
- Results data.frame contains non-zero AUC values for all targets without spurious intensity drops caused by empty-spectra filtering

## Limitations

- Sawtooth artefacts only manifest when multiple m/z scan windows overlap without mass_range separation; proper parameter configuration is prerequisite knowledge
- The fix requires manual re-execution and visual comparison of EIC plots; automated artefact detection is not provided in TARDIS
- No changelog is documented in the TARDIS repository, limiting traceability of mass_range routing behavior changes across versions

## Evidence

- [other] Peaks display a sawtooth profile when tardisPeaks() processes data with multiple overlapping m/z scan windows without mass_range separation, due to filtering of empty spectra within TARDIS.: "Peaks display a sawtooth profile when tardisPeaks() processes data with multiple overlapping m/z scan windows without mass_range separation, due to filtering of empty spectra within TARDIS."
- [other] Does the sawtooth artefact appear in extracted ion chromatogram (EIC) output when tardisPeaks() is run on LC-MS data with multiple overlapping m/z scan windows without proper mass_range separation?: "Does the sawtooth artefact appear in extracted ion chromatogram (EIC) output when tardisPeaks() is run on LC-MS data with multiple overlapping m/z scan windows without proper mass_range separation?"
- [other] Re-execute tardisPeaks() with correct mass_range argument routing to segregate scan windows by mass range, producing clean chromatographic peak profiles.: "Re-execute tardisPeaks() with correct mass_range argument routing to segregate scan windows by mass range, producing clean chromatographic peak profiles."
- [intro] compound ID, a unique identifier; A compound Name; Theoretical or measured *m/z*; Expected RT (in minutes); A column that indicates the polarity: "compound ID, a unique identifier; A compound Name; Theoretical or measured *m/z*; Expected RT (in minutes); A column that indicates the polarity"
- [intro] Input files need to be converted to the .mzML format and have to be centroided: "Input files need to be converted to the .mzML format and have to be centroided"