# Migration Time Extraction

> Use when you have OnDiskMSnExp CE-MS objects with known marker compounds (e.g., Paracetamol EOF marker) and need to extract their migration time positions to establish a calibration reference.

- Skill: `holobiomicslab/migration-time-extraction` (Agent Skill)
- Install (CLI): `npx skillmds@latest add holobiomicslab/migration-time-extraction`
- Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/migration-time-extraction/raw
- Safety review: pending
- 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/migration-time-extraction

---


# migration-time-extraction

## Summary

Extract migration time (MT) coordinates of marker peaks (e.g., EOF markers) from CE-MS data files by generating Extracted Ion Electropherograms (EIE) and applying xcms peak detection with specified m/z and MT range constraints. This preprocessing step is essential for calibrating and normalizing migration time scales before effective mobility transformation.

## When to use

Apply this skill when you have OnDiskMSnExp CE-MS objects with known marker compounds (e.g., Paracetamol EOF marker) and need to extract their migration time positions to establish a calibration reference. Specifically, use it when you require per-file MT values to correct for electroosmotic flow variations that cause migration time drift across replicate analyses.

## When NOT to use

- Input data are already effective mobility–transformed or already contain pre-computed migration time values; use getMtime only on raw OnDiskMSnExp CE-MS objects.
- No known internal standard or marker peak is available; getMtime requires a reference compound with known m/z to anchor the extraction.
- Migration time ranges are extremely broad or poorly constrained; wide MT-range parameters lead to spurious peak detection.

## Inputs

- OnDiskMSnExp object (CE-MS raw data)
- m/z range (numeric vector or single value with tolerance)
- Migration time range (numeric vector defining lower and upper MT bounds)
- Known marker compound mass and approximate migration time

## Outputs

- Per-file migration time table (file identifier × MT value)
- Structured output file (e.g., CSV or tabular format) with MT values and file metadata

## How to apply

Load CE-MS test files from the msdata package into R as OnDiskMSnExp objects. Call the getMtime() function, supplying the object, a narrow m/z range (mz-range parameter) centered on the marker's known mass, and a plausible migration time window (MT-range parameter). The function generates an Extracted Ion Electropherogram (EIE) by filtering the raw data to the specified m/z tolerance, then invokes xcms::findChromPeaks() to locate the peak within the MT range. Narrow m/z and MT ranges are critical to ensure correct peak detection and avoid false positives. Compile the extracted MT values into a per-file table with file identifiers. Export the result as a structured output file for use in downstream effective mobility calibration workflows.

## Related tools

- **MobilityTransformR** (Package providing getMtime() function for extraction of migration time from CE-MS OnDiskMSnExp objects) — https://github.com/LiesaSalzer/MobilityTransformR
- **xcms** (Provides findChromPeaks() algorithm for peak detection in Extracted Ion Electropherograms)
- **MSnbase** (Supplies OnDiskMSnExp class and spectral data handling for CE-MS files)
- **Spectra** (Provides spectral data representation and filtering infrastructure)
- **msdata** (Supplies CE-MS test data files for validation and example workflows)
- **MetaboCoreUtils** (Supplies core metabolomics data transformation and utility functions)

## Examples

```
getMtime(OnDiskMSnExp_object, mz = c(151.04, 151.08), mt = c(8.0, 12.0))
```

## Evaluation signals

- Extracted MT values fall within the specified MT-range parameter and are reproducible across replicate files.
- Per-file MT table contains no missing values (NA) for successfully processed files, indicating peak detection succeeded.
- MT values cluster around the expected migration time of the marker compound; outliers or bimodal distributions suggest m/z or MT range misconfiguration.
- Comparison of extracted MT values across replicate files shows expected drift consistent with electroosmotic flow variation, not random noise.
- Output file structure matches expected schema (file identifier column, MT value column, metadata columns); schema validation passes without errors.

## Limitations

- getMtime() requires narrow m/z and MT ranges to ensure correct peak detection; overly broad ranges cause false positives or missed detections.
- Migration time extraction depends on the quality and signal intensity of the marker peak; low-abundance or noisy peaks may not be detected reliably.
- The function is specific to CE-MS data; it cannot be applied to LC-MS or other chromatographic techniques.
- Effective mobility transformation for CE-MS data is not straightforward as in CE-UV, and migration time alone does not account for electroosmotic flow variations; extracted MT values must be combined with effective mobility calibration for reproducibility.

## Evidence

- [other] The getMtime() function accepts an OnDiskMSnExp object, mz-range, and MT-range as inputs and determines the migration time of a marker peak by generating an Extracted Ion Electropherogram (EIE) and using findChromPeaks from xcms to pick the peak, with narrow mz and mt ranges required to ensure correct peak detection.: "The getMtime() function accepts an OnDiskMSnExp object, mz-range, and MT-range as inputs and determines the migration time of a marker peak by generating an Extracted Ion Electropherogram (EIE) and"
- [intro] the effective mobility µ_eff of a compound remains stable in the same electrophoretic system. The use of an effective mobility scale instead of a migration time scale circumvents the drawback of MT: "the effective mobility µ_eff of a compound remains stable in the same electrophoretic system. The use of an effective mobility scale instead of a migration time scale circumvents the drawback of MT"
- [intro] Effective mobility transformation for CE-MS data is not as straightforward as in CE-UV and until now and to our knowledge there is no implementation in R that performs effective mobility: "Effective mobility transformation for CE-MS data is not as straightforward as in CE-UV and until now and to our knowledge there is no implementation in R that performs effective mobility"
- [intro] The CE-MS test data are from the `r BiocStyle::Biocpkg("msdata")` package: "The CE-MS test data are from the `r BiocStyle::Biocpkg("msdata")` package"
- [readme] To install MobilityTransformR, use the stable version available at Bioconductor.: "To install MobilityTransformR, use the stable version available at Bioconductor."