Extracted Ion Chromatogram Eic Visualization

---
name: extracted-ion-chromatogram-eic-visualization
description: Use when after running MS1 extraction and prescreening on mzML files
  with assigned adducts and tags, when you need to inspect detected compounds visually
  to verify peak shape, confirm retention time consistency across samples (e.
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_3214
  edam_topics:
  - http://edamontology.org/topic_3520
  - http://edamontology.org/topic_0121
  - http://edamontology.org/topic_3172
  tools:
  - shinyscreen
  - R
  - devtools
  - Docker
  techniques:
  - LC-MS
  license_tier: open
  provenance_tier: literature
derived_from:
- doi: 10.1186/s13321-025-01044-x
  title: Shinyscreen
evidence_spans:
- Shinyscreen is a Shiny application for visualizing and analyzing high resolution
  mass spectrometry data.
- Shinyscreen can be installed in R via `devtools`
- docker run -p 3838:3838 \ -v C:/your/path/project:/home/ssuser/projects
- docker pull registry.gitlab.com/uniluxembourg/lcsb/eci/shinyscreen:master
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_shinyscreen_cq
    doi: 10.1186/s13321-025-01044-x
    title: Shinyscreen
  dedup_kept_from: coll_shinyscreen_cq
schema_version: 0.2.0
attribution:
  generator: AgenticScienceBuilder
  original_doi: 10.1186/s13321-025-01044-x
  all_source_dois:
  - 10.1186/s13321-025-01044-x
  zenodo_doi: 10.5281/zenodo.20794027
  curators: []
  promoter: Louis-Félix Nothias
  sponsor: CNRS & Université Côte d'Azur
---

# extracted-ion-chromatogram-eic-visualization

## Summary

Visualization of extracted ion chromatograms (EICs) for individual compounds detected in high-resolution mass spectrometry data, enabling inspection of peak quality, retention time alignment, and ionization mode assignment across sample replicates and treatment groups.

## When to use

After running MS1 extraction and prescreening on mzML files with assigned adducts and tags, when you need to inspect detected compounds visually to verify peak shape, confirm retention time consistency across samples (e.g., KO+, WT−, STD+), and validate that the correct adduct ([M+H]+ or [M−H]−) was assigned to each file.

## When NOT to use

- Input mzML files have not yet been uploaded and tagged in Shinyscreen; extraction and prescreening must complete first.
- No prescreening summary table has been generated; EIC visualization requires prior Extract and Prescreen step execution.
- You are working with low-resolution MS data or data formats other than mzML; Shinyscreen is designed for high-resolution mass spectrometry.

## Inputs

- mzML file(s) loaded in Shinyscreen with assigned tags and adducts
- Prescreening summary table generated by Configure-Extract-Prescreen workflow
- Compound row selected from results table

## Outputs

- EIC plot (retention time vs. intensity) for the selected m/z and mzML file
- Visual confirmation of peak presence, shape, and quality
- MS2 peak and MS2 spectrum plots (co-displayed)

## How to apply

In the Shinyscreen Results Explorer tab, click on a compound row in the prescreening summary table to open the EIC visualization alongside MS2 peak and MS2 spectrum panels. The EIC displays the extracted ion chromatogram for the compound's m/z value (within the configured EIC window) across the selected mzML file. Inspect the peak height, width, and baseline noise; verify that the retention time falls within the expected range set during extraction configuration (default retention time window parameters). Cross-reference the EIC peak intensity and quality control scores in the summary table to judge whether the feature passed prescreening thresholds. If peaks are noisy, split, or absent, the compound may warrant exclusion or re-extraction with adjusted MS1 coarse/fine error or EIC window parameters.

## Related tools

- **shinyscreen** (Web application for extracting, prescreening, and visualizing EICs from mzML files; provides interactive Results Explorer tab to open EIC plots on compound selection) — https://gitlab.com/uniluxembourg/lcsb/eci/shinyscreen
- **R** (Underlying programming language for Shinyscreen; used to compute EIC extraction and rendering)
- **Docker** (Container for running Shinyscreen without local R installation; enables portability and reproducibility)

## Evaluation signals

- EIC plot displays a single, well-resolved peak at the expected m/z value and retention time for the compound.
- Peak intensity and baseline noise are consistent with the quality control score and adduct assignment reported in the summary table row.
- Retention time is within the configured retention time window (default parameters set during Extract step).
- EIC peak is present and visible for all expected sample tags (e.g., KO+, KO−, WT+, WT−) if compound was detected across replicates.
- MS2 peak and MS2 spectrum panels (co-displayed) show fragmentation patterns consistent with the compound's chemical structure or database entry.

## Limitations

- EIC visualization depends on prior correct assignment of adducts ([M+H]+ or [M−H]−) to each mzML file; incorrect adduct assignment will yield empty or artifactual EICs.
- EIC window and MS1 coarse/fine error parameters are applied globally during extraction; fine-tuning these for individual compounds requires re-running Extract, which may be computationally expensive.
- EIC visualization does not perform chromatographic peak deconvolution; overlapping peaks or co-eluting isomers will appear as merged or distorted peaks.
- No changelog or version history is documented in the repository, limiting traceability of changes to EIC rendering logic across releases.

## Evidence

- [methods] Retention time and intensity ranges inspection: "simply click on the corresponding row in the table. This will open up the extracted ion chromatogram (EIC), MS2 peak and MS2 spectrum"
- [methods] EIC extraction parameters: "extraction section will display a set of default parameters for MS1 coarse and fine error, EIC window, and retention time window"
- [methods] Tag and adduct assignment prerequisite: "assign a unique tag to each file (such as `KO+`, `STD+`, or `WT+`) in the tagging section. Next, select the appropriate adduct from the dropdown list"
- [methods] Prescreening workflow context: "Click the **Extract** button to perform MS1 coarse/fine error and EIC window extraction using default parameters. 8. Click the **Prescreen** button to run quality control checks on extracted features."
- [methods] Shinyscreen application purpose: "Shinyscreen is a Shiny application for visualizing and analyzing high resolution mass spectrometry data."