# Retention Time Intensity Extraction

> Use when when you have imported mass spectrometry data in .raw, .d, or mzXML format and need to generate a TIC plot to visualize overall sample ionization intensity as a function of retention time.

- Skill: `holobiomicslab/retention-time-intensity-extraction` (Agent Skill)
- Install (CLI): `npx skillmds@latest add holobiomicslab/retention-time-intensity-extraction`
- Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/retention-time-intensity-extraction/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/retention-time-intensity-extraction

---


# retention-time-intensity-extraction

## Summary

Extract and aggregate ion intensities across retention time from mass spectrometry data to prepare total ion chromatogram (TIC) data for visualization. This skill converts raw m/z and intensity observations into retention-time-indexed intensity profiles suitable for chromatographic analysis.

## When to use

When you have imported mass spectrometry data in .raw, .d, or mzXML format and need to generate a TIC plot to visualize overall sample ionization intensity as a function of retention time. Use this skill as a prerequisite step before rendering chromatographic visualizations or performing retention-time-based peak analysis.

## When NOT to use

- Input data is already in aggregated or feature-table format (e.g., peak intensity matrix or aligned feature table) — skip directly to visualization.
- Analysis goal is targeted identification of specific m/z features — use mass spectrum extraction at selected retention time points instead.
- Data contains only pre-processed peak lists without scan-level intensity arrays — TIC reconstruction from peak lists may introduce bias.

## Inputs

- Imported mass spectrometry data (formats: .raw, .d, mzXML)
- Scan-level ion intensity and retention time pairs
- Mass spectrum intensity matrix (scans × m/z)

## Outputs

- TIC data vector (retention time indexed intensity values)
- TIC plot (intensity versus retention time visualization)
- High-resolution image file of TIC plot

## How to apply

Load the imported mass spectrometry data into the R environment and extract scan-level ion intensity measurements indexed by retention time. Aggregate all m/z ion intensities within each scan (summing across the mass-to-charge dimension) to produce a single intensity value per retention time point. This aggregation produces a one-dimensional intensity profile indexed by retention time. Export the aggregated intensity-versus-retention-time vectors as data structures suitable for plotting. The rationale is that TIC aggregation compresses the full m/z dimension while preserving temporal (retention time) resolution, enabling visual inspection of ionization behavior across the entire chromatographic run.

## Related tools

- **R** (Programming environment for loading, aggregating, and manipulating mass spectrometry ion intensity and retention time data)
- **R GUI** (User-friendly graphical interface for SMART Data Visualization module to interactively extract and render TIC and mass spectrum plots) — github.com/YuJenL/SMART
- **SMART** (Integrated platform providing Data Visualization module that executes retention-time-intensity extraction and TIC rendering as part of the complete metabolomics analysis workflow) — github.com/YuJenL/SMART

## Evaluation signals

- TIC intensity values are positive and non-zero across the expected retention time range of the chromatographic run.
- Retention time values are monotonically increasing and span the full acquisition window (e.g., 0–60 minutes for typical LC–MS).
- TIC plot shows expected chromatographic peaks (local intensity maxima) at known or biologically plausible retention times.
- Exported high-resolution image file is readable and displays smooth intensity profile without artifacts or extreme spikes indicative of aggregation errors.
- Ion intensity sums per scan are consistent with raw scan-level total ion counts (summing TIC intensity across all scans should approximate total ions in raw file).

## Limitations

- Aggregation loses m/z resolution; multiplex features at the same retention time cannot be distinguished. For targeted or high-mass-resolution analyses, extract individual mass spectra at selected retention time points instead.
- Baseline drift and instrument noise are preserved in the aggregated TIC; downstream quality control and baseline correction may be required for accurate peak detection.
- TIC does not account for ionization efficiency variation across the mass range; m/z regions with naturally high ion abundance may dominate the TIC and obscure lower-abundance features.

## Evidence

- [other] Extract and prepare TIC data by aggregating ion intensities across retention time.: "Extract and prepare TIC data by aggregating ion intensities across retention time."
- [other] Generate a TIC plot displaying intensity versus retention time.: "Generate a TIC plot displaying intensity versus retention time."
- [other] Load imported mass spectrometry data (supporting .raw, .d, and mzXML formats) into the R environment.: "Load imported mass spectrometry data (supporting .raw, .d, and mzXML formats) into the R environment."
- [readme] Data Visualization: Visually represent various types of data features (e.g., total ion chromatogram (TIC) and mass spectra).: "Data Visualization: Visually represent various types of data features (e.g., total ion chromatogram (TIC) and mass spectra)."
- [other] Export all visualizations as high-resolution image files suitable for downstream analysis and reporting.: "Export all visualizations as high-resolution image files suitable for downstream analysis and reporting."