Chromascope

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Chromascope is a free, lightweight, easy-to-use, open-source, vendor-agnostic LC-MS workbench designed for targeted analysis. It opens mzML directly and works with any vendor file by converting it automatically with msconvert: download msconvert once and link it in Chromascope (how). Inspect batches, integrate peaks, build calibration curves, quantify and run QC. Use it like a normal desktop app, script it from the command line, or hand the controls to an AI assistant over MCP. The assistant does the reasoning; Chromascope does the maths, keeps the evidence and records exactly what happened.

https://github.com/user-attachments/assets/cfbe286f-962d-41b3-ad6f-ffa3f33bebf3

Video not playing? Open assets/demo.mp4 directly. It shows an AI client opening a file, extracting an XIC and previewing an integration in the Chromascope window; nothing is changed permanently.

Documentation

• Website and user manual: https://chromascope-ms.github.io/chromascope/
• MCP guide: set up an AI assistant, what it can do, ready-to-paste prompts, safety.
• Getting started: a ten-minute tutorial with the example file in test_file/.
• CHANGELOG.md and examples/README.md.

Install

1. Download the installer for your system from the releases page: .msi or portable .zip (Windows), .dmg (macOS), .deb, .rpm, .AppImage or .tar.gz (Linux).
2. The builds are not code-signed. On Windows choose More info, Run anyway in SmartScreen; on macOS use System Settings, Privacy & Security, Open Anyway.
3. Start Chromascope, choose File, Open data…, and follow the tutorial.

Details for every system, the checksums and building from source are on the download page. The desktop program checks GitHub once a day for a newer version; see Settings to turn that off.

What is in the package

Program	What it is
chromascope	The desktop app
chromascope-cli	The same analysis engine as JSON on the command line
chromascope-mcp	The desktop app as an MCP server: an AI assistant works in a visible window (74 tools)
chromascope-engine-mcp	A window-less MCP server with the 14 calculation tools, for scripts and servers

One engine sits behind all four, so a number from the window is the number from the CLI and from the assistant. Raw files are never modified, and results keep their units, settings, software versions and source hashes.

An assistant works in the window that its client started (chromascope-mcp). Its status bar shows how many requests the assistant made, with a link to the call log. When you ask it to propose instead of apply a change, for example new peak boundaries, the proposal appears in the window under Audit package, Review AI proposals, with its reason and evidence; only your Approve changes a result. Proposals saved in a project can be reviewed later in the plain chromascope.exe. See the guide to reviewing AI proposals.

Development

cargo fmt --all -- --check
cargo clippy --locked --all-targets -- -D warnings
cargo clippy --locked --all-targets --all-features -- -D warnings
cargo test --locked
cargo test --locked --features mcp
cargo test --locked --no-default-features --features mcp-headless
cargo test --locked --all-features

The package needs Rust 1.88 or newer. On Ubuntu the window also needs libxcb-render0-dev libxcb-shape0-dev libxcb-xfixes0-dev libxkbcommon-dev. The website is in website/ (MkDocs Material); build it from the repository root with pip install -r website/requirements.txt and mkdocs build --strict -f website/mkdocs.yml. See contributing: a change to the window or to the MCP tools updates the manual and the MCP guide in the same commit.

flowchart LR
  GUI[egui desktop] --> Engine[Shared analytical engine]
  CLI[JSON CLI] --> Engine
  DMCP[Desktop MCP server] --> GUI
  DMCP --> Engine
  HMCP[Headless MCP server] --> Engine
  Engine --> Rust[Rust kernels / mzdata]
  Engine --> Project[Immutable revisions and provenance]
  Project --> Delivery[JSON / CSV / TSV / SVG / HTML drafts]

Citation

If Chromascope helps with work you publish, please cite it and name the version you used (File, About Chromascope…). The metadata are in CITATION.cff, which GitHub shows under "Cite this repository".

Plain text:

Cseresznye, A. Chromascope: an open-source, AI-ready LC-MS workbench, version 0.3.1. Zenodo. https://doi.org/10.5281/zenodo.23542311

BibTeX:

@software{cseresznye_chromascope,
  author  = {Cseresznye, Adam},
  title   = {Chromascope: an open-source, AI-ready LC-MS workbench},
  version = {0.3.1},
  year    = {2026},
  doi     = {10.5281/zenodo.23542311},
  url     = {https://github.com/chromascope-ms/chromascope},
  license = {GPL-3.0-only}
}

Licence

Licensed under GPL-3.0-only. THIRD_PARTY_LICENSES.txt lists the notice of every dependency and of the embedded Inter and JetBrains Mono fonts.