Thermo Orbitrap (Instrument API) MCP Server

Let an AI agent watch and steer a Thermo Fisher Orbitrap mass spectrometer in real time: check the instrument mode and vacuum, read the scans streaming off the instrument (filtered by MS order, with the most intense centroids), place validated custom scans and pick up their results, set a repeating scan, and start, pause or stop acquisitions to a raw file. It does this through Thermo's own Instrument API (IAPI). Its 15 documented tools cover scan, acquisition, custom, scans.

People who work with scan, acquisition and custom and want it reachable from Claude, Cursor, VS Code, or another MCP client. The project is written in Python.

One of 32 MCP servers published from k-dense-ai/lab-instrument-mcps. Stars and repository activity are shared across all of them. See all 32 →

VERIFIED ACTIVE

LAST COMMIT 2026-09-26 · VERIFIED 2026-09-30

Apache-2.0 · Python servers · how we verify → /methodology

01 · Install Thermo Orbitrap (Instrument API)

Claude Code

claude mcp add k-dense-ai-lab-instrument-mcps-servers-c -- uvx labmcp-thermo-iapi

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "k-dense-ai-lab-instrument-mcps-servers-c": {
      "command": "uvx",
      "args": [
        "labmcp-thermo-iapi"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

repo age created 2026-09-25 - young repo, little track record yet

license Apache-2.0 - declared in the repository

pypi package labmcp-thermo-iapi - check the name against the project README before installing (PyPI has no namespace ownership)

registry namespace io.github.K-Dense-AI is GitHub-verified and matches the repo owner

03 · What Thermo Orbitrap (Instrument API) can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

With this server connected, an agent can cancel any pending custom scan and its processing delay (IAPI CancelCustomScan), cancel the repeating scan set with set_repeating_scan (IAPI CancelRepetition), report the instrument model, IAPI service/instrument connection, system mode and state (On/Standby/Off, and pause the running acquisition (IAPI Pause). Fails if the instrument reports it cannot pause.

Capability map

Tools grouped from the project's README - what Thermo Orbitrap (Instrument API) lets an agent do.

read & search

5 tools - e.g. Return the most recent raw commands sent to / replies received from the instrument (newest last). Useful for debugging and for recording what was done.; Report which instrument is connected (identity…

get_command_log · get_connection_info · get_instrument_status · get_possible_scan_parameters · get_recent_scans

Acquisition

4 tools - e.g. Pause the running acquisition (IAPI Pause). Fails if the instrument reports it cannot pause.; Resume a paused acquisition (IAPI Resume). Sample consumption continues.; Start an acquisition with the…

pause_acquisition · resume_acquisition · start_acquisition · stop_acquisition

Repeating

2 tools - e.g. Cancel the repeating scan set with set_repeating_scan (IAPI CancelRepetition).; Define or replace the scan the instrument repeats when no method or custom scan is running (IAPI…

cancel_repeating_scan · set_repeating_scan

delete

1 tool - e.g. Cancel any pending custom scan and its processing delay (IAPI CancelCustomScan).

cancel_custom_scans

Reconnect

1 tool - e.g. Close and re-open the connection to the instrument (e.g. after it was power cycled or a cable was re-plugged).

reconnect

Submit

1 tool - e.g. Place one custom scan to run next (IAPI CreateCustomScan/SetCustomScan); unset values fall back to the instrument's defaults. Every value is checked against Pos

submit_custom_scan

Wait

1 tool - e.g. Wait for the next scan that arrives after this call (optionally of one MS order, or the result of a custom scan by its access id) and return it. For a custom sc

wait_for_scan

Limitations (from the README)

- Instrument mode: scans only arrive in On mode, and custom scans and acquisitions need it too. stop_acquisition(standby=true) switches to Standby. This server has no tool to switch back to On (do that in Tune). - Custom scans: values you leave out come from the instrument's defaults, as Thermo documents for IScanDefinition.Values. running_number comes back as the scan's access_id (trailer item Access Id:). The serve

04 · Who maintains Thermo Orbitrap (Instrument API)

Thermo Orbitrap (Instrument API) is maintained by k-dense-ai. We track 32 MCP servers from k-dense-ai - 32 actively maintained, 9 combined GitHub stars, oldest repo from Sep 2026. Full record: all servers from k-dense-ai.

05 · Facts

repository: github.com/k-dense-ai/lab-instrument-mcps
website: https://github.com/K-Dense-AI/lab-instrument-mcps/tree/main/servers/chemistry/thermo-iapi
category: API integration - actively maintained as of 2026-09-30.
registry: io.github.K-Dense-AI/labmcp-thermo-iapi (active, first published 2026-09-26 · 2 versions)
packages: pypi:labmcp-thermo-iapi

06 · Thermo Orbitrap (Instrument API) FAQ

Is Thermo Orbitrap (Instrument API) still maintained?

Yes - as of 2026-09-30, its last commit was 2026-09-26. We re-verify nightly.

What can Thermo Orbitrap (Instrument API) do?

How do I install Thermo Orbitrap (Instrument API)?

Run `uvx labmcp-thermo-iapi`. You can also paste the ready-made client config above.

Does Thermo Orbitrap (Instrument API) run locally?

Yes - it's a stdio server: it runs on your machine (via uvx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to Thermo Orbitrap (Instrument API)

Alternatives to Thermo Orbitrap (Instrument API)

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