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Thermo Orbitrap (Instrument API) MCP server

by K-Dense-AI·io.github.K-Dense-AI/labmcp-thermo-iapi·v0.1.1·6 stars
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MCP server adapter for Thermo Fisher Orbitrap mass spectrometers via the licensed Instrument API.

A91/100grade A
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Safety scan
A91/100

full report

Adoption
Growing

6 stars167 downloads/wk

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If you have run it, two minutes of your experience saves the next person an afternoon.

Thermo Orbitrap (Instrument API) tools (12, 3 write)

write = sends, deletes, buys or posts

Read from the package source without running it. The installed server may list more.

  • cancel_custom_scanswrite action

    Cancel any pending custom scan and its processing delay (IAPI CancelCustomScan).

  • cancel_repeating_scanwrite action

    Cancel the repeating scan set with set_repeating_scan (IAPI CancelRepetition).

  • get_instrument_status

    Report the instrument model, IAPI service/instrument connection, system mode and state (On/Standby/Off; Running/ReadyToDownload/...), whether an acquisition can be paused or resumed, the IAPI licence where the API exposes it, requested readbacks, the latest scan status log (vacuum, source) and how many scans have arrived.

  • get_possible_scan_parameters

    List the scan parameters this instrument accepts for custom and repeating scans (IScans.PossibleParameters): name, allowed range or choices, default and help. The set depends on the model, licence and Tune version.

  • get_recent_scans

    Return the most recent scans received from the instrument (oldest first), optionally only one MS order or one custom scan's access id: scan number, MS order, precursor m/z, AGC target, injection time and the most intense centroids. Scans only arrive in On mode.

  • pause_acquisition

    Pause the running acquisition (IAPI Pause). Fails if the instrument reports it cannot pause.

  • resume_acquisition

    Resume a paused acquisition (IAPI Resume). Sample consumption continues.

  • set_repeating_scan

    Define or replace the scan the instrument repeats when no method or custom scan is running (IAPI CreateRepeatingScan/SetRepetitionScan). Values are validated like submit_custom_scan. Cancel with cancel_repeating_scan.

  • start_acquisition

    Start an acquisition with the instrument's current settings (IAPI StartAcquisition), recording to a raw file. This consumes sample. The instrument must be On; an acquisition must not already be running. Stop it with stop_acquisition. scan_count and until_stopped acquisitions are cancelled automatically after max_acquisition_duration_s.

  • stop_acquisition

    Stop the running acquisition (IAPI CancelAcquisition), by default also cancelling custom and repeating scans, and optionally switch the instrument to Standby (switch back to On in Tune). Every step is attempted even if an earlier one fails; failures are reported.

  • submit_custom_scanwrite action

    Place one custom scan to run next (IAPI CreateCustomScan/SetCustomScan); unset values fall back to the instrument's defaults. Every value is checked against PossibleParameters and the safety limits, and calls are rate-limited, before anything is sent. Fetch the result with wait_for_scan(access_id=running_number).

  • wait_for_scan

    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 scan placed with submit_custom_scan, a result that arrived since it was placed is returned at once. Returns found=false after timeout_s if nothing matching arrived (e.g. the instrument is in Standby).

Public scan report

scanner v0.1.9 · 2026-09-27 · same rubric, same numbers if you re-run it

no findings
  • Code scan9 source files scanned25/25
  • –Live reliabilityno gateway calls yet and no remote to proben/a
  • –Tool poisoningtools not inspected (local package is not executed); not countedn/a
  • Auth qualitylocal package, no credentials required12/15
  • Maintenancelast push 0 days ago15/15
  • Maintainer identityregistry namespace matches repository owner7/10
Overall 91/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

How Thermo Orbitrap (Instrument API) compares

Against every graded MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score
91/100
higher than 85% of 48,255 servers
Tools
12
the typical server has 7
Tools that change things
25%
typical: 0%. Fewer write tools means less an agent can break
GitHub stars
6
more than 85% of 28,688 servers
Downloads a week
167
more than 72% of 12,191 servers with a package

What its tools let an agent do: 6 read · 2 change · 2 delete · 2 run or deploy

Install Thermo Orbitrap (Instrument API) in Claude Code, Cursor or VS Code

claude mcp add labmcp-thermo-iapi -- uvx labmcp-thermo-iapi
Add to Cursor

What the publisher says

From the Thermo Orbitrap (Instrument API) repository's README, as published. We do not edit it. Read it on GitHub

LabMCP: Let AI Assistants Run Your Lab Instruments

<!-- COUNTS:START --> <!-- COUNTS:END -->

LabMCP lets an AI assistant such as Claude operate your laboratory instruments. You describe what you want in plain language, and the assistant weighs, heats, stirs, pumps, measures and logs for you. It stays inside safety limits you set, keeps a record of every command, and has a practice mode that needs no hardware.

It supports balances, hotplate stirrers, syringe pumps, spectrometers, mass spectrometers, potentiostats, lock-in amplifiers, temperature controllers, vacuum gauges, flow controllers, biosensors, clinical analyzers and more. You don't need to know how to program. Setup means installing one free helper program and pasting a few lines into your AI app's settings.

Free and open source, built by K-Dense.

You:        Tare the balance, then heat the stirrer to 60 °C at 400 rpm and log the pH every
            30 s until it's stable. Tell me when to add the reagent.

Assistant:  [tares the balance → sets stirring to 400 rpm → sets heating to 60 °C → logs pH …]
            "pH has been 7.41 ± 0.01 for 3 minutes. Ready for the reagent."

⭐ Help other scientists find this. If LabMCP is useful to you, please star the repo.

📋 Contents

  • How it works
  • Try it in 10 minutes (no instrument needed)
  • Supported instruments
  • Connect your real instrument
  • Safety
  • What every connector includes
  • Example requests
  • FAQ
  • Contributing
  • Roadmap

💡 How it works

You  ──type──▶  AI app  ──▶  LabMCP connector  ──USB / serial / network cable──▶  Instrument
                 (Claude,       (runs on the computer
                  Cursor, …)     attached to the instrument)
  • The AI app is where you type requests, e.g. Claude Desktop.
  • A LabMCP connector is a small program that knows one family of instruments and its command language, so the AI never has to guess it. You add one connector per type of instrument. (Technically these are MCP servers, which is the term you'll see in the tables and docs.)
  • MCP (Model Context Protocol) is the open standard that lets AI apps plug into tools like these. Think of it as USB for AI.
  • The AI can only use the actions a connector offers, like "tare", "set temperature" or "read pH". In the docs these actions are called tools. The connector checks every request against your limits and refuses anything unsafe before it reaches the instrument.

🚀 Try it in 10 minutes (no instrument needed)

Each connector has a practice mode (a simulator) that behaves like the real instrument and gives realistic replies. Nothing is connected, so nothing can go wrong.

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

Thermo Orbitrap (Instrument API): common questions

Is Thermo Orbitrap (Instrument API) MCP server safe?
Yes, by our scan: it is graded A (91/100). Read the Thermo Orbitrap (Instrument API) safety report
How do I install Thermo Orbitrap (Instrument API)?
It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.
Does Thermo Orbitrap (Instrument API) need an API key?
No secret keys are declared. It reads 4 settings from the environment.
Is Thermo Orbitrap (Instrument API) maintained?
The last commit was 38 days ago (2026-09-26). The latest release is v0.1.1.
How does Thermo Orbitrap (Instrument API) compare with other MCP servers?
safety score 91/100 (higher than 85% of 48,255 servers); tools 12 (the typical server has 7); tools that change things 25% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.

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