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Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) MCP server

by K-Dense-AI·io.github.K-Dense-AI/labmcp-ms-data·v0.1.1·6 stars
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MCP server for LC-MS data in mzML/mzMLb and Bruker timsTOF files; vendor formats via msconvert.

A91/100grade A
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Safety scan
A91/100

full report

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Growing

6 stars

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Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) tools (9, 2 write)

write = sends, deletes, buys or posts

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

  • convert_to_mzml

    Convert a vendor file (Thermo .raw, Waters .raw, Agilent .d, SCIEX .wiff, Shimadzu .lcd, Bruker .d) to mzML with the converter the user installed (ThermoRawFileParser, ProteoWizard msconvert, or msconvert in Docker; chosen with --option converter=...). Writes a new file in the data folder. Can take minutes; fails with install instructions if no converter is set up.

  • extract_ion_chromatogram

    Extracted ion chromatogram (XIC/EIC) for one or more m/z values: the summed intensity within ± tolerance (ppm or Da) in every MS1 spectrum (or another `ms_level`). For each target returns the apex RT and intensity, the apex peak's boundaries, area (intensity x min, no baseline subtraction) and FWHM, plus a downsampled trace. Reads every spectrum in the RT window, so restrict `rt_start_min`/`rt_end

  • find_ms2_scans

    Find the MS2 (MSn) spectra whose precursor m/z is within ± tolerance of `precursor_mz`, optionally within an RT window and for one charge state. Returns index, scan number, RT, precursor m/z, error in ppm, charge and intensity; open any hit with get_spectrum.

  • get_bpc

    Base peak chromatogram (intensity of the most intense peak per spectrum, with its m/z) vs retention time, downsampled to `max_points`. Cleaner than the TIC for spotting eluting compounds; the base-peak m/z tells you which ion dominates each part of the run.

  • get_run_infowrite action

    Describe one run: instrument vendor/model/serial (when the file records them), acquisition date, software, number of spectra per MS level, retention-time and m/z ranges, polarity, centroid/profile, and whether ion-mobility data is present. The first call on a large file indexes it (can take a while); later calls are instant.

  • get_spectrum

    Read one spectrum, chosen by `index`, `scan_number`, `native_id` or nearest `rt_min` (give exactly one). Returns MS level, RT, polarity, centroid/profile, precursor m/z and charge for MS2, a summary (peak count, TIC, base peak, m/z range) and the `top_n` most intense peaks; `save_path` writes the full peak list to CSV. For profile spectra the top peaks are local maxima of the profile.

  • get_tic

    Total ion chromatogram (sum of all intensities per spectrum vs retention time) for one MS level, downsampled to `max_points` (keeping the maximum in each bin so peaks survive). Returns the apex, median and area; `save_path` writes every point to CSV.

  • list_runs

    Find mass-spectrometry runs in the data folder and detect each one's vendor and format (mzML/mzML.gz/mzMLb, Bruker .d TDF or BAF, Agilent .d, Thermo .raw, Waters .raw folder, SCIEX .wiff/.wiff2, Shimadzu .lcd, mzXML). `readable_directly=false` means the run must be converted with convert_to_mzml before it can be analysed.

  • summarise_runwrite action

    Quick QC of a run: MS1/MS2 counts, TIC stability (CV, spray dropouts), where the signal elutes, cycle time, MS2 scans per cycle, median injection times and how often MS2 hit the maximum injection time, and precursor charge states. Returns plain-language warnings.

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 Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) 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
9
the typical server has 7
Tools that change things
22%
typical: 0%. Fewer write tools means less an agent can break
GitHub stars
6
more than 85% of 28,688 servers

What its tools let an agent do: 7 read · 2 change

Install Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) in Claude Code, Cursor or VS Code

claude mcp add labmcp-ms-data -- uvx labmcp-ms-data
Add to Cursor

What the publisher says

From the Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) 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.

Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion): common questions

Is Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) MCP server safe?
Yes, by our scan: it is graded A (91/100). Read the Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) safety report
How do I install Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion)?
It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.
Does Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) need an API key?
No secret keys are declared. It reads 4 settings from the environment.
Is Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) maintained?
The last commit was 38 days ago (2026-09-26). The latest release is v0.1.1.
How does Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) compare with other MCP servers?
safety score 91/100 (higher than 85% of 48,255 servers); tools 9 (the typical server has 7); tools that change things 22% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.

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