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

Let an AI agent find, read and analyse LC-MS data files from any vendor through open interfaces: list the runs in a folder, report the instrument and acquisition details, plot TIC/BPC chromatograms, extract ion chromatograms with apex and area, read spectra, find MS2 scans by precursor m/z, and run a quick QC. Vendor files are converted to mzML with a converter you have installed. This is a data server: it controls…. Its 12 documented tools cluster into read & search, convert, extract, reconnect.

People connecting this server to 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 Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion)

Claude Code

claude mcp add k-dense-ai-lab-instrument-mcps-servers-c -- uvx labmcp-ms-data

Claude Desktop / Cursor / VS Code - add to config

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

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-ms-data - 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 Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) can do

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

What you can build

An agent gets 12 documented tools across read & search, convert, extract, including convert_to_mzml, extract_ion_chromatogram, find_ms2_scans, get_bpc.

Capability map

Tools grouped from the project's README - what Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) lets an agent do.

read & search

8 tools - e.g. 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, sc; Base peak chromatogram (intensity of the…

find_ms2_scans · get_bpc · get_command_log · get_connection_info · get_run_info · get_spectrum…

Convert

1 tool - e.g. Convert a vendor file (Thermo .raw, Waters .raw, Agilent .d, SCIEX .wiff, Shimadzu .lcd, Bruker .d) to mzML with the converter the user installed (ThermoRawFile

convert_to_mzml

Extract

1 tool - e.g. 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)

extract_ion_chromatogram

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

Summarise

1 tool - e.g. 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

summarise_run

Limitations (from the README)

- Format support: mzML (indexed or not, optionally .gz) through pyteomics (Apache-2.0), using the PSI-MS vocabulary bundled with psims (no download). mzMLb needs the [mzmlb] extra (h5py, hdf5plugin). Gzipped mzML is decompressed to a temporary file for random access. - Bruker timsTOF (TDF): run metadata (instrument, serial, date, m/z and 1/K0 ranges), the TIC (Frames.SummedIntensities), BPC intensity (Frames.MaxInten

04 · Who maintains Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion)

Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) 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/ms-data
category: other - actively maintained as of 2026-09-30.
registry: io.github.K-Dense-AI/labmcp-ms-data (active, first published 2026-09-26 · 2 versions)
packages: pypi:labmcp-ms-data

06 · Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) FAQ

Is Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) still maintained?

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

What can Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) do?

An agent gets 12 documented tools across read & search, convert, extract, including convert_to_mzml, extract_ion_chromatogram, find_ms2_scans, get_bpc.

How do I install Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion)?

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

Does Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion) 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 Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion)

Alternatives to Mass Spectrometry Data (mzML, Bruker TDF, vendor conversion)

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