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

MCP server for LC-MS data in mzML/mzMLb and Bruker timsTOF files; vendor formats via msconvert.

Installation

MCP client config (paste into mcp.json)

{
  "mcpServers": {
    "labmcp-ms-data": {
      "command": "npx",
      "args": [
        "labmcp-ms-data"
      ]
    }
  }
}

Agent install prompt

Copy and paste into Cursor / Claude / other agents to install this MCP for you

Please read this MCP repository and install it into my current environment:
https://github.com/K-Dense-AI/lab-instrument-mcps

Known working client config (can write into mcp.json):
{
  "mcpServers": {
    "labmcp-ms-data": {
      "command": "npx",
      "args": [
        "labmcp-ms-data"
      ]
    }
  }
}

Please: 1) check README for deps and env vars; 2) write config for my client; 3) if secrets are missing, tell me what to fill — do not invent values.

GitHub

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