Koskamo

labmcp-ms-data MCP

An MCP server for analyzing LC-MS mass spectrometry data in mzML, mzMLb, and Bruker timsTOF formats. It allows agents to list runs, report instrument details, plot chromatograms, extract ion chromatograms, read spectra, find MS2 scans, and perform quality control. Vendor files are converted to mzML using external tools like msconvert or ThermoRawFileParser.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

labmcp-ms-data MCP logo, by K-Dense-AICommunity listingLocal stdioSource reviewed; not executedPublished by K-Dense-AI
You need:install a converter yourself; this package never bundles or downloads vendor libraries
Vendor documentation

What you can do with it

  • List runs in a data folder
  • Plot TIC/BPC chromatograms
  • Extract ion chromatograms with apex and area
  • Find MS2 scans by precursor m/z

Source and maintenance

Community listingRegistry 0.1.1
mcp-registry: io.github.K-Dense-AI/labmcp-ms-data@0.1.1Source repositoryProject website
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

labmcp-ms-data 0.1.1

pypi
labmcp-ms-data package definition
{
  "version": "0.1.1",
  "transport": "stdio",
  "identifier": "labmcp-ms-data",
  "registryType": "pypi",
  "registryBaseUrl": "https://pypi.org",
  "environmentVariables": [
    {
      "name": "LABMCP_ADDRESS",
      "description": "Instrument address, e.g. serial:///dev/ttyUSB0 or tcp://192.168.1.50:5025"
    },
    {
      "name": "LABMCP_SIMULATE",
      "description": "Set to 1 to use the built-in simulator (no hardware)"
    },
    {
      "name": "LABMCP_READ_ONLY",
      "description": "Set to 1 to disable all state-changing tools"
    },
    {
      "name": "LABMCP_LIMITS",
      "description": "Safety limit overrides, e.g. max_temperature_c=80"
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "labmcp-ms-data-mcp": {
      "command": "uvx",
      "args": [
        "labmcp-ms-data==0.1.1"
      ],
      "env": {
        "LABMCP_ADDRESS": "<YOUR_LABMCP_ADDRESS>",
        "LABMCP_SIMULATE": "<YOUR_LABMCP_SIMULATE>",
        "LABMCP_READ_ONLY": "<YOUR_LABMCP_READ_ONLY>",
        "LABMCP_LIMITS": "<YOUR_LABMCP_LIMITS>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "labmcp-ms-data-mcp": {
      "command": "uvx",
      "args": [
        "labmcp-ms-data==0.1.1"
      ],
      "env": {
        "LABMCP_ADDRESS": "<YOUR_LABMCP_ADDRESS>",
        "LABMCP_SIMULATE": "<YOUR_LABMCP_SIMULATE>",
        "LABMCP_READ_ONLY": "<YOUR_LABMCP_READ_ONLY>",
        "LABMCP_LIMITS": "<YOUR_LABMCP_LIMITS>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "labmcp-ms-data-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "labmcp-ms-data==0.1.1"
      ],
      "env": {
        "LABMCP_ADDRESS": "<YOUR_LABMCP_ADDRESS>",
        "LABMCP_SIMULATE": "<YOUR_LABMCP_SIMULATE>",
        "LABMCP_READ_ONLY": "<YOUR_LABMCP_READ_ONLY>",
        "LABMCP_LIMITS": "<YOUR_LABMCP_LIMITS>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "labmcp-ms-data-mcp": {
      "command": "uvx",
      "args": [
        "labmcp-ms-data==0.1.1"
      ],
      "env": {
        "LABMCP_ADDRESS": "<YOUR_LABMCP_ADDRESS>",
        "LABMCP_SIMULATE": "<YOUR_LABMCP_SIMULATE>",
        "LABMCP_READ_ONLY": "<YOUR_LABMCP_READ_ONLY>",
        "LABMCP_LIMITS": "<YOUR_LABMCP_LIMITS>"
      }
    }
  }
}

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