Koskamo

PRIDE Proteomics MCP Server

An MCP server that wraps the EBI PRIDE Archive, the largest public proteomics and mass-spectrometry dataset repository. It allows AI agents to search for projects by keyword and retrieve full metadata for specific projects by accession number, facilitating access to primary-source biological data without requiring authentication.

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Package and access

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

PRIDE Proteomics MCP Server logo, by PipeworxCommunity listingLocal stdioSource reviewed; not executedPublished by Pipeworx
You need:Install @pipeworx/sdk to call tools from any TypeScript/Node project.
Vendor documentation

What you can do with it

  • Search for proteomics projects by disease, organism, or technique
  • Retrieve full metadata for a specific PRIDE project by accession
  • Access public mass-spectrometry dataset repositories via MCP

Source and maintenance

Community listingRegistry 0.2.0
mcp-registry: io.github.pipeworx-io/pride@0.2.0Source repositoryProject website
Maintenance checked

Packages and installation

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

@pipeworx/mcp-pride 0.2.0

npm
@pipeworx/mcp-pride package definition
{
  "version": "0.2.0",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-pride",
  "registryType": "npm",
  "environmentVariables": [
    {
      "name": "PIPEWORX_API_KEY",
      "description": "Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap."
    }
  ]
}

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": {
    "pride-proteomics-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pride@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "pride-proteomics-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pride@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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": {
    "pride-proteomics-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pride@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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": {
    "pride-proteomics-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pride@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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