pepxml mcp for Gemini CLI

io.github.mrfentmen/pepxml-mcp

pepXML MCP: parse search results, validate runs, spectrum queries and hits.

client:Gemini CLI transport:stdio runtime:npm

Install pepxml mcp in Gemini CLI

~/.gemini/settings.json · windows: %USERPROFILE%\.gemini\settings.json

{
  "mcpServers": {
    "pepxml-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@mrfentmen/pepxml-mcp"
      ]
    }
  }
}

Gemini expands $VAR and ${VAR} inside env values, so a secret can live in your shell rather than this file. Gemini CLI docs