How to Use the EBI Proteins API MCP in VS Code Copilot

Q: How do I set up the EBI Proteins API MCP Server with VS Code Copilot?

Create a .vscode/mcp.json file in your repository root and add the server configuration. This MCP configuration is automatically loaded for anyone on your team using VS Code Copilot to run all 16 protein tools.

Q: Can VS Code Copilot query mass-spec data using the EBI Proteins API?

Yes, your agent calls getproteomics and getproteomicsptm to pull experimental peptide detections. It inserts this real-world mass-spec evidence straight into your active code.

Q: How does VS Code Copilot resolve taxonomy IDs with the EBI Proteins API?

The agent uses searchtaxonomy to find the correct NCBI taxon ID by organism name. It then calls gettaxonomy to retrieve the complete lineage for your code pipelines.

Q: What features can I filter by type in this server?

You can use searchfeaturesbytype to filter annotations like BINDING, ACTIVESITE, or TRANSMEM. This allows your agent to fetch targeted structural data without pulling full, bulky records.

Share UniProt queries, proteomics data, and taxonomy lookups across your engineering team in VS Code Copilot.

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Connect EBI Proteins API MCP to VS Code Copilot

Create your Vinkius account to connect EBI Proteins API to VS Code Copilot and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup EBI Proteins API with VS Code Copilot

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Query the MCP Server directly from VS Code Copilot

Equip your team with `get_protein` and `get_protein_features` inside their shared workspace. Your agent pulls down sequence lengths, domains, and active sites without forcing anyone to leave the editor. Committing this configuration to your repo ensures every developer uses the exact same tools. It standardizes how your engineering team fetches protein annotations during development.

Verify antigen and antibody targets

Retrieve validated targets from the Human Protein Atlas using `get_antigen`. Your agent displays peptide regions and experimental evidence directly inside the VS Code chat interface. This tool accelerates immunology research by letting your team analyze validated targets side-by-side with their active codebase. You bypass the slow process of manual web searches.

Retrieve gene-centric proteome counts

Use `get_genecentric` to return canonical proteins and related protein counts for specific genes. Your agent maps these counts directly to your active bioinformatic pipelines. Having these counts inside your editor simplifies the design of database schemas for proteomic applications. You write code based on real-world reference proteomes like UP000005640.

Setup guide

Set up EBI Proteins API MCP in VS Code Copilot

Prerequisites

VS Code 1.99 or later with GitHub Copilot extension
Active Vinkius subscription with a valid endpoint token

1

Open MCP configuration

Open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P) and run "MCP: Add Server". Select HTTP (Streamable) as the server type. VS Code will create .vscode/mcp.json in your workspace.
2

Add the EBI Proteins API MCP

Paste the JSON snippet shown on the right into your .vscode/mcp.json. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Switch to Agent mode

Open Copilot Chat (Cmd+Shift+I / Ctrl+Shift+I) and switch to Agent mode using the dropdown. MCP tools are only available in Agent mode — they do not appear in Edit or Ask modes.
4

Verify the connection

In the Copilot Chat input, type # to list available tools. You should see the EBI Proteins API tools listed. Try asking: "List my recent EBI Proteins API transactions" and Copilot will invoke them automatically.

.vscode/mcp.json

{
  "mcpServers": {
    "ebi-proteins-api-mcp": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

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Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by EMBL-EBI Proteins API. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about EBI Proteins API MCP in VS Code Copilot

Create a `.vscode/mcp.json` file in your repository root and add the server configuration. This MCP configuration is automatically loaded for anyone on your team using VS Code Copilot to run all 16 protein tools.

Yes, your agent calls `get_proteomics` and `get_proteomics_ptm` to pull experimental peptide detections. It inserts this real-world mass-spec evidence straight into your active code.

The agent uses `search_taxonomy` to find the correct NCBI taxon ID by organism name. It then calls `get_taxonomy` to retrieve the complete lineage for your code pipelines.

You can use `search_features_by_type` to filter annotations like BINDING, ACTIVE_SITE, or TRANSMEM. This allows your agent to fetch targeted structural data without pulling full, bulky records.

All requests to this MCP Server run inside isolated, ephemeral environments that handle authentication securely. Your private gene targets and sequence queries are never cached or logged by Vinkius.

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