SDRF And Metadata Prompts

Example 1: Load a local SDRF

User prompt

Load this SDRF file and tell me which raw files map to which assays and samples.

What the MCP should do

  • call load_sdrf

Expected output shape

  • grouped file metadata
  • assay/sample summaries
  • factor columns and instrument-related metadata when present

Example 2: Retrieve SDRF from PRIDE

User prompt

Retrieve the SDRF for this PRIDE accession and summarize the sample layout.

What the MCP should do

  • call retrieve_pride_sdrf

Expected output shape

  • PRIDE-derived SDRF summary
  • mapped raw file names, basenames, and stems

Example 3: Combine ID summaries with SDRF

User prompt

Inspect this PSM table and include SDRF-linked sample metadata if it matches the raw files.

What the MCP should do

  • call inspect_psm_table with sdrf_path or pride_project_accession

Expected output shape

  • normal inspection summary
  • additional sdrf_summary

Example 4: Ask for acquisition context

User prompt

For this scored peptide, tell me which runs, samples, fragmentation methods, and instruments support it.

What the MCP should do

  • if working from a scored table, call get_peptide_summary
  • optionally enrich through SDRF if available

Expected output shape

  • peptide-level support summary
  • run/sample context where available