Dataset Aggregation Prompts

Example 1: Summarize a scored table

User prompt

Summarize this scored PSM table into dataset, peptide, peptidoform, and run-level outputs.

What the MCP should do

  • call summarize_dataset

Expected output shape

  • dataset_metadata
  • identification_summary
  • sequence_summary
  • run_summary
  • confidence_summary
  • preview rows for peptide and peptidoform tables

Example 2: Retrieve one peptide summary

User prompt

Show me the peptide-level summary row for LQLETELEALKEELLFMK.

What the MCP should do

  • call get_peptide_summary

Expected output shape

  • one peptide-level aggregate row

Example 3: Retrieve one peptidoform summary

User prompt

Return the best peptidoform-level row for M[UNIMOD:35]PEPTIDE.

What the MCP should do

  • call get_peptidoform_summary

Expected output shape

  • one modification-aware aggregate row

Example 4: Inspect grouping structure

User prompt

List the dataset groups available in this scored table and tell me whether sample-level grouping is available.

What the MCP should do

  • call list_dataset_groups

Expected output shape

  • dataset/run/sample grouping keys
  • indication of whether SDRF-linked sample summaries exist