Table Inspection Prompts

Example 1: Inspect an upstream table

User prompt

Inspect this FragPipe PSM table and tell me how many PSMs, peptides, modified peptidoforms, and runs it contains.

What the MCP should do

  • call inspect_psm_table
  • use adapter="fragpipe"
  • summarize dataset_metadata, sequence_summary, and run_summary

Expected output shape

  • structured counts for PSMs, peptides, peptidoforms, and runs
  • preview rows from the normalized PSM table
  • no rescoring

Example 2: Inspect one peptide

User prompt

Show me the peptide summary for LQLETELEALKEELLFMK and list the supporting PSMs.

What the MCP should do

  • call inspect_peptide_table with peptide="LQLETELEALKEELLFMK"
  • optionally call inspect_psm_table to retrieve preview rows or supporting candidate IDs

Expected output shape

  • one collapsed peptide-level row
  • supporting PSM counts
  • modified/unmodified support if present

Example 3: Summarize score-like upstream fields

User prompt

Load this MaxQuant msms.txt file and summarize the confidence, charge-state, and precursor m/z distributions.

What the MCP should do

  • call summarize_numeric_field for confidence
  • call summarize_categorical_field for precursor_charge
  • call bin_numeric_field for precursor_mz

Expected output shape

  • numeric summary stats for confidence
  • counts/fractions for charge states
  • histogram-style bins for precursor m/z

Example 4: Inspect table fields before analysis

User prompt

List which fields in this Proteome Discoverer export can be summarized numerically or categorically.

What the MCP should do

  • call list_distribution_fields

Expected output shape

  • canonical fields
  • detected upstream source_columns.*
  • separation of numeric and categorical candidates