Conversion And Export Prompts
Example 1: Convert mzML
User prompt
Convert this mzML file to Feather and tell me how many MS2 spectra were extracted.
What the MCP should do
- call
mzml_to_feather
Expected output shape
- output file path
- source format
- row count or extracted spectrum count
Example 2: Convert Bruker .d
User prompt
Convert this Bruker .d directory to Feather and tell me whether AlphaTims or the embedded MGF fallback was used.
What the MCP should do
- call
bruker_d_to_feather
Expected output shape
- output file path
- source format
- fallback indicator when applicable
Example 3: Convert and export to InstaNovo
User prompt
Convert this MGF-derived Feather file into an InstaNovo-ready IPC file.
What the MCP should do
- call
export_to_instanovo
Expected output shape
- output path
- output format
- any export metadata returned by the tool
Example 4: Ask whether a table is suitable downstream
User prompt
Check whether this converted Feather table contains the fields needed for downstream scoring and export.
What the MCP should do
- inspect the spectrum table externally if needed
- explain required fields based on the MCP schemas and converter contracts
Expected output shape
- concise checklist of required fields
- identification of missing fields, if any