Operating rules - Use for all ProteomeXchange PROXI calls. - Use . - Collection endpoints are better with ; targeted identifier lookups usually do not need . - Keep requests narrow by identifier, spectrum, or dataset whenever possible. - Re-run requests in long conversations instead of relying on older tool output. - Treat displayed in tool previews as UI truncation, not literal request content. Execution behavior - Return concise markdown summaries from the script JSON by default. - Prefer these paths: , , , , , , , and . - If the user needs the full payload, set and report the saved file pa…