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proteomexchange-skill

Query ProteomeXchange PROXI endpoints for compact proteomics dataset and spectra summaries.

5.3k|765|Updated Mar 4, 2026
Search Tags:#mass spectrometry#datasets#proteomics#REST api#Spectra#proteomexchange#proxi
One-click install
npx skills add https://github.com/openai/plugins --skill proteomexchange-skill
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: proteomexchange-skill
Source: https://github.com/openai/plugins/tree/main/plugins/life-science-research/skills/proteomexchange-skill
Command: npx skills add https://github.com/openai/plugins --skill proteomexchange-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) components.

What problem does it solve?

Researchers querying the ProteomeXchange PROXI API often receive large, deeply nested JSON payloads that are hard to scan. This Skill submits narrow PROXI requests and returns compact, truncated summaries of datasets, libraries, peptidoforms, proteins, PSMs, spectra, and USI examples.

Core Features & Use Cases

  • Compact PROXI Queries: Calls ProteomeXchange PROXI endpoints such as datasets, libraries, peptidoforms, proteins, psms, spectra, and usi_examples with configurable item and depth limits.
  • Targeted Identifier Lookups: Fetches single records by identifier, for example datasets/PXD000001, without needing max_items truncation.
  • Raw Payload Archiving: Optionally saves the full JSON response to a file via save_raw and reports the saved path.
  • Use Case: A proteomics researcher asks for the ten most recent public datasets; the Skill queries the datasets endpoint with max_items=10 and returns a concise markdown summary instead of the full API payload.

Quick Start

Ask the assistant to list the latest 10 ProteomeXchange datasets or to fetch the PROXI record for dataset PXD000001.

Frequently Asked Questions about proteomexchange-skill

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query the ProteomeXchange PROXI API for datasets?▼

Send a JSON object with base_url set to the PROXI v0.1 endpoint and path set to datasets, optionally with max_items to limit results. The script returns a compact records list with truncation metadata instead of the full payload.

How do I look up a specific ProteomeXchange dataset by identifier?▼

Set the path field to datasets/<identifier>, for example datasets/PXD000001, and keep the same PROXI base_url. Targeted identifier lookups return a compact summary of the single record and usually do not need max_items.

What PROXI endpoints does this Skill support?▼

It supports the datasets, libraries, peptidoforms, proteins, psms, spectra, and usi_examples paths on the ProteomeXchange PROXI v0.1 API. Both collection endpoints and targeted identifier lookups are handled by the same REST script.

Can I save the full PROXI API response instead of a summary?▼

Yes, set save_raw to true in the JSON input and optionally provide raw_output_path. The full JSON payload is written to that file (or a default /tmp path) and the output reports the saved file location.

Why does the PROXI output show truncated records or ellipsis?▼

The script compacts responses using max_items and max_depth limits, truncating long strings and lists to keep summaries readable. Displayed ellipsis in previews is UI truncation, not literal request content; use save_raw for the complete payload.

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