ToolUniverse is a collection of tools, interfaces, and supporting components for building AI systems that perform scientific work. It is for developers creating AI scientist agents that use APIs, databases, machine-learning tools, and domain-specific utilities. The catalogue includes skills, commands, an MCP server, an agent, and a hook for working with the ecosystem.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add mims-harvard/ToolUniverse --skill tooluniverse-proteomics-data-retrievalgit clone --depth 1 https://github.com/mims-harvard/ToolUniverseWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-proteomics-data-retrieval)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-proteomics-data-retrieval"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-proteomics-data-retrieval/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-proteomics-data-retrieval"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-proteomics-data-retrieval.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00125 | $0.05199 |
| Opus 5.5 | $0.00050 | $0.02080 |
| Sonnet 5.5 | $0.00025 | $0.01040 |
| Haiku 4.5 | $0.00013 | $0.00520 |
Grade A, and why
tooluniverse-proteomics-data-retrieval scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 10d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 377 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Proteomics Data Retrieval
Find and retrieve metadata for publicly available proteomics datasets from MassIVE and ProteomeXchange repositories. Supports searching by species, keyword, or accession, and returns detailed dataset metadata including instruments, publications, species, and post-translational modifications.
When to Use This Skill
Triggers:
- "Find proteomics datasets for [organism/disease/protein]"
- "Search MassIVE for [keyword]"
- "Get details for PXD000001" or "Look up MSV000079514"
- "What public mass spectrometry datasets exist for [topic]?"
- "Find MS datasets with [PTM type] data"
- "List recent human proteomics datasets"
Use Cases:
- Dataset Discovery: Search repositories for proteomics experiments related to a research topic
- Accession Lookup: Get full metadata for a known dataset accession (PXD or MSV)
- Species-Filtered Search: Find all datasets for a specific organism
- Cross-Repository Search: Query both MassIVE and ProteomeXchange for comprehensive coverage
- Experimental Context: Find published datasets to validate or complement in-house results
COMPUTE, DON'T DESCRIBE
When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.
KEY PRINCIPLES
- ProteomeXchange is the aggregator -- it indexes datasets from PRIDE, MassIVE, PeptideAtlas, jPOST, and iProX
- MassIVE has richer metadata -- includes summaries, keywords, modifications, and contacts
- Search both repositories -- ProteomeXchange for breadth, MassIVE for detail
- Species uses NCBI taxonomy IDs -- human = 9606, mouse = 10090, rat = 10116
- Accession formats: PXD (ProteomeXchange), MSV (MassIVE) -- both accepted by MassIVE_get_dataset
- LOOK UP DON'T GUESS -- Never assume which datasets exist, their accessions, or their instrument types. Always search and retrieve metadata to confirm.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 10d ago Changed · +80 lines · +49 tokens per session ba2b399ae071
- 1mo ago First seen · 297 lines · 76 tokens per session scan A 446a8c6cc368
tooluniverse-proteomics-data-retrieval is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 125 tokens to every session and 5,199 once invoked, about $0.0005 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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