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tooluniverse-proteomics-data-retrieval

Search and retrieve proteomics dataset metadata from MassIVE and ProteomeXchange repositories.

1.7k|254|Updated Mar 3, 2025
Search Tags:#mass spectrometry#proteomics#metadata retrieval#dataset search#proteomexchange#pxd accession#massive
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-proteomics-data-retrieval
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-proteomics-data-retrieval
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-proteomics-data-retrieval
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-proteomics-data-retrieval

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Locating relevant public proteomics datasets across fragmented repositories is slow and error-prone. This Skill searches MassIVE and ProteomeXchange by keyword, species, or accession and returns structured metadata (instruments, publications, species, PTMs) so researchers can evaluate datasets before downloading or reanalyzing them.

Core Features & Use Cases

  • Cross-Repository Search: Query MassIVE by NCBI taxonomy ID and ProteomeXchange by keyword, then merge and deduplicate results by accession.
  • Accession Lookup: Retrieve full metadata for known PXD or MSV accessions, including instruments, publications, modifications, and file counts.
  • Dataset Quality Assessment: Apply an interpretation framework covering instrument resolution, publication status, and metadata completeness to judge dataset suitability.
  • Use Case: A researcher studying human phosphoproteomics asks for public datasets on the topic; the Skill searches ProteomeXchange by keyword, filters for human (taxonomy ID 9606), retrieves detailed MassIVE metadata, and compiles a structured report with accessions, instruments, and PubMed references.

Quick Start

Find public human phosphoproteomics datasets in MassIVE and ProteomeXchange and summarize their instruments and publications.

Frequently Asked Questions about tooluniverse-proteomics-data-retrieval

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

FAQPage Schema
How do I search MassIVE for proteomics datasets by species?▼

Use MassIVE_search_datasets with the species parameter set to an NCBI taxonomy ID as a string, such as "9606" for human or "10090" for mouse. MassIVE does not support keyword search, so filtering is species-based only.

How do I find proteomics datasets by keyword in ProteomeXchange?▼

Call ProteomeXchange_search_datasets with the query parameter set to your keyword, such as "phosphoproteomics" or "breast cancer", and a limit between 1 and 50. Results include accession, title, and species for each dataset.

What is the difference between MassIVE and ProteomeXchange for dataset search?▼

ProteomeXchange is an aggregator indexing PRIDE, MassIVE, PeptideAtlas, jPOST, and iProX, giving the broadest coverage with standardized PXD accessions. MassIVE hosts fewer datasets but provides richer metadata including summaries, keywords, modifications, and contacts.

Can I look up a dataset using either a PXD or MSV accession?▼

Yes. MassIVE_get_dataset accepts both MSV and PXD accession formats, while ProteomeXchange_get_dataset accepts only PXD identifiers. For PXD accessions, cross-reference both tools to combine file counts with richer summaries and keywords.

Can this skill download raw mass spectrometry data files?▼

No. These tools retrieve metadata only, such as titles, instruments, publications, and file counts. Raw data files must be downloaded separately from the MassIVE or ProteomeXchange repository websites.

What should I do when a MassIVE search returns no results?▼

Fall back to ProteomeXchange_search_datasets, which has broader coverage across multiple repositories. If keyword searches return nothing, simplify to single-term queries or search by species taxonomy ID instead.

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