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pride-database

Search and retrieve proteomics datasets from the PRIDE Archive REST API.

298|27|Updated Feb 18, 2026
Search Tags:#bioinformatics#mass spectrometry#data retrieval#proteomics#pride archive#peptide identification
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill pride-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pride-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/proteomics-protein-engineering/pride-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill pride-database

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill allows users to programmatically search and retrieve mass spectrometry-based proteomics datasets, peptide identifications, and raw data files from the PRIDE Archive, a crucial resource for biological research.

Core Features & Use Cases

  • Dataset Discovery: Find experiments by organism, tissue, disease, or instrument.
  • Data Retrieval: Download RAW/mzML files, peptide/PSM identifications, and protein-level evidence.
  • Use Case: A researcher wants to find all published proteomics studies on Alzheimer's disease in human brain tissue. They can use this Skill to query the PRIDE Archive, identify relevant datasets, and download the associated identification files for meta-analysis.

Quick Start

Use the pride-database skill to search for proteomics projects related to 'Alzheimer's disease' in 'Homo sapiens'.

Frequently Asked Questions about pride-database

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

FAQPage Schema
How do I search for proteomics datasets in the PRIDE Archive by organism and tissue?▼

Search for proteomics datasets in the PRIDE Archive by querying the REST API to filter experiments by organism, tissue, disease, or instrument. This returns relevant project metadata for discovering mass spectrometry studies.

Can I download raw mass spectrometry files and peptide identifications from PRIDE?▼

Yes, you can download RAW and mzML mass spectrometry files, peptide and PSM identifications, and protein-level evidence directly from the PRIDE Archive API. This facilitates retrieving complete proteomics datasets for analysis.

What is peptide identification retrieval from the PRIDE database used for?▼

Peptide identification retrieval from the PRIDE database is used to extract peptide and PSM evidence from public proteomics experiments. This supports meta-analysis and biological research by providing validated mass spectrometry results.

Does the PRIDE Archive API support filtering mass spectrometry data by disease?▼

Yes, the PRIDE Archive API supports filtering mass spectrometry data by disease. You can discover proteomics experiments related to specific conditions like Alzheimer's disease and download associated identification files.

Can I use pandas and matplotlib to analyze proteomics data retrieved from PRIDE?▼

Yes, you can use pandas and matplotlib to analyze proteomics data retrieved from PRIDE. The Skill leverages these dependencies to structure downloaded peptide identification files and visualize mass spectrometry results.

What is the best way to retrieve protein-level evidence from PRIDE for meta-analysis?▼

The best way to retrieve protein-level evidence from PRIDE for meta-analysis is using the PRIDE Archive REST API to programmatically search and download identification files. This provides structured evidence across multiple proteomics experiments.

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