PRIDE Archive REST API Reference

Overview

PRIDE (PRoteomics IDEntifications Database) at EMBL-EBI provides a full public REST API for querying proteomics datasets, proteins, peptides, and spectra.

Base URL

https://www.ebi.ac.uk/pride/ws/archive/v2

(Legacy v1 also exists but v2 is current)

Authentication

No authentication required for read access
Open and free to use

Key Endpoints

Endpoint	Description
`GET /projects`	Search/list proteomics projects
`GET /projects/{accession}`	Get a specific project by PXD accession
`GET /projects/{accession}/files`	List files for a project
`GET /spectra`	Search spectra
`GET /peptideevidences`	Search peptide evidences
`GET /proteinevidences`	Search protein evidences
`GET /stats`	Database statistics

Query Parameters

keyword — free-text search
filter — field-specific filters (e.g., species, instrument, modification)
pageSize — results per page (default 10, max 100)
page — page number (0-indexed)
sortDirection — ASC or DESC
sortFields — field to sort by

Example Calls

# Search projects by keyword
curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects?keyword=alzheimer&pageSize=5"

# Get a specific project
curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects/PXD010000"

# List files for a project
curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects/PXD010000/files?pageSize=10"

# Search by species (human = 9606)
curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects?filter=organisms_facet==9606&pageSize=5"

# Get database statistics
curl "https://www.ebi.ac.uk/pride/ws/archive/v2/stats"

Response Format

JSON. Example (project):

{
  "accession": "PXD010000",
  "title": "Project title here",
  "projectDescription": "...",
  "organisms": [{"accession": "9606", "name": "Homo sapiens"}],
  "instruments": [{"name": "Q Exactive"}],
  "submissionDate": "2018-05-01",
  "publicationDate": "2018-09-01",
  "numAssays": 12,
  "references": [{"pubmedId": 12345678}]
}

Rate Limits

No strict published rate limits, but standard EBI fair-use policies apply
Recommended: limit to a few requests per second
Bulk data available via FTP/Aspera at ftp.pride.ebi.ac.uk