pride-database
PRIDE Database
Overview
The PRIDE Archive (ProteomicsIDEntifications database) at EBI is the world's largest public repository of mass spectrometry-based proteomics data, containing 30,000+ datasets from peer-reviewed publications. The REST API v2 at https://www.ebi.ac.uk/pride/ws/archive/v2/ provides project discovery, file listing, peptide/PSM identification retrieval, and protein-level evidence — all without authentication. Data types include RAW files, peak lists (mzML, MGF), PRIDE XML result files, and processed identification tables.
When to Use
- Finding published proteomics datasets by organism, tissue, disease keyword, or instrument type for meta-analysis or benchmarking
- Downloading raw mass spectrometry data (RAW, mzML) or peak files (MGF) from a specific PRIDE project accession
- Retrieving peptide identification tables with sequence, modification, and confidence score for a project
- Querying protein-level evidence (PSMs, unique peptides) for a protein of interest across PRIDE projects
- Checking whether a protein has experimental proteomics evidence in a specific tissue or disease context
- Building training datasets of confident peptide-spectrum matches (PSMs) for proteomics ML applications
- For protein domain and family classification use
interpro-database; PRIDE provides experimental identification evidence only - For protein sequences, Swiss-Prot annotations, and ID mapping use
uniprot-protein-database
Prerequisites
More from jaechang-hits/sciagent-skills
scientific-brainstorming
Structured ideation methods: SCAMPER, Six Thinking Hats, Morphological Analysis, TRIZ, Biomimicry, plus more. Decision framework for picking methods by challenge type (stuck, improving, systematic exploration, contradiction). Use when generating research ideas or exploring interdisciplinary connections.
12gene-database
Query NCBI Gene via E-utilities for curated gene records across 1M+ taxa. Retrieve official gene symbols, aliases, RefSeq accessions, summary descriptions, genomic coordinates, GO annotations, and interaction data. Use for gene ID resolution, cross-species queries, and gene function summaries. For sequence retrieval use Ensembl; for expression data use geo-database.
10snakemake-workflow-engine
Python-based workflow management system for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake automatically determines the execution order and parallelism. Supports local, SLURM, LSF, AWS, and Google Cloud execution via profiles; per-rule conda/Singularity environments. Use for bioinformatics NGS pipelines, ML training workflows, and any multi-step file-processing analysis. Use Nextflow instead for Groovy-based dataflow pipelines or when nf-core ecosystem integration is required.
10esm-protein-language-model
Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and protein embeddings. Use when designing novel proteins, extracting sequence representations for downstream ML, or predicting structure from sequence. Local GPU or EvolutionaryScale Forge cloud API. For traditional structure prediction use AlphaFold; for small-molecule cheminformatics use RDKit.
10matchms-spectral-matching
Mass spectrometry spectral matching and metabolite identification with matchms. Use for importing spectra (mzML, MGF, MSP, JSON), filtering/normalizing peaks, computing spectral similarity (cosine, modified cosine, fingerprint), building reproducible processing pipelines, and identifying unknown metabolites from spectral libraries. For full LC-MS/MS proteomics pipelines, use pyopenms instead.
10chembl-database-bioactivity
Query ChEMBL via Python SDK. Search compounds by structure/properties, retrieve bioactivity (IC50, Ki, EC50), find target inhibitors, run SAR, access drug mechanism/indication data.
10