---
title: Proteomics on the platform
description: >-
  Search PRIDE mass spectrometry datasets and EMDB cryo-EM structures for
  protein identification, quantification, and structural analysis.
tags:
  - proteomics
---

Proteomics helps you find published mass-spectrometry datasets and cryo-EM structures for a protein of interest — searching PRIDE for proteomics experiments and EMDB for density maps, with the protocols, files, and linked structures behind each. Reach for it when you want existing experimental evidence — expression, post-translational modifications, or a solved structure — rather than a prediction. Where [genomics](/docs/genomics) works at the gene level, proteomics finds the protein-level and structural data that a gene-to-protein cross-reference points you toward. See [what you can achieve](/docs/capabilities#genomics-and-omics) for the full set.

## Proteomics overview

The Proteomics toolkit provides four tools for discovering mass spectrometry proteomics datasets and cryo-EM structural data from the two largest public repositories: PRIDE and EMDB. All tools use direct EBI REST API calls with no GPU compute, returning results in 2-6 seconds.

## Architecture

 I[Intent detection]
    I -->|Dataset search| PS[PRIDE Project Search]
    I -->|Dataset details| PD[PRIDE Dataset Details]
    I -->|Cryo-EM search| ES[EMDB Search]
    I -->|Map details| ED[EMDB Entry Details]
    PS & PD & ES & ED --> A["EBI REST API call (2-6 s)"]
    A --> Res[Structured results with database URLs]`}
  caption="A proteomics query is routed by intent to the matching EBI database, then returned as structured results."
/>

## Tool inventory

### PRIDE tools

| Lookup | Description |
|--------|-------------|
| PRIDE Project Search | Search the PRIDE archive for proteomics datasets by keyword, organism, instrument, or PTM type |
| PRIDE Dataset Details | Retrieve full metadata, protocols, file listings, and download links for a specific PXD project |

### EMDB tools

| Lookup | Description |
|--------|-------------|
| EMDB Search | Search the Electron Microscopy Data Bank for cryo-EM density maps |
| EMDB Entry Details | Get reconstruction parameters, map downloads, and linked PDB structures for an EMDB entry |

These lookups run inside a chat turn: ask Ivy in plain language and it picks the PRIDE or EMDB lookup. There is no form or job to submit for them.

## PRIDE: Proteomics Identifications Database

PRIDE is the world's largest public repository of mass spectrometry-based proteomics data, hosted by EMBL-EBI. It archives raw spectral data, peptide/protein identifications, post-translational modifications, and quantification results from published proteomics experiments.

### What you can search

| Category | Examples |
|----------|---------|
| Protein targets | "BRCA1", "p53", "insulin receptor" |
| Diseases | "Alzheimer", "breast cancer", "diabetes" |
| Organisms | "Homo sapiens", "Mus musculus", "E. coli" |
| PTM types | "phosphorylation", "acetylation", "ubiquitination" |
| Instruments | "Orbitrap", "Q Exactive", "timsTOF" |
| Techniques | "TMT", "SILAC", "label-free" |

### What you get back

- **Project metadata**: PXD accession, title, description, publication date
- **Experimental details**: Organisms, diseases, tissues, instruments, quantification methods
- **Protocols**: Sample processing and data processing protocols
- **References**: PubMed IDs and DOIs for associated publications
- **Files**: Raw data, processed results, search databases, and supplementary files with download links

## EMDB: Electron Microscopy Data Bank

EMDB is the global archive for 3D electron microscopy density maps of biological specimens. It stores cryo-EM maps ranging from sub-2 Angstrom to lower resolutions, covering proteins, complexes, viruses, and cellular structures.

### What you can search

| Category | Examples |
|----------|---------|
| Proteins/complexes | "ribosome", "proteasome", "RNA polymerase" |
| Viruses | "SARS-CoV-2 spike", "influenza hemagglutinin" |
| Organisms | "Homo sapiens", "Saccharomyces cerevisiae" |
| EMDB IDs | "EMD-13234", "EMD-1234" |
| Resolution range | Sub-3 Angstrom, sub-4 Angstrom |

### What you get back

- **Entry metadata**: EMDB ID, title, authors, deposition/release dates
- **Reconstruction**: Resolution, method (single particle, tomography, etc.), software
- **Sample**: Organism, macromolecule names, copy numbers
- **Cross-references**: Linked PDB structure IDs and related EMDB entries
- **Downloads**: Direct map download URLs (gzipped MRC format)

## What to ask for

| I want to... | Ivy answers it with |
|--------------|---------------------|
| Find proteomics datasets for a disease | A PRIDE project search |
| Get protocols for a PRIDE project | PRIDE dataset details |
| Download raw MS data | PRIDE dataset details (includes a file listing with FTP URLs) |
| Find cryo-EM maps for a protein | An EMDB search |
| Get reconstruction parameters | EMDB entry details |
| Find high-resolution cryo-EM structures | An EMDB search with a resolution cutoff (for example "better than 3 Å") |
| Find PDB structures linked to a density map | EMDB entry details |

## When to use other tools instead

| I want to... | Use this instead |
|--------------|------------------|
| Look up protein sequence/function | [UniProt](/docs/uniprot) |
| Search for X-ray crystal structures | [RCSB PDB](/docs/pdb) search and download |
| Get or predict protein structure | An [AlphaFold DB](/docs/alphafold) fetch or an [ESMFold](/docs/esmfold) prediction |
| Find protein-protein interactions | A STRING interaction lookup |
| Search for gene information | [Genomics](/docs/genomics) lookups (Entrez, Ensembl) |
| Run peptide identification from raw MS data | Not currently supported (PRIDE provides pre-processed results) |

## Licensing

| Database | License | Attribution |
|----------|---------|-------------|
| PRIDE | EMBL-EBI Terms of Use (open access) | Cite dataset DOI |
| EMDB | EMBL-EBI Terms of Use (open access) | Cite EMDB accession |

## Citations

> Perez-Riverol Y, et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. *Nucleic Acids Res*. 2022;50(D1):D543-D552. doi: [10.1093/nar/gkab1038](https://doi.org/10.1093/nar/gkab1038)

> Lawson CL, et al. EMDataBank unified data resource for 3DEM. *Nucleic Acids Res*. 2016;44(D1):D396-D403. doi: [10.1093/nar/gkv1126](https://doi.org/10.1093/nar/gkv1126)

## Chat Usage

### Example Prompts

- "Find PRIDE datasets studying phosphoproteomics in breast cancer"
- "Get the file listing and protocols for PXD012345"
- "Search EMDB for cryo-EM maps of the human proteasome"
- "What instruments were used in the latest Alzheimer's proteomics studies?"
- "Find sub-3 Angstrom cryo-EM structures of membrane proteins"

### Workflow Chaining

- **Feeds into**: UniProt (protein annotation), PDB/AlphaFold (structural analysis), STRING (interaction networks), Literature search (PubMed via references)
- **Accepts from**: UniProt (protein accessions), Genomics tools (gene-to-protein), Literature search (dataset references from papers)

## FAQ

### What databases does the Proteomics toolkit query?

  The toolkit queries PRIDE (PRoteomics IDEntifications Database) for mass spectrometry datasets and EMDB (Electron Microscopy Data Bank) for cryo-EM density maps. Both are accessed through the EBI REST APIs.

### Can I download raw MS data from PRIDE?

  Yes. Use PRIDE Dataset Details to get the file listing for a project. The output includes FTP download URLs for all raw data files, processed results, and supplementary materials.

### Does the toolkit run peptide identification or quantification?

  No. The proteomics tools search public dataset repositories, not process raw MS data. They help you find relevant datasets, protocols, and published results. For protein annotation, use UniProt tools. For protein structure, use AlphaFold or PDB tools.

### What resolution cryo-EM maps can I find?

  EMDB contains maps from sub-2 Angstrom to >20 Angstrom resolution. Ask for a resolution cutoff to find high-resolution structures (for example "sub-3 Angstrom maps").

## Read next