Proteomics on the platform

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 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 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

Rendering diagram…

Tool inventory

PRIDE tools

EMDB tools

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

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

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

When to use other tools instead

Licensing

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

Lawson CL, et al. EMDataBank unified data resource for 3DEM. Nucleic Acids Res. 2016;44(D1):D396-D403. doi: 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

Read next