Proteomics FAQ

These answers cover what the proteomics tools let you find in the PRIDE and EMDB repositories: what each database contains, how PRIDE project search works and how to reanalyze its raw data, how EMDB density maps relate to PDB atomic models, what resolution to filter for, and how to chain proteomics results into other platform tools.

Proteomics FAQ

What is PRIDE and what data does it contain?

PRIDE (PRoteomics IDEntifications Database) is the world's largest public repository of mass spectrometry-based proteomics data, hosted by EMBL-EBI. It archives raw spectral data, peptide and protein identifications, post-translational modifications, and quantification results from published experiments. As of 2026, PRIDE contains over 50,000 datasets across hundreds of organisms.

Can I search for a specific protein's expression data across studies?

PRIDE Project Search searches at the project level (titles, descriptions, metadata), not at the individual protein level. To find datasets that identified a specific protein, search by the protein name or gene symbol. The results will include projects that mention that protein, but you cannot query individual peptide-spectrum matches through these tools.

What is the difference between EMDB and PDB?

EMDB stores 3D electron microscopy density maps (volumes), while PDB stores atomic-resolution coordinate models. Many cryo-EM structures have both: an EMDB density map and a fitted PDB atomic model. The EMDB Entry Details tool shows linked PDB IDs for entries that have fitted models. Use EMDB Search when you specifically want cryo-EM maps; use PDB tools when you want atomic coordinates regardless of experimental method.

How do I reanalyze raw data from PRIDE?

The proteomics tools on the platform search the PRIDE repository and retrieve metadata, but they do not process raw mass spectrometry data. To reanalyze data: (1) use PRIDE Dataset Details to find the file listing and FTP download links, (2) download the RAW files using the FTP URL, (3) process with tools like MaxQuant, Proteome Discoverer, or MSFragger on your local workstation or compute cluster.

What resolution should I filter for in EMDB?

It depends on your use case. For molecular modeling and drug design, filter for sub-3 Angstrom (resolution_max: 3.0) to get maps with visible side chains. For fitting known structures into maps, 3-5 Angstrom is usually sufficient. For understanding overall architecture and subunit arrangement, even 6-10 Angstrom maps are useful. Omit the filter to see all available resolutions.

Are these tools free to use?

Yes. Both PRIDE and EMDB are open-access repositories funded by public research grants. The data is freely available for academic and commercial use. When publishing results that use these datasets, cite the original dataset DOI (for PRIDE) or EMDB accession.

Can I find datasets from specific mass spectrometry instruments?

Yes. Use the instrument filter in PRIDE Project Search. Common values include "Orbitrap", "Q Exactive", "Orbitrap Fusion", "timsTOF", and "TripleTOF". This is useful when you need data from a specific platform for method benchmarking or to find comparable datasets.

How do I chain proteomics results with other platform tools?

Common workflows include: (1) search PRIDE for datasets related to your protein of interest, then use UniProt for functional annotation of identified proteins; (2) find cryo-EM structures in EMDB, then look up the linked PDB structures for docking or visualization; (3) use EMDB to find density maps, then use AlphaFold for predicted structures to compare with experimental data. Ivy handles chaining automatically when you describe multi-step workflows.

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