Step-by-step workflows for searching PRIDE datasets, exploring EMDB cryo-EM structures, and retrieving detailed metadata.

You want to find published experimental evidence for a protein — mass-spectrometry datasets or a cryo-EM structure; this shows the fastest path through PRIDE and EMDB, from a keyword search to the protocols, files, and metadata behind each hit.

Proteomics quickstart

This guide covers four common workflows: searching for proteomics datasets, exploring dataset details, finding cryo-EM structures, and examining map metadata.

Workflow 1: Search PRIDE for proteomics datasets

Search by keyword

Ask Ivy in chat:

Find proteomics datasets for Alzheimer's disease

You can add filters in the same sentence, such as an organism ("in Homo sapiens") or a number of results ("the top 10").

Review the results

Each result includes key project metadata:

Field	Example Value
Accession	PXD032145
Title	Quantitative proteomics of Alzheimer's disease brain tissue
Organisms	Homo sapiens
Diseases	Alzheimer's disease
Instruments	Q Exactive HF
Quantification	TMT6plex
Publication Date	2023-06-15

Filter by instrument or PTM (optional)

Find phosphoproteomics studies in human using Orbitrap instruments

Ivy applies the organism, instrument, and modification (phosphorylation) as filters on the PRIDE search.

Workflow 2: Get PRIDE dataset details

Look up a specific project

Get the details and file listing for PRIDE project PXD000001

The file listing is included by default.

Review the metadata

The detailed output includes protocols, contacts, and files:

Section	Content
Sample processing protocol	Describes cell lysis, digestion, fractionation
Data processing protocol	Describes search engine, FDR threshold, quantification method
Submitters	Names and affiliations
File count	Total files available for download

Access the data

The output includes:

PRIDE URL: Direct link to the project page
FTP URL: FTP path for bulk file download
File listing: Individual file names, sizes, and types (RAW, mzML, result, search database)

Workflow 3: Search EMDB for cryo-EM structures

Search by protein or complex

Find cryo-EM structures of the human ribosome

Or with a resolution cutoff:

Find human ribosome cryo-EM maps better than 3 Angstrom, top 10

Review the results

Field	Example Value
EMDB ID	EMD-13234
Title	Human 80S ribosome
Resolution	2.8 Angstrom
Method	Single particle
Organism	Homo sapiens
Linked PDB	7P6Z

Find high-resolution structures

To focus on the best-resolved structures:

Find sub-2.5 Angstrom cryo-EM structures of membrane proteins

Workflow 4: Get EMDB entry details

Look up a specific entry

Get details for EMDB entry EMD-13234

Review reconstruction parameters

Field	Value
Resolution	2.8 Angstrom
Method	Single particle
Software	RELION, cryoSPARC
Sample	Human 80S ribosome
Macromolecules	40S subunit (1 copy), 60S subunit (1 copy)
Linked PDB	7P6Z

Download the map

The output includes:

EMDB URL: Link to the entry page with interactive viewer
Map download: Direct FTP link to the gzipped MRC density map
Linked PDB IDs: Fitted atomic models in the Protein Data Bank

Next steps

See inputs for filter options and accession formats
See outputs for result field descriptions and interpretation
Use UniProt for protein sequence and functional annotation
Use RCSB PDB for X-ray crystal structure search
Use ESMFold for predicted protein structures

Proteomics quickstart