---
title: Proteomics quickstart
description: >-
  Step-by-step workflows for searching PRIDE datasets, exploring EMDB cryo-EM
  structures, and retrieving detailed metadata.
tags:
  - proteomics
  - quickstart
---

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

### Step 1: 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").

### Step 2: 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 |

### Step 3: 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

### Step 1: Look up a specific project

```
Get the details and file listing for PRIDE project PXD000001
```

The file listing is included by default.

### Step 2: 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 |

### Step 3: 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

### Step 1: 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
```

### Step 2: 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 |

### Step 3: 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

### Step 1: Look up a specific entry

```
Get details for EMDB entry EMD-13234
```

### Step 2: 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 |

### Step 3: 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](/docs/proteomics/inputs) for filter options and accession formats
- See [outputs](/docs/proteomics/outputs) for result field descriptions and interpretation
- Use [UniProt](/docs/uniprot) for protein sequence and functional annotation
- Use [RCSB PDB](/docs/pdb) for X-ray crystal structure search
- Use [ESMFold](/docs/esmfold) for predicted protein structures

## Read next