---
title: Interpreting proteomics outputs
description: >-
  PRIDE project metadata, file listings, EMDB entry details, and cryo-EM
  reconstruction parameters.
tags:
  - proteomics
  - outputs
---

Searches return structured results with database URLs — PRIDE project metadata and file listings, or EMDB entry details and cryo-EM reconstruction parameters. From these you can follow accessions to the underlying datasets, download files, or jump to a linked structure.

## Interpreting proteomics outputs

## PRIDE Project Search output

| Field | Type | Description |
|-------|------|-------------|
| `query` | string | Search query used |
| `total_results` | number | Total matching projects in PRIDE |
| `returned` | number | Number of projects returned |
| `projects` | array | Project summaries |

### Project fields

| Field | Type | Description |
|-------|------|-------------|
| `accession` | string | PRIDE project accession (e.g., `PXD032145`) |
| `title` | string | Project title |
| `description` | string | Project description (truncated to 500 chars) |
| `submission_type` | string | Submission type (COMPLETE, PARTIAL, etc.) |
| `publication_date` | string | Date of public release |
| `organisms` | string[] | Organism names |
| `diseases` | string[] | Disease annotations |
| `tissues` | string[] | Tissue/organ types |
| `instruments` | string[] | Mass spectrometer names |
| `quantification` | string[] | Quantification methods (TMT, SILAC, label-free, etc.) |
| `keywords` | string[] | Author-assigned keywords |
| `tags` | string[] | Project tags |
| `references` | array | Publication references with PubMed IDs and DOIs |
| `pride_url` | string | Link to PRIDE project page |

### Submission types

| Type | Meaning |
|------|---------|
| COMPLETE | Full submission with raw data and identifications |
| PARTIAL | Partial submission (metadata and/or subset of files) |
| PRIDE | Legacy PRIDE submission format |

## PRIDE Dataset Details output

| Field | Type | Description |
|-------|------|-------------|
| `accession` | string | PRIDE project accession |
| `title` | string | Project title |
| `description` | string | Full project description |
| `sample_processing_protocol` | string | How samples were prepared |
| `data_processing_protocol` | string | How data was analyzed |
| `submission_type` | string | Submission type |
| `publication_date` | string | Public release date |
| `organisms` | array | Organisms with taxonomy IDs |
| `diseases` | string[] | Disease annotations |
| `tissues` | string[] | Tissue types |
| `instruments` | string[] | Instrument names |
| `quantification_methods` | string[] | Quantification approaches |
| `submitters` | array | Submitter names and affiliations |
| `lab_heads` | array | Lab head names and affiliations |
| `references` | array | Publication references (PubMed, DOI) |
| `keywords` | string[] | Keywords |
| `tags` | string[] | Project tags |
| `files` | array | File listing (if requested) |
| `file_count` | number | Total number of files |
| `files_by_category` | object | File count per category |
| `files_truncated` | boolean | `true` if more files exist than `max_files` returned |
| `sandbox_download_plan` | object | Ready-to-run download commands Ivy can use to pull the files into the chat's [code workspace](/docs/sandbox), when downloadable files exist |
| `pride_url` | string | Link to PRIDE project page |
| `ftp_url` | string | FTP directory for bulk download |

### File fields

| Field | Type | Description |
|-------|------|-------------|
| `name` | string | File name |
| `size` | number | File size in bytes |
| `size_human` | string | Human-readable file size (e.g., `"1.2 GB"`) |
| `category` | string | File category |
| `extension` | string | File extension |
| `download_url` | string | Direct HTTPS download URL, when available |
| `checksum` | string | File checksum, when available |
| `compressed` | boolean | `true` if the file is compressed |

### File types

| Type | Description | Common Extensions |
|------|-------------|-------------------|
| RAW | Vendor raw data | .raw, .d, .wiff |
| PEAK | Peak lists | .mgf, .mzML, .mzXML |
| RESULT | Search results | .mzid, .mzTab |
| SEARCH | Search databases | .fasta |
| OTHER | Supplementary files | .xlsx, .pdf, .txt |

## EMDB Search output

| Field | Type | Description |
|-------|------|-------------|
| `query` | string | Search query used |
| `total_results` | number | Total matching EMDB entries |
| `returned` | number | Entries returned |
| `entries` | array | Entry summaries |

### Entry fields

| Field | Type | Description |
|-------|------|-------------|
| `emdb_id` | string | EMDB accession (e.g., `EMD-13234`) |
| `title` | string | Entry title |
| `authors` | string[] | Author names |
| `deposition_date` | string | Date deposited |
| `release_date` | string | Date publicly released |
| `resolution` | number | Map resolution in Angstroms |
| `resolution_units` | string | Always `"Angstrom"` |
| `method` | string | Reconstruction method |
| `software` | string[] | Software used for reconstruction |
| `sample_name` | string | Sample description |
| `organism` | string | Organism scientific name |
| `ncbi_taxon` | string | NCBI taxonomy ID |
| `macromolecules` | array | Component molecules with copy numbers |
| `linked_pdb` | string[] | PDB structure IDs fitted to this map |
| `emdb_url` | string | Link to EMDB entry page |

### Resolution interpretation

| Resolution (Angstrom) | Quality | Structural Detail Visible |
|----------------------|---------|--------------------------|
| < 2.0 | Near-atomic | Individual atoms, water molecules |
| 2.0 - 3.0 | High | Side chain conformations, ligands |
| 3.0 - 4.0 | Good | Secondary structure, bulky side chains |
| 4.0 - 6.0 | Medium | Alpha-helices, beta-sheets, domain boundaries |
| 6.0 - 10.0 | Low | Domain shapes, subunit arrangement |
| > 10.0 | Very low | Overall molecular envelope |

### Reconstruction methods

| Method | Description |
|--------|-------------|
| Single particle | Individual molecule images averaged |
| Subtomogram averaging | Repeated structures within tomograms |
| Tomography | 3D reconstruction from tilt series |
| Helical | Filamentous structures with helical symmetry |
| 2D crystal | Ordered 2D arrays |

## EMDB Entry Details output

| Field | Type | Description |
|-------|------|-------------|
| `emdb_id` | string | EMDB accession |
| `title` | string | Entry title |
| `authors` | string[] | Author names |
| `deposition_date` | string | Deposition date |
| `release_date` | string | Release date |
| `resolution` | number | Resolution in Angstroms |
| `resolution_units` | string | `"Angstrom"` |
| `reconstruction_method` | string | Method used |
| `software` | string[] | Software tools |
| `sample` | object | Sample details |
| `sample.name` | string | Sample name |
| `sample.organism` | string | Organism scientific name |
| `sample.ncbi_taxon` | string | NCBI taxonomy ID |
| `sample.macromolecules` | array | Component molecules |
| `linked_pdb_ids` | string[] | Fitted PDB structure IDs |
| `related_emdb_ids` | string[] | Related EMDB entries |
| `emdb_url` | string | EMDB entry page |
| `map_download` | string | Direct FTP link to map file (.map.gz) |

## Read next