Interpreting proteomics outputs
PRIDE project metadata, file listings, EMDB entry details, and cryo-EM reconstruction parameters.
proteomicsoutputs
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, 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) |
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