Proteomexchange Tools#

Configuration File: proteomexchange_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the proteomexchange_tools.json configuration file.

Available Tools#

ProteomeXchange_get_dataset (Type: ProteomeXchangeTool)#

Get detailed metadata for a ProteomeXchange proteomics dataset by PX identifier. Returns title, s…

ProteomeXchange_get_dataset tool specification

Tool Information:

  • Name: ProteomeXchange_get_dataset

  • Type: ProteomeXchangeTool

  • Description: Get detailed metadata for a ProteomeXchange proteomics dataset by PX identifier. Returns title, species, instruments, publications (PubMed/DOI), file count, and cross-references to partner repositories (PRIDE, MassIVE, PeptideAtlas, jPOST). ProteomeXchange is the central hub for proteomics data sharing. Example: PXD000001 returns the first ProteomeXchange dataset (Erwinia carotovora TMT LC-MS/MS from Cambridge).

Parameters:

  • px_id (string) (required) ProteomeXchange dataset identifier (PXD format). Examples: ‘PXD000001’ (first PX dataset), ‘PXD000561’ (human proteome map).

Example Usage:

query = {
    "name": "ProteomeXchange_get_dataset",
    "arguments": {
        "px_id": "example_value"
    }
}
result = tu.run(query)

ProteomeXchange_get_spectrum_by_usi (Type: ProteomeXchangeTool)#

Retrieve a single mass spectrum (PSM) from ProteomeXchange by Universal Spectrum Identifier (USI)…

ProteomeXchange_get_spectrum_by_usi tool specification

Tool Information:

  • Name: ProteomeXchange_get_spectrum_by_usi

  • Type: ProteomeXchangeTool

  • Description: Retrieve a single mass spectrum (PSM) from ProteomeXchange by Universal Spectrum Identifier (USI) via the PROXI v0.1 interface. Unlike the dataset-level tools, this returns spectrum/peak-level data: scan number, charge state, precursor m/z, peptide sequence, all CV-term attributes, and the peak list (m/z + intensity pairs, capped to the first 200 peaks). A USI has the form ‘mzspec:<PXD accession>:<file>:scan:<scan>:<peptide>/<charge>’. Use ProteomeXchange_get_dataset or ProteomeXchange_search_datasets first to find dataset accessions and construct USIs.

Parameters:

  • usi (string) (required) Universal Spectrum Identifier. Example: ‘mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555:VLHPLEGAVVIIFK/2’.

  • resultType ([‘string’, ‘null’]) (optional) Level of detail returned by PROXI: ‘full’ (default, includes peak arrays) or ‘compact’.

Example Usage:

query = {
    "name": "ProteomeXchange_get_spectrum_by_usi",
    "arguments": {
        "usi": "example_value"
    }
}
result = tu.run(query)

ProteomeXchange_search_datasets (Type: ProteomeXchangeTool)#

Search the complete ProteomeXchange/ProteomeCentral dataset catalog. The upstream CGI ignores its…

ProteomeXchange_search_datasets tool specification

Tool Information:

  • Name: ProteomeXchange_search_datasets

  • Type: ProteomeXchangeTool

  • Description: Search the complete ProteomeXchange/ProteomeCentral dataset catalog. The upstream CGI ignores its keyword parameter, so this tool retrieves the catalog and applies the query across accession, title, species, keywords, publication, contact, and repository fields locally. Results support exact offset pagination and include exact match-count and continuation metadata.

Parameters:

  • query ([‘string’, ‘null’]) (optional) Optional case-insensitive search filter applied across accession, title, species, keywords, publication, contact, and repository fields. Examples: ‘PXD000001’, ‘cancer’, or ‘Homo sapiens’. Leave empty to paginate the complete catalog in the order returned by ProteomeCentral.

  • limit ([‘integer’, ‘null’]) (optional) Maximum results to return (1-1000, default 10).

  • offset ([‘integer’, ‘null’]) (optional) Zero-based offset into the complete locally filtered result set (default 0). Use metadata.next_offset to continue.

Example Usage:

query = {
    "name": "ProteomeXchange_search_datasets",
    "arguments": {
    }
}
result = tu.run(query)