Massive Tools#

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

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

Available Tools#

MassIVE_get_dataset (Type: MassIVETool)#

Get detailed information about a specific MassIVE proteomics dataset by its accession number (MSV…

MassIVE_get_dataset tool specification

Tool Information:

  • Name: MassIVE_get_dataset

  • Type: MassIVETool

  • Description: Get detailed information about a specific MassIVE proteomics dataset by its accession number (MSV or PXD format). Returns title, summary, species, instruments, keywords, contacts, publications, and post-translational modifications.

Parameters:

  • accession (string) (required) MassIVE dataset accession (e.g., ‘MSV000079514’) or ProteomeXchange accession (e.g., ‘PXD003971’)

Example Usage:

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

MassIVE_get_protein_identifications (Type: MassIVETool)#

Identification-level access to MassIVE datasets via the ProXI standard API. Keyed on ‘protein_acc…

MassIVE_get_protein_identifications tool specification

Tool Information:

  • Name: MassIVE_get_protein_identifications

  • Type: MassIVETool

  • Description: Identification-level access to MassIVE datasets via the ProXI standard API. Keyed on ‘protein_accession’ (e.g. ‘A2M_MOUSE’): with result_type=’proteins’ (default) it returns that protein’s cross-dataset identification counts (countPSM/countPeptides/countPeptidoforms/countDatasets); with result_type=’psms’ it returns that protein’s peptide-spectrum matches (peptide sequence + charge). Note: the MassIVE ProXI proteins/psms endpoints do not filter by dataset ‘accession’ (they return the same global summary regardless), so per-dataset identification listing is not supported here - use MassIVE_get_dataset for dataset-level metadata. Returns a structured success/error envelope.

Parameters:

  • accession ([‘string’, ‘null’]) (optional) Optional dataset accession (ProteomeXchange PXD or MassIVE MSV). NOTE: the MassIVE ProXI endpoints ignore this as a filter, so it does not restrict results to a dataset. Use ‘protein_accession’ to query; use MassIVE_get_dataset for dataset metadata.

  • protein_accession ([‘string’, ‘null’]) (optional) Protein accession for a cross-dataset lookup (e.g. ‘A2M_MOUSE’, ‘A2MP_MOUSE’). Returns the count of MassIVE datasets that identified this protein.

  • result_type (string) (optional) ‘proteins’ (default) for cross-dataset protein identification summaries, or ‘psms’ for that protein’s peptide-spectrum matches. Both require ‘protein_accession’.

Example Usage:

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

MassIVE_search_datasets (Type: MassIVETool)#

Search the MassIVE proteomics repository for mass spectrometry datasets through ProXI. Page numbe…

MassIVE_search_datasets tool specification

Tool Information:

  • Name: MassIVE_search_datasets

  • Type: MassIVETool

  • Description: Search the MassIVE proteomics repository for mass spectrometry datasets through ProXI. Page numbers start at 1 and page_size is strictly 1-100. Because ProXI exposes no total or next link, a short page proves completion while a full page only sets metadata.possible_more=true; continue with metadata.next_page until a short page is returned.

Parameters:

  • page_size (integer) (optional) Number of results to return (strictly 1-100; out-of-range values are rejected rather than silently clamped).

  • page_number (integer) (optional) One-based ProXI result page to return. Continue with metadata.next_page while metadata.possible_more is true.

  • species ([‘string’, ‘null’]) (optional) NCBI taxonomy ID to filter by species (e.g., ‘9606’ for human, ‘10090’ for mouse)

Example Usage:

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