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. MassIVE hosts thousands …

MassIVE_search_datasets tool specification

Tool Information:

  • Name: MassIVE_search_datasets

  • Type: MassIVETool

  • Description: Search the MassIVE proteomics repository for mass spectrometry datasets. MassIVE hosts thousands of proteomics datasets accessible via the ProXI standard API. Returns dataset accessions, titles, species, instruments, and keywords. Optionally filter by NCBI taxonomy ID for species.

Parameters:

  • page_size (integer) (optional) Number of results to return (max 100)

  • 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)