Peptideatlas Tools

Configuration File: peptideatlas_tools.json Tool Type: Local Tools Count: 1

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

Available Tools

PeptideAtlas_get_observed_peptides (Type: PeptideAtlasGetObservedPeptidesTool)

Query PeptideAtlas (SBEAMS PeptideAtlas, ISB) for the mass-spectrometry-OBSERVED peptides of a pr…

PeptideAtlas_get_observed_peptides tool specification

Tool Information:

  • Name: PeptideAtlas_get_observed_peptides

  • Type: PeptideAtlasGetObservedPeptidesTool

  • Description: Query PeptideAtlas (SBEAMS PeptideAtlas, ISB) for the mass-spectrometry-OBSERVED peptides of a protein/gene, the canonical record of which tryptic peptides have actually been seen in MS proteomics experiments and how often. Constrain by a UniProt accession or biosequence name (biosequence_name), or omit it to sample the whole build. Each record returns: peptide_accession (PAp…), peptide_sequence, n_observations (spectral count across the atlas), n_samples (number of samples), best_probability (PeptideProphet), empirical_proteotypic_score, SSRCalc_relative_hydrophobicity, n_protein_mappings, n_genome_locations, is_exon_spanning, protease_ids, and is_subpeptide_of. Distinct from sequence-derived peptide-coverage tools: PeptideAtlas adds empirical observation frequency and proteotypic scoring. Keyless public CGI; default build is Human 2024-01 (atlas_build_id=572).

Parameters:

  • biosequence_name (string) (optional) Protein/gene constraint: a UniProt accession or PeptideAtlas biosequence name. Example: ‘P02768’ (human serum albumin) -> several thousand observed peptides. Maps to biosequence_name_constraint. Omit to query the whole build (use a small row_limit).

  • atlas_build_id ([‘integer’, ‘string’]) (optional) PeptideAtlas build to query. Default 572 (Human 2024-01).

  • row_limit ([‘integer’, ‘string’]) (optional) Maximum number of peptide rows to return (default 500). Use a small value (e.g. 2-5) for whole-build sampling, since a build holds millions of peptides.

Example Usage:

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