ISPIDER Central

ISPIDER Central aggregates and queries proteomic identifications across multiple repositories to enable cross-dataset integration and annotation of mass spectrometry-based proteomics data.

Key Features:

• Integration Across Repositories: Queries and aggregates identifications from PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas, and the Global Proteome Machine to address heterogeneity in datasets and formats.
• Protein and Peptide Search Capabilities: Searches for proteins and peptides characterized in mass spectrometry-based proteomics experiments across multiple research groups and datasets.
• Resolution of Protein Accessions: Uses the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service to map and resolve protein accessions across sequence repositories.
• Annotation Integration via DAS and Dasty2: Integrates annotations from Distributed Annotation System (DAS) servers, including access via Dasty2, to enrich protein-level information.
• External Web Services Integration: Supports addition of further protein-centric information by invoking external web services that accept proteins as input.

Scientific Applications:

• Cross-Repository Identification Consolidation: Consolidates peptide and protein identifications across PRIDE, PepSeeker, PeptideAtlas, and the Global Proteome Machine for comparative analyses.
• Accession Mapping and Consistency: Provides consistent protein accession mapping across sequence repositories using PICR for integrative analyses.
• Annotation-Enriched Interpretation: Enables enrichment of proteomic hits with DAS-provided annotations and external web-service data to support functional interpretation.
• Integrative In Silico Proteomics Experiments: Facilitates integrative computational experiments that combine identifications and annotations from multiple public proteomics resources.

Methodology:

Queries PRIDE, PepSeeker, PeptideAtlas, and the Global Proteome Machine; maps protein accessions via EBI PICR; integrates annotations from DAS servers (including Dasty2) and invokes external protein-centric web services to collate search results.