neXtProt

neXtProt provides an integrated knowledgebase of human proteins by combining UniProtKB/Swiss-Prot curation with selected high-throughput datasets to support proteomics, protein function, interaction, modification, and variant analyses.

Key Features:

• Data integration: Integrates UniProtKB/Swiss-Prot curated entries with expression profiles, functional annotations, protein-protein binary interactions, post-translational modifications (PTMs), and variant information.
• Proteomics analysis tools: Includes a peptide uniqueness checker and a protein digestion tool to determine suitable proteases and identify trypsin-resistant proteins for mass spectrometry experiments.
• SPARQL federated queries: Provides a SPARQL endpoint that supports federated queries for integration with external RDF datasets.
• Programmatic access: Offers an API for programmatic data retrieval and integration.
• Data formats: Distributes proteomics-relevant data in PEFF 1.0 format.
• High-throughput dataset curation: Applies selection and filtering of high-throughput datasets to ensure relevance and quality of integrated data.

Scientific Applications:

• Protein annotation and function analysis: Enables exploration of protein expression, function, modifications, and variant annotations in a unified resource.
• Mass spectrometry proteomics: Supports protease selection, peptide uniqueness assessment, and identification of trypsin-resistant proteins for MS workflows.
• Interaction and network analysis: Facilitates analysis of protein-protein binary interactions and network-level studies.
• Variant and disease research: Allows investigation of protein variants and their potential roles in disease mechanisms.

Methodology:

Integrates curated UniProtKB/Swiss-Prot entries with selected and filtered high-throughput datasets, applies dataset selection and filtering procedures, and exposes data via a programmatic API and a SPARQL endpoint with federated query support.