Peptide Match

Peptide Match retrieves occurrences of query peptides from the UniProt Knowledgebase (UniProtKB), including isoforms, using an Apache Lucene-based search engine to identify peptide matches across protein datasets.

Key Features:

• Efficient Search Engine: Utilizes an Apache Lucene-based search engine for fast and accurate retrieval of peptide sequences within UniProtKB.
• Comprehensive Annotations: Reports matched proteins with specific sequence regions and provides links to proteomic and peptide spectral databases.
• Taxonomy-Based Grouping: Organizes results by organism, taxonomic group, or taxonomy tree for comparative context.
• Flexible Query Options: Supports treating isobaric leucine and isoleucine as equivalent, searching within UniRef100 representative sequences, and extending queries to major proteomic databases.
• RESTful Web Services: Offers programmatic access via RESTful web services for integration into automated workflows.
• Regular Data Updates: Underlying data are updated every four weeks in alignment with UniProt releases.

Scientific Applications:

• Protein Identification: Facilitates identification of proteins from peptide sequences obtained by mass spectrometry or other experimental methods.
• Comparative Proteomics: Enables comparison of peptide occurrences across different organisms and taxonomic groups.
• Functional Annotation: Assists in linking peptides to annotated UniProtKB entries to support functional interpretation of proteins.

Methodology:

Searches use an Apache Lucene-based engine against UniProtKB (including isoforms) with optional leucine/isoleucine equivalence and optional restriction to UniRef100 representative sequences, taxonomy-based grouping of results, annotated reporting of matched sequence regions with links to proteomic and peptide spectral databases, access via RESTful web services, and data updated every four weeks in alignment with UniProt releases.