PeptideAtlas

PeptideAtlas is a publicly accessible proteomics resource that compiles high-confidence peptide identifications observed in tandem mass spectrometry (MS/MS) experiments. It functions as an atlas of peptides and their protein mappings, drawing on data from multiple organisms and biological samples. The resource aims to document proteome coverage and support data validation, method development, and reproducibility in proteomics research.

Data and processing are central to PeptideAtlas. The atlas aggregates peptide identifications from public repositories and direct submissions, which are then reanalyzed using standardized search pipelines. Identifications are filtered to defined confidence levels with controlled error rates, enabling users to rely on the quality of the data. Each peptide entry includes the amino acid sequence, the supporting spectra, and the experimental context (sample, instrument, and protocol) along with the protein(s) to which the peptide maps. Peptides are linked to proteins, and proteins receive evidence-based annotations that reflect the supporting identifications.

Content and organization are designed to facilitate exploration. PeptideAtlas organizes data into builds, with each build representing a release that aggregates identifications from multiple experiments. Users can browse by peptide sequence or by protein, view associated spectra and metadata, and access cross-references to standard protein databases. The resource emphasizes reproducibility and interoperability through structured metadata and standardized identifiers.

Access and impact: The PeptideAtlas web interface supports querying, visualization, and data download, with options for programmatic access. The resource is used to assess proteome coverage, validate or refine protein identifications, and aid the design of targeted proteomics assays. It is maintained by a team of researchers and engages with the broader proteomics community to incorporate new data and standards.