Mass spec-based proteomics research typically uses protein reference databases for matching experimentally observed peptide fragmentation spectra to spectra predicted by large protein sequence databases like the UniProt Knowledgebase or Ensembl database.

These protein databases derive the bulk of their sequence information from translation of DNA sequences submitted to nucleic acid databases. However, these nucleic acid databases are not entirely stable – with gene models changing over time as the field incorporates new information and understandings.

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