Fig. 1.

A, A single PSM is represented within <SpectrumIdentificationItem> including scores as values associated with standard terms sourced from the PSI-MS controlled vocabulary. Unique identifiers and references to other objects in the file are underlined. B, The peptide identified is stored elsewhere in the file, within the <Peptide> element, which can be referenced by an unlimited number of PSMs. C, All the proteins within which a peptide sequence can be located (given the enzyme specificity as defined) are linked via the <PeptideEvidence> element. D, Database proteins are represented in <DBSequence>. E, An identified group of proteins is stored within <ProteinAmbiguityGroup> (“Protein group” on the right panel) and <ProteinDetectionHypothesis> (PDH) - evidence at the level of a single database accession.