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3. Relationship to Other Specifications

This format is not developed in isolation. It is designed to be complementary to, and used in conjunction with, several existing and emerging community models:

  • PSI Universal Spectrum Identifier (USI) - a universal mechanism for referring to a specific spectrum in public repositories. mzPeak uses USIs in the scan.spectrum_reference field and precursor.precursor_id for spectra drawn from external sources (see Spectrum metadata).
  • mzML - the current PSI recommendation for storing raw or processed mass spectrometry data. mzPeak draws on the mzML data model and re-uses concepts such as controlled vocabularies where feasible.
  • SDRF (Sample and Data Relationship Format) (Guidelines) - a representation of sample metadata. SDRF known at acquisition time may be carried alongside the data in an mzPeak archive with the other entity_type and data_kind.
  • imzML - the mzML-derived standard for mass-spectrometry imaging. mzPeak addresses imaging within the same archive via spatial coordinates in the scan metadata (see Imaging profile).

3.1 Controlled vocabularies

mzPeak metadata is anchored in the PSI-MS controlled vocabulary. The controlled vocabularies an archive relies on - with their versions and source URIs — are declared in the archive's cv_list (see file-level metadata), so a reader can resolve every CURIE unambiguously and reproducibly.