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27. Wavelength Spectra

Wavelength spectra — UV, DAD, and other electromagnetic-radiation (EMR) spectra --- are stored independently from mass spectra so the two modalities can have divergent schemas without inflating the number of empty columns, and so a reader need not sift through mass spectra to find EMR spectra (or vice versa). These files SHOULD be present only if wavelength spectra are included in the archive.

27.1 Wavelength spectrum signal data — wavelength_spectra_data.parquet

{
  "name": "wavelength_spectra_data.parquet",
  "entity_type": "wavelength spectrum",
  "data_kind": "data arrays"
}

The signal data is encoded using either point layout or chunked layout. The entity index column MUST be named wavelength_spectrum_index, and a co-located time column, if written, SHOULD be named wavelength_spectrum_time.

When using null marking, follow the null semantics for signal data carefully for profile data.

27.2 Wavelength spectrum metadata — wavelength_spectra_metadata.parquet

{
  "name": "wavelength_spectra_metadata.parquet",
  "entity_type": "wavelength spectrum",
  "data_kind": "metadata"
}

This table uses the packed parallel metadata table schema. It mirrors the spectrum metadata layout but omits the precursor and selected_ion facets, because EMR spectra have not been observed with isolation and fragmentation. spectrum.index and scan.source_index MUST be the first column of their respective facets.

27.2.1 spectrum (group)

  • index (uint64) — ascending 0-based index, incrementing by 1 per entry, SHOULD be time-sorted. Primary key.
  • id (string) — the "nativeID" string, per a native identifier format.
  • time (float64) — the data-acquisition start time. SHOULD be replicated from the parallel scan facet for simpler filtering; for a spectrum with multiple scans it SHOULD be the minimum value if the run is in acquisition-time order. The time unit MUST be minutes
  • data_processing_id (string) — the id of a data_processing that governs this spectrum if it deviates from the default in run.default_data_processing_id; null otherwise. This applies data processing reflects how properties or attributes of the spectrum are calculated. Data arrays are governed by the data processing methods defined in the array index
  • parameters (list).
  • number_of_auxiliary_arrays (integer) / auxiliary_arrays (list) — see auxiliary data arrays.
  • MS_1000559_spectrum_type (CURIE) — e.g. MS:1000804 "electromagnetic radiation spectrum".
  • MS_1003060_number_of_data_points (integer) — profile points stored in wavelength_spectra_data.parquet.
  • MAY supply a child of MS:1003058 (spectrum property) one or more times — e.g. λmax, lowest observed wavelength, total ion current.
  • MAY supply a child of MS:1000499 (spectrum attribute) one or more times — e.g. MS_1000796_spectrum_title.

27.2.2 scan (group)

  • source_index (uint64) — the spectrum this scan belongs to (foreign key).
  • instrument_configuration_id (integer) — the instrument_configuration governing this scan referenced by id.
  • parameters (list).
  • scan_windows (list) — see the equivalent substructure for spectra.
  • MAY supply a child of MS:1000503 (scan attribute) one or more times.