28. 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.
28.1 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. The main wavelength-axis array
SHOULD be named wavelength and the intensity array intensity, mirroring the
mz/intensity convention for mass spectra; as
elsewhere, readers resolve signal columns through the array index rather than by name.
When using null marking, follow the null semantics for signal data carefully for profile data.
28.2 Wavelength spectrum metadata — wavelength_spectra_metadata.parquet¶
{
"name": "wavelength_spectra_metadata.parquet",
"entity_type": "wavelength_spectrum",
"data_kind": "metadata"
}
This table uses the metadata table layout. It mirrors the spectrum metadata schema.
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 thescanstable 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 minutesdata_processing_id(string) — theidof adata_processingthat governs this spectrum if it deviates from the default inrun.default_data_processing_id;nullotherwise. 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 indexparameters(list).number_of_auxiliary_arrays(integer) /auxiliary_arrays(list) — see auxiliary data arrays.spectrum_type(CURIE) — e.g.MS:1000804"electromagnetic radiation spectrum".number_of_data_points(integer) — profile points stored inwavelength_spectra_data.parquet.- MAY supply a child of
MS:1003058(spectrum property) one or more times — e.g. - MAY supply a child of
MS:1000499(spectrum attribute) one or more times — e.g. spectra_combination (MS:1000570)(CURIE) — how multiple scans were combined to construct this spectrum. MUST be a child term ofMS:1000570|spectra combinationsuch asMS:1000795|no combinationorMS:1000571|sum of spectra. If this column is absent, this value SHOULD be assumed to beMS:1000795|no combination.
28.3 Wavelength spectrum scan metadata — wavelength_spectra_metadata_scans.parquet¶
{
"name": "wavelength_spectra_metadata_scans.parquet",
"entity_type": "wavelength_spectrum",
"data_kind": "scans"
}
This table uses the metadata table schema.
A scan or acquisition from the original raw file used to create a spectrum.
source_index(uint64) — the spectrum this scan belongs to (foreign key).instrument_configuration_id(integer) — theinstrument_configurationgoverning this scan referenced byid.parameters(list).scan_windows(list) — the list of windows in the main axis (wavelength array usually) that were acquired in this scan. This SHOULD be an empty list if no window metadata was stored.- (group)
scan_window_lower_limit(MS:1000501) (float32) — The lower wavelength bound of a mass spectrometer scan window.scan_window_upper_limit(MS:1000500) (float32) — The upper wavelength of a mass spectrometer scan window.
- MAY supply children of
MS:1000503(scan attribute),MS:1000018(scan direction, once), andMS:1000019(scan law, once).