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26. Chromatograms

Chromatograms are described by a signal file (chromatograms_data.parquet) and a metadata file (chromatograms_metadata.parquet). Diagnostic traces are currently carried here as well, pending their dedicated entity-type namespace.

26.1 Chromatogram signal data — chromatograms_data.parquet

{
  "name": "chromatograms_data.parquet",
  "entity_type": "chromatogram",
  "data_kind": "data arrays"
}

The signal data is encoded using either point layout or chunked layout. The entity index column MUST be named chromatogram_index. The default primary axis is a MS:1000595 time array, though the unit is up to the writer. For consistency, we recommend using minutes.

Column Encoding
chromatogram_index delta encoding
time arrays byte stream split (byte shuffling)

26.2 Chromatogram metadata — chromatograms_metadata.parquet

{
  "name": "chromatograms_metadata.parquet",
  "entity_type": "chromatogram",
  "data_kind": "metadata"
}

This table uses the packed parallel metadata table schema.

26.2.1 chromatogram (group)

  • index (integer) — the ascending 0-based index, incrementing by 1 per entry and SHOULD be time-sorted ascending. Primary key for the chromatogram facet.
  • id (string) — a unique string identifier. Unlike for spectra, there is no "nativeId" format definition for chromatograms at this time.
  • MS_1000465_scan_polarity (integer) — 1, -1, or null.
  • MS_1000626_chromatogram_type (CURIE) — e.g. total ion current (MS:1000235), selected ion current (MS:1000627), base peak (MS:1000628), absorption (MS:1000812), or selected ion current (MS:1000627).
  • data_processing_id (string) — the id of a data_processing that governs this chromatogram 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 chromatogram are calculated. Data arrays are governed by the data processing methods defined in the array index
  • parameters (list) — controlled or uncontrolled parameters; see the parameters list.
  • number_of_auxiliary_arrays (integer) and auxiliary_arrays (list) --- see auxiliary data arrays.
  • MS_1003060_number_of_data_points (integer) — data points stored in chromatograms_data.parquet.
  • MAY supply a child of MS:1000808 (chromatogram attribute) one or more times.

26.2.2 precursor (group)

The method of precursor-ion selection and activation. Outside of sequential, multiple or parallel reaction monitoring, this group will be unilaterally null.

  • source_index (integer) — the chromatogram this precursor belongs to (foreign key).
  • precursor_index (integer) — the chromatogram the precursor was created from (foreign key). See spectra for more details.
  • precursor_id (string) — the id of the chromatogram referenced by precursor_index. See spectra for more details.
  • isolation_window (group) — as for spectra: MUST supply children of MS:1000792.
  • activation (group) — as for spectra: MUST supply MS:1000044 (dissociation method) or a child.

26.2.3 selected_ion (group)

Like the precursor group, outside of sequential, multiple or parallel reaction monitoring, this group will be unilaterally null.

  • source_index (integer) / precursor_index (integer) — foreign keys.
  • ion_mobility_value (float) / ion_mobility_type (CURIE) — See the spectrum scan.ion_mobility_value for details storing scalar values. If multiple ion mobility values are available for the selected ion that have been combined, but no ion mobility centroid is available as when a ramp has been used, report multiple selected_ion records, one for the ramp start and one for the ramp end.
  • parameters (list) — controlled or uncontrolled parameters; see the parameters list.
  • MUST supply a child of MS:1000455 (ion selection attribute) one or more times — selected-ion m/z, charge state, intensity.

26.2.4 product (group) (optional)

When describing single reaction monitoring (SRM) or multiple reaction monitoring (MRM) experiments, each product ion is isolated separately with a different isolation window. This group is optional and MAY be omitted when the relevant data is absent.

  • source_index (integer) — the chromatogram this product belongs to (foreign key).
  • product_index (integer) — the ascending 0-based index, incrementing by 1 per entry. This number uniquely identifies each product ion selection across all rows.
  • isolation_window (group) — the isolation/selection window for this product ion, like the Q3 transmission window on a triple-quadrupole instrument.
    • parameters (list) — controlled or uncontrolled parameters; see the parameters list.
    • MUST supply children of MS:1000792 (isolation-window attribute) one or more times; promote to columns when available — e.g. isolation-window target m/z, lower offset, upper offset.
  • parameters (list) — controlled or uncontrolled parameters; see the parameters list.