27. 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.

27.1 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.

27.1.1 Recommended Parquet encodings¶

27.2 Chromatogram metadata — chromatograms_metadata.parquet¶

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

This table uses the metadata table schema.

• 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.
• scan_polarity (MS:1000465) (integer) — 1, -1, or null.
• chromatogram_type (MS:1000626) (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.
• number_of_data_points (MS:1003060) (integer) — data points stored in chromatograms_data.parquet.
• MAY supply a child of MS:1000808 (chromatogram attribute) one or more times.
  • chromatogram_title (MS:1000809)
  • lowest_observed_mz (MS:1000528)
  • highest_observed_mz (MS:1000527)
  • lowest_observed_wavelength (MS:1000619)
  • highest_observed_wavelength (MS:1000618)
  • lowest_observed_ion_mobility (MS:1003437)
  • highest_observed_ion_mobility (MS:1003438)

27.3 Chromatogram precursor metadata — chromatograms_metadata_precursors.parquet¶

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

The method of precursor-ion selection and activation. Outside of sequential, multiple or parallel reaction monitoring, this table will be empty or absent. Its schema is identical to the spectrum precursor schema

27.4 Chromatogram selected ion metadata — chromatograms_metadata_selected_ions.parquet¶

{
  "name": "chromatograms_metadata_selected_ions.parquet",
  "entity_type": "chromatogram",
  "data_kind": "selected_ions"
}

This table uses the metadata table schema.

Like the precursor group, outside of sequential, multiple or parallel reaction monitoring, this table will be empty or absent. Its schema is identical to the spectrum selected ion schema.

27.5 Chromatogram product selection metadata — chromatograms_metadata_products.parquet¶

{
  "name": "chromatograms_metadata_products.parquet",
  "entity_type": "chromatogram",
  "data_kind": "products"
}

This table uses the metadata table schema.

When describing single reaction monitoring (SRM) or multiple reaction monitoring (MRM) experiments, each product ion is isolated separately with a different isolation window. This table is usually empty or absent. Its schema is identical to the spectrum products schema.