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. For consistency, the units SHOULD be minutes.

26.1.1 Recommended Parquet encodings¶

26.2 Chromatogram metadata - chromatograms_metadata.parquet¶

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

This table uses the metadata table layout.

• index (integer) - the ascending 0-based index, incrementing by 1 per entry. 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), or absorption (MS:1000812).
• data_processing_id (string) - the id of a data_processing that governs this chromatogram if it differs from run.default_data_processing_id; null otherwise. This applies to how chromatogram properties were calculated. Data arrays for this chromatogram inherit these as well unless they specify a data processing methods 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)

26.3 Chromatogram precursor metadata - chromatograms_metadata_precursors.parquet¶

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

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

26.4 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 layout.

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.

26.5 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 layout.

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. For SRM or MRM acquisitions, the precursor isolation window and selected ion describe Q1 and the product isolation window describe Q3.