23. mzPeak metadata scan settings list¶

The list of scan settings pre-configuring acquisition settings. Analogous to https://peptideatlas.org/tmp/mzML1.1.0.html#scanSettingsList.

23.1 Use cases¶

This is used primarily used for high-level configuration of data-independent acquisition strategies like targeted MS, SWATH, and the like. Additionally used for imaging MS to define the spatial scanning parameters.

23.1.1 Targeted MS¶

Targeted mass spectrometry methods may list their targeted ions MAY be added to a 23.2.1 scan_settings entry's targets list. 23.2.2 Targets are described by any list of appropriate parameters, including terms like children of MS:1000455|ion selection attribute, MS:1000792|isolation window attribute or MS:1000510|precursor activation attribute

23.1.2 Data-Independent Acquisition (DIA)¶

Like targeted MS, DIA methods may define their windows scheme with terms like children of MS:1000455|ion selection attribute, MS:1000792|isolation window attribute or MS:1000510|precursor activation attribute, using a target for each window.

23.1.3 Imaging MS¶

The presence of the imaging mass spectrometry controlled vocabulary and the imaging key in the mzpeak_index.json#metadata. Imaging-specific parameters SHOULD be added to a 23.2.1 scan_settings entry's parameters list.

{
  "id": "scansettings1",
  "parameters": [
    {
      "accession": "IMS:1000401",
      "name": "top down",
    },
    {
      "accession": "IMS:1000413",
      "name": "flyback",
    },
    {
      "accession": "IMS:1000480",
      "name": "horizontal line scan",
    },
    {
      "accession": "IMS:1000491",
      "name": "linescan left right",
    },
    {
      "accession": "IMS:1000042",
      "name": "max count of pixels x",
      "value": 3
    },
    {
      "accession": "IMS:1000043",
      "name": "max count of pixels y",
      "value": 3
    },
    {
      "accession": "IMS:1000044",
      "name": "max dimension x",
      "unit": "UO:0000017",
      "value": 300
    },
    {
      "accession": "IMS:1000045",
      "name": "max dimension y",
      "unit": "UO:0000017",
      "value": 300
    },
    {
      "accession": "IMS:1000046",
      "name": "pixel size (x)",
      "unit": "UO:0000017",
      "value": 100.0
    },
    {
      "accession": "IMS:1000047",
      "name": "pixel size y",
      "unit": "UO:0000017",
      "value": 100.0
    }
  ],
  "source_file_refs": [],
  "targets": []
}

Specifics are yet to be determined.

Type: array Items: 23.2.1 scan_settings

23.2 Definitions¶

23.2.1 scan_settings¶

Description of the acquisition settings of the instrument prior to the start of the run. Analogous to https://peptideatlas.org/tmp/mzML1.1.0.html#scanSettings

Type: object

23.2.1.1 Properties¶

23.2.1.2 Property Details¶

id - string (required)

The unique identifier for this scan settings configuration

source_file_references - array of string (optional)

targets - array of 23.2.2 target (optional)

A list of targeted ions or intervals on an inclusion list.

parameters - array of param (required)

Additional parameters describing the scan settings.

23.2.2 target¶

Type: object

23.2.2.1 Properties¶

23.2.2.2 Property Details¶

parameters - array of param (required)

Additional parameters describing this target