22. 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.

22.1 Use cases¶

This is primarily used for high-level configuration of data-independent acquisition strategies like SWATH or targeted MS. Additionally used for imaging MS to define the spatial scanning parameters. These settings are associated with the rest of the data in the archive through a link to an instrument configuration.

22.1.1 Targeted MS¶

Targeted mass spectrometry methods may list their targeted ions MAY be added to a 22.2.1 scan_settings entry's targets list. 22.2.2 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.

22.1.2 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.

A target list describing a window list would look like:

[
  {
    "parameters": [
      {
        "accession": "MS:1000827",
        "name": "isolation window target m/z",
        "value": 813.0,
        "unit": "MS:1000040"
      },
      {
        "accession": "MS:1000828",
        "name": "isolation window lower offset",
        "value": 13.0,
        "unit": "MS:1000040"
      },
      {
        "accession": "MS:1000829",
        "name": "isolation window upper offset",
        "value": 13.0,
        "unit": "MS:1000040"
      },
      {
        "accession": "MS:1000045",
        "name": "collision energy",
        "value": 41.57222844344905,
        "unit": "UO:0000266"
      }
    ]
  },
  {
    "parameters": [
      {
        "accession": "MS:1000827",
        "name": "isolation window target m/z",
        "value": 413.0,
        "unit": "MS:1000040"
      },
      {
        "accession": "MS:1000828",
        "name": "isolation window lower offset",
        "value": 13.0,
        "unit": "MS:1000040"
      },
      {
        "accession": "MS:1000829",
        "name": "isolation window upper offset",
        "value": 13.0,
        "unit": "MS:1000040"
      },
      {
        "accession": "MS:1000045",
        "name": "collision energy",
        "value": 24.945128779395297,
        "unit": "UO:0000266"
      }
    ]
  }
  // and more
]

This pre-registration makes it possible for software to scan just the header metadata of the file to find the window schema, rather than scanning all unique entries in the spectrum precursor table.

22.1.3 Imaging MS¶

An imaging archive describes its pixel grid in the parameters list of one 22.2.1 scan_settings entry. The Imaging profile states which terms are required.

{
  "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_references": [],
  "targets": []
}

Type: array Items: 22.2.1 scan_settings

22.2 Definitions¶

22.2.1 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

22.2.1.1 Properties¶

Property	Type	Required	Description
`id`	`string`	Yes	The unique identifier for this scan settings configuration
`source_file_references`	`array` of `string`
`targets`	`array` of 22.2.2 `target`		A list of targeted ions or intervals on an inclusion list.
`parameters`	`array` of `param`	Yes	Additional parameters describing the scan settings.

22.2.1.2 Property Details¶

id - string (required)

The unique identifier for this scan settings configuration

source_file_references - array of string (optional)

targets - array of 22.2.2 target (optional)

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

parameters - array of param (required)

Additional parameters describing the scan settings.

22.2.2 target¶

Type: object

22.2.2.1 Properties¶

Property	Type	Required	Description
`parameters`	`array` of `param`	Yes	Additional parameters describing this target.

22.2.2.2 Property Details¶

parameters - array of param (required)

Additional parameters describing this target.