18. mzPeak metadata instrument configurations¶

Describe the JSON format of instrument configurations used to acquire a mass spectrometry experiment

18.1 Use cases¶

This describes which components are engaged for a particular scan configuration. This includes the inlet and ion source which may be configured independently of the mass analyzer. This is also the place to note the MS:1000031|instrument model, MS:1000529|serial number and any MS:1000032|customization done to the hardware.

18.1.1 Multiple configurations¶

When handling an instrument with multiple mass analyzers like an MS:1003971|ion trap fourier transform ion cyclotron resonance instrument, there SHOULD be multiple 18.2.1 instrument_configuration instances.

An example with two configurations, one using the ion trap, one using the fourier transform ion cyclotron resonance mass spectrometer (FT-ICR)

[
    {
    "components": [
    {
        "component_type": "ionsource",
        "order": 1,
        "parameters": [
        {
            "accession": "MS:1000073",
            "name": "electrospray ionization",
        },
        {
            "accession": "MS:1000057",
            "name": "electrospray inlet",
        }
        ]
    },
    {
        "component_type": "analyzer",
        "order": 2,
        "parameters": [
        {
            "accession": "MS:1000079",
            "name": "fourier transform ion cyclotron resonance mass spectrometer",
        }
        ]
    },
    {
        "component_type": "detector",
        "order": 3,
        "parameters": [
        {
            "accession": "MS:1000624",
            "name": "inductive detector",
        }
        ]
    }
    ],
    "id": 0,
    "parameters": [
    {
        "accession": "MS:1000448",
        "name": "LTQ FT",
    },
    {
        "accession": "MS:1000529",
        "name": "instrument serial number",
        "value": "SN06061F"
    }
    ],
    "software_reference": "Xcalibur"
    }
    {
    "components": [
        {
        "component_type": "ionsource",
        "order": 1,
        "parameters": [
            {
            "accession": "MS:1000073",
            "name": "electrospray ionization",
            },
            {
            "accession": "MS:1000057",
            "name": "electrospray inlet",
            }
        ]
        },
        {
        "component_type": "analyzer",
        "order": 2,
        "parameters": [
            {
            "accession": "MS:1000083",
            "name": "radial ejection linear ion trap",
            }
        ]
        },
        {
        "component_type": "detector",
        "order": 3,
        "parameters": [
            {
            "accession": "MS:1000253",
            "name": "electron multiplier",
            }
        ]
        }
    ],
    "id": 1,
    "parameters": [
        {
        "accession": "MS:1000448",
        "name": "LTQ FT",
        },
        {
        "accession": "MS:1000529",
        "name": "instrument serial number",
        "value": "SN06061F"
        }
    ],
    "software_reference": "Xcalibur"
    }
]

Type: array Items: 18.2.1 instrument_configuration

18.2 Definitions¶

18.2.1 instrument_configuration¶

Describes a single instrument configuration that was used. Analogous to https://peptideatlas.org/tmp/mzML1.1.0.html#instrumentConfiguration

Type: object

18.2.1.1 Properties¶

Property	Type	Required	Description
`components`	`array` of 18.2.2 `component_type`	Yes
`software_reference`	`string`	Yes	The identifier for a software that was associated with the data acquisition process. This MUST be a software_list[].id in the software list of the mzPeak archive.
`id`	`integer`	Yes	A unique identifier for this instrument configuration. This value is an integer for compact storage of references throughout the rest of the archive.
`parameters`	`array` of `param`	Yes	Additional parameters describing this configuration, like the instrument model and serial number
`scan_settings_reference`	`string` or `null`		The identifier for a scan settings that was associated with this instrument configuration. If present, this MUST be a scan_settings_list[].id in the scan settings list of the mzPeak archive.

18.2.1.2 Property Details¶

components - array of 18.2.2 component_type (required)

software_reference - string (required)

The identifier for a software that was associated with the data acquisition process. This MUST be a software_list[].id in the software list of the mzPeak archive.

id - integer (required)

A unique identifier for this instrument configuration. This value is an integer for compact storage of references throughout the rest of the archive.

parameters - array of param (required)

Additional parameters describing this configuration, like the instrument model and serial number

scan_settings_reference - string or null (optional)

The identifier for a scan settings that was associated with this instrument configuration. If present, this MUST be a scan_settings_list[].id in the scan settings list of the mzPeak archive.

18.2.2 component_type¶

Describes an instrument component like the ion source, mass analyzer, or detector

Type: object

18.2.2.1 Properties¶

Property	Type	Required	Description
`component_type`	`enum`	Yes	The kind of component this is
`order`	`integer`	Yes	The order in which the analytes travels through the component. The values must be contiguous, unique ascending integers.
`parameters`	`array` of `param`	Yes	Additional parameters describing this component, like the particular hardware type or components

18.2.2.2 Property Details¶

component_type - enum (required)

The kind of component this is

Allowed values: "ionsource", "analyzer", "detector"

order - integer (required)

The order in which the analytes travels through the component. The values must be contiguous, unique ascending integers.

parameters - array of param (required)

Additional parameters describing this component, like the particular hardware type or components