Class: MassSpectrometryConfiguration

Instrument configuration and setup for a mass spectrometry run.

URI: basalt_schema:MassSpectrometryConfiguration

 classDiagram
    class MassSpectrometryConfiguration
    click MassSpectrometryConfiguration href "../MassSpectrometryConfiguration/"
      Configuration <|-- MassSpectrometryConfiguration
        click Configuration href "../Configuration/"

      MassSpectrometryConfiguration : acquisition_strategy





        MassSpectrometryConfiguration --> "0..1" MassSpectrometryAcquisitionStrategyEnum : acquisition_strategy
        click MassSpectrometryAcquisitionStrategyEnum href "../MassSpectrometryAcquisitionStrategyEnum/"



      MassSpectrometryConfiguration : dd_ms2_resolution

      MassSpectrometryConfiguration : description

      MassSpectrometryConfiguration : fid

      MassSpectrometryConfiguration : fragmentation





        MassSpectrometryConfiguration --> "0..1" FragmentationEnum : fragmentation
        click FragmentationEnum href "../FragmentationEnum/"



      MassSpectrometryConfiguration : iat

      MassSpectrometryConfiguration : id

      MassSpectrometryConfiguration : injection

      MassSpectrometryConfiguration : ionization





        MassSpectrometryConfiguration --> "1" IonizationSourceEnum : ionization
        click IonizationSourceEnum href "../IonizationSourceEnum/"



      MassSpectrometryConfiguration : lims_protocol_instance_id

      MassSpectrometryConfiguration : loop_count

      MassSpectrometryConfiguration : mass_range_max

      MassSpectrometryConfiguration : mass_range_min

      MassSpectrometryConfiguration : name

      MassSpectrometryConfiguration : polarity





        MassSpectrometryConfiguration --> "1" PolarityEnum : polarity
        click PolarityEnum href "../PolarityEnum/"



      MassSpectrometryConfiguration : resolution





        MassSpectrometryConfiguration --> "1" MassSpecResolutionEnum : resolution
        click MassSpecResolutionEnum href "../MassSpecResolutionEnum/"

Inheritance

Configuration
- MassSpectrometryConfiguration

Slots

Name	Cardinality and Range	Description	Inheritance
injection	1 String	Type of injection used in the mass spectrometry method	direct
ionization	1 IonizationSourceEnum	Type of ionization used in the mass spectrometry method	direct
fragmentation	0..1 FragmentationEnum	fragmentation technique used in the mass spectrometry run	direct
polarity	1 PolarityEnum	Polarity setting used in the mass spectrometry method	direct
resolution	1 MassSpecResolutionEnum		direct
dd_ms2_resolution	1 Double	Data-dependent MS2 resolution setting used in the mass spectrometry method	direct
loop_count	1 String	Number of MS2 scans to be acquired between each full MS scan	direct
iat	0..1 Double	Ion accumulation time setting used in the mass spectrometry method	direct
fid	0..1 Double	Free induction decay	direct
mass_range_max	0..1 Float	The maximum mass observable by this run (in m/z)	direct
mass_range_min	0..1 Float	The minimum mass observable by this run (in m/z)	direct
acquisition_strategy	0..1 MassSpectrometryAcquisitionStrategyEnum	The acquisition strategy used in the mass spectrometry run	direct
lims_protocol_instance_id	0..1 Integer	Reference to the L7 protocol_instance that corresponds to this sample process...	direct
name	1 String	Human-readable name for the entity or activity	Configuration
description	0..1 String	Human-readable description for the entity or activity	Configuration
id	1 Uuid		Configuration

Usages

used by	used in	type	used
MassSpectrometryDataGenerationActivity	uses_ms_configuration	range	MassSpectrometryConfiguration

Identifier and Mapping Information

Schema Source

from schema: https://EMSL-Computing.github.io/BASALT-Schema

Mappings

Mapping Type	Mapped Value
self	basalt_schema:MassSpectrometryConfiguration
native	basalt_schema:MassSpectrometryConfiguration

LinkML Source

Direct

name: MassSpectrometryConfiguration
description: Instrument configuration and setup for a mass spectrometry run.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: Configuration
slots:
- injection
- ionization
- fragmentation
- polarity
- resolution
- dd_ms2_resolution
- loop_count
- iat
- fid
- mass_range_max
- mass_range_min
- acquisition_strategy
- lims_protocol_instance_id

Induced

name: MassSpectrometryConfiguration
description: Instrument configuration and setup for a mass spectrometry run.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: Configuration
attributes:
  injection:
    name: injection
    description: Type of injection used in the mass spectrometry method
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: injection
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: string
    required: true
  ionization:
    name: ionization
    description: Type of ionization used in the mass spectrometry method
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: ionization
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: IonizationSourceEnum
    required: true
  fragmentation:
    name: fragmentation
    description: fragmentation technique used in the mass spectrometry run
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: fragmentation
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: FragmentationEnum
  polarity:
    name: polarity
    description: Polarity setting used in the mass spectrometry method
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: polarity
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: PolarityEnum
    required: true
  resolution:
    name: resolution
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: resolution
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: MassSpecResolutionEnum
    required: true
  dd_ms2_resolution:
    name: dd_ms2_resolution
    description: Data-dependent MS2 resolution setting used in the mass spectrometry
      method
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: dd_ms2_resolution
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: double
    required: true
  loop_count:
    name: loop_count
    description: Number of MS2 scans to be acquired between each full MS scan.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: loop_count
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: string
    required: true
  iat:
    name: iat
    description: Ion accumulation time setting used in the mass spectrometry method.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: iat
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: double
  fid:
    name: fid
    description: Free induction decay
    todos:
    - is this a setting or a result?
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: fid
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: double
  mass_range_max:
    name: mass_range_max
    description: The maximum mass observable by this run (in m/z).
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: mass_range_max
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: float
  mass_range_min:
    name: mass_range_min
    description: The minimum mass observable by this run (in m/z).
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: mass_range_min
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: float
  acquisition_strategy:
    name: acquisition_strategy
    description: The acquisition strategy used in the mass spectrometry run.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_strategy
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: MassSpectrometryAcquisitionStrategyEnum
  lims_protocol_instance_id:
    name: lims_protocol_instance_id
    description: Reference to the L7 protocol_instance that corresponds to this sample
      processing step, if applicable.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: lims_protocol_instance_id
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: integer
  name:
    name: name
    description: Human-readable name for the entity or activity.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: name
    owner: MassSpectrometryConfiguration
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - Instrument
    - OntologyClass
    - ContainerAxis
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - Study
    - SoftwareControlledTermValue
    range: string
    required: true
  description:
    name: description
    description: Human-readable description for the entity or activity
    title: description
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: description
    owner: MassSpectrometryConfiguration
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - OntologyClass
    - ContainerType
    - LabDevice
    - Configuration
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - Study
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - QuantityValue
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/mass-spec
    alias: id
    owner: MassSpectrometryConfiguration
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - MAOMProduct
    - WEOMProduct
    - Site
    - Sample
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - ProcessedSample
    - CoreSection
    - SamplingActivity
    - AerosolArmSamplingActivity
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - EngineeredStrainSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true