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Edit slots and usages to accommodate multiple detection configurations for single MassSpectrometry instance #141

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Apr 30, 2024
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Original file line number Diff line number Diff line change
@@ -1,10 +1,13 @@
id: nmdc:dgms-99-zUCd5N
analyte_category: metabolome
mass_spectrum_collection_mode: profile
mass_spectrum_collection_modes:
- profile
acquisition_category: tandem_mass_spectrum
acquisition_strategy: data_independent_acquisition
resolution_category: high
mass_analyzer: Orbitrap
resolution_categories:
- high
mass_analyzers:
- Orbitrap
ionization_source: electrospray_ionization
polarity_mode: negative
alternative_identifiers:
Expand Down
36 changes: 32 additions & 4 deletions src/data/valid/Database-mass-spectrometry.yaml
Original file line number Diff line number Diff line change
@@ -1,11 +1,14 @@
data_generation_set:
- id: nmdc:dgms-99-zUCd5N
analyte_category: metabolome
mass_spectrum_collection_mode: full_profile
mass_spectrum_collection_modes:
- full_profile
acquisition_category: tandem_mass_spectrum
acquisition_strategy: data_independent_acquisition
resolution_category: high
mass_analyzer: Orbitrap
resolution_categories:
- high
mass_analyzers:
- Orbitrap
ionization_source: electron_ionization
polarity_mode: negative
alternative_identifiers:
Expand All @@ -19,4 +22,29 @@ data_generation_set:
type: nmdc:MassSpectrometry
associated_studies:
- nmdc:sty-00-555xxx

- id: nmdc:dgms-99-zUCd5x
analyte_category: lipidome
mass_spectrum_collection_modes:
- full_profile
- centroid
acquisition_category: tandem_mass_spectrum
acquisition_strategy: data_dependent_acquisition
resolution_categories:
- high
- low
mass_analyzers:
- Orbitrap
- ion_trap
ionization_source: electrospray_ionization
polarity_mode: negative
alternative_identifiers:
- emsl:123423
has_input:
- nmdc:bsm-00-red2
add_date: 30-OCT-14 12.00.00.000000000 AM
mod_date: 22-MAY-20 06.13.12.927000000 PM
has_output:
- nmdc:dobj-00-9n9n9x
type: nmdc:MassSpectrometry
associated_studies:
- nmdc:sty-00-555xxx
19 changes: 11 additions & 8 deletions src/schema/nmdc.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -156,10 +156,10 @@ classes:
- eluent_introduction
- acquisition_category
- acquisition_strategy
- resolution_category
- mass_analyzer
- resolution_categories
- mass_analyzers
- ionization_source
- mass_spectrum_collection_mode
- mass_spectrum_collection_modes
- polarity_mode

slot_usage:
Expand Down Expand Up @@ -695,21 +695,24 @@ slots:
range: PolarityModeEnum
description: the polarity of which ions are generated and detected

mass_spectrum_collection_mode:
mass_spectrum_collection_modes:
range: MassSpectrumCollectionModeEnum
description: Indicates whether mass spectra were collected in full profile, reduced profile, or centroid mode during acquisition.
multivalued: true

ionization_source:
range: IonizationSourceEnum
description: which kind of ionization source is used to introduce analytes into a mass spectrometer

mass_analyzer:
mass_analyzers:
range: MassAnalyzerEnum
description: which kind of mass analyzer is primarily used during the spectra collection.
description: which kind of mass analyzer(s) used during the spectra collection.
multivalued: true

resolution_category:
resolution_categories:
range: ResolutionCategoryEnum
description: whether mass spectra are collected at higher than unity resolution
description: whether mass spectra are collected at higher than unit resolution
multivalued: true

acquisition_strategy:
range: AcquisitionStrategyEnum
Expand Down
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