Object[Protocol, MassSpectrometry]
Protocol for determining the mass of compounds by ionizing them and measuring their mass-to-charge ratio.
Organizational Information
Name
Name of this Object.
Format: Single
Class: String
Programmatic Pattern: _String
Pattern Description: A string.
ID
ID of this Object.
Format: Single
Class: String
Programmatic Pattern: _String
Pattern Description: The ID of this object.
Object
Object of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, MassSpectrometry, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, MassSpectrometry]
Pattern Description: Object[Protocol, MassSpectrometry]
Notebook
Notebook this object belongs to.
Format: Single
Class: Link
Programmatic Pattern: _Link
Pattern Description: An object of that matches ObjectP[Object[LaboratoryNotebook]].
Relation: Object[LaboratoryNotebook][Objects]
Author
The investigator who created this protocol.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[User][ProtocolsAuthored]
General
DateConfirmed
The date on which the protocol first entered processing or a backlog.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateEnqueued
The date on which the protocol was accepted and added to the queue.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateStarted
The date on which the protocol moved from the front of the queue to begin running in the lab.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateCompleted
The date on which the last step of this protocol's execution was finished.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateCanceled
The date on which the protocol was canceled and removed from the queue.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
Script
The script that created this protocol.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Notebook][Protocols]
SubprotocolScripts
All scripts generated by this protocol as a list of subprotocols.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Notebook, Script][ParentProtocol]
Site
The ECL site at which this protocol was executed.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Container, Site]
SamplesIn
Input samples for this analytical or preparative experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ContainersIn
Any containers containing this protocols' SamplesIn.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
NumberOfReplicates
Indicates the number of times the experiment is repeated with identical parameters.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
Status
The current status of the protocol.
Format: Single
Class: Expression
Programmatic Pattern: ProtocolStatusP
CheckpointProgress
A listing of all the checkpoints passed in the execution of this protocol.
Format: Multiple
[[1]] Name
Header: Name
Class: String
Programmatic Pattern: _String
[[2]] Start Time
Header: Start Time
Class: Date
Programmatic Pattern: _?DateObjectQ
[[3]] End Time
Header: End Time
Class: Date
Programmatic Pattern: _?DateObjectQ|Null
SubprotocolDescription
A short title indicating what this subprotocol accomplishes.
Format: Single
Class: String
Programmatic Pattern: _String
BatchedUnitOperations
The individual batches of the protocol, as they will be executed in the lab.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[UnitOperation][Protocol]
ReplacementProtocol
If this protocol was aborted due to technical reasons, links to the replacement protocol run in its place.
Format: Single
Class: Link
Programmatic Pattern: _Link
Sterile
Indicates if the protocol is performed in a sterile environment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
LiquidHandlingLog
The instrumentation trace file that monitored and recorded the execution of this robotic liquid handling.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[EmeraldCloudFile]
PooledSamplesIn
The members of SamplesIn gathered into the pools that are mixed in each AliquotContainer.
Format: Multiple
Class: Expression
Programmatic Pattern: {ObjectReferenceP[Object[Sample]]..}
NestedIndexMatchingSamplesIn
The members of SamplesIn gathered into the pools that are mixed in each AliquotContainer.
Format: Multiple
Class: Expression
Programmatic Pattern: {ObjectReferenceP[Object[Sample]]..}
InitialNitrogenPressure
The pressure data of the nitrogen gas source before starting the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
NitrogenPressureLog
The pressure log for the nitrogen gas source for the relevant section of the facility.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
InitialCO2Pressure
The pressure data of the CO2 gas source before starting the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
CO2PressureLog
The pressure log for the CO2 gas source for the relevant section of the facility.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
InitialArgonPressure
The pressure data of the argon gas source before starting the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
HoldOrder
Indicates if the queue position of this protocol should be strictly enforced, regardless of the available resources in the lab.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
Priority
Indicates if this protocol should be prioritized to start at the given StartDate, have dedicated operation for its entirety, and not be interrupted by other protocols.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
StartDate
The date at which this protocol should be prioritized to start.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
Branch
The git branch that this protocol should be run on.
Format: Single
Class: String
Programmatic Pattern: _String
Detectors
Indicates the types of measurements performed for the experiment and available on the Instrument.
Format: Multiple
Class: Expression
Programmatic Pattern: ChromatographyDetectorTypeP
AcquisitionModes
For each member of SamplesIn, the type of acquisition being performed in this protocol. MS mode measures the masses of the intact analytes, whereas MSMS measures the masses of the analytes fragmented by collision-induced dissociation.
Format: Multiple
Class: Expression
Programmatic Pattern: AcquisitionModeP
MassAnalyzer
The type of the component of the mass spectrometer that performs ion separation based on m/z (mass-to-charge ratio).
Format: Single
Class: Expression
Programmatic Pattern: MassAnalyzerTypeP
Instrument
The instrument used to perform the mass spectrometry experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
IntegratedHPLC
The HPLC system that is coupled to the mass spectrometer instrument used for this experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
IonModes
For each member of SamplesIn, indicates if positively or negatively charged ions are analyzed.
Format: Multiple
Class: Expression
Programmatic Pattern: IonModeP
IonSource
The type of ionization used to create gas phase ions from the molecules in the sample. Electrospray ionization (ESI) produces ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol, and gas phase ions are formed from the fine spray of charged droplets as a result of solvent evaporation and Coulomb fission. In matrix-assisted laser desorption/ionization (MALDI), the sample is embedded in a laser energy absorbing matrix which is then irradiated with a pulsed laser, ablating and desorbing the molecules with minimal fragmentation and creating gas phase ions from the analyte molecules in the sample.
Format: Single
Class: Expression
Programmatic Pattern: IonSourceP
InjectionType
The type of injection used to inject the sample into the mass spectrometer. In DirectInfusion, the sample is directly injected into the instrument using the built-in fluidics pump system of the mass spectrometer without the use of any mobile phase. FlowInjection works by injecting the sample into a flowing solvent stream using a liquid chromatography autosampler and pumps, in the absence of chromatographic separation.
Format: Single
Class: Expression
Programmatic Pattern: InjectionTypeP
Buffer
The solvent pumped through the flow path, carrying the sample through the ionization source and into the mass spectrometer.
Format: Single
Class: Link
Programmatic Pattern: _Link
InitialBufferVolume
The volume of Buffer immediately before the experiment was started.
Format: Single
Class: Real
Unit: 1 liter
Programmatic Pattern: GreaterEqualP[0 Liter]
InitialBufferAppearance
An image of Buffer taken immediately before the experiment was started.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[EmeraldCloudFile]
MethodFiles
Method files used to conduct the mass spectrometry measurement of all SamplesIn zipped into one directory.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[EmeraldCloudFile]
ScanModes
For each member of SamplesIn, the mass scan mode for using in tandem mass analysis (ESI-QQQ).
Format: Multiple
Class: Expression
Programmatic Pattern: MassSpecScanModeP
Replicate Experiments
Template
The protocol whose option selections should be selected as the default options for this protocol.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol][ProtocolsTemplated]
ProtocolsTemplated
Protocols which were generated using this protocol's options as a starting point for its option defaults.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol][Template]
Sample Preparation
PreparatoryUnitOperations
A list of transfers, consolidations, aliquots, mixes and dilutions that will be performed in the order listed to prepare samples for the experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: _ | _
PreparatoryPrimitives
A list of transfers, consolidations, aliquots, mixes and dilutions that will be performed in the order listed to prepare samples for the experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: _ | _
VolumeCheckSamplePrep
Indicates if any liquid samples prepared by using the PreparatoryUnitOperations option should have their volumes measured and updated before running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
IncubateSamplePreparation
For each member of SamplesIn, parameters describing how the input samples should be heated prior to any aliquoting or the start of the experiment.
Format: Multiple
[Incubate]
Header: Incubate
Class: Boolean
[IncubationTemperature]
Header: IncubationTemperature
Class: Real
Unit: 1 degree Celsius
[IncubationTime]
Header: IncubationTime
Class: Real
Unit: 1 second
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[MixUntilDissolved]
Header: MixUntilDissolved
Class: Boolean
[MaxIncubationTime]
Header: MaxIncubationTime
Class: Real
Unit: 1 second
[IncubationInstrument]
Header: IncubationInstrument
Class: Link
[AnnealingTime]
Header: AnnealingTime
Class: Real
Unit: 1 second
[IncubateAliquotContainer]
Header: IncubateAliquotContainer
Class: Expression
[IncubateAliquot]
Header: IncubateAliquot
Class: Real
Unit: 1 liter
[IncubateAliquotDestinationWell]
Header: IncubateAliquotDestinationWell
Class: Expression
CentrifugeSamplePreparation
For each member of SamplesIn, parameters describing how the input samples should be spun down prior to any aliquoting or the start of the experiment.
Format: Multiple
[Centrifuge]
Header: Centrifuge
Class: Boolean
[CentrifugeInstrument]
Header: CentrifugeInstrument
Class: Link
[CentrifugeIntensity]
Header: CentrifugeIntensity
Class: VariableUnit
[CentrifugeTime]
Header: CentrifugeTime
Class: Real
Unit: 1 minute
[CentrifugeTemperature]
Header: CentrifugeTemperature
Class: Real
Unit: 1 degree Celsius
[CentrifugeAliquotContainer]
Header: CentrifugeAliquotContainer
Class: Expression
[CentrifugeAliquot]
Header: CentrifugeAliquot
Class: Real
Unit: 1 liter
[CentrifugeAliquotDestinationWell]
Header: CentrifugeAliquotDestinationWell
Class: Expression
FilterSamplePreparation
For each member of SamplesIn, parameters describing how particulates should be separated from the input samples prior to any aliquoting or the start of the experiment.
Format: Multiple
[Filtration]
Header: Filtration
Class: Boolean
[FiltrationType]
Header: FiltrationType
Class: Expression
[Filter]
Header: Filter
Class: Link
Relation: Object[Container] | Model[Container] | Object[Sample] | Model[Sample] | Object[Item] | Model[Item]
[FilterMaterial]
Header: FilterMaterial
Class: Expression
[FilterPoreSize]
Header: FilterPoreSize
Class: Real
Unit: 1 micrometer
[FilterContainerOut]
Header: FilterContainerOut
Class: Expression
[FilterInstrument]
Header: FilterInstrument
Class: Link
Relation: Model[Instrument, FilterBlock] | Object[Instrument, FilterBlock] | Model[Instrument, PeristalticPump] | Object[Instrument, PeristalticPump] | Model[Instrument, VacuumPump] | Object[Instrument, VacuumPump] | Model[Instrument, Centrifuge] | Object[Instrument, Centrifuge] | Model[Instrument, SyringePump] | Object[Instrument, SyringePump]
[FilterSyringe]
Header: FilterSyringe
Class: Link
[FilterHousing]
Header: FilterHousing
Class: Link
[FilterIntensity]
Header: FilterIntensity
Class: VariableUnit
[FilterTime]
Header: FilterTime
Class: Real
Unit: 1 minute
[FilterTemperature]
Header: FilterTemperature
Class: Real
Unit: 1 degree Celsius
[FilterSterile]
Header: FilterSterile
Class: Boolean
[FilterAliquotContainer]
Header: FilterAliquotContainer
Class: Expression
[FilterAliquot]
Header: FilterAliquot
Class: Real
Unit: 1 liter
[PrefilterMaterial]
Header: PrefilterMaterial
Class: Expression
[PrefilterPoreSize]
Header: PrefilterPoreSize
Class: Real
Unit: 1 micrometer
[FilterAliquotDestinationWell]
Header: FilterAliquotDestinationWell
Class: Expression
SamplePreparationProtocols
Protocols used to mix, centrifuge, incubate, and filter the SamplesIn prior to starting the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
PooledIncubateSample Preparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be incubated after aliquoting but prior to the start of the experiment.
Format: Multiple
[Incubate]
Header: Incubate
Class: Boolean
[IncubationTemperature]
Header: IncubationTemperature
Class: Real
Unit: 1 degree Celsius
[IncubationTime]
Header: IncubationTime
Class: Real
Unit: 1 second
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[MixUntilDissolved]
Header: MixUntilDissolved
Class: Boolean
[MaxIncubationTime]
Header: MaxIncubationTime
Class: Real
Unit: 1 second
[IncubationInstrument]
Header: IncubationInstrument
Class: Link
[AnnealingTime]
Header: AnnealingTime
Class: Real
Unit: 1 second
[IncubateAliquotContainer]
Header: IncubateAliquotContainer
Class: Expression
[IncubateAliquot]
Header: IncubateAliquot
Class: Real
Unit: 1 liter
[IncubateAliquotDestinationWell]
Header: IncubateAliquotDestinationWell
Class: Expression
NestedIndexMatchingIncubate SamplePreparation
For each member of NestedIndexMatchingSamplesIn, parameters describing how the pooled samples should be incubated after aliquoting but prior to the start of the experiment.
Format: Multiple
[Incubate]
Header: Incubate
Class: Boolean
[IncubationTemperature]
Header: IncubationTemperature
Class: Real
Unit: 1 degree Celsius
[IncubationTime]
Header: IncubationTime
Class: Real
Unit: 1 second
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[MixUntilDissolved]
Header: MixUntilDissolved
Class: Boolean
[MaxIncubationTime]
Header: MaxIncubationTime
Class: Real
Unit: 1 second
[IncubationInstrument]
Header: IncubationInstrument
Class: Link
[AnnealingTime]
Header: AnnealingTime
Class: Real
Unit: 1 second
[IncubateAliquotContainer]
Header: IncubateAliquotContainer
Class: Expression
[IncubateAliquot]
Header: IncubateAliquot
Class: Real
Unit: 1 liter
[IncubateAliquotDestinationWell]
Header: IncubateAliquotDestinationWell
Class: Expression
PooledCentrifugeSample Preparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be centrifuge after aliquoting and pooled mixing but prior to the start of the experiment.
Format: Multiple
[Centrifuge]
Header: Centrifuge
Class: Boolean
[CentrifugeInstrument]
Header: CentrifugeInstrument
Class: Link
[CentrifugeIntensity]
Header: CentrifugeIntensity
Class: VariableUnit
[CentrifugeTime]
Header: CentrifugeTime
Class: Real
Unit: 1 minute
[CentrifugeTemperature]
Header: CentrifugeTemperature
Class: Real
Unit: 1 degree Celsius
[CentrifugeAliquotContainer]
Header: CentrifugeAliquotContainer
Class: Expression
[CentrifugeAliquot]
Header: CentrifugeAliquot
Class: Real
Unit: 1 liter
[CentrifugeAliquotDestinationWell]
Header: CentrifugeAliquotDestinationWell
Class: Expression
NestedIndexMatchingCentrifuge SamplePreparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be centrifuge after aliquoting and pooled mixing but prior to the start of the experiment.
Format: Multiple
[Centrifuge]
Header: Centrifuge
Class: Boolean
[CentrifugeInstrument]
Header: CentrifugeInstrument
Class: Link
[CentrifugeIntensity]
Header: CentrifugeIntensity
Class: VariableUnit
[CentrifugeTime]
Header: CentrifugeTime
Class: Real
Unit: 1 minute
[CentrifugeTemperature]
Header: CentrifugeTemperature
Class: Real
Unit: 1 degree Celsius
[CentrifugeAliquotContainer]
Header: CentrifugeAliquotContainer
Class: Expression
[CentrifugeAliquot]
Header: CentrifugeAliquot
Class: Real
Unit: 1 liter
[CentrifugeAliquotDestinationWell]
Header: CentrifugeAliquotDestinationWell
Class: Expression
FilteredSamples
Samples corresponding to filtered eluents of SamplesIn generated during sample preparation and intended for use in this experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Sample]
MALDIPlate
The plate containing the spots of sample and calibrant embedded in laser energy absorbing matrix for matrix-assisted laser desorption/ionization (MALDI) analysis.
Format: Single
Class: Link
Programmatic Pattern: _Link
Calibrants
For each member of SamplesIn, a sample with known m/z (mass-to-charge ratios) used to calibrate the mass spectrometer.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Matrices
For each member of SamplesIn, the matrix co-spotted with the sample to assist in ionization.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
CalibrantMatrices
For each member of SamplesIn, the calibrant matrix co-spotted with the calibrant to assist in ionization.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
SpottingMethods
For each member of SamplesIn, the layering technique used to spot the MALDI plate with sample and matrix.
Format: Multiple
Class: Expression
Programmatic Pattern: SpottingMethodP
SpottingPattern
Indicates if all wells can be spotted (All) or if every other well is spotted (Spaced) to avoid contamination.
Format: Single
Class: Expression
Programmatic Pattern: SpottingPatternP
SpottingInstrument
The liquid handler used to spot the MALDI plate.
Format: Single
Class: Link
Programmatic Pattern: _Link
MixProtocols
The mix protocols used to mix the source samples prior to use in the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
SpottingDryTime
The amount of time the samples are left to dry after they have been aliquoted onto the MALDI plate.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
SampleVolumes
For each member of SamplesIn, the volume taken from the sample and aliquoted onto the MALDI plate (in MALDI mass spectrometry) or injected into the mass spectrometer (in ESI mass spectrometry).
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Microliter]
MALDIPlatePrep
A sample manipulation protocol used to transfer samples, matrices and calibrants onto the MALDI plate.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
PlateSeal
The package of pierceable, adhesive film used to cover plates of injection samples in this experiment in order to mitigate sample evaporation.
Format: Single
Class: Link
Programmatic Pattern: _Link
SampleTemperature
The nominal temperature of the autosampler where the input samples are incubated prior to injection into the mass spectrometer.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Kelvin]
Aliquoting
AliquotSamplePreparation
For each member of AliquotSamples, parameters describing how aliquots should be drawn from the input samples after initial sample preparation in order to create new aliquot samples upon which aliquot preparation and the experiment should proceed.
Format: Multiple
[Aliquot]
Header: Aliquot
Class: Boolean
[AliquotAmount]
Header: AliquotAmount
Class: Expression
[TargetConcentration]
Header: TargetConcentration
Class: Expression
[AssayVolume]
Header: AssayVolume
Class: Real
Unit: 1 milliliter
[AliquotContainer]
Header: AliquotContainer
Class: Expression
[AssayBuffer]
Header: AssayBuffer
Class: Link
[BufferDiluent]
Header: BufferDiluent
Class: Link
[BufferDilutionFactor]
Header: BufferDilutionFactor
Class: Real
[ConcentratedBuffer]
Header: ConcentratedBuffer
Class: Link
[DestinationWell]
Header: DestinationWell
Class: Expression
[TargetConcentrationAnalyte]
Header: TargetConcentrationAnalyte
Class: Expression
[AliquotSampleLabel]
Header: AliquotSampleLabel
Class: String
AliquotProtocols
Protocols used to create AliquotSamples prior to starting the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol]
AliquotPreparationProtocols
Protocols used to mix, centrifuge, incubate, and filter the AliquotSamples prior to starting the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol]
AliquotSamples
Samples corresponding to aliquots of SamplesIn generated during sample preparation and intended for use in this experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Sample]
AliquotContainers
Containers that hold AliquotSamples generated during sample preparation and intended for use in this experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
SaveAliquots
Indicates if the AliquotSamples should be stored after the experiment, rather than being discarded.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
ConsolidateAliquots
Indicates if identical aliquots should be consolidated in a single sample.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
AliquotPreparation
Indicates if the aliquotting should occur manually or on a robotic liquid handler.
Format: Single
Class: Expression
Programmatic Pattern: PreparationMethodP
AliquotVolumes
For each member of SamplesIn, the volume transferred from the sample into the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
AliquotMasses
For each member of SamplesIn, the mass of a solid transferred from the sample into the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Real
Unit: 1 milligram
Programmatic Pattern: GreaterP[0 Milligram]
AliquotAmounts
For each member of SamplesIn, the amount transferred from the sample into the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: VariableUnit
Programmatic Pattern: GreaterP[0 Milliliter] | GreaterP[0 Milligram] | GreaterP[0 Unit, 1 Unit]
TargetConcentrations
For each member of SamplesIn, the final concentration of analyte in the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: Milligram
Hold[GreaterP[0 Micro Molar] | GreaterP[0 ----------]]
Milliliter
AssayVolumes
For each member of SamplesIn (or PooledSamplesIn), the total volume of the reaction mixture which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Micro Liter]
AssayBuffers
For each member of SamplesIn (or PooledSamplesIn), the final buffers used to generate AliquotSamples by aliquoting SamplesIn.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ConcentratedBuffers
For each member of SamplesIn (or PooledSamplesIn), the concentrated buffer source which is added to the AliquotSamples to obtain 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
BufferDilutionFactors
For each member of SamplesIn (or PooledSamplesIn), he dilution factor by which the concentrated buffer is diluted in preparing the AliquotSamples to obtain a 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Multiple
Class: Real
Programmatic Pattern: GreaterP[0]
BufferDiluents
For each member of SamplesIn (or PooledSamplesIn), the diluent used to dilute the concentration of the concentrated buffer in preparing the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ConcentratedBuffer
The concentrated buffer source which is added to each of the AliquotSamples to obtain 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
BufferDilutionFactor
The dilution factor by which the concentrated buffer is diluted in preparing the AliquotSamples to obtain a 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0]
BufferDiluent
The diluent used to dilute the concentration of the concentrated buffer in preparing the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
AssayBuffer
The desired buffer for the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Sample Post-Processing
PostProcessingProtocols
Protocols used to perform post-processing such as sample imaging or volume measurement.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol]
ImageSample
Indicates if the samples that are modified in the course of the experiment are imaged after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
MeasureVolume
Indicates if the volume of the liquid samples modified in the course of the experiment are measured after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
MeasureWeight
Indicates if the weight of the solid samples modified in the course of the experiment are measured after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
Measure
Indicates if the volume/weight of the samples modified in the course of the experiment are measured after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
Storage
Indicates the conditions under which any samples generated by this experiment are stored after the protocol is completed.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
Experimental Results
Data
Any primary data generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
SamplesOut
Any preparative samples generated by the protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ContainersOut
Any containers holding SamplesOut generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
EnvironmentalData
Measurements of environmental conditions (temperature and humidity) recorded during the execution of this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
RawDataFiles
The raw data (in .raw Waters format) pertaining to the mass spectrometry measurement of all SamplesIn zipped into one directory.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[EmeraldCloudFile]
CalibrantData
Mass spectra of calibrants used in this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
MatrixData
Mass spectra for matrices used in this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
Troubleshooting
TroubleshootingReports
Reports for errors that require troubleshooting associated with the execution of this top-level protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Resources
AwaitingResources
Indicates if this protocol is awaiting the arrival of items before it can be begun or continued.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
ShippingMaterials
Indicates the transactions, and the specific products or samples therein, that must be received before this protocol can be begun or continued.
Format: Multiple
[[1]] Transaction
Header: Transaction
Class: Link
Programmatic Pattern: _Link
[[2]] Required Product
Header: Required Product
Class: Link
Programmatic Pattern: _Link
HazardousWaste
The types of waste generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
DispenserContainers
Containers gathered as destinations for any resources obtained from a chemical dispenser.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
GasSources
A list of containers that supplied gas to instruments in this protocol through plumbing connections.
Format: Multiple
[[1]] Gas Type
Header: Gas Type
Class: Expression
Programmatic Pattern: GasP
[[2]] Source Container
Header: Source Container
Class: Link
Programmatic Pattern: _Link
Relation: Object[Container]
[[3]] Supplied Instrument
Header: Supplied Instrument
Class: Link
Programmatic Pattern: _Link
Relation: Object[Instrument]
Cleaning
WasteGenerated
For each type of waste generated by this protocol, the total amount (in grams) generated during the conduct of the protocol.
Format: Multiple
[Waste]
Header: Waste
Class: Link
Relation: Model[Sample]
[Weight]
Header: Weight
Class: Real
Unit: 1 gram
NeedleWashSolution
The solution used to wash the exterior of the injection needle before, during, and after the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
TubingRinseSolution
The solution used to rinse buffers lines before and after and the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Storage Information
StoragePrice
The total monthly price for warehousing all user owned items associated with this protocol in an ECL facility under the storage conditions specified by each item.
Format: Single
Class: Real
Unit: 1 US dollar per month
Programmatic Pattern: USD
Hold[GreaterEqualP[0 -----]]
Month
Sample Storage
SamplesInStorage
For each member of SamplesIn, The storage conditions under which any input samples to this experiment should be stored after their usage in this experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
AliquotStorage
For each member of AliquotSamples, The storage conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
SamplesOutStorage
For each member of SamplesOut, the storage conditions under which any output samples generated by this experiment should be stored after the protocol is completed.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
CalibrantStorage
For each member of Calibrants, The storage conditions under which any input samples to this experiment should be stored after their usage in this experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
Option Handling
ResolvedOptions
The final options used as parameters for this protocol, after automatic options are resolved.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
UnresolvedOptions
The verbatim options originally input by the protocol author to generate this protocol, often with some options set to Automatic.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
Computations
ParallelComputations
List of computational jobs generated and run in parallel to the execution of this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ComputationsOutstanding
Indicates if any of the computation jobs in ParallelComputations have not yet completed.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
ErroneousComputations
List of computational jobs generated and run in parallel to the execution of this protocol in which a warning or error was thown, or that did not finish.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Ionization
SourceTemperatures
For each member of SamplesIn, the temperature that the source block is set to in order to discourage condensation and decrease solvent clustering in the reduced vacuum region of the source.
The source block is the metallic chamber with reduced pressure separating the sprayer (at atmospheric pressure) and the inside of the mass spectrometer (at 10^-7 Torr of pressure). It consists of the sampling cone, the isolation valve, and the ion block. The source temperature setting affects sensitivity and is adjusted according to InfusionFlowRates (the higher the flow rate, the higher the temperature).
Format: Multiple
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterP[0 Celsius]
DesolvationTemperatures
For each member of SamplesIn, the temperature setting for the ESI (electrospray ionization) desolvation heater that controls the nitrogen gas temperature used for solvent cluster evaporation, in order to produce single gas phase ions from the ion spray. This temperature setting affects sensitivity and is usually adjusted according to InfusionFlowRates (the higher the flow rate, the higher the temperature). Please refer to the documentation for details.
Format: Multiple
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterP[0 Celsius]
ESICapillaryVoltages
For each member of SamplesIn, the absolute voltage applied to the tip of the stainless steel ESI (electrospray ionization) capillary tubing in order to produce charged droplets.
Format: Multiple
Class: Real
Unit: 1 volt
Programmatic Pattern: UnitsP[0 Volt]
DesolvationGasFlows
For each member of SamplesIn, the nitrogen gas flow ejected around the ESI (electrospray ionization) capillary, used for solvent evaporation to produce single gas phase ions from the ion spray. This setting affects sensitivity and is usually adjusted according to InfusionFlowRates (the higher the flow rate, the higher the desolvation gas flow). Please refer to the documentation for details.
Format: Multiple
Class: VariableUnit
Programmatic Pattern: 1 Liter
Hold[GreaterP[-------] | GreaterP[0 PSI]]
Hour
ConeGasFlows
For each member of SamplesIn, the nitrogen gas flow ejected around the sample inlet cone (the spherical metal plate on the source block, acting as a first gate between the sprayer and the reduced-pressure ion block). This gas flow is used to minimize the formation of solvent ion clusters. It also helps reduce adduct ions and directing the spray into the ion block while keeping the sample cone clean.
Format: Multiple
Class: VariableUnit
Programmatic Pattern: 1 Liter
Hold[GreaterP[-------] | GreaterP[0 PSI]]
Hour
StepwaveVoltages
For each member of SamplesIn, the absolute voltage applied to the tip of the stainless steel ESI (electrospray ionization) capillary tubing in order to produce charged droplets.
Format: Multiple
Class: Real
Unit: 1 volt
Programmatic Pattern: GreaterP[0 Volt]
IonGuideVoltages
For each member of SamplesIn, the absolute voltage applied to the tip of the stainless steel ESI (electrospray ionization) capillary tubing in order to produce charged droplets. This option is diagrammed as IonSprayVoltage for ESI-QQQ.
Format: Multiple
Class: Real
Unit: 1 volt
Programmatic Pattern: UnitsP[0 Volt]
DeclusteringVoltages
For each member of SamplesIn, the voltage offset between the 1st and 2nd stage of the stepwave ion guide which leads ions coming from the sample cone (the metal shield covering the front of the source block), towards the quadrupole mass analyzer. For ESI-QTOF this was also known as SourceVoltageOffsets. This option also know as Sampling Cone Voltages and Declustering Potential (DP).
Format: Multiple
Class: Real
Unit: 1 volt
Programmatic Pattern: UnitsP[0 Volt]
MinLaserPowers
For each member of SamplesIn, the minimum laser power used to collect mass spectrometry data for the sample.
Format: Multiple
Class: Real
Unit: 1 percent
Programmatic Pattern: RangeP[0 Percent, 100 Percent]
MaxLaserPowers
For each member of SamplesIn, the maximum laser power used to collect mass spectrometry data for the sample.
Format: Multiple
Class: Real
Unit: 1 percent
Programmatic Pattern: RangeP[0 Percent, 100 Percent]
ShotsPerRaster
The number of repeated shots between each raster movement within a well.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
NumberOfShots
The number of times the mass spectrometer fires the laser to collect this mass spectrometry data.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
DelayTimes
For each member of SamplesIn, the delay between laser ablation and ion extraction accepted by the instrument.
Format: Multiple
Class: Real
Unit: 1 nanosecond
Programmatic Pattern: GreaterEqualP[0 Second]
Gains
For each member of SamplesIn, the signal amplification factor applied to the detector.
Format: Multiple
Class: Real
Programmatic Pattern: RangeP[1, 10]
LaserFrequency
The rate at which the mass spectrometer fires the laser onto the sample spots on the MALDI plate to create gas phase ions for mass analysis.
Format: Single
Class: Real
Unit: 1 hertz
Programmatic Pattern: GreaterP[0 Hertz]
Mass Analysis
MinMasses
For each member of SamplesIn, the lowest value of the range of measured mass-to-charge ratio (m/z).
Format: Multiple
Class: Real
Unit: 1 gram per mole
Programmatic Pattern: 0 Gram
Hold[GreaterEqualP[------]]
Mole
MaxMasses
For each member of SamplesIn, the highest value of the range of measured mass-to-charge ratio (m/z).
Format: Multiple
Class: Real
Unit: 1 gram per mole
Programmatic Pattern: 0 Gram
Hold[GreaterP[------]]
Mole
AcquisitionTime
Length of time during which samples are being injected and their m/z signal is sampled and digitized.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterP[0 Second]
InfusionSyringes
For each member of SamplesIn, the syringe used in ESI-QQQ instrument for direct infusion the sample via syringe pump.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
InfusionSyringeInnerDiameters
For each member of SamplesIn, the inner diameter of the syringes that are supposed to be used on syringe pump.
Format: Multiple
Class: Real
Unit: 1 millimeter
Programmatic Pattern: GreaterP[0 Millimeter]
InfusionSyringeNeedles
For each member of SamplesIn, the needle used by the syringe in the DirectInfusion process used in ESI-QQQ instrument via syringe pump.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
InfusionSyringeTubing
The tubing we used to connect the syringe from the syring pump to the mass spectrometer.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Alternatives[Object[Plumbing, Tubing]]
InfusionFlowRates
For each member of SamplesIn, the speed at which the sample is being injected into the mass spectrometer.
Format: Multiple
Class: Real
Unit: 1 microliter per minute
Programmatic Pattern: Microliter
Hold[GreaterP[0 ----------]]
Minute
InfusionVolumes
For each member of SamplesIn, the volume of sample being injected into the mass spectrometer by using syringe pumps, this is a unique field of ESI-QQQ.
Format: Multiple
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterP[0 Milliliter]
ScanTimes
For each member of SamplesIn, the duration of time allowed to pass between each spectral acquisition.
Format: Multiple
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterP[0 Second]
RunDurations
For each member of SamplesIn, the duration of time for which spectra are acquired for the sample currently being injected.
Format: Multiple
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterP[0 Minute]
AccelerationVoltages
For each member of SamplesIn, the voltage applied to the target plate to accelerate the ions.
Format: Multiple
Class: Real
Unit: 1 kilovolt
Programmatic Pattern: GreaterEqualP[0 Volt]
GridVoltages
For each member of SamplesIn, the voltage applied to the grid electrode.
Format: Multiple
Class: Real
Unit: 1 kilovolt
Programmatic Pattern: GreaterEqualP[0 Volt]
LensVoltages
For each member of SamplesIn, the voltage applied to the ion focusing lens located at the entrance of the mass analyser.
Format: Multiple
Class: Real
Unit: 1 kilovolt
Programmatic Pattern: GreaterEqualP[0 Volt]
CalibrationMethods
For each member of SamplesIn, the calibration settings used to calibrate the instrument.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Method]
CalibrantVolumes
The volumes taken from calibrants and aliquoted onto the MALDI plate.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Microliter]
MassSelections
For each member of SamplesIn, if the sample will be scan in tandem mass mode, this option represents the selected mass-to-charge ratio (m/z) value of the first mass analyzer in mass selection mode (MS1, Quadrupole for both ESI-QQQ).
Format: Multiple
Class: Expression
Programmatic Pattern: 0 Gram 0 Gram
Hold[{({GreaterP[------]..} | GreaterP[------] | Null)..}]
Mole Mole
FragmentMassSelections
For each member of SamplesIn, if the sample will be scan in tandem mass mode, this option represents the selected mass-to-charge ratio (m/z) value of the first mass analyzer in mass selection mode (MS2, unique option for the 2nd Quadrupole of ESI-QQQ).
Format: Multiple
Class: Expression
Programmatic Pattern: 0 Gram 0 Gram
Hold[{({GreaterP[------]..} | GreaterP[------] | Null)..}]
Mole Mole
CollisionEnergies
For each member of SamplesIn, if the sample will be scanned in tandem mass spectrometry mode, the value of the potential applied on collision cell to fragment the sample ions after passing MS1.
Format: Multiple
Class: Expression
Programmatic Pattern: {({UnitsP[0 Volt]..} | UnitsP[0 Volt] | Null)..}
FragmentMinMasses
For each member of SamplesIn, if the sample will be scanned in tandem mass spectrometry mode, the lowest value of the range of measured mass-to-charge ratio (m/z)for the second mass analyzer (MS2, Qudrapole analyzer for QQQ and TimeOfFlight analyzer for QTOF).
Format: Multiple
Class: Real
Unit: 1 gram per mole
Programmatic Pattern: 0 Gram
Hold[GreaterP[------]]
Mole
FragmentMaxMasses
For each member of SamplesIn, if the sample will be scanned in tandem mass spectrometry mode, the highest value of the range of measured mass-to-charge ratio (m/z) for the second mass analyzer (MS2,Quadrapole analyzer for QQQ and Time-Of-Flight analyzer for QTOF).
Format: Multiple
Class: Real
Unit: 1 gram per mole
Programmatic Pattern: 0 Gram
Hold[GreaterP[------]]
Mole
MassTolerances
For each member of SamplesIn, if the sample will be scanned in tandem mass spectrometry mode, the value for the mass tolerance in MS1 and MS2 in mass scan mode, indicating the step size of both MS1 and MS2 when both or either one of them are set in mass selection mode. This value indicate the mass range used to find a peak with twice the entered range.
Format: Multiple
Class: Real
Unit: 1 gram per mole
Programmatic Pattern: 0 Gram
Hold[GreaterP[------]]
Mole
CollisionCellExitVoltages
For each member of SamplesIn, if the sample will be scanned in tandem mass spectrometry mode in ESI-QQQ, the value of the potential applied between collision cell and the second Quadrupole mass analyzer (MS2) to guide and focus the ion beam into MS2.
Format: Multiple
Class: Real
Unit: 1 volt
Programmatic Pattern: UnitsP[0 Volt]
DwellTimes
For each member of SamplesIn, if the sample will be scan in SelectedIonMonitoring mode or MultipleReactionMonitoring mode, the length of time for each mass selection or mass selection pairs.
Format: Multiple
Class: Expression
Programmatic Pattern: {({GreaterP[0 Millisecond]..} | GreaterP[0 Millisecond] | Null)..}
MultipleReactionMonitoring Assays
For each member of SamplesIn, in ESI-QQQ, that firstly targets the ion corresponding to the compound of interest with subsequent fragmentation of that target ion to produce a range of daughter ions. One (or more) of these fragment daughter ions can be selected for quantitation purposes. Only compounds that meet both these criteria, i.e. specific parent ion and specific daughter ions corresponding to the mass of the molecule of interest are detected within the mass spectrometer. The mass assays (MS1/MS2 mass value combinations) for each scan, along with the CollisionEnergy and dwell time (length of time of each scan).
Format: Multiple
[MS1Mass]
Header: MS1Mass
Class: Expression
[CollisionEnergy]
Header: CollisionEnergy
Class: Expression
[MS2Mass]
Header: MS2Mass
Class: Expression
[DwellTime]
Header: DwellTime
Class: Expression
NeutralLosses
For each member of SamplesIn, if the sample will be scanned in tandem mass spectrometry mode with Neutral Ion Loss mode, the value for the mass offset values between MS1 and MS2 (neutral ion loss value.).
Format: Multiple
Class: Real
Unit: 1 gram per mole
Programmatic Pattern: 0 Gram
Hold[GreaterP[------]]
Mole
Plate Cleaning
Sonicator
The sonicator used to clean the MALDI plate.
Format: Single
Class: Link
Programmatic Pattern: _Link
PrimaryPlateCleaningSolvent
The initial solution used to clean the MALDI plate after the experimental run has completed.
Format: Single
Class: Link
Programmatic Pattern: _Link
SecondaryPlateCleaningSolvent
The secondary solution used to remove any remaining material on the MALDI plate after the experimental run has completed.
Format: Single
Class: Link
Programmatic Pattern: _Link
Last modified on Mon 26 Sep 2022 15:43:50