ECL`

ExperimentDegas

generates a Protocol which can use a variety of different techniques (freeze-pump-thaw, sparging, or vacuum degassing) to remove dissolved gases from liquid Samples.

Degassing is the removal of dissolved gases from liquids and is a useful preparatory step for solvents in many applications, such as in reactions that may be air-sensitive, or in experiments where the formation of air bubbles can cause issues for fluidic systems or can interfere with instrument measurements. There are a few ways degassing can be performed, most of which are based around Henry’s law, which states that at a given temperature, the amount of dissolved gas in a liquid is directly proportional to the partial pressure of the gas above the liquid. One of the most effective methods of degassing is freeze-pump-thaw cycling, which is used primarily for low volume samples. Freeze-pump-thaw cycling involves flash-freezing the liquid in a Schlenk flask, applying a vacuum and evacuating the headspace, then thawing the liquid to allow bubbles of gas to form and escape into the headspace; this process is repeated 2-3 times minimum. Another method of degassing is via sonication/vacuum draw, where the liquid is sonicated under light vacuum over a few cycles, with the headspace refilled with an inert gas each time. A third method of degassing is by sparging, which involves bubbling a chemically inert gas through the liquid for an extended period of time. This increases the area of the gas-liquid interface and allows other dissolved gases to diffuse into the sparging gas before escaping from the liquid. Sparging is the least effective of these methods but is useful for when large amounts of solvent need to be degassed.

Experimental Principles

Figure 1.1: Degassing via Vacuum Degassing. Step 1: The sample is attached to a Schlenk line. Step 2: The low vacuum is turned on to the specified vacuum pressure. Bubbles should appear in the liquid, indicating that degassing is occurring. As per Henry\[CloseCurlyQuote]s law, the amount of dissolved gas in the liquid will decrease as the partial pressure of the gas above the liquid is decreased; as the dissolved gas enters the headspace, it is evacuated by the vacuum. Step 3: As an optional step, the sample is sonicated while the vacuum is turned on. The additional agitation helps increase the surface area of the gas-liquid interface and promotes more dissolved gas to enter the headspace. Step 4: The vacuum is closed once degassing is completed. Step 5: As an optional step, the headspace gas is replaced with an inert gas.

Figure 1.2: Degassing via Freeze-Pump-Thaw. Step 1: The sample is attached to a Schlenk line. The sample may occupy no more than 50% of the volume of the container. Step 2: The sample is flash frozen in a dewar filled with liquid nitrogen. Step 3: The headspace above the frozen sample is evacuated by opening the Schlenk line towards the vacuum and turning on the vacuum pump. Step 4: The sample container is transferred to a heat block, and the sample allowed to thaw completely. As the liquid thaws, bubbles of gas will form and escape into the evacuated headspace. Step 5: The process of freezing, pumping vacuum, and thawing is repeated a suggested minimum of 3 cycles, until no more bubbles are released during the thawing stage. Step 6: As an optional step, the headspace gas is replaced with an inert gas.

Figure 1.3: Degassing via Sparging. Step 1: The sample is attached to a Schlenk line. Step 2: The overhead stirrer is turned on to ensure sample mixing. Step 3: The inert gas source is turned on, allowing gas to flow from the sparging frit through the sample. Bubbles should appear in the sample and should be distributed by the stirrer. Sparging allows for the displacement of dissolved gases with the inert gas and can be left on for a prolonged time period to ensure full degassing.

Instrumentation

High Tech Schlenk Line

Figure 2.1.1: A Schlenk line consisting of a dual vacuum/inert gas manifold is common throughout the degassing apparatuses. The dual vacuum/inert gas manifold allows both the inert gas source and the vacuum pump to be connected to the sample through the same connection. The inert gases that can be used on the Schlenk line are nitrogen, argon, and helium, which can be fine tuned through a pressure regulator that controls the input pressure of the gas into the manifold, and a flow regulator that controls the low rate of gas leading into the sample. Two levels of vacuum are supported on the Schlenk line, high and low. The vacuum pressure of the low vacuum pump can be further specified, while the overall vacuum level on the manifold from both the high/low vacuum is read by a vacuum gauge. A condenser ensures that the vacuum pumps remains clean of potential contaminants. Up to four samples can be simultaneously connected to the Schlenk line. For the sonication/vacuum draw instrument apparatus, the sample is placed in a sonicator and attached via the Schlenk line to a low vacuum. For the freeze-pump-thaw instrument apparatus, a liquid nitrogen dewar and a heat block are prepared in addition to the Schlenk line, which is open to the high vacuum. The dewar contains liquid nitrogen filled above the liquid level of the sample to allow for proper flash freezing. The heat block contains dry, thermal metal beads and is used for thawing the frozen sample. For the sparging instrument apparatus, a sparging frit with a porous metal sparger on the end is used to bubble the gas through the liquid, while an overhead impeller is used to stir and mix the sample.

Experiment Options

General

DegasType

Indicates which degassing type (freeze-pump-thaw, sparging, or vacuum degassing) should be used. Freeze-pump-thaw involves freezing the liquid, applying a vacuum to evacuate the headspace above the liquid, and then thawing the liquid to allow the decreased pressure of the headspace to lower the solubility of dissolved gases; this is usually repeated a few times to ensure thorough degassing. Sparging involves bubbling a chemically inert gas through the liquid for an extended period of time to aid in removal of dissolved gases. Vacuum degassing involves lowering the pressure of the headspace above the liquid to decrease solubility of the dissolved gases, while continually removing any bubbled out dissolved gases from the headspace.

Default Value: Automatic

Default Calculation: If no options are provided, the sample volume will be used to determine the degassing type. Volumes under 50ml will default to freeze-pump-thaw, volumes between 50ml and 1L will default to vacuum degassing, while volumes above 1L will default to sparging.

Pattern Description: FreezePumpThaw, Sparging, or VacuumDegas.

Programmatic Pattern: DegasTypeP | Automatic

Index Matches to: experiment samples

Instrument

Indicates which degassing instrument should be used.

Default Value: Automatic

Default Calculation: If no options are provided, the instrument will be selected based on the degassing type.

Pattern Description: An object of type or subtype Model[Instrument, SpargingApparatus], Model[Instrument, VacuumDegasser], Model[Instrument, FreezePumpThawApparatus], Object[Instrument, SpargingApparatus], Object[Instrument, VacuumDegasser], or Object[Instrument, FreezePumpThawApparatus]

Programmatic Pattern: ObjectP[{Model[Instrument, SpargingApparatus], Model[Instrument, VacuumDegasser], Model[Instrument, FreezePumpThawApparatus], Object[Instrument, SpargingApparatus], Object[Instrument, VacuumDegasser], Object[Instrument, FreezePumpThawApparatus]}] | Automatic

Index Matches to: experiment samples

DissolvedOxygen

Indicates whether dissolved oxygen measurements should be taken on a 25 milliliter aliquot of a sample using the dissolved oxygen meter, before and after the degassing procedure is performed. Aliquots are returned to their parent sample following measurements. The dissolved oxygen measurements can only be taken on aqueous solutions and will expose the degassed sample to air.

Default Value: False

Pattern Description: True or False.

Programmatic Pattern: BooleanP

Index Matches to: experiment samples

Freeze-Pump-Thaw

FreezeTime

The amount of time the sample will be flash frozen by submerging the container in a dewar filled with liquid nitrogen during the freeze-pump-thaw procedure. This is the first step in the freeze-pump-thaw cycle.

Default Value: Automatic

Default Calculation: If no options are provided, the freezing time will default to 3 minutes.

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 60 minutes or Null.

Programmatic Pattern: (RangeP[0*Minute, 60*Minute] | Automatic) | Null

Index Matches to: experiment samples

PumpTime

The amount of time the sample will be vacuumed during the pump step of the freeze-pump-thaw procedure. The pump step evacuates the headspace above the frozen sample in preparation for the thawing step.

Default Value: Automatic

Default Calculation: If no options are provided, the pump time will default to 2 minutes.

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 60 minutes or Null.

Programmatic Pattern: (RangeP[0*Minute, 60*Minute] | Automatic) | Null

Index Matches to: experiment samples

ThawTemperature

The temperature that the heat bath regulator will be set to for thawing the sample during the freeze-pump-thaw procedure.

Default Value: Automatic

Default Calculation: If no options are provided, automatically resolved to ambient temperature.

Pattern Description: Greater than or equal to 25 degrees Celsius and less than or equal to 40 degrees Celsius or Null.

Programmatic Pattern: (RangeP[$AmbientTemperature, 40*Celsius] | Automatic) | Null

Index Matches to: experiment samples

ThawTime

The minimum amount of time the sample will be thawed during the freeze-pump-thaw procedure. During the thaw step, the decreased headspace pressure from the pump step will decrease the solubility of dissolved gases in the thawed liquid, thereby causing dissolved gases to bubble out from the liquid as it thaws.

Default Value: Automatic

Default Calculation: If no options are provided, the sample volume will be used to determine an estimated thawing time.

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 6 hours or Null.

Programmatic Pattern: (RangeP[0*Minute, 6*Hour] | Automatic) | Null

Index Matches to: experiment samples

NumberOfCycles

The number of cycles of freezing the sample, evacuating the headspace above the sample, and then thawing the sample that will be performed as part of a single freeze-pump-thaw protocol.

Default Value: Automatic

Default Calculation: If no options are provided, will default to 3 cycles for effective degassing.

Pattern Description: Greater than or equal to 1 and less than or equal to 10 or Null.

Programmatic Pattern: (RangeP[1, 10] | Automatic) | Null

Index Matches to: experiment samples

FreezePumpThawContainer

The container that will hold the sample during Freeze Pump Thaw. No more than 50% of the volume of the container can be filled during Freeze Pump Thaw.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Container, Vessel] or Object[Container, Vessel] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Model[Container, Vessel], Object[Container, Vessel]}] | _String) | Automatic) | Null

Index Matches to: experiment samples

Vacuum Degas

VacuumPressure

The vacuum pressure that the vacuum pump regulator will be set to during the vacuum degassing procedure.

Default Value: Automatic

Default Calculation: If no options are provided, will default to house vacuum pressure (150 mbar).

Pattern Description: Greater than or equal to 1 millibar and less than or equal to 1050 millibars or Null.

Programmatic Pattern: (RangeP[1*Milli*Bar, 1050*Milli*Bar] | Automatic) | Null

Index Matches to: experiment samples

VacuumSonicate

Indicates whether or not the sample will be agitated by immersing the container in a sonicator during the vacuum degassing method.

Default Value: Automatic

Default Calculation: If no options are provided, will default to True.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

VacuumTime

The amount of time the sample will be vacuumed during the vacuum degassing method.

Default Value: Automatic

Default Calculation: If no options are provided, will default to 1 hour.

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.

Programmatic Pattern: (RangeP[0*Minute, $MaxExperimentTime] | Automatic) | Null

Index Matches to: experiment samples

VacuumUntilBubbleless

Indicates whether vacuum degassing should be performed until the sample is entirely bubbleless, during the vacuum degassing method.

Default Value: Automatic

Default Calculation: If no options are provided, will default to False.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

MaxVacuumTime

The maximum amount of time the sample will be vacuumed during the vacuum degassing procedure. This option is used when VacuumUntilBubbleless is set, and allows the user to set a maximum amount of experiment time that is allowed for the sample to reach a bubbleless state. The experiment will first vacuum degas the sample for the specified VacuumTime, then perform a check to see if the sample appears bubbleless. If not, additional vacuum time will be addded, up to a maximum of the specified MaxVacuumTime.

Default Value: Automatic

Default Calculation: If no options are provided, will default to null unless VacuumUntilBubbleless is turned on, in which case it will default to72 hours.

Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.

Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null

Index Matches to: experiment samples

Sparging

SpargingGas

Describes which inert gas (nitrogen, argon, or helium) will be used during the sparging method.

Default Value: Automatic

Default Calculation: If no options are provided, will default to nitrogen gas.

Pattern Description: Nitrogen, Helium, or Argon or Null.

Programmatic Pattern: (DegasGasP | Automatic) | Null

Index Matches to: experiment samples

SpargingTime

The amount of time the sample will be sparged during the sparging method.

Default Value: Automatic

Default Calculation: If no options are provided, will default based on the sample volume.

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.

Programmatic Pattern: (RangeP[0*Minute, $MaxExperimentTime] | Automatic) | Null

Index Matches to: experiment samples

SpargingMix

Indicates if the sample undergoing sparging will be mixed during the sparing method.

Default Value: Automatic

Default Calculation: Automatically resolved to False if DegasType is set to Sparging. Otherwise, set to Null.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

PostProcessing

HeadspaceGasFlush

Describes which inert gas will be used to replace the headspace after degassing. None indicates that no specific gas will be used and that the sample will be exposed to the atmosphere when capping. For sparging, no headspace gas flushing can be performed.

Default Value: Automatic

Pattern Description: None or {Nitrogen, Helium, Argon}

Programmatic Pattern: (None | DegasGasP) | Automatic

Index Matches to: experiment samples

HeadspaceGasFlushTime

The amount of time the sample will be flushed with the headspace gas after degassing.

Default Value: Automatic

Default Calculation: If HeadspaceGasFlush is None, will default to Null. If HeadspaceGasFlush is selected, will default based on the container volume. For sparging, no headspace gas flushing can be performed.

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.

Programmatic Pattern: (RangeP[0*Minute, $MaxExperimentTime] | Automatic) | Null

Index Matches to: experiment samples

Post Experiment

SamplesInStorageCondition

The non-default conditions under which the SamplesIn of this experiment should be stored after the protocol is completed. If left unset, SamplesIn will be stored according to their current StorageCondition.

Default Value: Null

Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.

Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null

Index Matches to: experiment samples

SamplesOutStorageCondition

The non-default conditions under which any new samples generated by this experiment should be stored after the protocol is completed. If left unset, the new samples will be stored according to their Models' DefaultStorageCondition.

Default Value: Null

Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null

Index Matches to: experiment samples

Model Input

PreparedModelAmount

Indicates the amount of a Model[Sample] specified as input to the experiment function that will be prepared in the PreparedModelContainer. When set to All and the input model sample is not preparable, the entire amount of the input model sample that comes from one of the Products is prepared. The selected product must have both Amount and DefaultContainerModel populated, and it must not be a KitProduct. When set to All and the input model is preparable such as water, 1 Milliliter of the input model sample is prepared.

Default Value: Automatic

Default Calculation: Automatically set to 1 Milliliter.

Pattern Description: All or Count or Count or Mass or Volume or Null.

Index Matches to: experiment samples

PreparedModelContainer

Indicates the container in which a Model[Sample] specified as input to the experiment function will be prepared.

Default Value: Automatic

Default Calculation: If PreparedModelAmount is set to All and the input model has a product associated with both Amount and DefaultContainerModel populated, automatically set to the DefaultContainerModel value in the product. Otherwise, automatically set to Model[Container, Vessel, "10 mL Schlenk Flask, 14/20 Outer Joint with Chem-Cap High Vacuum Valve"].

Pattern Description: An object of type or subtype Model[Container] or Null.

Programmatic Pattern: ((Null | ObjectP[Model[Container]]) | Automatic) | Null

Index Matches to: experiment samples

Sample Prep Options

Sample Preparation

PreparatoryUnitOperations

Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSamplePreparation.

Default Value: Null

Pattern Description: List of one or more unit Operation ManualSamplePreparation or RoboticSamplePreparation or unit Operation must match SamplePreparationP entries or Null.

Programmatic Pattern: {((ManualSamplePreparationMethodP | RoboticSamplePreparationMethodP) | SamplePreparationP)..} | Null

Preparatory Incubation

Incubate

Indicates if the SamplesIn should be incubated at a fixed temperature prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).

Default Value: Automatic

Default Calculation: Resolves to True if any of the corresponding Incubation options are set. Otherwise, resolves to False.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

IncubationTemperature

Temperature at which the SamplesIn should be incubated for the duration of the IncubationTime prior to starting the experiment.

Default Value: Automatic

Pattern Description: Ambient or greater than or equal to -20 degrees Celsius and less than or equal to 500 degrees Celsius or Null.

Programmatic Pattern: ((Ambient | RangeP[$MinIncubationTemperature, $MaxIncubationTemperature]) | Automatic) | Null

Index Matches to: experiment samples

IncubationTime

Duration for which SamplesIn should be incubated at the IncubationTemperature, prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.

Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null

Index Matches to: experiment samples

Mix

Indicates if this sample should be mixed while incubated, prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves to True if any Mix related options are set. Otherwise, resolves to False.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

MixType

Indicates the style of motion used to mix the sample, prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves based on the container of the sample and the Mix option.

Pattern Description: Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, or Nutate or Null.

Programmatic Pattern: (MixTypeP | Automatic) | Null

Index Matches to: experiment samples

MixUntilDissolved

Indicates if the mix should be continued up to the MaxIncubationTime or MaxNumberOfMixes (chosen according to the mix Type), in an attempt dissolve any solute. Any mixing/incubation will occur prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves to True if MaxIncubationTime or MaxNumberOfMixes is set.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

MaxIncubationTime

Maximum duration of time for which the samples will be mixed while incubated in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. This occurs prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves based on MixType, MixUntilDissolved, and the container of the given sample.

Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.

Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null

Index Matches to: experiment samples

IncubationInstrument

The instrument used to perform the Mix and/or Incubation, prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves based on the options Mix, Temperature, MixType and container of the sample.

Pattern Description: An object of type or subtype Model[Instrument, Roller], Model[Instrument, OverheadStirrer], Model[Instrument, Vortex], Model[Instrument, Shaker], Model[Instrument, BottleRoller], Model[Instrument, Roller], Model[Instrument, Sonicator], Model[Instrument, HeatBlock], Model[Instrument, Homogenizer], Model[Instrument, Disruptor], Model[Instrument, Nutator], Model[Instrument, Thermocycler], Model[Instrument, EnvironmentalChamber], Model[Instrument, Pipette], Object[Instrument, Roller], Object[Instrument, OverheadStirrer], Object[Instrument, Vortex], Object[Instrument, Shaker], Object[Instrument, BottleRoller], Object[Instrument, Roller], Object[Instrument, Sonicator], Object[Instrument, HeatBlock], Object[Instrument, Homogenizer], Object[Instrument, Disruptor], Object[Instrument, Nutator], Object[Instrument, Thermocycler], Object[Instrument, EnvironmentalChamber], or Object[Instrument, Pipette] or Null.

Programmatic Pattern: (ObjectP[Join[MixInstrumentModels, MixInstrumentObjects]] | Automatic) | Null

Index Matches to: experiment samples

AnnealingTime

Minimum duration for which the SamplesIn should remain in the incubator allowing the system to settle to room temperature after the IncubationTime has passed but prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.

Programmatic Pattern: (RangeP[0*Minute, $MaxExperimentTime] | Automatic) | Null

Index Matches to: experiment samples

IncubateAliquotContainer

The desired type of container that should be used to prepare and house the incubation samples which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.

Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null

Index Matches to: experiment samples

IncubateAliquotDestinationWell

The desired position in the corresponding IncubateAliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or Null.

Programmatic Pattern: (WellPositionP | Automatic) | Null

Index Matches to: experiment samples

IncubateAliquot

The amount of each sample that should be transferred from the SamplesIn into the IncubateAliquotContainer when performing an aliquot before incubation.

Default Value: Automatic

Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.

Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null

Index Matches to: experiment samples

Preparatory Centrifugation

Centrifuge

Indicates if the SamplesIn should be centrifuged prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).

Default Value: Automatic

Default Calculation: Resolves to True if any of the corresponding Centrifuge options are set. Otherwise, resolves to False.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

CentrifugeInstrument

The centrifuge that will be used to spin the provided samples prior to starting the experiment.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Instrument, Centrifuge] or Object[Instrument, Centrifuge] or Null.

Programmatic Pattern: (ObjectP[{Model[Instrument, Centrifuge], Object[Instrument, Centrifuge]}] | Automatic) | Null

Index Matches to: experiment samples

CentrifugeIntensity

The rotational speed or the force that will be applied to the samples by centrifugation prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.

Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null

Index Matches to: experiment samples

CentrifugeTime

The amount of time for which the SamplesIn should be centrifuged prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than 0 minutes or Null.

Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null

Index Matches to: experiment samples

CentrifugeTemperature

The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.

Default Value: Automatic

Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius or Null.

Programmatic Pattern: ((Ambient | RangeP[-10*Celsius, 40*Celsius]) | Automatic) | Null

Index Matches to: experiment samples

CentrifugeAliquotContainer

The desired type of container that should be used to prepare and house the centrifuge samples which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.

Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null

Index Matches to: experiment samples

CentrifugeAliquotDestinationWell

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or Null.

Programmatic Pattern: (WellPositionP | Automatic) | Null

Index Matches to: experiment samples

CentrifugeAliquot

The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.

Default Value: Automatic

Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.

Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null

Index Matches to: experiment samples

Preparatory Filtering

Filtration

Indicates if the SamplesIn should be filter prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).

Default Value: Automatic

Default Calculation: Resolves to True if any of the corresponding Filter options are set. Otherwise, resolves to False.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

FiltrationType

The type of filtration method that should be used to perform the filtration.

Default Value: Automatic

Default Calculation: Will automatically resolve to a filtration type appropriate for the volume of sample being filtered.

Pattern Description: PeristalticPump, Centrifuge, Vacuum, Syringe, or AirPressure or Null.

Programmatic Pattern: (FiltrationTypeP | Automatic) | Null

Index Matches to: experiment samples

FilterInstrument

The instrument that should be used to perform the filtration.

Default Value: Automatic

Default Calculation: Will automatically resolved to an instrument appropriate for the filtration type.

Pattern Description: An object of type or subtype 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], or Object[Instrument, SyringePump] or Null.

Programmatic Pattern: (ObjectP[{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]}] | Automatic) | Null

Index Matches to: experiment samples

Filter

The filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: Will automatically resolve to a filter appropriate for the filtration type and instrument.

Pattern Description: An object of type or subtype Model[Container, Plate, Filter], Model[Container, Vessel, Filter], or Model[Item, Filter] or Null.

Programmatic Pattern: (ObjectP[{Model[Container, Plate, Filter], Model[Container, Vessel, Filter], Model[Item, Filter]}] | Automatic) | Null

Index Matches to: experiment samples

FilterMaterial

The membrane material of the filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: Resolves to an appropriate filter material for the given sample is Filtration is set to True.

Pattern Description: Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, or AnoporeAlumina or Null.

Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null

Index Matches to: experiment samples

PrefilterMaterial

The material from which the prefilter filtration membrane should be made of to remove impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.

Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null

Index Matches to: experiment samples

FilterPoreSize

The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: Resolves to an appropriate filter pore size for the given sample is Filtration is set to True.

Pattern Description: 0.008 micrometers, 0.02 micrometers, 0.1 micrometers, 0.2 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.

Programmatic Pattern: (FilterSizeP | Automatic) | Null

Index Matches to: experiment samples

PrefilterPoreSize

The pore size of the filter; all particles larger than this should be removed during the filtration.

Default Value: Automatic

Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.

Programmatic Pattern: (FilterSizeP | Automatic) | Null

Index Matches to: experiment samples

FilterSyringe

The syringe used to force that sample through a filter.

Default Value: Automatic

Default Calculation: Resolves to an syringe appropriate to the volume of sample being filtered, if Filtration is set to True.

Pattern Description: An object of type or subtype Model[Container, Syringe] or Object[Container, Syringe] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Model[Container, Syringe], Object[Container, Syringe]}] | _String) | Automatic) | Null

Index Matches to: experiment samples

FilterHousing

The filter housing that should be used to hold the filter membrane when filtration is performed using a standalone filter membrane.

Default Value: Automatic

Default Calculation: Resolve to an housing capable of holding the size of the membrane being used, if filter with Membrane FilterType is being used and Filtration is set to True.

Pattern Description: An object of type or subtype Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], or Object[Instrument, FilterBlock] or Null.

Programmatic Pattern: (ObjectP[{Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], Object[Instrument, FilterBlock]}] | Automatic) | Null

Index Matches to: experiment samples

FilterIntensity

The rotational speed or force at which the samples will be centrifuged during filtration.

Default Value: Automatic

Default Calculation: Will automatically resolve to 2000 GravitationalAcceleration if FiltrationType is Centrifuge and Filtration is True.

Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.

Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null

Index Matches to: experiment samples

FilterTime

The amount of time for which the samples will be centrifuged during filtration.

Default Value: Automatic

Default Calculation: Will automatically resolve to 5 Minute if FiltrationType is Centrifuge and Filtration is True.

Pattern Description: Greater than 0 minutes or Null.

Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null

Index Matches to: experiment samples

FilterTemperature

The temperature at which the centrifuge chamber will be held while the samples are being centrifuged during filtration.

Default Value: Automatic

Default Calculation: Will automatically resolve to 22 Celsius if FiltrationType is Centrifuge and Filtration is True.

Pattern Description: Greater than or equal to 4 degrees Celsius or Null.

Programmatic Pattern: ((Alternatives[GreaterEqualP[4*Celsius]]) | Automatic) | Null

Index Matches to: experiment samples

FilterContainerOut

The desired container filtered samples should be produced in or transferred into by the end of filtration, with indices indicating grouping of samples in the same plates, if desired.

Default Value: Automatic

Default Calculation: Automatically set as the PreferredContainer for the Volume of the sample. For plates, attempts to fill all wells of a single plate with the same model before using another one.

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.

Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1] | Automatic, (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null

Index Matches to: experiment samples

FilterAliquotDestinationWell

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or Null.

Programmatic Pattern: (WellPositionP | Automatic) | Null

Index Matches to: experiment samples

FilterAliquotContainer

The desired type of container that should be used to prepare and house the filter samples which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.

Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null

Index Matches to: experiment samples

FilterAliquot

The amount of each sample that should be transferred from the SamplesIn into the FilterAliquotContainer when performing an aliquot before filtration.

Default Value: Automatic

Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.

Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null

Index Matches to: experiment samples

FilterSterile

Indicates if the filtration of the samples should be done in a sterile environment.

Default Value: Automatic

Default Calculation: Resolve to False if Filtration is indicated. If sterile filtration is desired, this option must manually be set to True.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

Aliquoting

Aliquot

Indicates if aliquots should be taken from the SamplesIn and transferred into new AliquotSamples used in lieu of the SamplesIn for the experiment. Note that if NumberOfReplicates is specified this indicates that the input samples will also be aliquoted that number of times. Note that Aliquoting (if specified) occurs after any Sample Preparation (if specified).

Default Value: Automatic

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

AliquotAmount

The amount of a sample that should be transferred from the input samples into aliquots.

Default Value: Automatic

Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container if a liquid, or the current Mass or Count if a solid or counted item, respectively.

Pattern Description: All or Count or Count or Mass or Volume or Null.

Index Matches to: experiment samples

TargetConcentration

The desired final concentration of analyte in the AliquotSamples after dilution of aliquots of SamplesIn with the ConcentratedBuffer and BufferDiluent which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

Default Calculation: Automatically calculated based on aliquot and buffer volumes.

Pattern Description: Greater than 0 molar or greater than 0 grams per liter or Null.

Programmatic Pattern: ((GreaterP[0*Molar] | GreaterP[0*(Gram/Liter)]) | Automatic) | Null

Index Matches to: experiment samples

TargetConcentrationAnalyte

The substance whose final concentration is attained with the TargetConcentration option.

Default Value: Automatic

Default Calculation: Automatically set to the first value in the Analytes field of the input sample, or, if not populated, to the first analyte in the Composition field of the input sample, or if none exist, the first identity model of any kind in the Composition field.

Pattern Description: An object of type or subtype Model[Molecule], Model[Molecule, cDNA], Model[Molecule, Oligomer], Model[Molecule, Transcript], Model[Molecule, Protein], Model[Molecule, Protein, Antibody], Model[Molecule, Carbohydrate], Model[Molecule, Polymer], Model[Resin], Model[Resin, SolidPhaseSupport], Model[Lysate], Model[ProprietaryFormulation], Model[Virus], Model[Cell], Model[Cell, Mammalian], Model[Cell, Bacteria], Model[Cell, Yeast], Model[Tissue], Model[Material], or Model[Species] or Null.

Programmatic Pattern: (ObjectP[IdentityModelTypes] | Automatic) | Null

Index Matches to: experiment samples

AssayVolume

The desired total volume of the aliquoted sample plus dilution buffer.

Default Value: Automatic

Default Calculation: Automatically determined based on Volume and TargetConcentration option values.

Pattern Description: Greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: (RangeP[1*Microliter, 20*Liter] | Automatic) | Null

Index Matches to: experiment samples

ConcentratedBuffer

The concentrated buffer which should be diluted by the BufferDilutionFactor in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

Index Matches to: experiment samples

BufferDilutionFactor

The dilution factor by which the concentrated buffer should be diluted in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentratedBufferDilutionFactor of that sample; otherwise, set to Null.

Pattern Description: Greater than or equal to 1 or Null.

Programmatic Pattern: (GreaterEqualP[1] | Automatic) | Null

Index Matches to: experiment samples

BufferDiluent

The buffer used to dilute the aliquot sample such that ConcentratedBuffer is diluted by BufferDilutionFactor in the final solution. The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is specified; otherwise, resolves to Null.

Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

Index Matches to: experiment samples

AssayBuffer

The buffer that should be added to any aliquots requiring dilution, where the volume of this buffer added is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is not specified; otherwise, resolves to Null.

Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

Index Matches to: experiment samples

AliquotSampleStorageCondition

The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.

Default Value: Automatic

Programmatic Pattern: ((SampleStorageTypeP | Disposal) | Automatic) | Null

Index Matches to: experiment samples

DestinationWell

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or list of one or more any well from A1 to H12 or any well from A1 to H12 entries or Null.

Programmatic Pattern: ((WellPositionP | {((Automatic | Null) | WellPositionP)..}) | Automatic) | Null

AliquotContainer

The desired type of container that should be used to prepare and house the aliquot samples, with indices indicating grouping of samples in the same plates, if desired. This option will resolve to be the length of the SamplesIn * NumberOfReplicates.

Default Value: Automatic

Default Calculation: Automatically set as the PreferredContainer for the AssayVolume of the sample. For plates, attempts to fill all wells of a single plate with the same model before aliquoting into the next.

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null or {Index, Container} or list of one or more an object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null entries or list of one or more Automatic or Null or {Index, Container} entries.

Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null) | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | {((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null))..} | {({GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | (Automatic | Null))..}) | Automatic) | Null

AliquotPreparation

Indicates the desired scale at which liquid handling used to generate aliquots will occur.

Default Value: Automatic

Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.

Pattern Description: Manual or Robotic or Null.

Programmatic Pattern: (PreparationMethodP | Automatic) | Null

ConsolidateAliquots

Indicates if identical aliquots should be prepared in the same container/position.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Protocol Options

Organizational Information

Template

A template protocol whose methodology should be reproduced in running this experiment. Option values will be inherited from the template protocol, but can be individually overridden by directly specifying values for those options to this Experiment function.

Default Value: Null

Pattern Description: An object of type or subtype Object[Protocol] or an object of type or subtype of Object[Protocol] with UnresolvedOptions, ResolvedOptions specified or Null.

Programmatic Pattern: (ObjectP[Object[Protocol]] | FieldReferenceP[Object[Protocol], {UnresolvedOptions, ResolvedOptions}]) | Null

Name

A object name which should be used to refer to the output object in lieu of an automatically generated ID number.

Default Value: Null

Pattern Description: A string or Null.

Programmatic Pattern: _String | Null

Post Experiment

MeasureWeight

Indicates if any solid samples that are modified in the course of the experiment should have their weights measured and updated after running the experiment. Please note that public samples are weighed regardless of the value of this option.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MeasureVolume

Indicates if any liquid samples that are modified in the course of the experiment should have their volumes measured and updated after running the experiment. Please note that public samples are volume measured regardless of the value of this option.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

Indicates if any samples that are modified in the course of the experiment should be freshly imaged after running the experiment. Please note that public samples are imaged regardless of the value of this option.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Example Calls

Degas a sample

Degas a sample:

Degas multiple samples in the same protocol:

Degas using different degassing methods

Degassing via the freeze-pump-thaw method may be specified:

Degassing via the vacuum sonication method may be specified:

Degassing via the sparging method may be specified:

The instrument for the degassing instrument may be specified:

Degas while specifying vacuum degas options

If running a vacuum degas experiment, options specific to vacuum degas may be specified:

If running a vacuum degas experiment, VacuumUntilBubbleless can be used to specify that the vacuum degassing should be run past the VacuumTime until the sample has no more visible bubbles during vacuum sonication, up to a maximum time of MaxVacuumTime:

Degas while specifying freeze pump thaw options

If running a freeze pump thaw experiment, options specific to freeze pump thaw may be specified:

Degas while specifying sparging options

If running a sparging experiment, options specific to sparging may be specified:

Post Experiment

At the conclusion of the freeze-pump-thaw and vacuum sonication degassing methods, the container headspace may be swapped with a specified inert gas:

Preferred Input Containers

For Degas experiments using freeze-pump-thaw, the experiment will automatically transfer aliquots of your samples into a Schlenk flask if they are not already in compatible Schlenk flasks.

For Degas experiments using vacuum degassing, the VacuumDegasser can only be operated on glass bottles or 50mL tubes (no carboys and no tubes less than 50mL in volume). Use the SamplePreparation option to prepare the samples if your samples are not in compatible vessels.

For Degas experiments using sparging, the VacuumDegasser can only be operated on bottles and carboys (no tubes). Use the SamplePreparation option to prepare the samples if your samples are not in compatible vessels.

Warnings and Errors

Messages (46)

DegasDissolvedOxygenError (1)

Return $Failed if the DissolvedOxygen specified is True for a non-aqueous sample:

DegasDissolvedOxygenVolumeError (1)

Return $Failed if the Sample Volume is <50 mL and DissolvedOxygen is set to True:

DegasFreezePumpThawNullMismatch (1)

If the DegasType provided is FreezePumpThaw but FreezePumpThaw-related options are Null, an error will be thrown:

DegasGeneralOptionMismatch (1)

If options specific to more than one DegasType are specified simultaneously, an error will be thrown:

DegasHeadspaceGasFlushOptions (1)

If HeadspaceGasFlushTime is set but HeadspaceGasFlush is None, an error will be thrown:

DegasHeadspaceGasFlushTimeOptions (1)

If HeadspaceGasFlushTime is Null but HeadspaceGasFlush is set, an error will be thrown:

DegasHeadspaceGasFlushTypeMismatch (1)

If the DegasType provided is not VacuumDegas or FreezePumpThaw but HeadspaceGasFlush-related options are given, an error will be thrown:

DegasInstrumentOptionMismatch (1)

If an option for a degas type is specified and options from a conflicting degas type are also specified, an error will be thrown:

DegasMaxVacuumTimeMismatch (1)

Return $Failed if the MaxVacuumTime is less than the VacuumTime:

DegasMaxVacuumUntilBubbleless (1)

If MaxVacuumTime is set but VacuumUntilBubbleless is False, an error will be thrown:

DegasNotLiquid (1)

Return $Failed if the Sample State is not liquid:

DegasNoVolume (1)

Return $Failed if Sample contains Null in the Volume field:

DegasSpargingNullMismatch (1)

If the DegasType provided is Sparging but Sparging-related options are Null, an error will be thrown:

DegasSpargingTimeLow (1)

Throw a warning if the SpargingTime is <15 minute:

DegasTypeInstrumentMismatch (1)

If the DegasType and Instrument do not agree, an error will be thrown:

DegasVacuumDegasNullMismatch (1)

If the DegasType provided is VacuumDegas but VacuumDegas-related options are Null, an error will be thrown:

DegasVacuumTimeLow (1)

Throw a warning if the VacuumTime is <15 minute:

DiscardedSamples (1)

If the provided sample is discarded, an error will be thrown:

FreezePumpThawContainerError (1)

Return $Failed if the FreezePumpThawContainer specified is not a suitable Schlenk flask or does not have a max volume of at least double the sample volume:

FreezePumpThawInstrument (1)

If the degas type is specified as freeze pump thaw and options from a conflicting degas instrument type are also specified, an error will be thrown:

FreezePumpThawOnlyMismatch (1)

If the DegasType provided is not FreezePumpThaw but FreezePumpThaw-specific options are given, an error will be thrown:

FreezePumpThawVolumeError (1)

Return $Failed if the Sample Volume is >50 mL and the DegasType is FreezePumpThaw:

HeadspaceGasFlushSpargingError (1)

If the DegasType resolved is not VacuumDegas or FreezePumpThaw but HeadspaceGasFlush-related options are given, an error will be thrown:

InstrumentPrecision (9)

If a FreezeTime with a greater precision than 1 Second is given, it is rounded:

If a HeadspaceGasFlushTime with a greater precision than 1 Second is given, it is rounded:

If a MaxVacuumTime with a greater precision than 1 Second is given, it is rounded:

If a PumpTime with a greater precision than 1 Second is given, it is rounded:

If a SpargingTime with a greater precision than 1 Second is given, it is rounded:

If a ThawTemperature with a greater precision than 1 Celsius is given, it is rounded:

If a ThawTime with a greater precision than 1 Second is given, it is rounded:

If a VacuumPressure with a greater precision than 1 Milli*Bar is given, it is rounded:

If a VacuumTime with a greater precision than 1 Second is given, it is rounded:

ObjectDoesNotExist (6)

Do NOT throw a message if we have a simulated container but a simulation is specified that indicates that it is simulated:

Do NOT throw a message if we have a simulated sample but a simulation is specified that indicates that it is simulated:

Throw a message if we have a container that does not exist (ID form):

Throw a message if we have a container that does not exist (name form):

Throw a message if we have a sample that does not exist (ID form):

Throw a message if we have a sample that does not exist (name form):

SpargingInstrument (1)

If the degas type is specified as sparging and options from a conflicting degas instrument type are also specified, an error will be thrown:

SpargingOnlyMismatch (1)

If the DegasType provided is not Sparging but Sparging-specific options are given, an error will be thrown:

SpargingVolumeContainerLow (1)

For sparging, if the volume of the sample is less than half of the max volume of the container, the container will need to be transferred and a warning will be thrown:

SpargingVolumeError (1)

Return $Failed if the Sample Volume is <50 mL or >4L and the DegasType is Sparging:

VacuumDegasInstrument (1)

If the degas type is specified as vacuum degas and options from a conflicting degas instrument type are also specified, an error will be thrown:

VacuumDegasOnlyMismatch (1)

If the DegasType provided is not VacuumDegas but VacuumDegas-specific options are given, an error will be thrown:

VacuumDegassingSuitableContainer (1)

If the container of the sample is not either a glass bottle or a 50mL tube, the container will need to be transferred and a warning will be thrown:

VacuumDegasVolumeError (1)

Return $Failed if the Sample Volume is >1 L or <10 mL and the DegasType is VacuumDegas:

Possible Issues

Sample volume incompatibility with selected degassing methods.

Given instrument and method restrictions, degassing with different degas types can only be performed on samples within certain volume limitations. To ensure that degassing can be performed efficiently, make sure to specify the right degas type for the volume desired.

Sample exposed to atmospheric air post sparging.

Given instrument and method restrictions, degassing using the sparging method will result in temporary exposure to atmosphere as the sparging cap is replaced with a normal bottle or carboy cap. If temporary exposure to atmosphere must be avoided, please select the vacuum degassing or freeze-pump-thaw methods of degassing.

Rapid temperature changes during freeze pump thaw risks breaking freeze-pump-thaw glassware.

During freeze-pump-thaw, the sample container cycles between freezing in liquid nitrogen, having vacuum pumped while submerged in liquid nitrogen, and thawing out in a heat block. Rapid and extreme temperatures can cause glass to break and samples to be lost. To avoid breaking the freeze-pump-thaw container, avoid setting a thaw temperature too high. Ambient temperature is recommended.

Degassing samples in serial.

Given current instrument and fume hood restrictions, degassing is currently be performed on one sample at a time, using one degassing method at a time.

Last modified on Mon 18 Aug 2025 10:47:49