ExperimentIRSpectroscopy
ExperimentIRSpectroscopy[Samples]⟹Protocol
generates a Protocol to measure Infrared (IR) absorbance of the provided sample or container 'objects'.
Infrared Spectroscopy (IR spectroscopy or vibrational spectroscopy) involves the interaction of infrared radiation with matter. The technique is mostly based on absorption spectroscopy, though emission and reflection spectroscopy can also be utilised. IR spectroscopy can be used to identify and study chemical substances by measuring the vibrational and rotational energy levels within the molecule. The method or technique of infrared spectroscopy is conducted with an instrument called an infrared spectrometer (or spectrophotometer) to produce an infrared spectrum using a sample in its solid or liquid phase. The output, an IR spectrum, can be visualized in a graph of infrared light absorbance (or transmittance) on the vertical axis vs. frequency or wavelength on the horizontal axis. Typical units of frequency used in IR spectra are reciprocal centimeters (sometimes called wave numbers), with the symbol cm−1. A common laboratory instrument that uses this technique is a Fourier transform infrared (FTIR) spectrometer using attenuated total reflection (ATR).
Experimental Principles
Figure 1.1: Procedural overview of an Infrared (IR) Spectroscopy experiment. Step 1: If the user specifies the use of a blank, place the blank on the surface of ATR sample holder, run an IR spectrum of the blank, and clean the surface of the ATR sample holder. Step 2: Place the sample on the surface of ATR sample holder. If a suspension solution is specified, pipette the solution onto the sample. Step 3: If pressure application is specified, apply the pressure applicator. Step 4: Run an IR spectrum of the sample. Step 5: Analyze or visualize IR spectroscopy data.
Instrumentation
Bruker ALPHA
Figure 2.1: The Alpha-P Bruker is a Fourier Transform Infrared (FTIR) Spectrometer that consists of a source, interferometer, sample holder, detector, amplifier, and A/D convertor. The infrared source for the Alpha-P Bruker uses a silicon carbide rod that is heated to 1300 Celsius. The source emits an infrared beam at the Michelson interferometer. The interferometer consists of two perpendicular mirrors and a beamsplitter. One of the mirrors is a stationary mirror and the other is a movable mirror. The beamsplitter is designed to transmit half of the light and reflect half of the light. Subsequently, the transmitted light and the reflected light strike the stationary mirror and the movable mirror, respectively. When reflected back by the mirrors,two beams of light recombine with each other at the beamsplitter. When the mirrors are equidistant from the beamsplitter the distance travelled by two beams is the same, the situation is defined as zero path difference (ZPD). At the ZPD the wavelengths undergo constructive interference and the intensity of the signal is at a maximum. As the movable mirror changes it distance, the signal undergoes constructive and destructive interference, and the distance that it moves away from the ZPD is called the optical path difference (OPD). As the mirror moves back and forth, the intensity of the signal moves between a maximum and minimum giving rise to a cosine wave.
Attenuated total reflection (ATR) is a sampling technique used in conjunction with infrared spectroscopy which enables samples to be examined by the IR wavelength in the solid or liquid state without further preparation. ATR uses a property of total internal reflection resulting in an evanescent wave. A beam of infrared light is passed through the ATR crystal in such a way that it reflects at least once off the internal surface in contact with the sample. The resultant wave is examined and the plot created is called a interferogram. The interferogram is a function of time and the values outputted by this function of time are said to make up the time domain. The time domain is Fourier transformed to get a frequency domain, which is deconvolved and visualized in a graph of infrared light absorbance (or % transmittance) on the vertical axis vs. frequency or wavelength on the horizontal axis. This graph is the IR absorption spectrum. The IR absorption spectrum that is commonly recognizable with absorption intensity or % transmittance plotted against the wavelength or wavenumber. The ratio of radiant power transmitted by the sample (I) relative to the radiant power of incident light on the sample (I0) results in quantity of Transmittance,(T). Absorbance (A) is the logarithm to the base 10 of the reciprocal of the transmittance (T).
Experiment Options
Protocol
Instrument
Pattern Description: An object of type or subtype Model[Instrument, Spectrophotometer] or Object[Instrument, Spectrophotometer]
Programmatic Pattern: ObjectP[{Model[Instrument, Spectrophotometer], Object[Instrument, Spectrophotometer]}]
SampleModule
The type of instrument apparatus used to hold the sample for this Infrared (IR) measurement. Affects the manner of the IR beam through the sample and the amount required.
Default Calculation: For samples with enough volume and requisite chemical compatibility, the Reflection module will be picked. This entails directly measuring the sample on an Attenuated total reflection (ATR) surface. Low volume/mass samples can otherwise be measured using KBr or ZnSe plates.
NumberOfReplicates
The number of times to repeat spectroscopy reading on each provided sample. If Aliquot -> True, this also indicates the number of times each provided sample will be aliquoted.
Sample Handling
SampleAmount
Default Calculation: Automatically resolves to 20 uL is the sample state is a Liquid; otherwise, resolves to 20 mg.
Pattern Description: Greater than or equal to 1 microliter and less than or equal to 500 microliters or greater than or equal to 1 milligram and less than or equal to 500 milligrams.
Programmatic Pattern: (RangeP[1*Microliter, 500*Microliter] | RangeP[1*Milligram, 500*Milligram]) | Automatic
PressSample
Indicates if the sample should have pressure application through measurement on the ATR measurement surface.
Default Calculation: Automatically resolves to False for liquid samples and solid samples with a specified SuspensionSolution. Resolves to True for solid samples without a SuspensionSolution specified.
SuspensionSolution
The model or sample (e.g. mineral oil), which will be directly added after the input sample and pipette mixed on the sampling apparatus before measurement.
Default Calculation: Resolves to mineral oil if a SuspensionSolutionVolume is supplied, otherwise Null.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
SuspensionSolutionVolume
The model or sample (e.g. mineral oil), which will be directly added to the input sample and pipette mixed on the sampling apparatus before measurement.
Default Calculation: Automatically resolves to Null if SuspensionSoluton is Null. Otherwise, resolves to 20 microliters.
Pattern Description: Greater than or equal to 20 microliters and less than or equal to 500 microliters or Null.
Blanks
The model or sample whose absorbance will be subtract as background from the absorbance measurement of the SamplesIn. The numeric index indicates when these subtracting samples are shared for different input samples.
Default Calculation: Automatically set to the so that Blank index matches across samples. If no Blank is specified, then set to Null.
Programmatic Pattern: (((ObjectP[{Model[Sample], Object[Sample]}] | _String) | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Sample], Object[Sample]}] | _String) | (Automatic | Null)}) | Automatic) | Null
BlankAmounts
Default Calculation: Automatically resolves to Null if Blanks is Null. Otherwise, resolves to SampleAmount + SuspensionSolutionVolume (if defined).
Pattern Description: Greater than or equal to 20 microliters and less than or equal to 500 microliters or greater than or equal to 20 milligrams and less than or equal to 500 milligrams or Null.
Programmatic Pattern: ((RangeP[20*Microliter, 500*Microliter] | RangeP[20*Milligram, 500*Milligram]) | Automatic) | Null
PressBlank
Indicates if the Blanks should have pressure application through measurement on the ATR measurement surface.
Default Calculation: Automatically resolves to False for liquid Blanks samples. Resolves to True for solid samples.
RecoupSample
Indicates if the transferred liquid used for IR measurement will be recouped or transferred back into the original container upon completing the measurement.
Absorbance Parameters
IntegrationTime
The amount of time for which the spectroscopy measurement reading should occur for a given sample and background measurement. Readings occur in discrete readings. The resulting spectrum is the averaged reading for each discrete reading.
Default Calculation: If neither IntegrationTime nor NumberOfReadings are set, then IntegrationTime is resolved to 1 minute. If NumberOfReadings is set, IntegrationTime is resolved to Null.
Pattern Description: Greater than or equal to 0.1 minutes and less than or equal to 10 minutes or Null.
NumberOfReadings
Number of redundant readings which should be taken by the detector to determine a single averaged IR spectrum measurement. Either IntegrationTime or NumberofReadings can be set but not both.
Pattern Description: Greater than or equal to 1 and less than or equal to 200 in increments of 1 or Null.
MinWavenumber
The minimum wavenumber of the spectrum range to be measured and viewed. Either MinWavenumber or MaxWavelength can be specified but not both.
Default Calculation: If neither MinWavenumber nor MaxWavelength are set, then MinWavenumber is resolved to 400 1/centimeter. If MaxWavelength is set, MinWavenumber is resolved to Null.
Pattern Description: Greater than or equal to 100 reciprocal centimeters and less than or equal to 8000 reciprocal centimeters or Null.
MaxWavenumber
The maximum wavenumber of the spectrum range to be measured and viewed. Either MinWavenumber or MaxWavelength can be specified but not both.
Default Calculation: If neither MaxWavenumber nor MinWavelength are set, then MaxWavenumber is resolved to 4000/centimeter. If MinWavelength is set, MaxWavenumber is resolved to Null.
Pattern Description: Greater than or equal to 100 reciprocal centimeters and less than or equal to 8000 reciprocal centimeters or Null.
MinWavelength
The minimum wavelength of the spectrum range to be measured and viewed. Either MinWavenumber or MinWavelength can be set but not both. This value will be convert to Wavenumber for measurement.
Default Calculation: If neither IntegrationTime nor NumberOfReadings are set, then NumberOfReadings is resolved to Null because IntegrationTime will be set. If IntegrationTime is set, NumberOfReadings is resolved to Null.
Pattern Description: Greater than or equal to 1250 nanometers and less than or equal to 100 micrometers or Null.
MaxWavelength
The maximum wavelength of the spectrum range to measured and viewed. Either MaxWavenumber or ManWavelength can be set but not both. This value will be convert to Wavenumber for measurement.
Pattern Description: Greater than or equal to 1250 nanometers and less than or equal to 100 micrometers or Null.
WavenumberResolution
Pattern Description: Greater than or equal to 2 reciprocal centimeters and less than or equal to 256 reciprocal centimeters.
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.
Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting, Oven} or Disposal or Null.
Model Input
PreparedModelContainer
Indicates the container in which a Model[Sample] specified as input to the experiment function will be prepared.
Default Calculation: If PreparedModelAmount is set to All and when the input model has a product associated with both Amount and DefaultContainerModel populated, automatically set to the DefaultContainerModel value in the product. Otherwise set to Model[Container, Vessel, "2mL Tube"].
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.
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.
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 Calculation: Resolves to True if any of the corresponding Incubation options are set. Otherwise, resolves to False.
IncubationTemperature
Temperature at which the SamplesIn should be incubated for the duration of the IncubationTime prior to starting the experiment.
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
IncubationTime
Duration for which SamplesIn should be incubated at the IncubationTemperature, prior to starting the experiment.
Mix
Default Calculation: Automatically resolves to True if any Mix related options are set. Otherwise, resolves to False.
MixType
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.
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 Calculation: Automatically resolves to True if MaxIncubationTime or MaxNumberOfMixes is set.
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 Calculation: Automatically resolves based on MixType, MixUntilDissolved, and the container of the given sample.
IncubationInstrument
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.
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.
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.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
IncubateAliquotDestinationWell
The desired position in the corresponding IncubateAliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
IncubateAliquot
The amount of each sample that should be transferred from the SamplesIn into the IncubateAliquotContainer when performing an aliquot before incubation.
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.
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 Calculation: Resolves to True if any of the corresponding Centrifuge options are set. Otherwise, resolves to False.
CentrifugeInstrument
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
CentrifugeIntensity
The rotational speed or the force that will be applied to the samples by centrifugation prior to starting the experiment.
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
CentrifugeTime
CentrifugeTemperature
The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.
Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius or Null.
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.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
CentrifugeAliquotDestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
CentrifugeAliquot
The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.
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.
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 Calculation: Resolves to True if any of the corresponding Filter options are set. Otherwise, resolves to False.
FiltrationType
Default Calculation: Will automatically resolve to a filtration type appropriate for the volume of sample being filtered.
FilterInstrument
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
Filter
The filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
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
FilterMaterial
The membrane material of the filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
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.
PrefilterMaterial
The material from which the prefilter filtration membrane should be made of to remove impurities from the SamplesIn prior to starting the experiment.
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.
FilterPoreSize
The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.
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.
PrefilterPoreSize
The pore size of the filter; all particles larger than this should be removed during the filtration.
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.
FilterSyringe
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
FilterHousing
The filter housing that should be used to hold the filter membrane when filtration is performed using a standalone filter membrane.
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
FilterIntensity
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
FilterTime
Default Calculation: Will automatically resolve to 5 Minute if FiltrationType is Centrifuge and Filtration is True.
FilterTemperature
The temperature at which the centrifuge chamber will be held while the samples are being centrifuged during filtration.
Default Calculation: Will automatically resolve to 22 Celsius if FiltrationType is Centrifuge and Filtration is True.
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 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
FilterAliquotDestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
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.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
FilterAliquot
The amount of each sample that should be transferred from the SamplesIn into the FilterAliquotContainer when performing an aliquot before filtration.
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.
FilterSterile
Default Calculation: Resolve to False if Filtration is indicated. If sterile filtration is desired, this option must manually be set to True.
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).
AliquotAmount
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.
Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All) | Automatic) | Null
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.
TargetConcentrationAnalyte
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.
AssayVolume
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.
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.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
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 Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentratedBufferDilutionFactor of that sample; otherwise, set to Null.
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 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.
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 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.
AliquotSampleStorageCondition
The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting, Oven} or Disposal or Null.
DestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
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 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
Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.
ConsolidateAliquots
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.
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.
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.
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.
ImageSample
Example Calls
ExperimentIRSpectroscopy can work with any combination of liquid or solid samples.The procedure will transfer an amount of sample, determined by the option SampleAmount, onto an attenuated total reflectance (ATR) surface in order to obtain the absorbance measurement.
Basic
Dry samples can be mixed with a suspension solution (via the SuspensionSolution option) in order to generate a slurry directly on the ATR surface, which is consequently measured:
Blanking
A blanking sample can be specified using the Blanks option and will be run with each input sample. The spectrum of this sample is subtracted from that of the input sample's spectrum in order to generate the final spectrum. Blank samples are certainly optional and can be turned off by specifying Blanks -> Null. Blank samples of the same model can also be shared between or separated for different input samples using our flexible, but powerful option format:
Detection
Additionally, parameters of the spectroscopy measurement are under option control.The range of absorbance can be specified with options MinWavenumber/MaxWavenumber or MinWavelength/MaxWavelength. The measurement time can be specified either by total time, using the IntegrationTime option, or the number of scans performed, using the NumberOfReadings option:
Warnings and Errors
Messages (43)
BlankHasNoQuantity (1)
BlankIndexSpecifiedNull (1)
BlankSpecifiedNull (1)
DryNoPressureBlanks (1)
ImproperBlankAmount (1)
ImproperSampleAmount (1)
IncompatibleBlanks (1)
IncompatibleSample (1)
IncompatibleSuspensionSolution (1)
IndexDifferentSameObject (1)
IntegrationReadingsNull (1)
IntegrationReadingsSpecified (1)
IntegrationTimePrecision (1)
IRSpectroscopyTooManySamples (1)
MaxWavelengthPrecision (1)
MaxWavenumberMinWavelengthBothNull (1)
MaxWavenumberMinWavelengthBothSpecified (1)
MaxWavenumberPrecision (1)
MinWavelengthPrecision (1)
MinWavenumberGreaterThanMax (1)
MinWavenumberMaxWavelengthBothNull (1)
MinWavenumberMaxWavelengthBothSpecified (1)
MinWavenumberPrecision (1)
ObjectDoesNotExist (4)
PressureApplicationWithFluidSample (1)
PressureApplicationWithFluidSampleBlanks (1)
RecoupSuspensionSolution (1)
SameBlankIndexDifferentObjects (1)
SampleHasNoQuantity (1)
SuspensionSolutionNull (1)
SuspensionSolutionResolved (1)
SuspensionSolutionVolumePrecision (1)
SuspensionVolumeNull (1)
Last modified on Wed 3 Sep 2025 15:29:41