ExperimentLCMS

generates a Protocol to separate and analyze Samples via Liquid Chromatography Mass Spectrometry (LCMS).

Liquid chromatography - Mass Spectrometry (LC-MS) separates samples injected into a liquid flow by passage through an adsorbent column (see ExperimentHPLC). After separation, analytes are ionized, selected, and detected in the Mass Spectrometer device (see ExperimentMassSpectrometry). Within, ions are resolved by their mass versus charge state. Optionally, ions can be fragmented by collision with an inert gas, and the resulting product ions can, in turn, be resolved and detected for more information. In total, LC-MS can answer composition questions; for example, proteins, lipids, and metabolites can be identified in a sample. Furthermore, LC-MS can answer concentration questions; for instance, nucleotides can be quantified in a biological sample.

Experimental Principles

Figure 1.1: Procedural overview of a LCMS experiment. Step 1: The system is rinsed with cleaning solutions. Step 2: The stationary column is installed and equilibrated to measurement conditions. Step 3: Samples are then introduced into the flow path. Step 4: The analytes are selectively retained on the downstream column. Step 5: Upon exit from the column, the now separated analytes are analyzed according to their physical property using a mass spectrometer. Step 6: After final sample measurement, the Column(s) are rinsed, removed from the system, and stowed. Step 7: After the column is removed, the system is rinsed with cleaning solution.

Instrumentation

Waters Acquity UPLC I-Class PDA

Figure 2.1.1: Instrument diagram for the H-Class and I-Class systems. Buffer solutions (up to 4) are steadily pumped through the instrument, consisting of a 6-port valve system, adsorbent column, detectors, and terminates at fraction collection or waste. Samples within the autosampler are loaded into the sample loop via positive displacement from the syringe. The rotation of the valve exposes the sample loop, thereby carrying the sample downstream to the column. Within the column, molecular constituents are separated by adsorption -- a function of the buffers, column, sample properties and temperature. Analytes are continuously carried downstream to the detectors, where they can elicit quantifiable peak signals.

Figure 2.1.2: Principle of PhotodiodeArray detection. Filtered light (across a range of wavelengths) passes through the flow downstream of the column. Presence of light-absorbing molecules will result in less light transmission to the recipient Diode, thereby producing a chromatographic peak for each specific wavelength.

Xevo G2-XS QTOF

Figure 2.2.1: Principles of an electrospray quadrupole time of flight mass spectrometer (QTOF). Analytes are flowed through a capillary tube into a heated source box (SourceTemeprature) at the desired InfusionFlowRate. A confluence of the source box temperature, DesolvationTemperature, DesolvationGasFlow, and ESICapillaryVolage result in neubilization, vaporization, and ionization of the analyte stream to generate an electrospray. The electrospray enters the mass spectrometer through the source cone, which serves to focus the ions and excludes contimation via a ConeGasFlow. Within the mass spectrometer, the electrospray is futher refined via an applied voltage (DeclusteringVoltage) to yeild isolated gas-phase ions. Ions are then focused through a stepwave ion guide path via another applied voltage (StepwaveVoltage) into an ion beam. The ions travel through a quadrupole and a collision cell. Lastly, they enter a time-of-flight analyzer which resolves the ions by their mass to charge ratio according to their travel time. Spectra are continuously acquired for ions inside MassDetection hitting the detector during ScanTime until the end of RunDuration. For time independent samples, an average mass spectrum is generated. When coupled with liquid chromatography (see ExperimentLCMS) time-dependent mass spectra are generated instead.

QTRAP 6500

Figure 2.3.1: Principles of an electrospray triple quadrupole mass spectrometer (ESI-QQQ). Analytes are injected through the capillary tube into the source block at the desired InfusionFlowRate. Once the sample enters the source block, it is evaporated at the DesolvationTemperature under a stream of nitrogen gas with a pressure of DesolvationGasFlow. ESICapillaryVoltage is then applied to the capillary tubing tip to produce an electrospray, which turns into single gas-phase ions due to additional evaporation and desolvation SourceTemperature. Ions, focused by the ConeGasFlow, enter the mass spectrometer through the source cone and follow the ion path via an applied voltage (DeclusteringVoltage). They are then guided through an ion guide path via another applied voltage (IonGuideVoltange) to generate a focused ion beam. Ions travel through the first quadrupole mass analyzer (MS1), where their mass is resolved by their mass-to-charge ratio (m/z, MassDetection). After the MS1, ions enter the collision cell, where they can be fragmented by collision-induced dissociation, resulting in bond breakage and the fragmentation of the molecular ions into smaller fragments. CollisionCellExitVoltage accelerates and guides the fragmented ions to enter the second quadrupole mass analyzer (MS2), where their mass can be resolved again by their m/z (FragmentMassDetection). Spectra are continuously acquired for ions either inside MassDetection as a ranged value or as a fixed value, hitting the detector during ScanTime until the end of RunDuration, and a total mass spectrum is generated.

Experiment Options

General

SeparationMode

The category of method used to elicit differential column retention due to interaction between molecules in the mobile phase with those on the stationary phase (column).

Default Value: Automatic

Default Calculation: Automatically set to match the Separation Mode listed with the provided column.

Pattern Description: NormalPhase, ReversePhase, IonExchange, SizeExclusion, Affinity, or Chiral.

Programmatic Pattern: SeparationModeP | Automatic

MassAnalyzer

The manner of detection used to resolve and detect molecules. QTOF accelerates ions through an elongated flight tube and separates ions by their flight time (related to mass to charge ratio).

Default Value: Automatic

Default Calculation: Is automatically set to the QTOF.

Pattern Description: QTOF or TripleQuadrupole.

Programmatic Pattern: (QTOF | TripleQuadrupole) | Automatic

ChromatographyInstrument

The device used to separate molecules from the sample mixture using mobile liquid through an adsorbent column.

Default Value: Model[Instrument, HPLC, Waters Acquity UPLC I-Class PDA]

Default Calculation: Automatically set to an instrument model that is available for the best MassSpectrometerInstrument.

Pattern Description: An object of type or subtype Model[Instrument, HPLC] or Object[Instrument, HPLC]

Programmatic Pattern: ObjectP[{Model[Instrument, HPLC], Object[Instrument, HPLC]}]

MassSpectrometerInstrument

The device used to ionize, separate, fragment (optionally), and detect analyte species.

Default Value: Automatic

Default Calculation: Is automatically set according to MassAnalyzer: Model[Instrument, MassSpectrometer, "Xevo G2-XS QTOF"] for QTOF, Model[Instrument, MassSpectrometer, "QTRAP 6500"] for using TripleQuadrupole.

Pattern Description: An object of type or subtype Model[Instrument, MassSpectrometer] or Object[Instrument, MassSpectrometer]

Programmatic Pattern: ObjectP[{Model[Instrument, MassSpectrometer], Object[Instrument, MassSpectrometer]}] | Automatic

Detector

Default Value: Automatic

Default Calculation: Automatically set from SeparationMode or the objects specified by the Gradient option.

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

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

Sample Parameters

InjectionTable

The order of Sample, Standard and Blank sample injected into the Instrument during measurement and/or collection. This also includes the priming and flushing of the column(s).

Default Value: Automatic

Default Calculation: Samples are inserted in the order of the input samples based with the number of replicates. Standard and Blank samples are inserted based on the determination of StandardFrequency and BlankFrequency options. For example, StandardFrequency -> FirstAndLast and BlankFrequency -> Null result in Standard samples injected first, then samples, and then the Standard sample set again at the end. Column priming is inserted at the beginning and repeated according to ColumnPrimeFrequency. Column flushing is inserted at the end.

Pattern Description: List of one or more {Type, Sample, InjectionVolume, Column Temperature, Gradient, Mass Spectrometry} entries.

Programmatic Pattern: {{Standard | Sample | Blank | ColumnPrime | ColumnFlush, (ObjectP[{Model[Sample], Object[Sample]}] | _String) | (Automatic | Null), RangeP[0*Microliter, 50*Microliter, 1*Microliter] | (Automatic | Null), RangeP[30*Celsius, 90*Celsius] | (Ambient | Automatic), ObjectP[Object[Method, Gradient]] | (Automatic | New), ObjectP[Object[Method, MassAcquisition]] | (Automatic | New)}..} | Automatic

SampleTemperature

The temperature of the chamber in which the samples, Standard, and Blank are stored while waiting for the Injection.

Default Value: Ambient

Pattern Description: Ambient or greater than or equal to 5 degrees Celsius and less than or equal to 40 degrees Celsius.

Programmatic Pattern: RangeP[5*Celsius, 40*Celsius] | Ambient

ColumnTemperature

The temperature of the Column throughout the measurement and/or collection. If ColumnnTemperature is set to Ambient, column oven temperature control is not used. Otherwise, ColumnTemperature is maintained by temperature control of the column oven.

Default Value: Automatic

Default Calculation: Automatically set to the corresponding gradient temperature specified in the Gradient option or the column temperature for the sample in the InjectionTable option; otherwise, set to Ambient.

Pattern Description: Ambient or greater than or equal to 30 degrees Celsius and less than or equal to 90 degrees Celsius.

Programmatic Pattern: (RangeP[30*Celsius, 90*Celsius] | Ambient) | Automatic

Index Matches to: experiment samples

InjectionVolume

The physical quantity of sample loaded into the flow path for measurement.

Default Value: Automatic

Default Calculation: If InjectionTable is specified, automatically set from the Injection Volume entry for the sample. Otherwise set to 5 Microliter.

Pattern Description: Greater than or equal to 0 microliters and less than or equal to 50 microliters.

Programmatic Pattern: RangeP[0*Microliter, 50*Microliter] | Automatic

Index Matches to: experiment samples

NeedleWashSolution

The net speed of the fluid flowing through the pump inclusive of the composition of BufferA, BufferB, BufferC, and BufferD specified in the gradient options. This speed is linearly interpolated such that consecutive entries of {Time, Flow Rate} will define the intervening fluid speed. For example, {{0 Minute, 0.3 Milliliter/Minute},{30 Minute, 0.5 Milliliter/Minute}} means flow rate of 0.4 Milliliter/Minute at 15 minutes into the run.

Figure 3.1: ESI source settings should be adjusted according to the flow rate used to infuse the sample into the mass spectrometer to ensure successful spray formation and solvent desolvation. This table provides recommended settings for typical flow rate ranges for both ESI-QTOF and ESI-QQQ. Note that ESI-QTOF and ESI-QQQ take different input ranges and units. Desolvation gas flow is input as gas flow rate for ESI-QTOF and gas pressure for ESI-QQQ; ESI-QQQ has different polarity for the capillary voltage for positive and negative ion mode, while ESI-QTOF only takes positive capillary voltage as the input.

Default Value: Automatic

Default Calculation: If Gradient option is specified, automatically set from the method given in the Gradient option. If NominalFlowRate of the column model is specified, set to lesser of the NominalFlowRate for each of the columns, guard columns or the instrument's MaxFlowRate. Otherwise set to 1 Milliliter / Minute.

Pattern Description: Greater than or equal to 0 milliliters per minute and less than or equal to 2 milliliters per minute or list of one or more {Time, Flow Rate} entries.

Programmatic Pattern: (RangeP[0*(Milliliter/Minute), 2*(Milliliter/Minute)] | {{RangeP[0*Minute, $MaxExperimentTime], RangeP[0*(Milliliter/Minute), 2*(Milliliter/Minute)]}..}) | Automatic

Index Matches to: experiment samples

Gradient

The composition of different specified buffers in BufferA, BufferB, BufferC and BufferD over time in the fluid flow. Specific parameters of a gradient object can be overridden by specific options.

Default Value: Automatic

Default Calculation: Automatically set to best meet all the Gradient options (e.g. GradientA, GradientB, GradientC, GradientD, FlowRate).

Pattern Description: An object of type or subtype Object[Method, Gradient] or list of one or more {Time, Buffer A Composition, Buffer B Composition, Buffer C Composition, Buffer D Composition, Flow Rate} entries.

Programmatic Pattern: (ObjectP[Object[Method, Gradient]] | {{RangeP[0*Minute, $MaxExperimentTime], RangeP[0*Percent, 100*Percent], RangeP[0*Percent, 100*Percent], RangeP[0*Percent, 100*Percent], RangeP[0*Percent, 100*Percent], RangeP[0*(Milliliter/Minute), 2*(Milliliter/Minute)]}..}) | Automatic

Index Matches to: experiment samples

Separation

MaxAcceleration

When ramping up the FlowRate of solvent through the instrument, the maximum allowed change per time in the FlowRate.

Default Value: Automatic

Default Calculation: For Waters instruments, automatically set to the lowest value from Max the Column, Instrument, and GuardColumn models. For other instruments, automatically set to Null.

Pattern Description: Greater than 0 milliliters per minute squared or Null.

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

Mass Analysis

Calibrant

The sample with components of known mass-to-charge ratios (m/z) used to calibrate the mass spectrometer. In the chosen ion polarity mode, the calibrant should contain at least 3 masses spread over the mass range of interest.

Figure 3.2: Various calibrants available.

Default Value: Automatic

Default Calculation: If using QTOF as the mass analyzer, set to sodium iodide for peptide samples, cesium iodide for intact protein analysis. For other types of samples, is set to cesium iodide if molecular weight is above 2000 Da, to sodium iodide if molecular weight between 1200 and 2000 Da, and to sodium formate for all others (small molecule range). If using TripleQuadrupole as the mass analyzer, this option will be set automatically based on the first IonMode: Model[Sample, "id:zGj91a71kXEO"] or Model[Sample, "id:bq9LA0JA1YJz"] for Positive and Negative, respectively.

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

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

The method by which spectra are collected. DataDependent will depend on the properties of the measured mass spectrum of the intact ions. DataIndependent will systemically scan through all of the intact ions. MS1 will focus on defined intact masses. MS1MS2 will focus on fragmented masses.

Figure 3.3: (a),(b) and (c):Various acquisition modes available for ExperimentLCMS using QTOF as the MassAnalyzer. For MS1FullScan mode, the collision cell is turned off, and ions are measured and resolved with just the quadrupole time of flight. For MS1FullScanMS2 mode, one intact mass (MassDetection) is selected in the first quadruple and disassociated into fragment ions with the collision cell. Fragment ions are resolved and detected with the quadrupole time of flight. For DataIndependent mode, scans are alternated between scanning a range of MS1FullScan masses (no fragmentation) and scanning fragmentation of a range of masses (MS2). For DataDependent mode, acquisition is split into cycles. For the first scan of each cycle, a survey is taken where the collision cell is off and only intact masses are measured. The top ranking intact ions are noted, then for each consequent scan of the cycle, a ranking intact ion is fragmented, and the resultant fragment ions are resolved and measured on the quadrupole time of flight. A suite of options are available to control how many ions are ranked, which ones are, and to eliminate redundancies. (d):Various mass spectrometry scan modes available for ExperimentLCMS using TripleQuad as the MassAnalyzer. In Full Scan Mode, the entire MS1 range is scanned and fragmentation is off. In SelectedIonMonitoring, select MS1 masses (per the MassDetection option) are monitored and measured without fragmentation. In PrecursorIonScan mode, fragmentation is on, and fragment ion is selected (per the FragmentMassDetection option), while MS1 masses are scanned across a range (MassDetection). In NeutralIonLoss mode, both MS1 and MS2 masses are scanned, to track specific MS1/MS2 combinations for neutral ion loss. In ProductIonScan, an MS1 mass is selected (MassDetection) and a range of MS2 mass is scanned to survey fragmentation patterns of the parent mass. In MultipleReactionMonitoring mode, both MS1 and MS2 are selected - specific intact and fragment ion pairs are monitored.

Default Value: Automatic

Default Calculation: Set to MS1FullScan unless DataDependent related options are set, then set to DataDependent.

Pattern Description: DataIndependent, DataDependent, MS1FullScan, MS1MS2ProductIonScan, SelectedIonMonitoring, NeutralIonLoss, PrecursorIonScan, or MultipleReactionMonitoring or list of one or more DataIndependent, DataDependent, MS1FullScan, MS1MS2ProductIonScan, SelectedIonMonitoring, NeutralIonLoss, PrecursorIonScan, or MultipleReactionMonitoring entries.

Programmatic Pattern: (MSAcquisitionModeP | {MSAcquisitionModeP..}) | Automatic

Index Matches to: experiment samples

Fragment

Indicates if ions should be collided with neutral gas and dissociated in order to measure the resulting product ions. Also known as tandem mass spectrometry or MS/MS (as opposed to MS).

Default Value: Automatic

Default Calculation: Set to True if AcquisitionMode is MS1MS2ProductIonScan, DataDependent, or DataIndependent. Set True if any of the Fragmentation related options are set (e.g. FragmentMassDetection).

Pattern Description: List of one or more True or False entries or True or False.

Programmatic Pattern: (BooleanP | {BooleanP..}) | Automatic

Index Matches to: experiment samples

MassDetection

The lowest and the highest mass-to-charge ratio (m/z) to be recorded or selected for intact masses. When Fragment is True, the intact ions will be selected for fragmentation.

Figure 3.4: MassDetection, IonMode, and Calibrant should be adjusted according to the type of analyte in the sample and the chosen ion mode. This table lists mass ranges and calibrants that this experiment automatically defaults to. For QTOF, the calibrant will be determined according to analyte types, if not user-specified: small molecules, peptides, and large molecules such as intact protein/antibodies and nucleic acid oligomers. For ESI-QQQ, the Calibrant and SecondCalibrant will be determined based on IonMode.

Default Value: Automatic

Default Calculation: For Fragment -> False, automatically set to one of three default mass ranges according to the molecular weight of the Analytes to encompass them.

Pattern Description: DataDependent or DataIndependent or MS1FullScan, NeutralIonLoss, DataDependent, DataIndependent or PrecursorIonScan or MS1MS2ProductIonScan or SelectedIonMonitoring or SelectedIonMonitoring or MultipleReactionMonitoring or list of one or more DataDependent or DataIndependent or MS1FullScan, NeutralIonLoss, DataDependent, DataIndependent or PrecursorIonScan or MS1MS2ProductIonScan or SelectedIonMonitoring or SelectedIonMonitoring or MultipleReactionMonitoring entries.

Programmatic Pattern: ((RangeP[2*(Gram/Mole), 100000*(Gram/Mole)] ;; RangeP[2*(Gram/Mole), 100000*(Gram/Mole)] | RangeP[2*(Gram/Mole), 100000*(Gram/Mole)] | {RangeP[2*(Gram/Mole), 100000*(Gram/Mole)]..} | MSAnalyteGroupP) | {(RangeP[2*(Gram/Mole), 100000*(Gram/Mole)] ;; RangeP[2*(Gram/Mole), 100000*(Gram/Mole)] | RangeP[2*(Gram/Mole), 100000*(Gram/Mole)] | {RangeP[2*(Gram/Mole), 100000*(Gram/Mole)]..} | MSAnalyteGroupP)..}) | Automatic

Index Matches to: experiment samples

MassDetectionStepSize

Indicate the step size for mass collection in range when using TripleQuadruploe as the MassAnalyzer.

Default Value: Automatic

Default Calculation: This option will be set to Null if using ESI-QTOF. For ESI-QQQ, if both of the mass anaylzer are in mass selection mode (SelectedIonMonitoring and MultipleReactionMonitoring mode), this option will be auto resolved to Null. In all other mass scan modes in ESI-QQQ, this option will be automatically resolved to 0.1 g/mol.

Pattern Description: Greater than or equal to 0.01 grams per mole and less than or equal to 1 gram per mole or list of one or more greater than or equal to 0.01 grams per mole and less than or equal to 1 gram per mole or Null entries or Null.

Programmatic Pattern: ((RangeP[0.01*(Gram/Mole), 1*(Gram/Mole)] | {(RangeP[0.01*(Gram/Mole), 1*(Gram/Mole)] | Null)..}) | Automatic) | Null

Index Matches to: experiment samples

The collision energy profile at the end of the scan from CollisionEnergy or CollisionEnergyScanProfile, as related to analyte mass.

Default Value: Automatic

Programmatic Pattern: ((RangeP[0.1*Volt, 255*Volt] ;; RangeP[0.1*Volt, 255*Volt] | {(RangeP[0.1*Volt, 255*Volt] ;; RangeP[0.1*Volt, 255*Volt] | Null)..}) | Automatic) | Null

Index Matches to: experiment samples

SurveyChargeStateExclusion

Indicates if redundant ions that differ by ionic charge (+1/-1, +2/-2, etc.) should be excluded and if ChargeState exclusion-related options should be automatically filled in.

Default Value: Automatic

Default Calculation: Set to True, if any of the ChargeState options are set; otherwise, False.

Pattern Description: List of one or more True or False or Null entries or True or False or Null.

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

Index Matches to: experiment samples

SurveyIsotopeExclusion

Indicates if redundant ions that differ by isotopic mass (e.g. 1, 2 Gram/Mole) should be exlcuded and if MassIsotope exclusion-related options should be automatically filled in.

Default Calculation: Is automatically set to the first IonGuideVoltage.

Pattern Description: Greater than or equal to -15 volts and less than or equal to -2 volts or greater than or equal to 2 volts and less than or equal to 15 volts or Null.

Programmatic Pattern: ((RangeP[-15*Volt, -2*Volt] | RangeP[2*Volt, 15*Volt]) | Automatic) | Null

Index Matches to: Blank

ColumnPrimeIonGuideVoltage

Default Value: Automatic

Default Calculation: Is automatically set to first IonGuideVoltage.

Pattern Description: Greater than or equal to -15 volts and less than or equal to -2 volts or greater than or equal to 2 volts and less than or equal to 15 volts or Null.

Programmatic Pattern: ((RangeP[-15*Volt, -2*Volt] | RangeP[2*Volt, 15*Volt]) | Automatic) | Null

Index Matches to: experiment samples

MinimumThreshold

The minimum number of total ions detected within ScanTime durations needed to trigger the start of data dependent acquisition when AcquisitionMode is set to DataDependent.

Default Value: Automatic

Default Calculation: Automatically set to (100000/Second)*ScanTime if AcquisitionMode is DataDependent; otherwise, set to Null.

Pattern Description: Greater than or equal to 0 ArbitraryUnits and less than or equal to 8000000 ArbitraryUnits or list of one or more greater than or equal to 0 ArbitraryUnits and less than or equal to 8000000 ArbitraryUnits or Null entries or Null.

Programmatic Pattern: ((RangeP[0*ArbitraryUnit, 8000000*ArbitraryUnit] | {(RangeP[0*ArbitraryUnit, 8000000*ArbitraryUnit] | Null)..}) | Automatic) | Null

Index Matches to: experiment samples

The range above and below each ion in ExclusionMasses to consider for omission when ExclusionMass is set to All or Once.

Default Value: Automatic

Default Calculation: If ExclusionMass -> All or Once, set to 0.5 Gram/Mole; otherwise, Null.

Programmatic Pattern: ((RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | {(RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | Null)..}) | Automatic) | Null

Index Matches to: experiment samples

ExclusionRetentionTimeTolerance

The range of time above and below the ExclusionDomain to consider for exclusion.

Default Value: Automatic

Default Calculation: If ExclusionMass and ExclusionDomain options are set, this is set to 10 seconds; otherwise, Null.

Pattern Description: Greater than or equal to 0 seconds and less than or equal to 3600 seconds or list of one or more greater than or equal to 0 seconds and less than or equal to 3600 seconds or Null entries or Null.

Programmatic Pattern: ((RangeP[0*Second, 3600*Second] | {(RangeP[0*Second, 3600*Second] | Null)..}) | Automatic) | Null

The range above and below each ion in InclusionMasses to consider for prioritization. For example, if set to 0.5 Gram/Mole, the total range is 1 Gram/Mole.

Default Value: Automatic

Default Calculation: Set to 0.5 Gram/Mole if InclusionMass is given; otherwise, Null.

Programmatic Pattern: ((RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | {(RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | Null)..}) | Automatic) | Null

Index Matches to: experiment samples

ChargeStateExclusionLimit

The number of ions to survey first with exclusion by ionic state. For example, if AcquisitionSurvey is 10 and this option is 5, then 5 ions will be surveyed with charge-state exclusion. For candidate ions of rank 6 to 10, no exclusion will be performed.

Default Value: Automatic

Default Calculation: Inherited from any supplied method; otherwise, set the same to AcquisitionSurvey, if any ChargeState option is set.

Pattern Description: Greater than or equal to 0 and less than or equal to 30 in increments of 1 or list of one or more greater than or equal to 0 and less than or equal to 30 in increments of 1 or Null entries or Null.

Programmatic Pattern: ((RangeP[0, 30, 1] | {(RangeP[0, 30, 1] | Null)..}) | Automatic) | Null

Index Matches to: experiment samples

ChargeStateExclusion

The specific ionic states of intact ions to redundantly exclude from the survey for further fragmentation/acquisition. 1 refers to +1/-1, 2 refers to +2/-2, etc.

Default Value: Automatic

Default Calculation: When SurveyChargeStateExclusion is True, set to {1,2}; otherwise, Null.

Pattern Description: Greater than or equal to 1 and less than or equal to 6 in increments of 1 or list of one or more greater than or equal to 1 and less than or equal to 6 in increments of 1 or Null entries or Null.

Programmatic Pattern: ((RangeP[1, 6, 1] | {(RangeP[1, 6, 1] | Null)..}) | Automatic) | Null

Index Matches to: experiment samples

The range of m/z around a mass to consider for exclusion. This applies for both ChargeState and mass shifted Isotope. If set to 0.5 Gram/Mole, then the total range should be 1 Gram/Mole.

Default Value: Automatic

Default Calculation: When SurveyIsotopeExclusion or SurveyChargeStateExclusion is True, set to 0.5 Gram/Mole; otherwise, set to Null.

Programmatic Pattern: ((RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | {(RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | Null)..}) | Automatic) | Null

Index Matches to: experiment samples

IsotopeRatioTolerance

The range of relative magnitude around IsotopeRatio to consider for isotope exclusion.

Default Calculation: If StandardGradient option is specified, automatically set from the method given in the StandardGradient option. If NominalFlowRate of the column model is specified, set to lesser of the NominalFlowRate for each of the columns, guard columns or the instrument's MaxFlowRate. Otherwise set to 1 Milliliter / Minute.

Pattern Description: Greater than or equal to 0 milliliters per minute and less than or equal to 2 milliliters per minute or list of one or more {Time, Flow Rate} entries or Null.

Programmatic Pattern: ((RangeP[0*(Milliliter/Minute), 2*(Milliliter/Minute)] | {{RangeP[0*Minute, $MaxExperimentTime], RangeP[0*(Milliliter/Minute), 2*(Milliliter/Minute)]}..}) | Automatic) | Null

Index Matches to: Standard

StandardGradient

The composition of different specified buffers in BufferA, BufferB, BufferC and BufferD over time in the fluid flow for Standard measurement. Specific parameters of a gradient object can be overridden by specific options.

Default Value: Automatic

Default Calculation: Automatically set to best meet all the StandardGradient options (e.g. StandardGradientA, StandardGradientB, StandardGradientC, StandardGradientD, StandardFlowRate).

Programmatic Pattern: ((ObjectP[Object[Method, Gradient]] | {{RangeP[0*Minute, $MaxExperimentTime], RangeP[0*Percent, 100*Percent], RangeP[0*Percent, 100*Percent], RangeP[0*Percent, 100*Percent], RangeP[0*Percent, 100*Percent], RangeP[0*(Milliliter/Minute), 2*(Milliliter/Minute)]}..}) | Automatic) | Null

The duration of time allowed to pass between each spectral acquisition. When StandardAcquisitionMode is DataDependent, this value refers to the duration for measuring spectra from the intact ions. Increasing this value improves sensitivity whereas decreasing this value allows for more data points and spectra to be acquired.

Default Value: Automatic

Default Calculation: Set to 0.2 seconds unless a method is given.

Programmatic Pattern: ((RangeP[0.015*Second, 10*Second] | {RangeP[0.015*Second, 10*Second]..}) | Automatic) | Null

Index Matches to: Standard

StandardFragmentMassDetection

The lowest and the highest mass-to-charge ratio (m/z) to be recorded or selected for product ions. When StandardAcquisitionMode is DataDependent|DataIndependent, all of the product ions in consideration for measurement. Null if StandardFragment is False.

Default Value: Automatic

Default Calculation: When StandardFragment is False, set to Null. Otherwise, 20 Gram/Mole to the maximum StandardMassDetection.

Pattern Description: All or Range or Specific or list of one or more All or Range or Specific or Null entries or Null.

Programmatic Pattern: ((({RangeP[20*(Gram/Mole), 16000*(Gram/Mole)]..} | All | RangeP[20*(Gram/Mole), 16000*(Gram/Mole)] ;; RangeP[100*(Gram/Mole), 16000*(Gram/Mole)]) | {({RangeP[20*(Gram/Mole), 16000*(Gram/Mole)]..} | All | Null | RangeP[20*(Gram/Mole), 16000*(Gram/Mole)] ;; RangeP[100*(Gram/Mole), 16000*(Gram/Mole)])..}) | Automatic) | Null

Index Matches to: Standard

StandardCollisionEnergy

The voltage by which intact ions are accelerated through inert gas in order to dissociate them into measurable fragment ion species when StandardFragment is True. StandardCollisionEnergy cannot be defined simultaneously with StandardCollisionEnergyMassProfile.

Default Value: Automatic

Default Calculation: Is automatically set to 40 Volt when StandardFragment is True, otherwise is set to Null.

Index Matches to: Standard

StandardCollisionEnergyMassProfile

The relationship of collision energy with the StandardMassDetection.

Default Value: Automatic

Default Calculation: Set to StandardCollisionEnergyMassScan if defined; otherwise, set to Null.

Programmatic Pattern: ((RangeP[0.1*Volt, 255*Volt] ;; RangeP[0.1*Volt, 255*Volt] | {(RangeP[0.1*Volt, 255*Volt] ;; RangeP[0.1*Volt, 255*Volt] | Null)..}) | Automatic) | Null

Index Matches to: Standard

The time range when the StandardExclusionMasses are omitted in the chromatogram. Full indicates for the entire period.

Default Value: Automatic

Default Calculation: Set to the entire StandardAcquisitionWindow.

Index Matches to: Standard

StandardExclusionMass

The intact ions (Target Mass) to omit. When set to All, the mass is excluded for the entire StandardExclusionDomain. When set to Once, the mass is excluded in the first survey appearance, but considered for consequent ones.

Default Value: Automatic

Default Calculation: If any StandardExclusionMode-related options are set (e.g. StandardExclusionMassTolerance), a target mass of the first Analyte (if not in StandardInclusionMasses) is chosen and retention time is set to 0*Minute.

Pattern Description: List of one or more list of one or more {Mode, Target Mass} entries entries or list of one or more {Mode, Target Mass} or Null entries or {Mode, Target Mass} or Null.

Index Matches to: Standard

StandardExclusionMassTolerance

The range above and below each ion in StandardExclusionMasses to consider for omission when StandardExclusionMass is All or Once.

Default Value: Automatic

Default Calculation: If StandardExclusionMass -> All or Once, set to 0.5 Gram/Mole; otherwise, Null.

Programmatic Pattern: ((RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | {(RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | Null)..}) | Automatic) | Null

Index Matches to: Standard

StandardExclusionRetentionTimeTolerance

The range of time above and below the StandardExclusionDomain to consider for exclusion.

Default Value: Automatic

Default Calculation: If StandardExclusionMass and StandardExclusionDomain options are set, this is set to 10 seconds; otherwise, Null.

Programmatic Pattern: ((RangeP[0*Second, 3600*Second] | {(RangeP[0*Second, 3600*Second] | Null)..}) | Automatic) | Null

Index Matches to: Standard

Indicates if redundant ions that differ by ionic charge (+1/-1, +2/-2, etc.) should be excluded and if StandardChargeState exclusion-related options should be automatically filled in.

Default Value: Automatic

Default Calculation: Set to True, if any of the StandardChargeState options are set; otherwise, False.

Pattern Description: List of one or more True or False or Null entries or True or False or Null.

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

Index Matches to: Standard

StandardSurveyIsotopeExclusion

Indicates if redundant ions that differ by isotopic mass (e.g. 1, 2 Gram/Mole) should be excluded and if StandardMassIsotope exclusion-related options should be automatically filled in.

Default Value: Automatic

Default Calculation: Set to True, if any of the StandardIsotopeExclusion options are set; otherwise, False.

Pattern Description: List of one or more True or False or Null entries or True or False or Null.

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

Index Matches to: Standard

StandardChargeStateExclusionLimit

The number of ions to survey first with exclusion by ionic state. For example, if StandardAcquisitionSurvey is 10 and this option is 5, then 5 ions will be surveyed with charge-state exclusion. For candidate ions of rank 6 to 10, no exclusion will be performed.

Default Value: Automatic

Default Calculation: Inherited from any supplied method; otherwise, set the same to StandardAcquisitionSurvey, if any ChargeState option is set.

Programmatic Pattern: ((RangeP[0, 30, 1] | {(RangeP[0, 30, 1] | Null)..}) | Automatic) | Null

Index Matches to: Standard

StandardChargeStateExclusion

The specific ionic states of intact ions to redundantly exclude from the survey for further fragmentation/acquisition. 1 refers to +1/-1, 2 refers to +2/-2, etc.

Default Value: Automatic

Default Calculation: When StandardSurveyChargeStateExclusion is True, set to {1,2}; otherwise, Null.

Programmatic Pattern: ((RangeP[1, 6, 1] | {(RangeP[1, 6, 1] | Null)..}) | Automatic) | Null

Index Matches to: Standard

StandardChargeStateMassTolerance

The range of m/z to consider for exclusion by ionic state property when StandardSurveyChargeStateExclusion is True.

Default Value: Automatic

Default Calculation: When StandardSurveyChargeStateExclusion is True, set to 0.5 Gram/Mole; otherwise, Null.

Programmatic Pattern: ((RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | {(RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | Null)..}) | Automatic) | Null

Index Matches to: Standard

A neutral loss scan is performed on ESI-QQQ mass spectrometry by scanning the sample through the first quadrupole (Q1). The ions are then fragmented in the collision cell. The second mass analyzer is then scanned with a fixed offset to MS1. This option represents the value of this offset.

Default Value: Automatic

Default Calculation: Is set to 500 g/mol if using NeutralIonLoss as StandardAcquisitionMode, and is Null in other modes.

Pattern Description: Greater than 0 grams per mole or list of one or more greater than 0 grams per mole or Null entries or Null.

Programmatic Pattern: ((GreaterP[0*(Gram/Mole)] | {(GreaterP[0*(Gram/Mole)] | Null)..}) | Automatic) | Null

Index Matches to: Standard

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

Default Value: Null

Pattern Description: {AmbientStorage, 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: Standard

Blanks

Blank

The object(s) (samples) to inject typically as negative controls (e.g. to test effects stemming from injection, sample solvent, impurities on the column or buffer).

Default Value: Automatic

Default Calculation: If any other Blank option is specified or RefractiveIndex Detector is selected, automatically set to the specified BufferA or Model[Sample, "Milli-Q water"].

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: Blank

BlankInjectionVolume

The physical quantity of Blank sample that is loaded into the flow path on the selected instrument along with the mobile phase onto the stationary phase.

Default Value: Automatic

Default Calculation: Automatically set equal to the first entry in InjectionVolume.

Pattern Description: Greater than or equal to 0 microliters and less than or equal to 500 microliters or Null.

Programmatic Pattern: (RangeP[0*Microliter, 500*Microliter] | Automatic) | Null

The net speed of the fluid flowing through the pump inclusive of the composition of BufferA, BufferB, BufferC, and BufferD specified in the BlankGradient options during Blank measurement. This speed is linearly interpolated such that consecutive entries of {Time, Flow Rate} will define the intervening fluid speed. For example, {{0 Minute, 0.3 Milliliter/Minute},{30 Minute, 0.5 Milliliter/Minute}} means flow rate of 0.4 Milliliter/Minute at 15 minutes into the run.

Default Value: Automatic

Default Calculation: If BlankGradient option is specified, automatically set from the method given in the BlankGradient option. If NominalFlowRate of the column model is specified, set to lesser of the NominalFlowRate for each of the columns, guard columns or the instrument's MaxFlowRate. Otherwise set to 1 Milliliter / Minute.

Pattern Description: Greater than or equal to 0 milliliters per minute and less than or equal to 2 milliliters per minute or list of one or more {Time, Flow Rate} entries or Null.

Programmatic Pattern: ((RangeP[0*(Milliliter/Minute), 2*(Milliliter/Minute)] | {{RangeP[0*Minute, $MaxExperimentTime], RangeP[0*(Milliliter/Minute), 2*(Milliliter/Minute)]}..}) | Automatic) | Null

Index Matches to: Blank

BlankGradient

The composition of different specified buffers in BufferA, BufferB, BufferC and BufferD over time in the fluid flow during Blank measurement. Specific parameters of a gradient object can be overridden by specific options.

Default Value: Automatic

Default Calculation: Automatically set to best meet all the BlankGradient options (e.g. BlankGradientA, BlankGradientB, BlankGradientC, BlankGradientD, BlankFlowRate).

Default Value: Automatic

Default Calculation: Is automatically set to any specified MassAcquisition method; otherwise, set to 40 Volt.

Pattern Description: Greater than or equal to 0.1 volts and less than or equal to 150 volts or Null.

Programmatic Pattern: (RangeP[0.1*Volt, 150*Volt] | Automatic) | Null

Index Matches to: Blank

BlankStepwaveVoltage

Default Value: Automatic

Default Calculation: Is automatically set to the first StepwaveVoltage.

Pattern Description: Greater than or equal to 0.1 volts and less than or equal to 200 volts or Null.

Programmatic Pattern: (RangeP[0.1*Volt, 200*Volt] | Automatic) | Null

Index Matches to: Blank

BlankSourceTemperature

Default Value: Automatic

Default Calculation: Is automatically set to the first SourceTemperature.

Pattern Description: Greater than or equal to 25 degrees Celsius and less than or equal to 150 degrees Celsius or Null.

Programmatic Pattern: (RangeP[25*Celsius, 150*Celsius] | Automatic) | Null

Index Matches to: Blank

BlankDesolvationTemperature

The temperature setting for the ESI desolvation heater that controls the nitrogen gas temperature used for solvent evaporation to produce single gas phase ions from the ion spray. Similar to BlankDesolvationGasFlow, this setting is dependent on solvent flow rate and composition. A typical range is from 150 to 650 Celsius.

Default Value: Automatic

BlankMassDetection

The lowest and the highest mass-to-charge ratio (m/z) to be recorded or selected for intact masses. When BlankFragment is True, the intact ions will be selected for fragmentation.

Default Value: Automatic

Default Calculation: For BlankFragment -> False, automatically set to one of three default mass ranges according to the molecular weight of the BlankAnalytes to encompass them.

Pattern Description: All or Range or Single or Specific List or list of one or more All or Range or Single or Specific List entries or Null.

Index Matches to: Blank

BlankScanTime

The duration of time allowed to pass between each spectral acquisition. When BlankAcquisitionMode is DataDependent, this value refers to the duration for measuring spectra from the intact ions. Increasing this value improves sensitivity whereas decreasing this value allows for more data points and spectra to be acquired.

Default Value: Automatic

Default Calculation: Set to 0.2 seconds unless a method is given.

Programmatic Pattern: ((RangeP[0.015*Second, 10*Second] | {RangeP[0.015*Second, 10*Second]..}) | Automatic) | Null

Index Matches to: Blank

BlankFragmentMassDetection

The lowest and the highest mass-to-charge ratio (m/z) to be recorded or selected for product ions. When BlankAcquisitionMode is DataDependent|DataIndependent, all of the product ions in consideration for measurement. Null if BlankFragment is False.

Default Value: Automatic

Default Calculation: When BlankFragment is False, set to Null. Otherwise, 20 Gram/Mole to the maximum BlankMassDetection.

Pattern Description: All or Range or Specific or list of one or more All or Range or Specific or Null entries or Null.

Index Matches to: Blank

BlankCollisionEnergy

The voltage by which intact ions are accelerated through inert gas in order to dissociate them into measurable fragment ion species when BlankFragment is True. BlankCollisionEnergy cannot be defined simultaneously with BlankCollisionEnergyMassProfile.

Default Value: Automatic

Default Calculation: Is automatically set to 40 Volt when BlankFragment is True, otherwise is set to Null.

Index Matches to: Blank

BlankCollisionEnergyMassProfile

The relationship of collision energy with the BlankMassDetection.

Default Value: Automatic

Default Calculation: Set to BlankCollisionEnergyMassScan if defined; otherwise, set to Null.

Programmatic Pattern: ((RangeP[0.1*Volt, 255*Volt] ;; RangeP[0.1*Volt, 255*Volt] | {(RangeP[0.1*Volt, 255*Volt] ;; RangeP[0.1*Volt, 255*Volt] | Null)..}) | Automatic) | Null

Index Matches to: Blank

The time range when the BlankExclusionMasses are omitted in the chromatogram. Full indicates for the entire period.

Default Value: Automatic

Default Calculation: Set to the entire BlankAcquisitionWindow.

Index Matches to: Blank

BlankExclusionMass

The intact ions (Target Mass) to omit. When the Mode is set to All, the mass is excluded for the entire ExclusionDomain. When the Mode is set to Once, the Mass is excluded in the first survey appearance, but considered for consequent ones.

Default Value: Automatic

Default Calculation: If any BlankExclusionMode-related options are set (e.g. BlankExclusionMassTolerance), a target mass of the first Analyte (if not in BlankInclusionMasses) is chosen and retention time is set to 0*Minute.

Pattern Description: List of one or more list of one or more {Mode, Target Mass} entries entries or list of one or more {Mode, Target Mass} or Null entries or {Mode, Target Mass} or Null.

Index Matches to: Blank

BlankExclusionMassTolerance

The range above and below each ion in BlankExclusionMasses to consider for omission when BlankExclusionMass is All or Once.

Default Value: Automatic

Default Calculation: If BlankExclusionMass -> All or Once, set to 0.5 Gram/Mole; otherwise, Null.

Programmatic Pattern: ((RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | {(RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | Null)..}) | Automatic) | Null

Index Matches to: Blank

BlankExclusionRetentionTimeTolerance

The range of time above and below the BlankExclusionDomain to consider for exclusion.

Default Value: Automatic

Default Calculation: If BlankExclusionMass and BlankExclusionDomain options are set, this is set to 10 seconds; otherwise, Null.

Programmatic Pattern: ((RangeP[0*Second, 3600*Second] | {(RangeP[0*Second, 3600*Second] | Null)..}) | Automatic) | Null

Index Matches to: Blank

Indicates if redundant ions that differ by ionic charge (+1/-1, +2/-2, etc.) should be left out and if BlankChargeState exclusion-related options should be automatically filled in.

Default Value: Automatic

Default Calculation: Set to True, if any of the BlankChargeState options are set; otherwise, False.

Pattern Description: List of one or more True or False or Null entries or True or False or Null.

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

Index Matches to: Blank

BlankSurveyIsotopeExclusion

Indicates if redundant ions that differ by isotopic mass (e.g. 1, 2 Gram/Mole) should be excluded and if BlankMassIsotope exclusion-related options should be automatically filled in.

Default Value: Automatic

Default Calculation: Set to True, if any of the BlankIsotopeExclusion options are set; otherwise, False.

Pattern Description: List of one or more True or False or Null entries or True or False or Null.

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

Index Matches to: Blank

BlankChargeStateExclusionLimit

The number of ions to survey first with exclusion by ionic state. For example, if BlankAcquisitionSurvey is 10 and this option is 5, then 5 ions will be surveyed with charge-state exclusion. For candidate ions of rank 6 to 10, no exclusion will be performed.

Default Value: Automatic

Default Calculation: Inherited from any supplied method; otherwise, set the same to BlankAcquisitionSurvey, if any ChargeState option is set.

Programmatic Pattern: ((RangeP[0, 30, 1] | {(RangeP[0, 30, 1] | Null)..}) | Automatic) | Null

Index Matches to: Blank

BlankChargeStateExclusion

The specific ionic states of intact ions to redundantly exclude from the survey for further fragmentation/acquisition. 1 refers to +1/-1, 2 refers to +2/-2, etc.

Default Value: Automatic

Default Calculation: When BlankSurveyChargeStateExclusion is True, set to {1,2}; otherwise, Null.

Programmatic Pattern: ((RangeP[1, 6, 1] | {(RangeP[1, 6, 1] | Null)..}) | Automatic) | Null

Index Matches to: Blank

BlankChargeStateMassTolerance

The range of m/z to consider for exclusion by ionic state property when BlankSurveyChargeStateExclusion is True.

Default Value: Automatic

Default Calculation: When BlankSurveyChargeStateExclusion is True, set to 0.5 Gram/Mole; otherwise, Null.

Programmatic Pattern: ((RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | {(RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | Null)..}) | Automatic) | Null

Index Matches to: Blank

Indicate the step size for mass collection in range when using TripleQuadruploe as the MassAnalyzer.

Default Value: Automatic

Programmatic Pattern: ((RangeP[0.01*(Gram/Mole), 1*(Gram/Mole)] | {(RangeP[0.01*(Gram/Mole), 1*(Gram/Mole)] | Null)..}) | Automatic) | Null

Index Matches to: Blank

BlankMultipleReactionMonitoringAssays

Default Value: Automatic

Default Calculation: Is set based on BlankMassDetection, BlankCollissionEnergy, BlankDwellTime and BlankFramentMassDetection.

Pattern Description: List of one or more list of one or more Individual Multiple Reaction Monitoring Assay or None entries or Null entries or Null.

Index Matches to: Blank

Default Value: Automatic

Pattern Description: Greater than or equal to 0 percent and less than or equal to 100 percent or list of one or more {Time, Buffer D Composition} entries or Null.

Programmatic Pattern: ((RangeP[0*Percent, 100*Percent] | {{RangeP[0*Minute, $MaxExperimentTime], RangeP[0*Percent, 100*Percent]}..}) | Automatic) | Null

ColumnPrimeFlowRate

The net speed of the fluid flowing through the pump inclusive of the composition of BufferA, BufferB, BufferC, and BufferD specified in the ColumePrimeGradient options during column prime. This speed is linearly interpolated such that consecutive entries of {Time, Flow Rate} will define the intervening fluid speed. For example, {{0 Minute, 0.3 Milliliter/Minute},{30 Minute, 0.5 Milliliter/Minute}} means flow rate of 0.4 Milliliter/Minute at 15 minutes into the run.

Default Value: Automatic

Default Calculation: If ColumnPrimeGradient option is specified, automatically set from the method given in the ColumnPrimeGradient option. If NominalFlowRate of the column model is specified, set to lesser of the NominalFlowRate for each of the columns, guard columns or the instrument's MaxFlowRate. Otherwise set to 1 Milliliter / Minute.

Pattern Description: Greater than or equal to 0 milliliters per minute and less than or equal to 2 milliliters per minute or list of one or more {Time, Flow Rate} entries or Null.

Default Value: Automatic

Default Calculation: Is automatically set to any specified MassAcquisition method; otherwise, set to 40 Volt.

Pattern Description: Greater than or equal to 0.1 volts and less than or equal to 150 volts or Null.

Programmatic Pattern: (RangeP[0.1*Volt, 150*Volt] | Automatic) | Null

ColumnPrimeStepwaveVoltage

Default Value: Automatic

Default Calculation: Is automatically set to the first StepwaveVoltage.

Pattern Description: Greater than or equal to 0.1 volts and less than or equal to 200 volts or Null.

Programmatic Pattern: (RangeP[0.1*Volt, 200*Volt] | Automatic) | Null

ColumnPrimeSourceTemperature

Default Value: Automatic

Default Calculation: Is automatically set to the first SourceTemperature.

Pattern Description: Greater than or equal to 25 degrees Celsius and less than or equal to 150 degrees Celsius or Null.

Programmatic Pattern: (RangeP[25*Celsius, 150*Celsius] | Automatic) | Null

ColumnPrimeDesolvationTemperature

The temperature setting for the ESI desolvation heater that controls the nitrogen gas temperature used for solvent evaporation to produce single gas phase ions from the ion spray. Similar to ColumnPrimeDesolvationGasFlow, this setting is dependent on solvent flow rate and composition. A typical range is from 150 to 650 Celsius.

Default Value: Automatic

Default Calculation: Is automatically set to the first DesolvationTemperature.

Pattern Description: Greater than or equal to 20 degrees Celsius and less than or equal to 650 degrees Celsius or Null.

Programmatic Pattern: (RangeP[20*Celsius, 650*Celsius] | Automatic) | Null

ColumnPrimeDesolvationGasFlow

The rate at which nitrogen gas is flowed around the ESI capillary. It is used for solvent evaporation to produce single gas phase ions from the ion spray. Similar to ColumnPrimeDesolvationTemperature, this setting is dependent on solvent flow rate and composition. Higher desolvation temperatures usually result in increased sensitivity, but too high values can cause spray instability. Typical values are between 300 to 1200 L/h.

Default Value: Automatic

Default Calculation: Is automatically set to the first DesolvationGasFlow.

Programmatic Pattern: ((RangeP[55*(Liter/Hour), 1200*(Liter/Hour)] | RangeP[0*PSI, 85*PSI]) | Automatic) | Null

ColumnPrimeConeGasFlow

The rate at which nitrogen gas flow is flowed around the sample inlet cone (the spherical metal plate acting as a first gate between the sprayer and the reduced pressure chamber, the ion block). This gas flow is used to minimize the formation of solvent ion clusters. It also helps reduce adduct ions and directing the spray into the ion block while keeping the sample cone clean. Typical values are between 0 and 150 L/h.

Default Value: Automatic

Default Calculation: Is automatically set to the first ConeGasFlow.

Programmatic Pattern: ((RangeP[0*(Liter/Hour), 300*(Liter/Hour)] | RangeP[30*PSI, 55*PSI]) | Automatic) | Null

The relationship of collision energy with the ColumnPrimeMassDetection.

Default Value: Automatic

Default Calculation: Set to ColumnPrimeCollisionEnergyMassScan if defined; otherwise, set to Null.

Programmatic Pattern: (RangeP[0.1*Volt, 255*Volt] ;; RangeP[0.1*Volt, 255*Volt] | Automatic) | Null

Index Matches to: ColumnPrimeAcquisitionWindow

THe time range when the ColumnPrimeExclusionMasses are omitted in the chromatogram. Full indicates for the entire period.

Default Value: Automatic

Default Calculation: Set to the entire ColumnPrimeAcquisitionWindow.

Programmatic Pattern: (((GreaterEqualP[0*Minute] ;; GreaterEqualP[0*Minute] | Full) | {(GreaterEqualP[0*Minute] ;; GreaterEqualP[0*Minute] | Full)..}) | Automatic) | Null

Index Matches to: ColumnPrimeAcquisitionWindow

ColumnPrimeExclusionMass

The intact ions (Target Mass) to omit. When the Mode is set to All, the mass is excluded for the entire ExclusionDomain. When set to Once, the mass is excluded in the first survey appearance, but considered for consequent ones.

Default Value: Automatic

Default Calculation: If any ColumnPrimeExclusionMode-related options are set (e.g. ColumnPrimeExclusionMassTolerance), a target mass of the first Analyte (if not in ColumnPrimeInclusionMasses) is chosen and retention time is set to 0*Minute.

Pattern Description: List of one or more {Mode, Target Mass} entries or {Mode, Target Mass} or Null.

Programmatic Pattern: (({All | Once, RangeP[2*(Gram/Mole), 100000*(Gram/Mole)]} | {{All | Once, RangeP[2*(Gram/Mole), 100000*(Gram/Mole)]}..}) | Automatic) | Null

Index Matches to: ColumnPrimeAcquisitionWindow

ColumnPrimeExclusionMassTolerance

The range above and below each ion in ColumnPrimeExclusionMasses to consider for omission when ColumnPrimeExclusionMass is set to All or Once.

Default Value: Automatic

Default Calculation: If ColumnPrimeExclusionMass -> All or Once, set to 0.5 Gram/Mole; otherwise, Null.

Pattern Description: Greater than or equal to 0 grams per mole and less than or equal to 3000 grams per mole or Null.

Programmatic Pattern: (RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | Automatic) | Null

Index Matches to: ColumnPrimeAcquisitionWindow

ColumnPrimeExclusionRetentionTimeTolerance

The range of time above and below the ColumnPrimeExclusionDomain to consider for exclusion.

Default Value: Automatic

Default Calculation: If ColumnPrimeExclusionMass and ColumnPrimeExclusionDomain options are set, this is set to 10 seconds; otherwise, Null.

Pattern Description: Greater than or equal to 0 seconds and less than or equal to 3600 seconds or Null.

Programmatic Pattern: (RangeP[0*Second, 3600*Second] | Automatic) | Null

Index Matches to: ColumnPrimeAcquisitionWindow

The maximum charge state of the ColumnPrimeInclusionMass to also consider for inclusion. For example, if this is set to 3 and the polarity is Positive, then +1,+2,+3 charge states will be considered as well.

Default Value: Automatic

Default Calculation: Inherited from any supplied method.

Programmatic Pattern: ((RangeP[0, 6, 1] | {RangeP[0, 6, 1]..}) | Automatic) | Null

Index Matches to: ColumnPrimeAcquisitionWindow

The specific ionic states of intact ions to redundantly exclude from the survey for further fragmentation/acquisition. 1 refers to +1/-1, 2 refers to +2/-2, etc.

Default Value: Automatic

Default Calculation: When ColumnPrimeSurveyChargeStateExclusion is True, set to {1,2}; otherwise, Null.

Programmatic Pattern: ((RangeP[1, 6, 1] | {RangeP[1, 6, 1]..}) | Automatic) | Null

Index Matches to: ColumnPrimeAcquisitionWindow

ColumnPrimeChargeStateMassTolerance

The range of m/z to consider for exclusion by ionic state property when ColumnPrimeSurveyChargeStateExclusion is True.

Default Value: Automatic

Default Calculation: When ColumnPrimeSurveyChargeStateExclusion is True, set to 0.5 Gram/Mole; otherwise, Null.

Pattern Description: Greater than or equal to 0 grams per mole and less than or equal to 3000 grams per mole or Null.

Programmatic Pattern: (RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | Automatic) | Null

Index Matches to: ColumnPrimeAcquisitionWindow

Default Value: Automatic

Default Calculation: Is set to 500 g/mol if using NeutralIonLoss as the ColumnPrimeAcquisitionMode, and is Null in other modes.

Pattern Description: Greater than 0 grams per mole or Null.

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

Index Matches to: ColumnPrimeAcquisitionWindow

Default Value: Automatic

Default Calculation: Is set based on ColumnPrimeMassDetection, ColumnPrimeCollissionEnergy, ColumnPrimeDwellTime and ColumnPrimeFramentMassDetection.

Pattern Description: List of one or more Individual Multiple Reaction Monitoring Assay or None entries or Null.

Programmatic Pattern: (({({GreaterP[0*(Gram/Mole)], (RangeP[5*Volt, 180*Volt] | RangeP[-180*Volt, 5*Volt]) | Automatic, GreaterP[0*(Gram/Mole)], GreaterP[0*Second] | Automatic} | Null)..} | Null) | Automatic) | Null

Index Matches to: ColumnPrimeAcquisitionWindow

Default Value: Automatic

Default Calculation: Automatically set to best meet the values specified in ColumnFlushGradient options (e.g. ColumnFlushGradientA, ColumnFlushGradientB, ColumnFlushGradientC, ColumnFlushGradientD, ColumnFlushFlowRate).

ColumnFlushIonMode

Indicates if positively or negatively charged ions are analyzed.

Default Value: Automatic

Default Calculation: Set to the first IonMode for an analyte input sample.

Pattern Description: Negative or Positive or Null.

Programmatic Pattern: (IonModeP | Automatic) | Null

ColumnFlushMassSpectrometryMethod

The previously specified instruction(s) for the analyte ionization, selection, fragmentation, and detection.

Default Value: Automatic

Default Calculation: If ColumnFlush samples exist and MassSpectrometryMethod is specified, then set to the first available ColumnFlushMassSpectrometryMethod.

Pattern Description: An object of type or subtype Object[Method, MassAcquisition] or New or Null.

Programmatic Pattern: ((ObjectP[Object[Method, MassAcquisition]] | New) | Automatic) | Null

ColumnFlushESICapillaryVoltage

The absolute voltage applied to the tip of the stainless steel capillary tubing in order to produce charged droplets. Adjust this voltage to maximize sensitivity. Most compounds are optimized between 0.5 and 3.2 kV in ESI positive ion mode and 0.5 and 2.6 in ESI negative ion mode, but can be altered according to sample type. For low flow applications, best sensitivity will be achieved with a relatively high value in ESI positive (e.g. 3.0 kV), for columnFlush flow UPLC a value of 0.5 kV is typically best for maximum sensitivity.

Default Value: Automatic

Default Calculation: Is automatically set to the first ESICapillaryVoltage.

Pattern Description: Greater than or equal to -4 kilovolts and less than or equal to 5 kilovolts or Null.

Programmatic Pattern: (RangeP[-4*Kilovolt, 5*Kilovolt] | Automatic) | Null

ColumnFlushDeclusteringVoltage

Default Value: Automatic

Default Calculation: Is automatically set to any specified MassAcquisition method; otherwise, set to 40 Volt.

Pattern Description: Greater than or equal to 0.1 volts and less than or equal to 150 volts or Null.

Programmatic Pattern: (RangeP[0.1*Volt, 150*Volt] | Automatic) | Null

ColumnFlushStepwaveVoltage

Default Value: Automatic

Default Calculation: Is automatically set to the first StepwaveVoltage.

Pattern Description: Greater than or equal to 0.1 volts and less than or equal to 200 volts or Null.

Programmatic Pattern: (RangeP[0.1*Volt, 200*Volt] | Automatic) | Null

ColumnFlushSourceTemperature

Default Value: Automatic

Default Calculation: Is automatically set to the first SourceTemperature.

Pattern Description: Greater than or equal to 25 degrees Celsius and less than or equal to 150 degrees Celsius or Null.

Programmatic Pattern: (RangeP[25*Celsius, 150*Celsius] | Automatic) | Null

ColumnFlushDesolvationTemperature

The temperature setting for the ESI desolvation heater that controls the nitrogen gas temperature used for solvent evaporation to produce single gas phase ions from the ion spray. Similar to ColumnFlushDesolvationGasFlow, this setting is dependent on solvent flow rate and composition. A typical range is from 150 to 650 Celsius.

Default Value: Automatic

Default Calculation: Is automatically set to the first DesolvationTemperature.

Pattern Description: Greater than or equal to 20 degrees Celsius and less than or equal to 650 degrees Celsius or Null.

Programmatic Pattern: (RangeP[20*Celsius, 650*Celsius] | Automatic) | Null

ColumnFlushDesolvationGasFlow

The rate at which nitrogen gas is flowed around the ESI capillary. It is used for solvent evaporation to produce single gas phase ions from the ion spray. Similar to ColumnFlushDesolvationTemperature, this setting is dependent on solvent flow rate and composition. Higher desolvation temperatures usually result in increased sensitivity, but too high values can cause spray instability. Typical values are between 300 to 1200 L/h.

Default Value: Automatic

Default Calculation: Is automatically set to the first DesolvationGasFlow.

Programmatic Pattern: ((RangeP[55*(Liter/Hour), 1200*(Liter/Hour)] | RangeP[0*PSI, 85*PSI]) | Automatic) | Null

ColumnFlushConeGasFlow

Default Value: Automatic

Default Calculation: Is automatically set to the first ConeGasFlow.

Programmatic Pattern: ((RangeP[0*(Liter/Hour), 300*(Liter/Hour)] | RangeP[30*PSI, 50*PSI]) | Automatic) | Null

The lowest and the highest mass-to-charge ratio (m/z) to be recorded or selected for intact masses. When ColumnFlushFragment is True, the intact ions will be selected for fragmentation.

Default Value: Automatic

Default Calculation: For ColumnFlushFragment -> False, automatically set to one of three default mass ranges according to the molecular weight of the ColumnFlushAnalytes to encompass them.

Pattern Description: All or Range or Single or Specific List or Null.

Index Matches to: ColumnFlushAcquisitionWindow

ColumnFlushScanTime

The duration of time allowed to pass between each spectral acquisition. When ColumnFlushAcquisitionMode is DataDependent, this value refers to the duration for measuring spectra from the intact ions. Increasing this value improves sensitivity whereas decreasing this value allows for more data points and spectra to be acquired.

Default Value: Automatic

Default Calculation: Set to 0.2 seconds unless a method is given.

Pattern Description: Greater than or equal to 0.015 seconds and less than or equal to 10 seconds.

Programmatic Pattern: RangeP[0.015*Second, 10*Second] | Automatic

Index Matches to: ColumnFlushAcquisitionWindow

ColumnFlushFragmentMassDetection

The lowest and the highest mass-to-charge ratio (m/z) to be recorded or selected for product ions. When ColumnFlushAcquisitionMode is DataDependent|DataIndependent, all of the product ions in consideration for measurement. Null if ColumnFlushFragment is False.

Default Value: Automatic

Default Calculation: When ColumnFlushFragment is False, set to Null. Otherwise, 20 Gram/Mole to the maximum ColumnFlushMassDetection.

Pattern Description: All or Range or Specific or Null.

Programmatic Pattern: (({RangeP[20*(Gram/Mole), 16000*(Gram/Mole)]..} | All | RangeP[20*(Gram/Mole), 16000*(Gram/Mole)] ;; RangeP[100*(Gram/Mole), 16000*(Gram/Mole)]) | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

ColumnFlushCollisionEnergy

The voltage by which intact ions are accelerated through inert gas in order to dissociate them into measurable fragment ion species when ColumnFlushFragment is True. Cannot be defined simultaneously with ColumnFlushCollisionEnergyMassProfile.

Default Value: Automatic

Default Calculation: Is automatically set to 40 Volt when ColumnFlushFragment is True, otherwise is set to Null.

Programmatic Pattern: (((RangeP[5*Volt, 255*Volt] | RangeP[-180*Volt, 5*Volt]) | {(RangeP[5*Volt, 180*Volt] | RangeP[-180*Volt, 5*Volt])..}) | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

ColumnFlushCollisionEnergyMassProfile

The relationship of collision energy with the ColumnFlushMassDetection.

Default Value: Automatic

Default Calculation: Set to ColumnFlushCollisionEnergyMassScan if defined; otherwise, set to Null.

Programmatic Pattern: (RangeP[0.1*Volt, 255*Volt] ;; RangeP[0.1*Volt, 255*Volt] | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

The tune range when the ColumnFlushExclusionMasses are omitted in the chromatogram. Full indicates for the entire period.

Default Value: Automatic

Default Calculation: Set to the entire ColumnFlushAcquisitionWindow.

Programmatic Pattern: (((GreaterEqualP[0*Minute] ;; GreaterEqualP[0*Minute] | Full) | {(GreaterEqualP[0*Minute] ;; GreaterEqualP[0*Minute] | Full)..}) | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

The time range when the ColumnFlushInclusionMass applies with respect to the chromatogram.

Default Value: Automatic

Default Calculation: Set to the entire ColumnFlushAcquisitionWindow.

Programmatic Pattern: (((GreaterEqualP[0*Minute] ;; GreaterEqualP[0*Minute] | Full) | {(GreaterEqualP[0*Minute] ;; GreaterEqualP[0*Minute] | Full)..}) | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

ColumnFlushInclusionMass

The ions (Target Mass) to prioritize during the survey scan for further fragmentation When ColumnFlushAcquisitionMode is DataDependent. ColumnFlushInclusionMass set to Only will solely be considered for surveys. When Mode is Preferential, the InclusionMass will be prioritized for survey.

Default Value: Automatic

Default Calculation: When ColumnFlushInclusionMode Only or Preferential, an entry mass is added based on the mass of the most salient analyte of the sample.

Pattern Description: List of one or more {Mode, Target Mass} entries or {Mode, Target Mass} or Null.

Programmatic Pattern: (({Only | Preferential, RangeP[2*(Gram/Mole), 4000*(Gram/Mole)]} | {{Only | Preferential, RangeP[2*(Gram/Mole), 4000*(Gram/Mole)]}..}) | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

ColumnFlushInclusionCollisionEnergy

The overriding collision energy value that can be applied to the ColumnFlushInclusionMass. Null will default to the ColumnFlushCollisionEnergy option and related.

Default Value: Automatic

Default Calculation: Inherited from any supplied method.

Pattern Description: Greater than or equal to 0 volts and less than or equal to 255 volts or list of one or more greater than or equal to 0 volts and less than or equal to 255 volts entries or Null.

Programmatic Pattern: ((RangeP[0*Volt, 255*Volt] | {RangeP[0*Volt, 255*Volt]..}) | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

ColumnFlushInclusionDeclusteringVoltage

The overriding source voltage value that can be applied to the ColumnFlushInclusionMass. Null will default to the ColumnFlushDeclusteringVoltage option.

Default Value: Automatic

Default Calculation: Inherited from any supplied method.

Programmatic Pattern: ((RangeP[0.1*Volt, 150*Volt] | {RangeP[0.1*Volt, 150*Volt]..}) | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

ColumnFlushInclusionChargeState

The maximum charge state of the ColumnFlushInclusionMass to also consider for inclusion. For example, if this is set to 3 and the polarity is Positive, then +1,+2,+3 charge states will be considered as well.

Default Value: Automatic

Default Calculation: Inherited from any supplied method.

Programmatic Pattern: ((RangeP[0, 6, 1] | {RangeP[0, 6, 1]..}) | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

The specific ionic states of intact ions to redundantly exclude from the survey for further fragmentation/acquisition. 1 refers to +1/-1, 2 refers to +2/-2, etc.

Default Value: Automatic

Default Calculation: When ColumnFlushSurveyChargeStateExclusion is True, set to {1,2}; otherwise, Null.

Programmatic Pattern: ((RangeP[1, 6, 1] | {RangeP[1, 6, 1]..}) | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

ColumnFlushChargeStateMassTolerance

The range of m/z to consider for exclusion by ionic state property when ColumnFlushSurveyChargeStateExclusion is True.

Default Value: Automatic

Default Calculation: When ColumnFlushSurveyChargeStateExclusion is True, set to 0.5 Gram/Mole; otherwise, Null.

Pattern Description: Greater than or equal to 0 grams per mole and less than or equal to 3000 grams per mole or Null.

Programmatic Pattern: (RangeP[0*(Gram/Mole), 3000*(Gram/Mole)] | Automatic) | Null

Index Matches to: ColumnFlushAcquisitionWindow

Default Value: Automatic

Default Calculation: Is set to 500 g/mol if using NeutralIonLoss as the ColumnFlushAcquisitionMode, and is Null in other modes.

Pattern Description: Greater than 0 grams per mole or Null.

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

Index Matches to: ColumnFlushAcquisitionWindow

Default Value: Automatic

Default Calculation: Is set based on ColumnFlushMassDetection, ColumnFlushCollissionEnergy, ColumnFlushDwellTime and ColumnFlushFramentMassDetection.

Pattern Description: List of one or more Individual Multiple Reaction Monitoring Assay or None entries or Null.

Index Matches to: ColumnFlushAcquisitionWindow

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 ExperimentSampleManipulation.

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

PreparatoryPrimitives

Index Matches to: experiment samples

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

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

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

Basics

High performance liquid chromatography (HPLC) separates sample mixtures into analyzable molecular constituents by injection into flowing liquid that passes through a retentive column:

MassAnalyzer

Use MassAnalyzer option to select TripleQuadruploe as the mass analyzer

Separation Mode and Gradient

More specific buffers and gradient profiles can also be articulated. For example:

A full gradient table can be specified:

Ionization

The polarity of the ions analyzed can be set along with the desired reference solution for the sample masses:

Specific settings for electrospray ionization source can be controlled in order to maximize ionization capability:

Acquisition Windows and Modes

Different acquisition modes can be specified within different time periods for the same chromatogram. Here, for all of the samples, during the time period from 2 minutes to 5 minutes, an MS1FullScan acquisition is employed (no fragmentation; measure intact ions). From 7 minutes to 9, a data dependent acquisition is performed (see the appropriate section above):

Similarly, different fragmentation instructions can be specified for different time periods:

Multiple Reaction Monitoring

Specified MassAnalyzer, AcquisitionMode, MassSelection and FragmentMassSelection to conduct multiple reaction monitoring analysis by using QTRAP 6500:

Specified MassAnalyzer, AcquisitionMode and MultipleReactionMonitoringAssays to conduct multiple reaction monitoring analysis by using QTRAP 6500:

Data Dependent Acquisition

In data dependent acquisition, the measurement is split into cycles (see the figure above). In the first part of the cycle, the intact ions (no fragmentations) are surveyed and considered for fragmentation analysis:

A threshold can be specified on whether to consider an intact ion for fragmentation analysis. Likewise, a limit can be placed so that a highly abundant ion is not overly analyzed:

Various m/z can be excluded from the acquisition program:

Masses can be prioritized for fragmentation as they surface during the surveys:

Redundant isotopes can excluded from acquisition surveys:

Redundant charge states can excluded from acquisition surveys:

Standards and Blanks

ExperimentLCMS can be used to quantify analytes in a sample, in which case, a Standard sample is employed to serve as reference. A standard can be submitted before and after the injection sequence of the samples simply by running:

Likewise, a Blank sample can be used to see if there is any background from the injection process. To run a blank to occur between every 5 samples, use the following command:

PhotoDiodeArray detection

PhotoDiodeArray detection involves passes light across a range of wavelengths and measures how much light is absorbed for each even wavelength:

Injection Table

In addition to specifying frequencies of running standards and blanks, now the injection sequence of samples, standards, blanks, and column primes/flushes can be explicitly articulated as well. In this case, an additional column flush is specified after the injection of the second sample:

Preferred Input Containers

The autosampler can take 2mL deep well plates.

The autosampler can take normal vials routinely used in HPLC analysis.

Data Processing

The data can be viewed by PlotChromatographyMassSpectra:

The data can be viewed by different types by spcifying PlotType options:

Use the PlotType and MassSpectrumTimeRange to plot mass spectrum data with in a certain time range:

Use ExcludeRange to specify one or more ranges of m/z values to exclude from different type of plots:

Warnings and Errors

Messages (90)

AbsorbanceRateAdjusted (1)

Adjust the sampling rate if not an available value:

AcquisitionLimitConflict (1)

When AcquisitionLimit is set, AcquisitionMode must be DataDependent; otherwise, throw an error and return $Failed:

AcquisitionSurveyConflict (1)

When AcquisitionSurvey is set, AcquisitionMode must be DataDependent; otherwise, throw an error and return $Failed:

AcquisitionWindowTooLong (1)

Specified acquisition windows cannot exceed the gradient:

AirFlowRatePrecision (1)

Return a warning when an air flow rate value is specified to unfeasible precision:

BlankFrequencyNoBlanks (1)

BlankFrequency must be Automatic, Null, or None when there are no Blank samples:

BlankOptionsButNoFrequency (1)

BlankFrequency cannot be None if other blank options are defined:

ChargeStateExclusionConflict (1)

When ChargeStateExclusion options are set, AcquisitionMode must be DataDependent; otherwise, throw an error and return $Failed:

ChargeStateExclusionLimitConflict (1)

When ChargeStateExclusionLimit exceeds AcquisitionSurvey throw an error and return $Failed:

ChargeStateMassToleranceConflict (1)

ChargeStateMassTolerance must be set when ChargeStateExclusion options are; otherwise, throw an error and return $Failed:

CollisionEnergyConflict (1)

When CollisionEnergy is incompatible with the AcquisitionMode throw an error and return $Failed:

CollisionEnergyProfileConflict (1)

When CollisionEnergy and CollisionEnergyScan are both defined throw an error and return $Failed:

CollisionEnergyScanConflict (1)

CollisionEnergyMassScan can only be defined when AcquisitionMode is DataDependent:

ColumnFlushConflict (1)

Throw an error when column flush turned off, but an option is specified:

ColumnGap (1)

Columns specified in series cannot have gaps within:

ColumnPrimeConflict (1)

Throw an error when column prime turned off, but an option is specified:

ColumnSelectorConflict (1)

If ColumnSelector is specified, then any specified Columns must be represented within:

CycleTimeLimitConflict (1)

When CycleTimeLimit is set, AcquisitionMode must be DataDependent; otherwise, throw an error and return $Failed:

DataIndependentSoleWindow (1)

Return an error when DataIndependent is specified in a multi-acquisition window run:

DimensionlessPrecision (1)

Return a warning when a dimensionless value is specified to unfeasible precision:

ExclusionMassToleranceConflict (1)

ExclusionMassTolerance must be set when ExclusionMass is; otherwise, throw an error and return $Failed:

ExclusionModeConflict (1)

When ExclusionMass options are set, AcquisitionMode must be DataDependent; otherwise, throw an error and return $Failed:

ExclusionModeMustBeSame (1)

ExclusionMasses must all have the same exclusion mode:

ExclusionRetentionTimeConflict (1)

ExclusionRetentionTime must be set when ExclusionMass options are; otherwise, throw an error and return $Failed:

FlowRatePrecision (1)

Return a warning when the FlowRate is specified to unfeasible precision:

FragmentConflict (1)

When Fragment disagrees with the AcquistionMode throw an error and return $Failed:

FragmentDetectionConflict (1)

When FragmentMassDetection is incompatible with the AcquisitionMode throw an error and return $Failed:

FragmentScanTimeConflict (1)

When FragmentScanTime is set, AcquisitionMode must be DataDependent; otherwise, throw an error and return $Failed:

GradientAmbiguity (1)

If Gradient is a table, then auxillary options lead to ambiguity:

GradientOutOfOrder (2)

If Gradient is a table, each entry must be ascending in time:

GradientPercentPrecision (1)

Return a warning when the percent in Gradient is specified to unfeasible precision:

GradientSingleton (1)

Return an error when the specified gradient only has one entry:

GuardColumnSelector (1)

If ColumnSelector and GuardColumn are both specified, then they must match:

HPLCIncompatibleAliquotContainer (1)

Error if the specified container in which to aliquot the samples is not compatible with an HPLC instrument:

InclusionMassToleranceConflict (1)

InclusionMassTolerance must be set when InclusionMass options are; otherwise, throw an error and return $Failed:

InclusionModeConflict (1)

When InclusionMass related options are defined, AcquisitionMode must be DataDependent; otherwise, throw an error and return $Failed:

IncompatibleColumnTechnique (2)

Warning is thrown if specified Column's ChromatographyType is not HPLC:

If multiple columns are specified, a warning is thrown if any specified Column's ChromatographyType is not HPLC:

IncompatibleColumnTemperature (1)

If multiple columns are specified, a warning is thrown if the specified column temperature is outside any specified Column's compatible temperature range:

IncompatibleColumnType (3)

Warning is thrown if specified Column's SeparationMode does not match the specified SeparationMode:

Warning is thrown if specified GuardColumn's SeparationMode does not match the specified SeparationMode:

If multiple columns are specified, a warning is thrown if any specified Column's SeparationMode does not match the specified Type:

IncompatibleContainerModel (1)

Error if aliquot is explicity prohibited and the input samples are in a container type that is not compatible with an HPLC instrument:

IncompatibleMaterials (1)

Return a warning when a sample incompatible with the instrument:

InjectionTableBlankConflict (1)

Both InjectionTable and Blank are specified but have a mismatch:

InjectionTableBlankFrequencyConflict (1)

Both InjectionTable and (StandardFrequency, BlankFrequency, nor ColumnRefreshFrequency) cannot be set at the same time:

InjectionTableForeignSamples (1)

The InjectionTable contains samples that are not in the input or doesn't account for all of the samples:

InjectionTableStandardConflict (1)

Both InjectionTable and Standard are specified but have a mismatch:

InvalidCollisionVoltageOptions (2)

QQQ must speicify CollisionEnergy and CollisionCellExitVoltage that are consistent with ion mode:

QTOF must use positive CollisionEnergy and CollisionCellExitVoltage must be Null:

InvalidGasFlowOptions (2)

QQQ must use pressure for gas flow options:

QTOF must use flow rate for gas flow options:

InvalidGradientCompositionOptions (5)

Error if a specified gradient's total buffer composition is greater than 100%:

Error if a specified standard gradient's total buffer composition is greater than 100%:

Error if a specified blank gradient's total buffer composition is greater than 100%:

Error if a specified column prime gradient's total buffer composition is greater than 100%:

Error if a specified column flush gradient's total buffer composition is greater than 100%:

InvalidVoltageOptions (3)

QQQ must use 150 Celsius as the Source Temperature:

QTOF must use positive voltages:

QQQ must use voltages that are consistent with ion mode:

IsotopeMassToleranceConflict (1)

IsotopeMassTolerance must be set when ChargeStateExclusion or IsotopicExclusionMass options are; otherwise, throw an error and return $Failed:

IsotopeRatioToleranceConflict (1)

IsotopeRatioTolerance must be set when IsotopicExclusionMass options are; otherwise, throw an error and return $Failed:

IsotopicExclusionLimitConflict (1)

When IsotopicExclusionMass exceeds two entries throw an error and return $Failed:

IsotopicExclusionMassConflict (1)

When IsotopicExclusionMass options are set, AcquisitionMode must be DataDependent; otherwise, throw an error and return $Failed:

LargeVoltagePrecision (1)

Return a warning when a large voltage value is specified to unfeasible precision:

LCMSAutoResolvedNeutralLoss (1)

Need to specify NeutralLoss:

LCMSCollisionEnergyAcquisitionModeConflict (1)

If the AcquisitionMode is not MultipleReactionMonitoring, the CollisionEnergies cannot be set to a list of single values.

LCMSInvalidMultipleReactionMonitoringLengthOfInputOptions (1)

If using MultipleReactionMonitoring, all inputs (MassDetection,FragmentMassDetection,CollisionEnerigy and DwellTime) should have same length for each sample:

LCMSInvalidScanTime (1)

When the instrumentation is unable to scan a mass range in the specified ScanTime the function fails and an error is returned:

MassAnalyzerAndAcquitionModeMismatched (1)

QTOF must use flow rate for gas flow options:

MassAnalyzerAndMassSpecInstrumentConflict (1)

MassAnalyzer and MassSpectrometerInstrument should matched with each other:

MassDetectionConflict (1)

When MassDetection is incompatible with AcquisitionMode throw an error and return $Failed:

MassPrecision (1)

Return a warning when a mass is specified to unfeasible precision:

NonBinaryHPLC (2)

Non-binary gradients are not supported in ExperimentLCMS:

Non-binary gradients are not supported in ExperimentLCMS (2):

OnlyHPLCAvailable (1)

If a liquid chromatography device not amendable to LCMS is requested, an error is thrown:

OnlyOneCalibrantWillBeRan (1)

Only one calibrant will be run for using QTOF as the mass analyzer:

OverlappingAcquisitionWindows (1)

Acquisition Windows cannot be overlapping:

OverwritingGradient (1)

If a value in a supplied gradient is overwritten, then a new gradient method should be made:

PercentPrecision (1)

Return a warning when a percent value is specified to unfeasible precision:

PerSecondPrecision (1)

Return a warning when a 1/Second value is specified to unfeasible precision:

RemovedExtraGradientEntries (1)

Duplicate times in the gradients will be removed but a warning will be thrown:

RepeatedDetectors (1)

Duplicate entries in the Detector option are removed:

StandardOptionsButNoFrequency (1)

StandardFrequency cannot be None if other standard options are defined:

StandardsButNoFrequency (1)

StandardFrequency must not be None or Infinity when there are Standard samples:

TemperaturePrecision (1)

Return a warning when a temperature value is specified to unfeasible precision:

TimePrecision (1)

Return a warning when a time value is specified to unfeasible precision:

VoltagePrecision (1)

Return a warning when a voltage is specified to unfeasible precision:

WavelengthPrecision (1)

Return a warning when the AbsorbanceWavelength is specified to unfeasible precision:

Possible Issues

Equilibration

Equilibrate to the correct buffer conditions at the end of each gradient to reach a state that is appropriate for the start of the next gradient.

Column flush

The column will end up being stored in whatever the final gradient solvent conditions are so that should be considered for column protection.

Column fouling

Consider using a GuardColumn to preserve column lifetime. Examine injections of standards over time to ensure that the column is performing to satisfaction.

Filter sample and buffer

Samples should not have particulates; otherwise, the system will over-pressurize. Consider filtering any samples or buffers used for the LCMS experiment.

Last modified on Sun 14 Apr 2024 14:58:35