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Object[Method, MassAcquisition]

A set of parameters used to conduct acquisition on a mass spectrometer.

Organizational Information

    Name

    Name of this Object.
    Format: Single
    Class: String
    Programmatic Pattern: _String
    Pattern Description: A string.

    ID

    ID of this Object.
    Format: Single
    Class: String
    Programmatic Pattern: _String
    Pattern Description: The ID of this object.

    Object

    Object of this Object.
    Format: Single
    Class: Expression
    Programmatic Pattern: Object[Method, MassAcquisition, _String]
    Pattern Description: The object reference of this object.

    Type

    Type of this Object.
    Format: Single
    Class: Expression
    Programmatic Pattern: Object[Method, MassAcquisition]
    Pattern Description: Object[Method, MassAcquisition]

    Notebook

    Notebook this object belongs to.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Pattern Description: An object of that matches ObjectP[Object[LaboratoryNotebook]].

General

    Template

    The method whose option selections should be selected as the default options for this method.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link

    MethodsTemplated

    Methods which were generated using this method's options as a starting point for its option defaults.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link

    MassAnalyzer

    The type of the component of the mass spectrometer that performs ion separation based on m/z (mass-to-charge ratio). QTOF accelerates ions through a flight tube and resolves by their flight time.
    Format: Single
    Class: Expression
    Programmatic Pattern: MassAnalyzerTypeP

Ionization

    IonSource

    The type of ionization used to create gas phase ions from the molecules in the sample. Electrospray ionization (ESI) produces ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol, and gas phase ions are formed from the fine spray of charged droplets as a result of solvent evaporation and Coulomb fission.
    Format: Single
    Class: Expression
    Programmatic Pattern: IonSourceP

    ESICapillaryVoltage

    The applied voltage differential between the injector and the inlet for the mass spectrometry in order to ionize analyte molecules.
    Format: Single
    Class: Real
    Unit: 1 volt
    Programmatic Pattern: UnitsP[0 Volt]

    DesolvationTemperature

    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.
    Format: Single
    Class: Real
    Unit: 1 degree Celsius
    Programmatic Pattern: GreaterP[0 Celsius]

    SourceTemperature

    The temperature that the source block is set to in order to discourage condensation and decrease solvent clustering in the reduced vacuum region of the source. The source block is the metallic chamber with reduced pressure separating the sprayer (at atmospheric pressure) and the inside of the mass spectrometer (at 10^-7 Torr of pressure). It consists of the sampling cone, the isolation valve, and the ion block. The source temperature setting affects sensitivity.
    Format: Single
    Class: Real
    Unit: 1 degree Celsius
    Programmatic Pattern: GreaterP[0 Celsius]

    DeclusteringVoltage

    The applied voltage between the sample inlet on the mass spectrometry and the first stage of the ion filter.
    Format: Single
    Class: Real
    Unit: 1 volt
    Programmatic Pattern: UnitsP[0 Volt]

    ConeGasFlow

    The rate of nitrogen gas flow ejected around the sample inlet cone (the spherical metal plate on the source block, acting as a first gate between the sprayer and the reduced-pressure ion block). This gas flow is used to minimize the formation of solvent ion clusters. It also helps reduce adduct ions and directs the spray into the ion block while keeping the sample cone clean.
    Format: Single
    Class: VariableUnit
    Programmatic Pattern: 1 Liter Hold[GreaterP[-------] | GreaterP[0 PSI]] Hour

    DesolvationGasFlow

    The nitrogen gas flow ejected around the ESI (electrospray ionization) capillary, used for solvent evaporation to produce single gas phase ions from the ion spray.
    Format: Single
    Class: VariableUnit
    Programmatic Pattern: 1 Liter Hold[GreaterP[-------] | GreaterP[0 PSI]] Hour

    StepwaveVoltage

    The applied voltage between the two stages of the ion filter.
    Format: Single
    Class: Real
    Unit: 1 volt
    Programmatic Pattern: GreaterP[0 Volt]

    IonMode

    The polarity of the charged analyte.
    Format: Single
    Class: Expression
    Programmatic Pattern: IonModeP

    IonGuideVoltage

    The absolute voltage applied to the tip of the stainless steel ESI (electrospray ionization) capillary tubing in order to produce charged droplets. This is an unique option for ESI-QQQ, and also referred as IonSprayVoltages.
    Format: Single
    Class: Real
    Unit: 1 volt
    Programmatic Pattern: UnitsP[0 Volt]

Sample Preparation

    Calibrant

    The sample with known mass-to-charge ratios used to calibrate the mass spectrometer.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Sample]

    SecondCalibrant

    The second sample with known mass-to-charge ratios used to calibrate the mass spectrometer.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Sample]

Mass Analysis

    AcquisitionWindows

    The time blocks to acquire measurement.
    Format: Multiple

    [StartTime]

      Header: StartTime
      Class: Real
      Unit: 1 minute

    [EndTime]

      Header: EndTime
      Class: Real
      Unit: 1 minute

    AcquisitionModes

    For each member of AcquisitionWindows, the manner of scanning and/or fragmenting intact and resultant ions.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: MSAcquisitionModeP

    Fragmentations

    For each member of AcquisitionWindows, indicates whether the intact ions collide with inert gas to dissociate into product ions. Also known as Tandem mass spectrometry or MS/MS.
    Format: Multiple
    Class: Boolean
    Programmatic Pattern: BooleanP

    MinMasses

    For each member of AcquisitionWindows, the lowest measured or selected mass-to-charge ratio (m/z) intact ions.
    Format: Multiple
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: 0 Gram Hold[GreaterEqualP[------]] Mole

    MaxMasses

    For each member of AcquisitionWindows, the highest measured or selected mass-to-charge ratio (m/z) intact ions.
    Format: Multiple
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: 0 Gram Hold[GreaterP[------]] Mole

    MassSelections

    For each member of AcquisitionWindows, all of the measured or selected mass-to-charge ratio (m/z) intact ions.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: 0 Gram Hold[{GreaterP[------]..}] Mole

    ScanTimes

    For each member of AcquisitionWindows, the duration of time allowed to pass between each spectral acquisition.
    Format: Multiple
    Class: Real
    Unit: 1 second
    Programmatic Pattern: GreaterP[0 Second]

    FragmentMinMasses

    For each member of AcquisitionWindows, the lowest measured or selected mass-to-charge ratio (m/z) dissociation product ions.
    Format: Multiple
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: 0 Gram Hold[GreaterEqualP[------]] Mole

    FragmentMaxMasses

    For each member of AcquisitionWindows, the highest measured or selected mass-to-charge ratio (m/z) dissociation product ions.
    Format: Multiple
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: 0 Gram Hold[GreaterP[------]] Mole

    FragmentMassSelections

    For each member of AcquisitionWindows, all of the measured or selected mass-to-charge ratio (m/z) dissociation product ions.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: 0 Gram Hold[{GreaterP[------]..}] Mole

    CollisionEnergies

    For each member of AcquisitionWindows, all of the measured or selected mass-to-charge ratio (m/z) dissociation product ions.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {UnitsP[0 Volt]..} | UnitsP[0 Volt]

    LowCollisionEnergies

    For each member of AcquisitionWindows, the lowest value of the linear function for applied potential as mapped to the MinMass.
    Format: Multiple
    Class: Real
    Unit: 1 volt
    Programmatic Pattern: GreaterP[0 Volt]

    HighCollisionEnergies

    For each member of AcquisitionWindows, the highest value of the linear function for applied potential as mapped to the MinMass.
    Format: Multiple
    Class: Real
    Unit: 1 volt
    Programmatic Pattern: GreaterP[0 Volt]

    FinalLowCollisionEnergies

    For each member of AcquisitionWindows, at the end of the spectral scan, the lowest value of the linear function for applied potential as mapped to the MinMass.
    Format: Multiple
    Class: Real
    Unit: 1 volt
    Programmatic Pattern: GreaterP[0 Volt]

    FinalHighCollisionEnergies

    For each member of AcquisitionWindows, at the end of the spectral scan, the highest value of the linear function for applied potential as mapped to the MinMass.
    Format: Multiple
    Class: Real
    Unit: 1 volt
    Programmatic Pattern: GreaterP[0 Volt]

    FragmentScanTimes

    For each member of AcquisitionWindows, the duration of time allowed to pass between each spectral acquisition for the product ions when AcquistionMode -> DataDependent.
    Format: Multiple
    Class: Real
    Unit: 1 second
    Programmatic Pattern: GreaterP[0 Second]

    AcquisitionSurveys

    For each member of AcquisitionWindows, indicates the number of intact ions to consider for fragmentation and acquisition in DataDependent acquistion mode.
    Format: Multiple
    Class: Integer
    Programmatic Pattern: GreaterP[0, 1]

    MinimumThresholds

    For each member of AcquisitionWindows, the least number of total intact ions needed to be measured to elicit an acquisition program.
    Format: Multiple
    Class: Integer
    Programmatic Pattern: GreaterP[0, 1]

    AcquisitionLimits

    For each member of AcquisitionWindows, the maximum number measured ions allowed during a fragmentation measurement of a survey ion. Will proceed to the next intact ion/fragmentation once reached.
    Format: Multiple
    Class: Integer
    Programmatic Pattern: GreaterP[0, 1]

    CycleTimeLimits

    For each member of AcquisitionWindows, the maximum duration allowable for a survey. Will proceed to the next cycle once reached.
    Format: Multiple
    Class: Real
    Unit: 1 second
    Programmatic Pattern: GreaterP[0 Second]

    ExclusionDomains

    For each member of AcquisitionWindows, the time blocks within to consider for specific mass exclusion.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {{UnitsP[Minute], UnitsP[Minute]}..}

    ExclusionMasses

    For each member of AcquisitionWindows, indicates the manner of omitting intact ions for acquisition survey.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: 0 Gram Hold[{{ExclusionModeP, GreaterP[------]}..}] Mole

    ExclusionMassTolerances

    For each member of AcquisitionWindows, the range above and below each ion in ExclusionMassSelection to consider for omission.
    Format: Multiple
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: GreaterP[0 Dalton]

    ExclusionRetentionTime Tolerances

    For each member of AcquisitionWindows, the range above and below each retention time in ExclusionMassSelection to consider for omission.
    Format: Multiple
    Class: Real
    Unit: 1 second
    Programmatic Pattern: GreaterP[0 Second]

    InclusionDomains

    For each member of AcquisitionWindows, the time blocks within to consider for specific mass inclusion.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {{UnitsP[Minute], UnitsP[Minute]}..}

    InclusionMasses

    For each member of AcquisitionWindows, the intact ions to prioritize during survey acquisition.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: 0 Gram Hold[{{InclusionModeP, GreaterP[------]}..}] Mole

    InclusionCollisionEnergies

    For each member of AcquisitionWindows, the overriding collision energy to use for the corresponding InclusionMass.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {GreaterEqualP[0 Volt]..}

    InclusionDeclusteringVoltages

    For each member of AcquisitionWindows, the overriding source voltage to use for the corresponding InclusionMass.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {GreaterEqualP[0 Volt]..}

    InclusionChargeStates

    For each member of AcquisitionWindows, the charge state isotopes to also consider for inclusion.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {GreaterEqualP[0, 1]..}

    InclusionScanTimes

    For each member of AcquisitionWindows, the overriding scan time to use for the corresponding InclusionMass.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {GreaterEqualP[0 Second]..}

    InclusionMassTolerances

    For each member of AcquisitionWindows, the range above and below each ion in InclusionMassSelection to consider for omission.
    Format: Multiple
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: GreaterP[0 Dalton]

    ChargeStateLimits

    For each member of AcquisitionWindows, the number of ions to survey before excluding for ion state properties.
    Format: Multiple
    Class: Integer
    Programmatic Pattern: GreaterEqualP[0, 1]

    ChargeStateSelections

    For each member of AcquisitionWindows, the specific ionic states of intact ions to redundantly exclude from the survey for further fragmentation/acquisition.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {GreaterEqualP[1, 1]..}

    ChargeStateMassTolerances

    For each member of AcquisitionWindows, the range of m/z to consider for exclusion by ionic state property.
    Format: Multiple
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: GreaterP[0 Dalton]

    IsotopeMassDifferences

    For each member of AcquisitionWindows, the delta between monoisotopic ions as a criterion for survey exclusion.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {GreaterP[0 Dalton]..}

    IsotopeRatios

    For each member of AcquisitionWindows, the minimum relative magnitude between monoisotopic ions as a criterion for survey exclusion.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {GreaterP[0]..}

    IsotopeDetectionMinimums

    For each member of AcquisitionWindows, the acquisition rate of a given intact mass to consider for isotope exclusion in the survey.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: 1 Hold[{GreaterP[0 ------]..}] Second

    IsotopeRatioTolerances

    For each member of AcquisitionWindows, the range of relative magnitude around IsotopeRatio and SecondaryIsotopeRatio to consider for isotope exclusion.
    Format: Multiple
    Class: Real
    Unit: 1 percent
    Programmatic Pattern: GreaterP[0 Percent]

    IsotopeMassTolerances

    For each member of AcquisitionWindows, the range of m/z to consider for exclusion by ionic state property.
    Format: Multiple
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: GreaterP[0 Dalton]

    CollisionCellExitVoltages

    For each member of AcquisitionWindows, if the sample will be scanned in tandem mass spectrometry mode in ESI-QQQ, the value of the potential applied between collision cell and the second Quadrupole mass analyzer (MS2) to guide and focus the ion beam into MS2.
    Format: Multiple
    Class: Real
    Unit: 1 volt
    Programmatic Pattern: UnitsP[0 Volt]

    MassDetectionStepSizes

    For each member of AcquisitionWindows, the mass-to-charge value at which the mass spectrometer will record a data of the mass scan.
    Format: Multiple
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: 0 Gram Hold[GreaterP[------]] Mole

    NeutralLosses

    In ESI-QQQ analysis, if the sample will be scanned in tandem mass spectrometry mode with Neutral Ion Loss mode, the value for the mass offset values between MS1 and MS2 (neutral ion loss value.).
    Format: Multiple
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: 0 Gram Hold[GreaterP[------]] Mole

    DwellTimes

    For each member of AcquisitionWindows, if the sample will be scan in SelectedIonMonitoring mode or MultipleReactionMonitoring mode, the length of time for each mass selection or mass selection pairs.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {({GreaterP[0 Millisecond]..} | GreaterP[0 Millisecond] | Null)..}

    MultipleReactionMonitoring Assays

    For each member of AcquisitionWindows, in ESI-QQQ, that firstly targets the ion corresponding to the compound of interest with subsequent fragmentation of that target ion to produce a range of daughter ions. One (or more) of these fragment daughter ions can be selected for quantitation purposes. Only compounds that meet both these criteria, i.e. specific parent ion and specific daughter ions corresponding to the mass of the molecule of interest are detected within the mass spectrometer. The mass assays (MS1/MS2 mass value combinations) for each scan, along with the CollisionEnergy and dwell time (length of time of each scan).
    Format: Multiple

    [MS1Mass]

      Header: MS1Mass
      Class: Expression

    [CollisionEnergy]

      Header: CollisionEnergy
      Class: Expression

    [MS2Mass]

      Header: MS2Mass
      Class: Expression

    [DwellTime]

      Header: DwellTime
      Class: Expression
Last modified on Mon 26 Sep 2022 15:43:47