Advion Expression CMS - DataApex · AdvionExpressionCMS 4Usingthecontrolmodule ScanMode-SelectedMassRange IntheSelectedMassRangemode,thedatabeingacquiredarewhole spectralscansdefinedusingStart

ADVION EXPRESSION CMS

Clarity Control Module ENG

CodeRev M17250EDate 24102017

Phone +420251013400 DataApex Ltd

Fax +420251013401 Petrzilkova 258313

claritydataapexcom 15800Prague 5

wwwdataapexcom TheCzech Republic

Clarityreg DataApexreg and reg are trademarks of DataApex Ltd Microsoftreg and WindowsTM aretrademarks of Microsoft CorporationDataApex reserves the right to make changes to manuals without prior notice Updated manuals can bedownloaded fromwwwdataapexcom

Author DM

Advion Expression CMS Table of Contents

Contents1 Advion Expression CMS Control Module 12 Requirements 23 Installation Procedure 331 Hardware - Wiring 332 Clarity Configuration 4

4 Using the control module 641 Method Setup - MS - General 6411 Method Setup - MS - Contact Closures 10412 Method Setup - MS - Analog IO 12

42 Device Monitor 14421 Tuning Ion Source 17

43 Expression CMS Setup 225 Report Setup 24

Table of Contents ClarityControlModule

To facilitate the orientation in the Advion Expression CMS manual and Clarity chromatographystation different fonts are used throughout themanual Meanings of these fonts are

Instrument (blue text) marks the nameof thewindow to which the text refersOpenFile (italics) describes the commands and names of fields in Clarity parameters that canbe entered into themor a window or dialog name (when you already are in the topic describingthewindow)WORK1 (capitals) indicates the nameof the file andor directoryACTIVE (capital italics) marks the state of the station or its part

The bold text is sometimes also used for important parts of the text and the name of the Claritystation Moreover some sections are written in format other than normal text These sections areformatted as follows

Note Notifies the reader of relevant information

Caution Warns the user of possibly dangerous or very importantinformation

Marks the problem statement or trouble questionDescription Presents more detailed information on the problem describes its causes

etcSolution Marks the response to the question presents a procedure how to remove it

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Advion Expression CMS 1 Advion Expression CMSControlModule

1 Advion Expression CMS ControlModule

This manual describes the setting of the Advion Expression CMSdetector The control module enables direct control of the instrument overUSB line

Fig 1 Advion Expression CMSdetector

Direct control means that the MS detector can be completely controlledfrom the Clarity environment Instrument method controlling the analysisconditions will be saved in the measured chromatograms

Advion Expression CMS 2Requirements

2 RequirementsClarity Installation CD ROM with LC Control module (pn A24) and MSExtension (pn A38)USB A-B cable (pn SK06)

Note Cables are not part of Clarity Control Module It is stronglyrecommended to order required cables together with the ControlModule

Advion Expression CMS 3 Installation Procedure

3 Installation Procedure31 Hardware - Wiring

The Advion Expression CMS detector is controlled by USBcommunication It uses standard USB A-B cable

Note In some cases the Advion Expression CMS detector loses thecommunication with the control software In such case it is necessary tounplug the communication cable from the computer and plug it back

3 Installation Procedure ClarityControlModule

32 Clarity Configuration

Fig 2 How to add Advion Expression CMS

Start the Clarity station by clicking on the icon on the desktopInvoke the System Configuration dialog accessible from the Claritywindow using the System - Configuration commandPress the Add button ① (see Fig 2 on pg 4 ) to invoke the AvailableControl Modules dialogYou can specify the searching filter② to simplify the finding of the driver

Select the Expression CMS and press the Add ③ button

The Expression CMS Setup dialog will appear (see Fig 3 on pg 5)

Fig 3 Expression CMSSetup

Select the correct Communication mode and press the AutoDetect buttonto check the presence of the detector

Note Other fields from this dialog are described later in the description of theExpression CMSSetup dialog

Press the OK button

The Expression CMS will appear in the Setup Control Modules list ④ ofthe System Configuration dialog

Drag and drop the Expression CMS icon from the Setup Control Moduleslist ④ on the left side of the System Configuration dialog to the desiredInstrument⑤ tab on the right side ⑥ (or use the button ⑦ to do so)

Note The configuration dialog of the Advion Expression CMS detector(Expression CMS Setup) can be displayed any time by double-clicking onits icon or using theSetup button

Advion Expression CMS 4Using the controlmodule

4 Using the control moduleNew MS tab is created in the Method Setup dialog It can be accessed byusing the Method - MS Controlhellip command from the Instrument window

41 Method Setup - MS - GeneralThe Method Setup - MS tab for the Advion Expression CMS detector hasthree sub-tabs General where all information on the acquisition of thesignal is set Contact Closures settings for the detectors digital inputs andoutputs are set and the Analog IO sub-tab containing the settings for theexternal signals processed by the Advion Expression CMS and analogoutput signal settings

Fig 4 Method Setup - MS - General

Instrument SettingsThis section allows to set the Ion Source Settings file and Tune Settingsfile Both of these files are saved in Mass Express-compatible format andsaved in the ADVIONMS subdirectory of the Clarity installation directory(CCLARITYBIN by default) The preparation of your own Ion SourceSettings and Tune Settings files can be performed in the Tuning IonSource dialogIon Source SettingsDefines the particular Ion Source Settings file used for the givenmethod In case of two ion sources a setting for each ion source is

4 Using the controlmodule ClarityControlModule

presentTune SettingsDefines the particular Tune Settings file used for the given method Incase of two ion sources a setting for each ion source is present

Acquisition MethodSome fields in this section change depending on whether the method isused for Single Ion Monitoring (SIM) or Scan acquisitionSignal RangeParameter specifying how intense single ion signals are expectedfrom the Advion Expression CMS The higher the setting is thehigher signals can be acquired but the precision of data on intensityaxis becomes lower Signal of a single ion exceeding the set value willbe trimmed to the set value Maximum TIC signal intensity in Clarity is10000 times higher than Signal Range setScan ModeAllows to select between SIM mode and Selected Mass Range (Scan)mode

Scan Mode - Selected Mass RangeIn the Selected Mass Range mode the data being acquired are wholespectral scans defined using Start End and Scan Time parametersMoreover some of the mz ion signals may be extracted from thegathered spectra which is important for some devices (eg coupling ofthe fraction collector to the Advion Expression CMS detector) Themaximum number of extracted signals to be set here is dependent onthe maximum signals set in the Expression CMS Setup dialogParticular signals are enabled by using the checkbox in the Enablecolumn on a particular row

Mass [mz]Defines the central mass of the ion being acquired The value must layin the range of mz 10 - 1200 including the Span [mz] of the ionwindow

Span [mz]Sets the span of the given ion being acquired This span issymmetrically divided around the Mass [mz] and must be larger than0 Default value is 02

Start [mz]Sets the lowest mz value being scanned This parameter must belower than End [mz] value but cannot go below 10

End [mz]Sets the highest mz value being scanned This parameter must behigher than Start [mz] value but cannot go above 1200

Scan TimeDefines the time during which the detector takes one complete scanfrom Start [mz] to End [mz] The data resolution is 005 mz

Note The maximum scanning speed of the Advion Expression CMSdetector varies according to its subtype for basic CMS it is 5000 AMUswhichmeans the lowest possible value ofScan Time is dependent on therange selected The lower the scan time is the better results will beobtained from the chromatographic point of view (more data points on apeak) but the higher the scan time is the better sensitivity the detector willhave (obtaining eachmz value over longer time)

Full RangeSets the values in the Start [mz] and End [mz] to their maximumvalues according to the subtype of the Advion Expression CMSdetector

Scan Mode - SIM

Fig 5 ScanMode - SIM

In the SIM mode the section is reduced to just the table allowing to setthe SIM signals numbers and their mz values The table has oneadditional column Dwell Time

Dwell Time [ms]Sets the time for which the detector will gather the data for a given SIMion The value must be at least 1 ms the default value is 50 ms

Smooth DataDefines whether spectral data will be smoothed by using Savitzky-Golayfilter While checked the spectral data are smoother but might be lesspreciseRemove NoiseDefines whether the noise will be deducted from the measured dataBefore the acquisition the Advion Expression CMS detector calculatesthe average electronic signal noise and then sets all the data withintensity of less then the average noise plus three times its standarddeviation to zeroUse Two Ion SourcesAccesses the second ion source setting and second tune setting for theAdvion Expression CMS detectors which have two ion sources The UseTwo Ion Sources checkbox must be also checked in the Expression CMSSetup dialog

411 Method Setup - MS - Contact Closures

Fig 6 Method Setup - Acquisition - Output

This sub-tab contains means to control the digital inputs and outputs of theAdvion Expression CMSContact Closure InputSection defining the options to start and stop the analysis of AdvionExpression CMS If the analysis should be started based on digital inputselect the particular Input in the first line check the Start On checkboxselect the expected input level change (Low to High or High to Low ) andthe Delay [ms] which should precede the stating of the analysis after thecontact closure input is invoked Same behavior can be set for stoppingthe analysis based on an input just using the Stop On checkbox andappropriate row

Note Under standard conditions Clarity does not use digital inputs organizedthis way to start and stop analyses Analysis is usually started by anautosampler (whose inject marker may however be connected to aselected contact closure input and used thisway if the autosampler is notcontrolled by Clarity) and ended by elapsing the End Time as set on theMethod Setup - Measurement tab

Contact Closure OutputsSection defining the behavior of the contact closure outputs of the AdvionExpression CMS To use the functionality select the output to betriggered in the Set up Output row select the event which will produce thetriggering of the output in the Enable Output section (either Close Contact

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on Time [s] or Close Contact on Peak) and particular parameters for thetriggering (time in case of the first option TIC signal or extracted ion (XIC )with its Start [mz] and End [mz] values The parameters for the detectionof a peak can be set in the Set up Contact Closure Output Thresholdsdialog invoked by using the Thresholdshellip button

Sets up the conditions when the Close Contact on Peak parameter istriggered Basic setting contains setting just the signal threshold -signal value which is satisfied when the signal is Above or Below thevalue set in the Intensity field It is possible to define the time for whichthe signal has to be above or below the mentioned value before thecontact closure is triggered in the Past Threshold Time [s] fieldAdditionally further condition may be defined using the Gradientcheckbox - this row also specifies whether the signal must beconcurrently to the given threshold rising or falling by defining thesignal SlopeOnce the conditions are met the contact closure output is triggeredafter the time defined in the Delay [s] field

Note Each of the four contact closure outputs may be triggered only onceduring the course of the analysis

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412 Method Setup - MS - Analog IO

Fig 7 Method Setup - MS - Analog IO

The Analog IO tab allows to set parameters for analog inputs and outputsAdvion Expression CMS detector can receive up to four analog signalsand process them in the same manner as the native signals areprocessed and can put voltages on up to four analog outputs to providethe analog signal to other devicesAnalog InputsThis section allows to set the behavior of up to four analog inputs Eachanalog input is enabled by checking the appropriate checkbox (Input 14)which consecutively allows to add the name of the input in Clarity andmap the input voltages (as set in the Max Voltage field) to signal intensityin Clarity (as set in the Max Intensity field) The value set in the MaxIntensity will always correspond to the input voltage set in the Max Voltagefield higher voltage will be trimmed Values allowed in the Max Voltagefield are 100 mV 1 V or 10 V

Note Analog signals received in this way are stored in Clarity as Auxiliarysignals which means no Integration is possible on them They arehowever sufficient for monitoring other devices flow pressuretemperature etc

Analog OutputsSection allowing to set the behavior of up to four analog outputs To setthe behavior of the particular output it is necessary to select it in the Setup Output field By checking the Enable checkbox the output will be

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provided based on either TIC signal or XIC signal (as created with a rangefrom Start [mz] to End [mz]) The mapping of the signal intensity fromAdvion Expression CMS detector to output voltage is provided by MaxIntensity and Max Voltage fields - the two values set correspond to eachother where Max Voltage may be set between 1 V and 10 VAdditionally the signal being sent to analog output connector may befurther processed in Advion Expression CMS by applying baselineremoval andor signal smoothing If Remove Baseline checkbox ischecked the output signal will be zero until the time specified in the firstfield on the row (in seconds) is reached Before that time the averagebaseline signal is calculated in a time window as long as defined in thesecond field on the row (again set in seconds) For this reason thesecond field value must always be smaller or equal to the value in the firstfieldThe smoothing of the analog signal is defined by checking the Smoothcheckbox the time parameter of the smoothing is set in the field on therow It governs the time for which the signal will be smoothed delaying theanalog output by several seconds It is recommended if the smoothing isto be used to set the interval long enough so that at least 5 data pointscan be gathered in the interval (thus when the scan time is 500 ms thetime set should be at least 25 seconds

Note The baseline removal and smoothing must be set for each output signalindependently

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42 Device MonitorThe window with the detector status can be invoked by the Monitor -Device Monitor command from the Instrument window or using the LCMonitor icon It displays the actual values for most detector parametersallows to set the detector to OPERATE and STANDBY state work with thedetector vacuum and also enter the Tuning Ion Source dialog for settingit up

Fig 8 DeviceMonitor

StatusShows the general status of the Advion Expression CMS detector Uponstarting Clarity the detector is VENTED and needs to be first switched toSTANDBY state by using the Pump Down button then to the OPERATEstate to be able to gather data

Caution Please head the instructions by Advion company on working with theAdvion Expression CMS detector to prevent possible damage done tothe detector

MS StatusButton allowing to display the Hardware Configuration dialog displayingthe status of the detector including its Firmware version and the version ofthe control libraries (SDK) used to operate it

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Fig 9 Hardware Configuration

OperateSwitches the Advion Expression CMS detector to OPERATE state Thecommand is only available when the detector is in the STANDBY stateStandbyButton switching the detector to STANDBY state when it is in theOPERATE state It is recommended to keep the detector in the STANDBYstate instead of switching it down completely unless the powering downshould be for a long period of timeVentButton allowing to vent the detector when it is in the STANDBY state Aconfirmation message is issued upon using the Vent buttonPump DownPress the Pump Down button when the detector is VENTED and you wantto shift it to the STANDBY state The vacuum will be built in the AdvionExpression CMS detector but the detector itself will not be switched tothe STANDBY state unless 30-minutes timer in the VENTED state iselapsed The timer can be seen in the Status fieldTuningIon SourceOpens the Tuning Ion Source dialog serving for maintenance andcalibration of the Advion Expression CMS detectorCapillary Heater OnMonitors (and allows to control) the status of the ion source capillaryheater The heater is automatically switched on when the detector is putinto OPERATE mode but is not switched off when it is then put toSTANDBY mode You can switch the heater on and off manually Theactual temperature of the capillary heater can be seen in the CapillaryTemp field of the Readback TableNebulization Gas Flow OnMonitors (and allows to control) the status of the nebulization gas flowThe flow is automatically switched on when the detector is put intoOPERATE mode and is switched off when it is then put to STANDBYmode You can switch the flow on and off manuallyStandby Nebulization Gas Flow OnMonitors the status of the nebulization gas flow when the AdvionExpression CMS detector is in STANDBY state Compared to the

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OPERATE state the nebulization gas flow is greatly reduced during theSTANDBYIon Source Gas OnMonitors (and allows to control) the status of the ion source heated gasflow The flow is automatically switched on when the detector is put intoOPERATE mode and is switched off when it is then put to STANDBYmode You can switch the flow on and off manuallyIon Source Gas Heater OnMonitors the status of the ion source gas heater which should beautomatically switched on when the when the Ion Source Gas Flow isstartedTurn Left Calibrant OnSwitches the valve to the left calibrant vial When the checkbox ischecked the calibrant from the left vial flows into the detectorTurn Right Calibrant OnSwitches the valve to the right calibrant vial When the checkbox ischecked the calibrant from the right vial flows into the detectorOther parameters status may be monitored in the Device Monitor windowincluding the Turbo At Speed Vacuum OK Safety Switch High Voltages Positive Ion FIA Signal and the states of Digital Inputs These servemostly for diagnostic reasons when the Ad does not work and cannot bechanged from the Device Monitor windowReadback TableTable showing the readbacks from the Advion Expression CMS detector

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421 Tuning Ion SourceThe dialog for performing maintenance operations on the AdvionExpression CMS detector like performing manual and automatic tunesmz calibration and performance tests The dialog consists of several tabseach of which is described in its own section

Fig 10 Tuning Ion Source

Reference CompoundSelects and loads the preset parameters for the calibration compound It is

possible to save your own Reference Compound sets by using thebutton where you will be prompted to enter the desired file nameLoading a fresh Reference Compound tune set loads the values into theMasses sectionMassesSection showing the values as set in the Reference Compound tune fileYou can display the section in two modes - either showing the CenterMass and the Span (symetricaly divided around it) or Start Mass modeshowing the Start Mass and the End Mass in the Masses TableMasses TableA table showing the parameters of the Reference Compound namelytheir Mass [mz] and Scan Time [ms]Smooth DataWhen checked smoothes the Tune Graphs for the display

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PerformanceSection showing the results of the Advion Expression CMS detectoroverall performance under the given ion source settings tune settings andon the given calibration reference compoundTest PerformanceWhen pressed performs the Performance test Its results are thenshown in the Performance TablePerformance TableTable showing the results of the Performance test The table containsa row for each mass defined in the Masses Table showing Referenceand Measured mass peak Resolution (peak width at half height) andpeak Intensity The expected and measured mass should not differ bymore than 01 mz while the Resolution should be in 05 - 07 mzrange

Tune GraphsLower section of the Tuning Ion Source dialog is filled with Tune Graphs- one graph for each mass as set in the Masses Table The X axis displaysthe mz values as defined in the Span [mz] column the vertical axisshows the peak intensity The graphs can be zoomed independently ofeach other

Ion SourceSection showing (and allowing to change) various parameters of the IonSource settings The values can be changed the changes can be then

saved using the button Changes may also be cancelled by using the

button The individual parameters available in the list may changeaccording to the Ion Source Type installed The list shows the values setin the Ion Source settings file (modifiable) and the actual readbacks fromthe Advion Expression CMS detectorIon Source SettingsAllows to select the particular ion source settings file to be displayed andchanged

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Manual TuneTab for performing manual tune

Fig 11 Manual Tune

This tabs allows the user to manually change the parameters setautomatically during the Auto Tune program and also few others Thechanges are made to the tune file selected in the Tune Settings field and

must be saved after the change is done using the button Changes

may also be cancelled by using the button

Caution Changing any of the parameters on the Manual Tune tab is stronglyrecommended only to people with deep understanding of how theAdvion Expression CMS detector and MS Detectors in general workandmay lead to damage done to the hardware

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Auto TuneTab for performing automatic tune

Fig 12 Auto Tune

Auto TuneButton allowing to perform the tune adjustment The received tune settingsare saved into the _CURRENTTUNE file which can be then saved underanother name The tune program expect for the particular calibrant to beswitched and correct ion source settings loadedTune TypeAllows to select between various tune types Three types of the auto tunetake differing amount of time to perform and adjust differing number ofparameters

Tune Resolution Only (fast) is the default choice of tune It only adjuststhe Resolution parameters and can only be performed when peaksare visible in the tune graphs for all masses that are to be tunedTune All Parameters (regular) is tune program which will first adjustthe Extraction Electrode and Hexapole Bias parameters and later tuneIon Energy and Resolution settings It also requires peaks be presentin all tuning graphsFind Peaks and Tune All Parameters (extreme) is the most extremetune program which first performs the peak search and then the TuneAll Parameters program

ResultsThe table showing the results of the automatic tune in respect to valuespreviously contained in the tune file and values of the same parametersafter the tune was performed

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CalibrationTab for performing the mz calibration

Fig 13 Calibration

CalibrateUsing the button performs the mz calibration on a set of masses asdefined in the Masses Table in the left side of the Tuning Ion Sourcedialog It is necessary to have the peaks visible in all tune graphs for thesuccessful finish of the mz calibrationCalibration TableShows the resulting correlation factors on different mass rangesResetButton allowing to return to current settings rather than using the newlycalibrated results

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43 Expression CMS SetupThe Expression CMS Setup dialog serves for the correct setting of thecommunication between Clarity and the Advion Expression CMSdetector

Fig 14 Expression CMS Setup

CommunicationSection allowing to set the communication with the Advion ExpressionCMS detector Two communication modes are available - USB (forconnecting to the live detector) and Simulation (for DEMO regime withoutthe detector)AutoDetectServes for detecting the Advion Expression CMS detector If thecommunication attempt is successful the serial number of the detectoris displayed next to the button

SIM (EIC) SignalsSection allowing to set the behavior of the Advion Expression CMSdetector while in the SIM (Single Ion Monitoring) modeNumber of SignalsSets the maximum number of EIC (Extracted Ion Chromatograms)signals usable in the SIM mode

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Note Clarity allows to work with the signals in SIM mode in the same way aswith standard chromatographic signals The number of signals set in thisfield is reserved for SIM signals and cannot be used while working in theScan mode - therefore if you will only be working in the Scan mode itmight be useful to set the number of SIM signals used to 0 not to blockother functionsof theMS Evaluation extension (like extracting additionalsignals from the acquired spectra on request)

SIM NameAllows to set custom names to the EIC signals in the SIM mode

Note The actual valuesof mz used for particular signals are defined later in theMethod Setup - MS - General dialog

Use Two Ion SourcesAllows to use two ion sources in the same analysis The particular usageof both ion sources (or either of them) is later set per method in theMethod Setup - MS dialog Availability of the Use Two Ion Sources optiondepends on the autodetected model of the detectorTIC 1(2) NameAllows to set a custom name for TIC (Total Ion Current) signalMS Spectrum 1(2) NameAllows to set a custom name for the acquired spectrum Spectra (if thereare more of them in a single chromatogram) will be referenced based onthis name

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Advion Expression CMS 5Report Setup

5 Report SetupAll of the detector settings accessible on the Method Setup - MS tab for theAdvion Expression CMS detector are reported To do so the InstrumentControl parameter on the Method tab of the Report Setup dialog must bechecked

Fig 15 Report Setup

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1 Advion Expression CMS Control Module

2 Requirements

3 Installation Procedure

31 Hardware - Wiring


4 Using the control module

41 Method Setup - MS - General



42 Device Monitor

421 Tuning Ion Source

43 Expression CMS Setup

5 Report Setup

Clarityreg DataApexreg and reg are trademarks of DataApex Ltd Microsoftreg and WindowsTM aretrademarks of Microsoft CorporationDataApex reserves the right to make changes to manuals without prior notice Updated manuals can bedownloaded fromwwwdataapexcom

Author DM

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Fig 13 Calibration

- 21 -

- 22 -

- 23 -

Fig 15 Report Setup

- 24 -

2 Requirements







42 Device Monitor



5 Report Setup

- 18 -

Fig 11 Manual Tune

- 19 -

Fig 12 Auto Tune

- 20 -

Fig 13 Calibration

- 21 -

- 22 -

- 23 -

Fig 15 Report Setup

- 24 -

2 Requirements







42 Device Monitor



5 Report Setup

Fig 11 Manual Tune

- 19 -

Fig 12 Auto Tune

- 20 -

Fig 13 Calibration

- 21 -

- 22 -

- 23 -

Fig 15 Report Setup

- 24 -

2 Requirements







42 Device Monitor



5 Report Setup

Fig 12 Auto Tune

- 20 -

Fig 13 Calibration

- 21 -

- 22 -

- 23 -

Fig 15 Report Setup

- 24 -

2 Requirements







42 Device Monitor



5 Report Setup

Fig 13 Calibration

- 21 -

- 22 -

- 23 -

Fig 15 Report Setup

- 24 -

2 Requirements







42 Device Monitor



5 Report Setup

- 22 -

- 23 -

Fig 15 Report Setup

- 24 -

2 Requirements







42 Device Monitor



5 Report Setup

- 23 -

Fig 15 Report Setup

- 24 -

2 Requirements







42 Device Monitor



5 Report Setup

Fig 15 Report Setup

- 24 -

2 Requirements







42 Device Monitor



5 Report Setup

Documents

Advion Expression CMS - DataApex · AdvionExpressionCMS 4Usingthecontrolmodule ScanMode-SelectedMassRange IntheSelectedMassRangemode,thedatabeingacquiredarewhole spectralscansdefinedusingStart