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Surveyor Plus User Guide for the Xcalibur Data

1. Wash tube Needle tubing assembly gt Concentric syringe Solvent path for Flush Syringe at Fill Position command Outer plunger moves upward pushing solvent out of the needle tubing into the injection port of the autosampler through the transfer tube and into the 6 port injection valve Solvent path for Flush Syringe command Injection port of i autosampler ZS Transfer tube From pump Injection valve in the inject position Waste container Injection port of autosampler Transfer tube From pump Injection valve in the inject position Waste container Mobile phase m Wash solvent 198 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls Autosampler Direct Controls Removing and Installing Sample Trays If you did not select the Verify Door Is Closed check box when you specified the configuration options for the autosampler the XYZ arm does not move to the back of the tray compartment when you open the tray compartment door For information on specifying the configuration settings for the Surveyor Autosampler Plus see Surveyor Autosampler Plus Configuration Settings on page 45 To remove or install a sample tray 1 Open the Direct Control dialog box for the autosampler 2 In the Direct Command list select Position Arm to Access T
2. Parameter Description Error Log Error Log Displays errors that are generated by the PDA detector The error log can hold up to 100 errors When the error log is full the newest error log entry replaces the oldest error log entry The error log is protected by a backup battery when the detector is turned off Tip For best results save the error log print to file before you clear it The error log is useful during preventive and problem maintenance Buttons Request Log Downloads the error log that is stored in the PDA detector and displays the results in the Error Log box Clear Log Erases the current error log Tip For best results save the error log print to file before you clear it The error log is useful during preventive and problem maintenance Export Log Exports the log to a comma separated values file that you can open with the Excel application Versions Versions display box Displays the version number for the detector firmware This information is useful to determine if firmware upgrades are necessary Have this information handy whenever you contact your Thermo Fisher Scientific service representative Date and Time Date and time 182 Surveyor Plus User Guide for LC Devices Displays the current system date and time This is the time that the data system uses for entries in the error log and the time stamp on the snapshot file Thermo Scientific 6 Direct Controls UV Vis Detector Direct Controls UV Vi
3. Solvent colors His Mis Lic Mp LULU UAE E RA 0 0 00 00 0 0 Type of view Solvent Gradient v Solvent Gradient view The program must contain at least two time lines Surveyor Plus User Guide for LC Devices 81 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings 6 For a gradient separation method do the following a For each row in the program type the solvent composition and the flow rate and then press ENTER The pump program can contain from 2 to 398 rows time lines The last row in the gradient program is a placeholder and has no effect on the pump conditions The last row does not have a time entry in the Time column The flow rate range is the same as for an isocratic run see step 4b on page 80 To produce a stable gradient enter a flow rate of at least 25 pL min b To return the solvent conditions to those specified in the first line of the gradient program select First Line Conditions in the Method Finalizing list First Line Conditions is the default selection Figure 52 shows the gradient program entries for the gradient program in Table 17 After 30 minutes the gradient program returns to the first line conditions for the remainder of the run To equilibrate the LC column at the first line conditions for 10 minutes you must set the run time for the PDA detector or MS detector to 40 minutes Tip If you do not want the detector to acquire data during
4. d Push the LED holder down until it meets resistance from the needle mount e Make sure that the light fixture cable is routed so that it does not obstruct the movement of the XYZ arm 3 Install the target port fixture as follows a Remove the aluminum retention clip see Figure 199 from the wash station housing pull it forward and then upward Figure 199 Retention clip for the autosampler injection port Retention clip Thermo Scientific Surveyor Plus User Guide for LC Devices 295 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler b Pull the injection port out from the wash station see Figure 200 Figure 200 Autosampler injection port connected to the transfer tube nut Injection port Transfer tube nut 4 Insert the target port fixture see Figure 189 on page 287 into the position previously held by the injection port 5 Click Next to proceed to the next page of the wizard Go to the next procedure Moving the XYZ Arm to the Home Position Moving the XYZ Arm to the Home Position Use this page of the Arm Calibration wizard see Figure 201 to move the XYZ arm to the home position In the home position the XYZ arm is aligned over the autosampler injection port Figure 201 Move the Arm to the Home Position button page Diagnostic Arm Calibration Move the arm to the home position Press Next when movement stops To move the XYZ arm to the home positi
5. 2011Thermo Fisher Scientific Inc All rights reserved Surveyor and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc in the United States The following are registered trademarks in the United States and other countries Teflon is a registered trademark of E I du Pont de Nemours and Company Windows Excel and XP are registered trademarks of Microsoft Corporation All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries Thermo Fisher Scientific Inc provides this document to its customers with a product purchase to use in the product operation This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc The contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Scientific Inc makes no representations that this document is complete accurate or error free and assumes no responsibility and will not be liable for any errors omissions damage or loss that might result from any use of this document even if the information in the document is followed properly This document is not part of any sales contract between Thermo Fisher Scientific Inc an
6. Syringe size Minimum speed Maximum speed Default speed uL uL s pL s uL s 100 0 01 13 20 3 00 250 0 04 33 00 8 00 500 0 08 66 11 8 00 2500 0 41 330 80 25 00 Reservoir Content Page Use the Reservoir Content page see Figure 56 to enter descriptions for the contents of the four 16 mL reservoir vials located on the right side of the tray compartment and the wash solvent bottle located in the solvent platform at the top of the LC system stack You can type up to 80 characters in each box Figure 55 shows the relative size of the 1 liter wash bottle and the 16 mL reservoir vials Figure 55 Reservoir vials and wash solvent bottle Wash bottle Reservoir vials Bede 92 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Autosampler Instrument Method Parameters To specify the solvents in the wash bottle and reservoir vials 1 Click the Reservoir Content tab The Reservoir Content page appears see Figure 56 Figure 56 Reservoir Content page for the autosampler Reservoir Content Reservoir 1 o Reservoir 2 P Reservoir 3 P Reservoir 4 FO OE Wash Bottle 2 Identify the solvents contained in the 16 mL reservoir vials and the 1 L wash bottle by typing their names in their respective boxes Timed Events Page for the Autosampler Thermo Scientific You can use the TF terminals see Figure 57 on the back panel of the autosampler to control peripheral devices tha
7. The autosampler injection valve switches to the inject position allowing the mobile phase to backflush the contents of the sample loop onto the column The autosampler then issues a momentary Inject Out signal to the detector The detector starts acquiring data Each of the Surveyor Plus LC devices has a panel of four status LEDs located on the front of the left door All of the devices have these three LEDs Power Comm and Run In addition the detector has a Lamps LED the autosampler has a Temp LED and the analytical pump has a Degas LED These topics describe the meanings of the LED states Thermo Scientific Surveyor MS Pump Plus LED States Surveyor LC Pump Plus LED States Autosampler LED States PDA Detector LED States UV Vis Detector LED States Surveyor Plus User Guide for LC Devices 35 1 Introduction to the Surveyor Plus LC System Status LEDs Surveyor MS Pump Plus LED States 36 Table 1 lists the states of the Surveyor MS Pump Plus LEDs Table 1 Pump status LEDs and their meaning LED Status Meaning Power Green The pump is on and receiving power Comm Amber The pump is not communicating with the data system Green Communication to the data system has been established Flashing green A pump program is downloading from the data system computer Run Amber The power is switched on but the pistons are idle producing no flow Flashing amber A firmware download is in progress
8. Table 52 describes the direct control parameters for the Surveyor LC Pump Plus Table 52 Operation Surveyor LC Pump Direct Control parameters Sheet 1 of 2 Parameter Description Pump PumpOn sTurnsonthesolvent flow from the pump sssssi i lt CO Pump Off Turns off the solvent flow from the pump Error Condition Clear Clears the error log You must clear the error log before you can restart the solvent flow from the pump Method Flow Rate Specifies the flow rate in mL min Range 0 000 to 9 999 mL min Component A B C or D Specifies the percent composition of solvent A B C or D Download Downloads the new mobile phase settings to the on board CPU of the Surveyor LC Pump Plus Purge Purge Time Specifies the length of time that the pump draws solvent through the system at approximately 10 mL min Range 0 1 to 9 9 minutes Solvent Valve Specifies the solvent proportioning valve that is activated The pump draws solvent from the solvent line connected to this proportioning valve Note The Surveyor LC Pump Plus is a quaternary gradient pump that can be set up to pump four solvents The solvent lines are labeled A B C and D You must purge each separately 186 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls Pump Direct Controls Table 52 Operation Surveyor LC Pump Direct Control parameters Sheet 2 of 2 Param
9. 1 Introduction to the Surveyor Plus LC System Analytical Pump Analytical Pump Thermo Scientific part of Thermo Fisher Scientific Inc offers two analytical pumps in the Surveyor Plus product line the Surveyor MS Pump Plus which provides optimum performance in the lower flow rate ranges needed for mass spectrometry and the Surveyor LC Pump Plus which provides optimum performance in the flow rate ranges needed for chromatography Both analytical pumps contain a built in solvent degassing system that consists of four independent chambers maintained at a constant vacuum of approximately 27 in Hg Each chamber contains an 18 in length of 0 045 in ID Teflon AF tubing This translates to a volume of less than 500 pL per channel adding very little to the quantity of solvent required to purge the lines when you replace an eluent These topics describe the features of the Surveyor analytical pumps e Surveyor MS Pump Plus e Surveyor LC Pump Plus Surveyor MS Pump Plus 2 The Surveyor MS Pump Plus is a dual piston quaternary low pressure mixing pump with a built in vacuum degasser and pulse dampener The pumping system provides flow rates from 1 to 2000 pL min which is the range needed to perform LC and LC MS applications You can run precise gradients from 200 to 2000 pL min while the extremely low gradient delay volume of 65 pL ensures minimum system cycle times The pulse dampening assembly consists of a low volume T conne
10. 1x 512 photo diode array aQ Fixed grating Tungsten halogen lamp 22 Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Solvent Platform The PDA detector does not have independent controls such as a keypad to create data acquisition methods Instead you create instrument methods for data acquisition with the data system The only manual controls for the PDA detector are the On Off switch that controls line power the attenuators that control the light throughput to the diode array and the holmium oxide wheel that controls the position of the wavelength calibration solution UV Vis Detector The UV Vis detector is a full featured time programmable variable wavelength UV Vis ultraviolet visible absorbance detector It operates in either the single wavelength mode the dual wavelength UV wavelength mode or the dual wavelength Visible mode The wavelength range in the single wavelength mode is 190 to 800 nm In the dual wavelength UV mode the range is 190 to 450 nm and in the dual wavelength Visible mode the range is 366 to 700 nm The wavelength time table is available in all three modes The time table can contain up to 10 lines If you enable the Zero On Wavelength Change feature the baseline absorbance returns to zero between each line in the time table even if the wavelengths remain the same The baseline absorbance does not return to
11. 322 Surveyor Plus User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Performing a Dark Current Calibration The function of the array calibration is to measure and correct for the dark current produced by the diodes of the photodiode array The dark current is the small amount of background signal that is produced by the diodes of the array even when both lamps are turned off The environmental conditions of your laboratory can cause the dark current of the diode array to increase over time For best results perform an array calibration dark current after any of the following events occur e After 100 hours of use or monthly whichever comes first e Whenever a 5 C change in the operating environment occurs e After you move the detector e After you replace the lamp e After you download a new firmware file Because the dark current produced by the diodes rises as the temperature within the detector rises warm up the lamps for one hour before you perform a dark current calibration Warming up the lamps for one hour allows the detector to equilibrate to its normal operating temperature The lamps turn off during the dark current calibration routine After the dark current calibration routine finishes the lamps turn back on To perform the dark current calibration 1 Pump methanol through the flow cell at 1 mL min 2 Turn on both lamps and wait one hour f
12. C calibur 2 m Plot properties Raw file cA xcalburdataipahs Olraw 0000 ml Detector jv x Scan filter a ns Peak algorithm JAvaion F Plot type ChannelB O z P LJ Delay min joo Fangels p Fix scale to f1000000 00 Cancel Help 5 In the Range area set the displayed time range of the chromatogram e Fora generic layout file leave an asterisk in the Time Range box When you open a raw data file the x axis of the chromatogram is scaled to the run time for your detector in the instrument setup method used to acquire the data e To specify a specific time range type a beginning time point and an ending time point separated by a dash in the Time Range box 6 In the Plot Properties area select the following a In the Detector list select UV b In the Peak Algorithm list select Avalon c In the Plot Type list select Channel A Channel B or Channel C 7 Click OK to exit the dialog box and view your discrete chromatogram Figure 145 shows a discrete channel chromatogram Thermo Scientific Surveyor Plus User Guide for LC Devices 237 8 Qual Browser Creating a Layout for PDA Data To modify the layout for the spectrum cell go to Specifying the Spectrum Range on page 238 Figure 145 Chromatogram view with a chromatogram for a PDA discrete channel Discrete Channel B wavelength C Xcaliburdatai PAHs_01 03 04 2003 05 50 29 PM RT 0 00 14 98 9 NL 1 19E6 Channel B UY PAHs_
13. The first time line in the time program table is set to 0 00 minutes and is uneditable The second time line in the program is a placeholder line and has no effect on the pumping conditions For example the pump program shown in Figure 47 produces a proportioned mobile phase consisting of 80 methanol and 20 water v v The proportions of the solvents remain constant throughout the run The mobile phase flow rate remains constant at 1 mL min throughout the run 3 To create a gradient pump method enter at least two steps in the Gradient Program table For each additional line in the program type these values e A time value in the Time column e A flow rate in the Flow column e The solvent percentages for the mobile phase in the solvent columns 4 Press ENTER The last line in the gradient table which has an in place of a line number is a placeholder and has no effect on the pump conditions Table 14 lists the gradient conditions used to create the gradient profile shown in Figure 48 Table 14 Gradient program Time min Solvent composition 0 00 to 5 00 Held constant at 90 10 water methanol 5 00 to 25 00 Linear ramp from 10 to 90 methanol 25 00 to 25 01 Stepped down to initial solvent composition of 90 10 water methanol 25 01 to 40 00 Column is equilibrated at the initial solvent composition of 90 10 water methanol At 25 01 minutes the program returns to its initial solvent composition To equilibrate th
14. To view the spectrum for a particular peak in the chromatogram 1 To unlock the display click the Lock Display button After you unlock the display data collection continues off screen 2 Pin the spectrum cell by clicking the pin in the upper right corner of the cell The pin in the upper right corner of the spectrum cell turns green Cursor actions in other cells such as the chromatogram cell affect the view displayed in the pinned spectrum cell Thermo Scientific Surveyor Plus User Guide for LC Devices 215 7 Sequence Setup Working with the Real Time Plot View 3 In the chromatogram cell click the peak of interest In the spectrum cell a spectrum appears for the time point that you clicked 4 Click the Lock Display button to resume monitoring real time data acquisition 5 Pin the chromatogram cell by clicking the pin in the upper right corner of the cell The pin in the upper right corner of the chromatogram cell turns green Cursor actions in other cells such as the spectrum cell affect the view displayed in the pinned chromatogram cell 6 In the spectrum cell click the wavelength of interest In the chromatogram cell that contained the Total Scan chromatogram a scan chromatogram appears for the specific wavelength that you clicked 7 Click the Lock Display button to resume monitoring real time data acquisition Adding Cells to the Display You can display multiple cells in the Real Time Plot view
15. b From the Surveyor LC Pump view choose Surveyor LC Pump gt Direct Control gt Operation The Operation Surveyor LC Pump Direct Control dialog box appears see Figure 171 Surveyor Plus User Guide for LC Devices Thermo Scientific 9 LC Pump Calibration and Record Keeping Calibrating the Surveyor LC Pump Plus Figure 171 Operation Surveyor LC Pump Direct Control dialog box Operation Surveyor LC Pump Direct Control Method Flow Rate 1 000 mL min Component Pump Off Component B Component C Component D Download Error Condition Purge Time 3 0 min Solvent Valve A Help Close c Inthe Method area enter the specified flow rate in the Flow Rate box and enter the specified mobile phase composition in the Component A through Component D boxes d Click Download to send these parameters to the onboard CPU of the Surveyor LC Pump Plus e Click Pump On to turn on the pump flow 3 Record the pressure trace 4 If the pressure pulsation is too high for your application change the compressibility setting Then repeat steps 2 and 3 Continue to change the compressibility setting until the level of pump pulsation is adequate for your application Note Changing the compressibility setting affects the flow rate 5 After you change the compressibility setting to minimize the pressure pulsation check the flow rate If necessary adjust the flow rate adjustment setting as described
16. on page 52 when you specify the configuration settings for the autosampler and leave the counters at the default setting the autosampler status displays Maintenance Due and the data system prevents you from starting a run For information about changing the counter settings on the Maintenance Information page see Autosampler Maintenance Information on page 309 Thermo Scientific Surveyor Plus User Guide for LC Devices xv Preface Related Documentation In addition to Help that you can access from the data system these manuals are provided with LC Devices as PDF files for the Surveyor Plus family of high performance LC instruments Surveyor Plus User Guide for LC Devices formerly entitled Surveyor Plus User Guide for the Xcalibur Data System Surveyor Plus Preinstallation Requirements Guide e Surveyor Plus Getting Connected Guide e Surveyor Autosampler Plus Hardware Manual Surveyor LC Pump Plus Hardware Manual Surveyor MS Pump Plus Hardware Manual Surveyor PDA Plus Detector Hardware Manual e Surveyor UV Vis Plus Detector Hardware Manual To view manuals for your Surveyor Plus LC devices Go to Start gt Programs gt Thermo Instruments gt Manuals gt LC Devices gt Surveyor gt d Thermo Instruments d Manuals D LC Devices D Surveyor Getting Connected Preinstall Requirements Surveyor AS Surveyor LC Pump Surveyor MS Pump Plus Surveyor PDA Plus Surveyor UVVIS User
17. Axis Normalization C Stack Overlay 3D Density map 3D Elevation Ki E gt 0 30 60 Skew a T gt 0 30 45 Intensity shaded Rettue hsortance M Draw backdrop Time min Cancel Help h Select the appropriate style i Click OK to save your settings and close the Display Options dialog box Thermo Scientific Surveyor Plus User Guide for LC Devices 247 8 Qual Browser Creating a Layout for PDA Data Saving the New Layout Now that you have created a layout for displaying your PDA data save the layout so that you can apply it to other data files containing PDA data To save the layout 1 From the Qual Browser window choose File gt Layout gt Save As The Save Layout File dialog box appears see Figure 156 Figure 156 Save Layout File dialog box Save Layout File Save in B methods gt ac EE templates PDA yt File name fi Save as type Layout Files lpt Cancel Header Information 2 Type a file name in the File name box 3 Click Save 248 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Viewing the Spectrum for a Specific Time Point Viewing the Spectrum for a Specific Time Point To view a spectrum for a specific time point 1 Open a raw data file with PDA data and apply an appropriate layout file see Opening a Raw Data File in Qual Browser on page 219 2 Pin the spectrum
18. Labels Axis Normalization Normalize method RT 0 00 15 00 C Intensity range 200000 Total Scan 150000 PDA Normalize each plot to gt 100000 PAHs_01 C Largest peak in subsection 50000 Largest peak in selected time range Largest peak in all times 0 Time min Cancel Help 240 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Creating a Layout for PDA Data b In the Normalize Method area select the Auto Range option Selecting Auto Range ensures that the entire dynamic range of the chromatogram is displayed in the active view normalized over the full range of the y axis c Inthe Normalize Each Plot To area select the Largest Peak in Selected Time Range option 5 Specify the Axis parameters as follows a Click the Axis tab The Axis page appears see Figure 148 b In the Units area select the Absolute option Selecting Absolute sets the y axis to the absolute units of pAU Figure 148 Axis page in the Display Options dialog box Display Options Style Color Labels Axis Normalization Name Show name Offset RT 0 00 15 00 Time min Always v T 200000 I Split time range Divisions je Sonat Total Scan PDA PAHs_01 100000 50000 From detector 0 C Custom Relative Name Show name Offset fusu Always v a Time min Cancel Help 6 Specify the labels for the peaks in the chromatogram
19. Stack Address OK O pee tee 2 In the Stack Address box type the appropriate number unit ID The Stack Address setting must match the rotary switches on the back panel of the detector 3 Click OK to close the Surveyor UV Vis Configuration dialog box When you have finished configuring all of your LC devices go to the next topic Closing the Foundation Application Closing the Foundation Application Before you can open your Thermo Scientific data system you must close the Foundation application To save the instrument configuration and close the Instrument Configuration window Click Done at the bottom of the Thermo Foundation Instrument Configuration window The Windows desktop appears Tip You must close the Instrument Configuration window before you open the Xcalibur data system The two applications cannot be open at the same time 66 Surveyor Plus User Guide for LC Devices Thermo Scientific Instrument Method Setup Thermo Scientific This chapter describes the instrument control parameters for the Surveyor Plus LC devices It does not describe the instrument control parameters for your Thermo Scientific mass spectrometer For information about setting up the data acquisition parameters for a Thermo Scientific mass spectrometer refer to the getting started guide or Help for the mass spectrometer To automate control of the liquid chromatography devices you must create an instrument method and
20. To align the light beam over the hole in the target port fixture 1 In the Step list of the Arm Calibration wizard select 25x 793 75 microns This selection moves the arm 793 75 micrometers 0 03125 inches each time you click Left Right Forward or Backward 1 micrometer 3 937 x 10 inches 2 Click Left Right Forward and Backward to align the position of the light beam with the hole in the center of the target port fixture 3 In the Step list select a smaller step size and continue aligning the position of the light beam 4 After you align the light beam with the hole in the center of the target port fixture click Next to proceed to the next page of the wizard Go to the next procedure Applying the Arm Calibration Setting 298 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Applying the Arm Calibration Setting Use this page of the Arm Calibration wizard see Figure 204 to download the new arm calibration settings Figure 204 Set Calibration button page Diagnostic Arm Calibration Warning The light beam must be directly over the injector port Incorrect alignment will make the autosampler unusable Set Calibration Cancel Help To apply the current calibration settings for the arm position 1 Ensure that the light beam is centered over the hole in the target port fixture see Figure 205 Figure 205
21. 254 Filter Bandwidth nm Three Channels m Channel C 7 Sample Rate Hz hoo x Wavelength nm 280 Filter Bandwidth nim 3 Timed Events Time min Type Channel Level m4U Delay sec Thermo Scientific Surveyor Plus User Guide for LC Devices 95 3 Instrument Method Setup PDA Detector Instrument Method Parameters 2 In the Run Length min box type a run time from 0 to 600 minutes 3 In the Filter Rise Time sec list select a rise time from 0 to 10 0 seconds Rise time is inversely proportional to the amount of baseline noise If your chromatogram contains closely eluting peaks minimize baseline noise while retaining maximum resolution by selecting a rise time that is approximately one tenth of the narrowest peak s width at half height FWHM Increasing the rise time above this level increases peak tailing which can reduce the resolution of closely eluting peaks Figure 60 shows the effect of rise time on peak tailing Figure 60 Effect of rise time on peak tailing 500 0 1 s rise time 2 0 s rise time 400 5 0 s rise time 300 mAU 10 0 s rise time 200 2 0 2 1 2 2 23 24 2 5 26 27 Minutes 4 In the Units area select the Wavelength Absorbance option Note For information about using the Diode Intensity option to perform diagnostics see Creating a Display Method on page 313 Methods that record light intensities for the PDA detector have the spda fil
22. 3 Confirm that you have a vial in the position specified in the sequence row P 4 From the toolbar click the Run Sample button The Run Sequence dialog box appears see Figure 122 The User box contains your login name and the Run Rows box contains the row number that you selected in the sequence spreadsheet Figure 122 Run Sequence dialog box Run Sequence m Acquisition Options Instrument Start Instrument User Surveyor PDA Surveyor AS Yes Surveyor LC Pump Run Rows f I Priority Sequence V Start When Ready Change Instruments Processing Actions Instrument Method Start Up Browse f Quan M Qual Shut Down Browse r Programs Programs Pre Acquisition Browse r Post Acquisition Browse Run Synchronously Pre Acquisition Post Acquisition After Sequence Set System C On C Standby Off Cancel Help 212 Surveyor Plus User Guide for LC Devices Thermo Scientific 7 Sequence Setup Starting Data Acquisition 5 Confirm the following e The MS detector and LC components are configured for operation as Xcalibur devices in the Instrument list e The autosampler is specified as the start instrument Yes is displayed in the Start Instrument column next to Surveyor AS see Figure 123 Figure 123 Surveyor AS specified as the start instrument Instrument Start Instrument Surveyor PDA Surveyor 4S Yes Surveyor LC Pump After the autosampler injectio
23. Click Apply To turn the column oven off 1 Select Turn Off Tray Temperature from the list of commands 2 Click Apply 200 Surveyor Plus User Guide for LC Devices Thermo Scientific o Sequence Setup This chapter describes how to acquire and view chromatographic and PDA spectral data using the Xcalibur data system Contents e Creating a Single Sample Sequence e Equilibrating the Chromatographic Column e Loading the Autosampler e Starting Data Acquisition e Working with the Real Time Plot View Creating a Single Sample Sequence To set up a sequence to inject a single sample follow these procedures in order 1 Opening the Sequence Setup Window 2 Creating the Sequence 3 Optional Selecting the Vial Locations Interactively 4 Saving the Sequence Opening the Sequence Setup Window To open the New Sequence Template dialog box Anan 1 Click the Sequence Setup icon on the Home Page m The Thermo Xcalibur Sequence Setup window appears see Figure 112 Thermo Scientific Surveyor Plus User Guide for LC Devices 201 7 Sequence Setup Creating a Single Sample Sequence Figure 112 Sequence Setup window Thermo Xcalibur Sequence Setup Open elk File Edit Change Actions Yiew GoTo Help Sample Type FileName SampleID Path InstMeth ProcMeth Position Inj Vol Level 0 1 For Help press F1 NUM 9 26 2008 7 13PM 2 From the Sequence Setup window choose File gt New The New Sequen
24. Click Continue to close the File Save Audit Trail dialog box and save the instrument method Thermo Scientific Surveyor Plus User Guide for LC Devices 111 ee B Sample Preparation Routines Sample preparation routines are part of the instrument method Use the Sample Preparation ple prep P P P page to create a multitask routine containing up to 512 tasks A task consists of a sample preparation operation and its associated parameters The ability to add 512 tasks to a sample preparation routine gives you considerable flexibility however the arrangement of the tasks in the task list must follow a logical order For example you cannot add a task that deposits liquid before you add a task that draws liquid In addition if you are using the 250 uL dual concentric syringe that ships with the autosampler you must follow an additional set of rules that maintain the proper positioning of the inner and outer plungers of the syringe Contents e Opening the Sample Preparation Page e Sample Preparation Rules e Building the Sample Preparation Routine e Sample Locations for the Sample Preparation Tasks e Draw Eject and Transfer Volumes for Sample Preparation Tasks e Syringe Speed Range for Sample Preparation Tasks e Sample Preparation Routine Example Opening the Sample Preparation Page The Sample Preparation page is part of the instrument method To open the Sample Preparation page 1 Open the autosampler view from your dat
25. Click Power The Power Options Properties dialog box opens to the Power Schemes page see Figure 21 Thermo Scientific Surveyor Plus User Guide for LC Devices 25 1 Introduction to the Surveyor Plus LC System Turning Off the Computer s Energy Saving Features Figure 21 Power Options Properties Power Options Properties Power Schemes Advanced Hibernate UPS ef Select the power scheme with the most appropriate settings for this computer Note that changing the settings below will modify the selected scheme Power schemes Home Office Desk v Settings for Home Office Desk power scheme Turn off monitor After 20 mins Turn off hard disks Never System standby 7 Modify the power scheme settings as follows In the Turn Off Monitor list select Never e In the System Standby list select Never 8 Modify the hibernate setting as follows a Click the Hibernate tab The Hibernate page appears see Figure 22 26 Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Turning Off the Computer s Energy Saving Features Figure 22 Hibernate page Power Options Properties Power Schemes Advanced Hibernate UPS Cy When your computer hibernates it stores whatever it has in memory on your hard disk and then shuts down When your computer comes out of hibernation it returns to its previous
26. Comment User text that provides additional information The text string can consist of up to 255 alphanumeric characters Solvent A B C and D check boxes and adjacent boxes Thermo Scientific When these check boxes are selected the associated solvent column on the Gradient Program page is available Select the check boxes corresponding to the solvent bottles to be used to create the mobile phase Type a description of the solvent in the adjacent box Clearing the check box associated with a solvent A B C or D makes the solvent column unavailable on the Gradient Program page Surveyor Plus User Guide for LC Devices 77 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings Table 16 Thermo pump method parameters Sheet 2 of 3 Parameter Operating Mode Description Specifies the operating mode for the pump The selection is 0 7000 PSI Start settings Specifies the device that triggers the start of a run and the run synchronization signals between the pump and the autosampler The selections are as follows Surveyor AS injection At the start of a run the Surveyor Autosampler Plus waits for the logic pump to issue the Pump Ready and the Release Injection signal before making an injection The pump then waits for the Start gradient signal from the autosampler before starting the pump program When you use this injection logic set up the Surveyor Autosampler Plus as the start
27. Displays the state of the UV Vis detector Ready The detector is ready to start data acquisition Off The detector is not ready to start data acquisition because one or both lamps are off Depending on the acquisition wavelengths specified in the downloaded instrument method one or both lamps must be on e For the UV range the deuterium lamp must be on e For the visible range the tungsten lamp must be on e When the wavelength table specifies wavelengths in both the UV and visible ranges both lamps must be on Running The detector is acquiring data Displays the current absorbance value for the first wavelength channel AU2 184 Surveyor Plus User Guide for LC Devices Displays the current absorbance value for the second wavelength channel Thermo Scientific 6 Direct Controls Pump Direct Controls Pump Direct Controls The Surveyor product line includes the Surveyor LC Pump Plus and the Surveyor MS Pump Plus These topics describe the direct controls for your Surveyor Plus pump e Surveyor LC Pump Plus Direct Controls e Surveyor MS Pump Plus Direct Controls Surveyor LC Pump Plus Direct Controls Use the Surveyor LC Pump Direct Control dialog box to quickly draw fresh solvent through the solvent lines clear an error condition download new solvent conditions to the pump and start and stop the solvent flow from the pump For information on opening the Direct Control dialog box and using the d
28. Dual UV D2 Dual Visible W or Single Wavelength Lambda 1 nm Displays the current wavelength setting for the Wavelength 1 channel Lambda 2 nm Displays the current wavelength setting for the Wavelength 2 channel Absorbance 1 AU Displays the current absorbance level for the Wavelength channel Absorbance 1 AU Thermo Scientific Displays the current absorbance level for the Wavelength 2 channel Surveyor Plus User Guide for LC Devices 153 5 Daily Operation Turning Devices On Off or into Standby from the Info View Turning Devices On Off or into Standby from the Info View You can turn on certain activities for a device from its device listing in the Info View To use this feature the device must be powered on and communicating with the data system To turn on a device from the Info View Right click the device listing on the Status page and choose Turn Device On Depending on the device the following actions occur e When you turn on the pump it begins pumping solvents from the last set of downloaded parameters e When you turn on the detector its lamps turn on e When you turn on the autosampler it adjusts its controlled temperature zones to the last set of downloaded parameters To place a device in Standby mode Right click the device listing on the Status page and choose Turn Device into Standby Depending on the device the following actions occur e When you place the
29. LED light beam centered over the hole in the target port fixture LED light beam aligned with the hole in the target port fixture 2 Click Set Calibration The Next button becomes available 3 Click Next to proceed to the final page of the wizard Go to the next procedure Checking the Arm Calibration Offset Values Thermo Scientific Surveyor Plus User Guide for LC Devices 299 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Checking the Arm Calibration Offset Values Use this page of the Arm Calibration wizard to check the calibration values and close the wizard see Figure 206 Figure 206 Final page of the Arm Calibration wizard with the Finish button Diagnostic Arm Calibration Current calibration values x offset microns 540 00 Y offset microns 1586 00 Finish To verify the calibration setting 1 In the Current Calibration Values area verify the following e The X Offset readback displays a value from 900 to 900 um e The Y Offset readback displays a value from 1500 to 2500 pm Tip 1000 microns 1000 micrometers 0 04 inches The diameter of the hole in the center of the target port fixture is 0 047 inches 2 Click Finish to accept the settings and close the Arm Calibration wizard 3 Remove the LED and target port calibration fixtures 4 Reinstall the injection port as follows a Insert the injection port into the port in front of the was
30. Pressure Recorder Full Scale on page 264 Range 1 to 10 in integer steps For information on setting the full scale range for the pressure recorder see Scaling the Output of the Pressure Recorder Terminals on page 268 Flow Rate Adjustment Alpha Thermo Scientific Makes fine adjustments to the flow rate see Flow Rate Adjustment Alpha on page 265 For information on calibrating the alpha value see Updating the Flow Rate Adjustment Setting on page 268 Surveyor Plus User Guide for LC Devices 261 9 LC Pump Calibration and Record Keeping Calibrating the Surveyor LC Pump Plus Table 56 Calibration parameters for the Surveyor LC Pump Plus Sheet 2 of 2 Parameter Pressure Sensor Description Adjusts the pressure sensor reading see Pressure Sensor Adjustment on page 265 Adjustment For information on adjusting the pressure sensor reading see Updating the Pressure Sensor Adjustment Setting on page 269 Set Downloads the new setting to the pump Pressure Transducer Zero Calibrates the current pressure reading as the zero point see Pressure Transducer Zero on page 265 For information on setting the zero point for the pressure transducer see Zeroing the Pressure Transducer on page 269 Calibration Options for the Surveyor LC Pump Plus Compressibility The Xcalibur data system provides the following calibration options see Figure 168 for
31. Table 43 Surveyor LC Pump Plus status readbacks Readback Description Status Displays the following pump states READY The pump is ready to take a command Not Connected The pump is not communicating with the data system computer Off The pump pistons are stopped Running Isocratic The pump flow is on Running Gradient The pump is running a gradient program Degasser Displays the following degasser states READY or Not Connected Run Time Displays the run time Time Remaining Displays the remaining time for the run Flow Displays the user specified flow rate Pressure Displays the pressure monitored by the pump A Displays the user specified percent composition for solvent A B Displays the user specified percent composition for solvent B C Displays the user specified percent composition for solvent C D Displays the user specified percent composition for solvent D 150 Surveyor Plus User Guide for LC Devices Thermo Scientific Surveyor PDA Plus Detector Status View 5 Daily Operation Checking the Status of the LC Devices Figure 85 shows the Status view for the Surveyor PDA Plus Detector You can view the status of the lamps and the wavelength and dark current calibrations from this view Figure 85 Surveyor PDA Plus Detector Status view Status Acquisition Queue Run Manager Ready To Download Sequence Sample Name Working On Position Raw File Inst Method E Sur
32. Use this button to clear all tasks from the task list in the Method area Import Thermo Scientific Use this button to open the Open dialog box where you can select an instrument method with the sample preparation routine that you want to add to the current instrument method After you select an instrument method and click Import the File Name read only box displays the file name of the instrument method you want to import Surveyor Plus User Guide for LC Devices 121 4 Sample Preparation Routines Sample Locations for the Sample Preparation Tasks Sample Locations for the Sample Preparation Tasks For the sample preparation tasks you can select an absolute or a relative location For the Relative Location option the selections are Current Current 1 Current 2 and Current 3 Current is the sample location in the current sequence row Current 1 is the next adjacent vial or well location in the tray and so on For example if the vial location in the current sequence row is B 1 Current is B 1 then Current 1 is B 2 and so on For the Absolute Location option you specify an absolute vial or well location The vial or well locations depend on the tray configuration see Table 30 Tip Remember to place a vial at the selected location Table 30 Vial and well positions Tray configuration Vial or well positions Standard 1 8 mL vials A 1 to E 20 96 Well Plate A Al to C H12 384 Well Plate A Al to C P
33. io ae a D C3 nina e gt pe o i UNITID ENET ano 3 v n al O v luvls dvyo gt AQVaY dANd Q10H LOAfN gt 2 a Pad a oO 3 gt Use the Signal Polarity page of the Surveyor Autosampler Configuration dialog box to specify the signal polarities for the input and output run signals For the Surveyor LC Pump Plus and the Surveyor MS Pump Plus ensure that the Pump Ready Active High and the Injection Hold Release Active High check boxes in the Input area are selected To specify the signal polarities for the autosampler 1 Open the Surveyor Autosampler Configuration dialog box see Surveyor Autosampler Plus Configuration Settings on page 45 2 Click the Signal Polarity tab The Signal Polarity page appears see Figure 39 56 Surveyor Plus User Guide for LC Devices Thermo Scientific 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Figure 39 Signal Polarity page parameters Tray Communication Signal polarity Firmware IV Pump ready active high ki m x Ensure that these check boxes I Injection hold release active high are selected for a Surveyor Plus LC system Output F Autosampler ready active high Injection out active high Gradient start active high Pump stop active high Timed events active high 3 In the Input area ensure that the Pump Ready Active High and Injection Hold Release Ac
34. peak coverage ee 5 400000 Peak start Peak stop 3 J 200000 125 130 135 140 145 150 155 160 165 170 1 75 Time min 258 Surveyor Plus User Guide for LC Devices Thermo Scientific ee LC Pump Calibration and Record Keeping This chapter describes the calibration and record keeping procedures for the Surveyor LC Pump Plus Contents e Calibrating the Surveyor LC Pump Plus e Recording Maintenance Information for the Surveyor LC Pump Plus e Firmware Version Information for the Surveyor LC Pump Plus The Surveyor LC Pump Plus is factory calibrated to produce an accurate flow rate while pumping water at 1 mL min Its ability to accurately proportion binary mobile phases is also tested at a flow rate of 1 mL min The Surveyor LC Pump Plus does not require calibration upon arrival at its shipping destination However over time the pressure readings from its built in pressure transducer can drift and require re zeroing If you are running the LC pump at high backpressures you might notice an increase in its pressure pulsation You can reduce this pressure pulsation by adjusting the compressibility setting of the LC pump Thermo Scientific Surveyor Plus User Guide for LC Devices 259 9 LC Pump Calibration and Record Keeping Calibrating the Surveyor LC Pump Plus Calibrating the Surveyor LC Pump Plus Two calibration options for the Surveyor LC Pump Plus affect its performance the alpha setting which affects the flow rate
35. select the Auto Range option Selecting Auto Range ensures that the entire dynamic range of the spectrum is displayed in the active view normalized over the full range of the y axis c Inthe Normalize Spectrum To area select the Largest Peak in Range option 5 Specify the Axis parameters as follows a Click the Axis tab The Axis page appears see Figure 151 b In the Units area select the Absolute option Selecting Absolute sets the y axis to the absolute units of pAU 6 Click OK to close the Display Options dialog box Thermo Scientific Surveyor Plus User Guide for LC Devices 243 8 Qual Browser Creating a Layout for PDA Data Figure 151 Axis page in the Display Options dialog box Display Options wavelength nm always z a p awas E Inserting Cells Occasionally you might want to add more cells to the Qual Browser window For example you might want to add a cell containing a map plot contour or 3D to the view screen or you might want to display several discrete or scan wavelengths in separate cells To add a cell containing a map plot to the window 1 Click a cell to make it the active cell 2 Choose Grid gt Insert Cells gt Left Right Above or Below The location of the new cell is relative to the active cell Initially the new cell contains the same information as the existing cell see Figure 152 244 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Cr
36. 0 200 220 240 260 280 300 320 340 360 380 400 wavelength nm 250 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Determining Peak Areas Determining Peak Areas In a chromatogram the area of an isolated peak is directly proportional to the concentration of the analyte 1 bd 1 2 6 Thermo Scientific To make a peak area determination using the Qual Browser application Open the Qual Browser application Open the data file raw of interest see Opening a Raw Data File in Qual Browser on page 219 Ensure that the chromatogram cell is the active cell as indicated by a gray border Select the chromatogram that you want to integrate as follows a Right click the chromatogram and from the shortcut menu choose Ranges The Chromatogram ranges dialog box appears b In the Detector list select the detector type e To integrate a scan wavelength select PDA e To integrate a discrete wavelength channel select UV c Ensure that Avalon is selected as the Peak Algorithm d Select the appropriate wavelength e To display the chromatogram for a scan wavelength select Wavelength Range from the Plot Type list and then type a value for a wavelength within your scan range in the Range box e To display the chromatogram for a discrete wavelength channel select Channel A B or C from the Plot Type list Turn on peak detection by right clicking the chromatogram cell and choosing
37. 140 Surveyor Plus User Guide for LC Devices e The Verify Door Is Closed Check box is selected and the tray compartment door is closed e The Verify Door Is Closed check box is clear and the door is open or closed Thermo Scientific 5 Daily Operation Checking the Status of the LC Devices Table 36 Status readbacks for the autosampler Sheet 3 of 3 Readback Description Maintenance Due Displays Yes or No No The Enable Maintenance Log check box is clear none of the maintenance counters has exceeded its limit or both Yes The Enable Maintenance Log check box is selected and one or more of the maintenance counters has exceeded its limit The autosampler cannot start a run until you zero the counter or clear the Enable Maintenance Log check box For information about setting up the maintenance counters see Autosampler Maintenance Information on page 309 For information about clearing the Enable Maintenance Log check box see Communication Page on page 52 Firmware Version Displays the firmware version of the autosampler Oven Page Figure 78 shows the Oven page of the status view for the autosampler Figure 78 Oven page AS Status Oven Tray Error log Oven Control on Yes Current temperature C 24 4 Set temperature C 30 0 Ready status Ready Thermo Scientific Surveyor Plus User Guide for LC Devices 141 5 Daily Operation Checking the Status of the LC Devices Table 37 descri
38. 232 serial connection To check the communication connections 1 Check the settings of the rotary switches on the back panels of the Surveyor Autosampler Plus the Surveyor UV Vis Plus Detector or the Surveyor PDA Plus Detector and the Surveyor LC Pump Plus 2 For the Surveyor MS Pump Plus verify that the serial communication cable connecting the MS pump to the data system computer is attached to COM port 1 42 Surveyor Plus User Guide for LC Devices Thermo Scientific 2 Thermo Foundation Instrument Configuration Opening the Thermo Foundation Instrument Configuration Application Opening the Thermo Foundation Instrument Configuration Application To open the Thermo Foundation Instrument Configuration application From the Windows taskbar choose Start gt Programs gt Thermo Foundation 1 0 gt Instrument Configuration The Thermo Foundation Instrument Configuration window appears see Figure 33 This window lists the installed device drivers Figure 33 Thermo Foundation Instrument Configuration window 23 Thermo Foundation Instrument Configuration Device Types ee Available Devices Configured Devices I Surveyor MS Pump Surveyor 4S Plus Surveyor LC Pump Surveyor PDA Plus o Surveyor UV ZIS C Ce Thermo Scientific Surveyor Plus User Guide for LC Devices 43 2 Thermo Foundation Instrument Configuration Adding Devices to the Instrument Configuration Adding
39. 4 Sample Preparation Routines Sample Preparation Routine Example 7 Review the task list by expanding the tasks in the Method list see Figure 74 Figure 74 Method area with an expanded task list Method Sample Preparation Transfer from sample to sample Volume ful is 50 0 Source relative sample location is cu Destination relative sample location i Syringe speed ul s is 8 00 Source vial needle height mm is 2 Air bubble volume ul is 3 Destination vial needle height mm Transfer from reservoir to sample Volume ful is 225 0 Sample relative location is current Source reservoir is AY1 Syringe speed ul s is 8 00 Needle height mm is 2 0 Transfer from reservoir to sample Volume ul is 225 0 Sample relative location is current z b 8 Save the instrument method see Saving the Instrument Method on page 109 To perform this sample routine you must insert empty vials into your sample tray For example to dilute five samples place the samples in vial locations A1 A3 A5 A7 and A9 Place empty vials in vial locations A2 A4 A6 A8 and A10 Fill reservoir vial 1 with an appropriate diluent that matches the sample matrix If you do not want to inject the diluted samples create a five line sequence that lists the vial locations of the original samples A1 A3 A5 A7 and A9 The original samples are not injected If you want to inject the
40. 50 29 PM RT 0 00 15 00 9 453 NL 200000 2 12E5 Total Scan PDA 150000 PAHs_01 7 65 8 28 9 05 10 33 1255 13 52 0 0 1 2 3 4 5 6 7 8 9 10 1 12 13 14 45 Time min PAHs_01 1 RT 0 01 AV 1 NL 135E6 Ez T c sid 8 00 Q1MS 127 60 254 60 ae 253 1 oO O 80 ke 5 60 a lt g 254 1 20 X 1282 1292 102 2021 2032 2041 228 2 2292 2302 252 2 128 129 130 202 203 204 228 229 230 252 253 254 miz miz miz mz Displaying Discrete Wavelength Chromatograms To display a discrete chromatogram for the PDA data 1 If you have not already done so open a data file raw that has PDA data and MS data see Opening a Raw Data File in Qual Browser on page 219 The data file opens with the MS TIC chromatogram in the upper cell and a mass range spectrum in the lower cell 2 Pin the chromatogram cell see Active and Pinned Cells on page 225 3 Right click the chromatogram cell 4 From the shortcut menu choose Ranges The Chromatogram Ranges dialog box appears Figure 141 on page 234 shows the default settings Figure 144 shows the settings for a discrete channel wavelength 236 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Creating a Layout for PDA Data Figure 144 Chromatogram Ranges dialog box with the selection of a discrete channel wavelength Chromatogram Ranges Ranges Automatic processing Range Time range minutes ii Il Fixed scale Scan filter
41. A B or C Row A through P Column through 24 Figure 9 shows the notation for 384 well microplates Figure 9 Notation for 384 well microplates Top Left Bottom Right CAI A 29000099990900099900000 299990099990000999900009 P 206060906 OOS8SOG0806 900666669086666000506008 8OOG8G6G980G98G0G8H00088 elelelefelelelelelelelefeleleleleleleerelelele 894060990066600900060000 900000099096600900566009 896060690066660000860000 900090999056000900566000 leleretefelelelelelelelelelelelelelelelelelelele 900906999086000000506008 8O0O8G9G98GG98GOGSH000S6 908000699H080060HH0800000 90G0009900HHG09900H6000O 900060999086000990560009 899660990866660000566000 90000009906660O900560000 806060699866666000806006 900666999056606800566000 lelelefofelelelelelelelefelelelelelelelelelelele 900066989080606900800008 8OOO8G0G90H98G0G8H00088 8O0098G0G9G09H8G9S9HG00H 809060990066600000560000 900090099096600900506009 8O9060990066660000880000 900660099056600900566000 866098060 leefelelelereleleleje 800606999066600000806008 CA1 P 066660006 56665666556 606666665066666650506668 AL 1 74 24 1 B Al A 299099099000 QQQQQQQ QQQQQQQQQQQQQQQQQQQQQQQQ P 999960990866600000066000 900600099066600900560009 889660O90866668000506000 900060990056606000566000 lelelefefelelelelelejelefeleleleleleleeielelele 900966909066666800506008 8O0O8G0O98GO88G0GHH000S8 9080869G908066G900506008 90G0G09900GG600900HG00
42. C Absolute location fan elative location Curent 1 gt Volume ful 150 0 Syringe speed ul s 18 00 Source vial needle height mm 2 0 H Default settings Air bubble volume ful 3 0 Destination vial needle height mm 2 0 c Click Add To Task List to add the task to the sample preparation routine When the autosampler performs this task it withdraws 50 pL of sample from the current vial location in the sequence table and deposits it in the current 1 vial location 4 Add a task that transfers diluent with the inner syringe plunger from a reservoir vial to the sample location a In the Prep Operations list select Transfer from Reservoir to Sample The parameters for the task appear below the Add To Task List button 128 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 4 Sample Preparation Routines Sample Preparation Routine Example b Keep all the default parameter settings for the Transfer from Reservoir to Sample task except those that are shown below see Figure 71 Tip When accuracy is important keep the transfer volume below the nominal syringe size so that the autosampler uses the inner syringe plunger Solvent transfers made with the inner plunger are more accurate than solvent transfers made with the outer plunger because the stepper motor for the inner plunger takes smaller steps and provides finer control than th
43. Calibration Surveyor LC Pump Direct Control dialog box 1 Turn on the power to the Surveyor LC Pump 2 Open the Surveyor LC Pump view in the Instrument Setup window 3 Choose Surveyor LC Pump gt Direct Control gt Calibration The Calibration Surveyor LC Pump Direct Control dialog box appears see Figure 168 Surveyor Plus User Guide for LC Devices Thermo Scientific 9 Lc Pump Calibration and Record Keeping Calibrating the Surveyor LC Pump Plus Figure 168 Calibration page for the Surveyor LC Pump Calibration Surveyor LC Pump Direct Control Settings Compressibility 0 45 GPa Default value Pressure Recorder Full Scale 1 00 x 4 9 MPa Flow Rate Adjustment Alpha 5 0 rA Pressure Sensor Adjustment 4962 Pressure Transducer Zero neo C Calibration Surveyor LC Pump Direct Control Parameters Table 56 describes the calibration parameters for the Surveyor LC Pump Plus Table 56 Calibration parameters for the Surveyor LC Pump Plus Sheet 1 of 2 Parameter Description Settings Compressibility Specifies the compressibility of the mobile phase see Compressibility on page 262 For information on determining the appropriate value for your solvent conditions see Updating and Optimizing the Compressibility Setting on page 266 Pressure Recorder Full Scale Specifies the full scale range of the recorder connected to the pressure terminals on the back panel of the pump see
44. Command To apply a direct command 1 Select a command from the list of commands If the command requires additional parameters these parameters appear below the list Make the appropriate entries and selections 2 To execute the command click Apply Direct Control Commands for the Autosampler Table 53 describes the direct control commands for the autosampler Table 53 Direct control commands for the autosampler Sheet 1 of 3 Command Description Position Arm to Moves the XYZ arm to the back of the tray compartment so that you can remove trays from Access Tray or place trays into the tray compartment Note If the tray compartment door is open and you selected the Verify Door Is Closed check box when you configured the autosampler the autosampler does not execute this command until you close the tray compartment door Flush Syringe Flushes the needle tubing and the interior of the needle with flush solvent Parameter Selections or range Reservoir RV1 RV2 RV3 RV4 or Bottle Volume 0 to 6000 pL Flush Speed Depends on the syringe type as follows Syringe type Range Concentric syringes 1 65 to 661 38 pL s Standard 2500 pL syringe 0 83 to 330 85 pL s Flush Syringe at Flushes the needle tubing the interior of the needle and the sample loop with flush solvent Fill Position For the parameter descriptions see Flush Syringe Wash Needle Washes the exterior of the needle with solvent Pa
45. Devices to the Instrument Configuration To control a device from the data system the device must be listed in the Configured Devices y 8 pane of the Thermo Foundation Instrument Configuration window 1 To add the LC device drivers to the Thermo Foundation instrument configuration In the Available Devices list double click the icons for your LC devices A copy of the icon appears in the Configured Devices list see Figure 34 Figure 34 Thermo Foundation Instrument Configuration window with devices added to the Configured Devices list 23 Thermo Foundation Instrument Configuration Device Types an Available Devices Configured Devices Surveyor MS Pump Surveyor AS Surveyor LC Pump Surveyor 4S Plus Surveyor LC Pump Surveyor PDA Plus Surveyor PDA Plus Surveyor UV VIS 44 Surveyor Plus User Guide for LC Devices Thermo Scientific 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Specifying the Configuration Settings After you add the devices to the Configured Devices list specify the configuration settings for each device as described in these topics e Surveyor Autosampler Plus Configuration Settings e Surveyor MS Pump Plus Configuration Settings e Surveyor LC Pump Plus Configuration Settings e Surveyor PDA Plus Detector Configuration Settings e Surveyor UV Vis Plus Detector Configuration Settings After specifying the configuration options for the i
46. Dual valve Diffusion barrier cartridge cartridge Manual bleeder valve 2 mL dampening loop for priming To prime the pulse dampener of the Surveyor MS Pump Plus 1 Fill a solvent bottle with particulate free HPLC grade methanol 2 Connect an HPLC column or a flow restrictor to the LDA outlet 3 Insert the tip of the 10 mL syringe into the tubing connected to the manual bleeder valve see Figure 88 156 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 5 Daily Operation Priming the Pulse Dampener of the Surveyor MS Pump Plus Figure 88 Manual bleeder valve with attached tubing Outlet of pulse dampener Manual bleeder valve with attached tubing 4 Open the valve by turning it counterclockwise 5 To open the direct controls for the Surveyor MS Pump Plus do one of the following e From the Surveyor MS Pump Plus view choose Surveyor MS Pump Plus gt Direct Control The Direct Control dialog box appears Note For information about using the Direct Control dialog box for the Surveyor MS Pump Plus see Pump Direct Controls on page 185 or e From the tune window for your Thermo Scientific mass spectrometer choose Setup gt Inlet Direct Control The Inlet Direct Control dialog box that contains tabbed pages for each configured LC device appears Click the Surveyor MS Pump Plus tab Note For information about using the Inlet Direct Control dialog box see Chapter 1
47. EEC and harmonized standard EN 61010 1 2001 Surveyor MS Pump Plus When the Surveyor MS Pump Plus is delivered to you it meets all pertinent electromagnetic compatibility EMC and safety standards as described below EMC Directive 89 336 EEC amended by 92 31 EEC and 93 68 EEC EMC compliance has been evaluated by Underwriters Laboratories Inc EN 55011 1998 EN 61000 4 3 2002 EN 61000 3 2 1995 Al 1998 A2 1998 A14 2000 EN 61000 4 4 1995 Al 2001 A2 2001 IEC 61000 3 2 2000 EN 61000 4 5 1995 Al 2001 EN 61000 3 3 1995 EN 61000 4 6 1996 A1 2001 IEC 61000 3 3 1994 EN 61000 4 11 1994 Al 2001 EN 61326 1 1997 EN 61000 4 2 1995 Al 1998 A2 2001 CISPR 11 1999 A1 1999 A2 2002 FCC Class A CFR 47 Part 15 Subpart B 2004 Low Voltage Safety Compliance Low voltage safety compliance has been evaluated by TUV Rheinland of North America Inc This device complies with Low Voltage Directive 73 23 EEC and harmonized standard EN 61010 1 2001 Surveyor Autosampler Plus When the Surveyor Autosampler Plus is delivered to you it meets all pertinent electromagnetic compatibility EMC and safety standards as described below EMC Directive 89 336 EEC amended by 92 31 EEC and 93 68 EEC EMC compliance has been evaluated by Underwriters Laboratories Inc EN 55011 1998 EN 61000 4 3 2002 EN 61000 3 2 1995 Al 1998 A2 1998 A14 2000 EN 61000 4 4 1995 Al 2001 A2 2001 IEC 61000 3 2 2000 EN 61000 4 5 1995 Al 2001 E
48. File Summary Information User Finn Header File ID Finn Created Monday January 05 2004 1 46 36 PM User ID Finn Logon ID Finn Not changed Description New Method Cancel Help 2 In the Description box type an appropriate description Then click OK The Save As dialog box appears see Figure 119 Figure 119 Save As dialog box showing the file extension for a sequence file Save in methods gt ex EE P templates File name tes sld Save as type Xcalibur Sequences sld Cancel Help 3 Browse to the appropriate folder where you want to save the sequence Header Information 208 Surveyor Plus User Guide for LC Devices Thermo Scientific 7 Sequence Setup Equilibrating the Chromatographic Column 4 In the File Name box type a file name 5 Click Save Equilibrating the Chromatographic Column Warming up the deuterium lamp and equilibrating the LC column reduces baseline drift For information about warming up the D2 lamp see Turning the Lamps On or Off on page 163 An LC column requires 10 to 20 column volumes to equilibrate to the initial mobile phase conditions of an instrument method For example it takes approximately 17 mL of mobile phase to equilibrate a typical 4 6 mm IDX10 cm length column To calculate the volume of an LC column use the following equation Vin tr x L Where Vim volume in mL r column radius in cm rad
49. Guide To open Help e From the Instrument Setup window choose Help gt product name Help e Ifavailable for a specific window or dialog box click Help or press F1 for information about setting parameters For more information visit www thermoscientific com xvi Surveyor Plus User Guide for LC Devices Thermo Scientific Preface Safety and Special Notices Make sure you follow the precautionary statements presented in this guide The safety and other special notices appear in boxes Safety and special notices include the following CAUTION Highlights hazards to humans property or the environment Each CAUTION notice is accompanied by an appropriate CAUTION symbol IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or might contain information that is critical for optimal performance of the system Note Highlights information of general interest Tip Highlights helpful information that can make a task easier Thermo Scientific Surveyor Plus User Guide for LC Devices xvii Preface Contacting Us There are several ways to contact Thermo Fisher Scientific for the information you need To contact Technical Support Phone 800 532 4752 Fax 561 688 8736 E mail us techsupport analyze thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at mssupport thermo com To contact Customer Service
50. LC Devices 75 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings To specify the parameters on the Pump General page 1 Open the view for your pump For information about opening the device views from the Xcalibur 2 1 x data system see Opening the Instrument Setup Window on page 68 The pump view includes a Pump 1 area for a single pump system or a Pump 1 area and a Pump 2 area for a dual pump system 2 On the Pump General page specify the parameters as follows a Inthe Name box use the default label Pump 1 for a single pump system or type a label The label can be up to 16 alphanumeric characters The data system uses this label for the pump view on the Status page of the Information view b In the Comment box type additional information about the chromatographic method for example the specifications for the liquid chromatography column c Identify the solvents that make up the mobile phase All of the solvent check boxes are selected by default Clearing a solvent check box makes the solvent unavailable on the Gradient Program page In the boxes to the right of the solvent check boxes type the names of the solvents that make up the mobile phase e Inthe Operating Mode list the only selection for the Surveyor MS Pump Plus is Low Pressure d In the Start Settings list select how the system is triggered to start a run Surveyor AS Autosampler Injection Logic or Manual To trig
51. Motor speed 29 4 rpm Table 42 describes the status readbacks on the Degasser page of the pump status view Table 42 General page of the pump status view Readback Description Degasser Status The states of the degasser are as follows Ready The vacuum level has reached a sufficient level to degas the mobile phase solvents Not Connected The pump is not communicating with the data system computer Error An error condition has occurred Vacuum Level Displays the vacuum level of the solvent degassing chambers Motor Speed Displays the motor speed of the vacuum degasser 148 Surveyor Plus User Guide for LC Devices Thermo Scientific 5 Daily Operation Checking the Status of the LC Devices Surveyor LC Pump Plus Figure 84 shows the Status view for the Surveyor LC Pump Plus You can view the system pressure from this view Figure 84 Surveyor LC Pump Plus Status view Status Acquisition Queue E Run Manager Ready To Download Sequence Sample Name Working On Position Raw File Inst Method Surveyor AS Ready to Download Surveyor LC Pump Ready to Download Surveyor PDA Plus i OFf Status READY Degasser Run Time 0 00 min Time Remaining 0 00 min Flow 1 00 mL min Pressure 0 00 psi 10 x Thermo Scientific Surveyor Plus User Guide for LC Devices 149 5 Daily Operation Checking the Status of the LC Devices Table 43 describes the readbacks on the pump status view
52. Peak Detection gt Toggle Detection in This Plot from the shortcut menu To display numerical values for areas of the chromatographic peaks do the following a Right click the chromatogram cell and choose Display Options The Display Options dialog box appears b Click the Labels tab The Labels page appears see Figure 159 Surveyor Plus User Guide for LC Devices 251 8 Qual Browser Determining Peak Areas Figure 159 Labels page in the Display Options dialog box Display Options E T Ej Bj c Select the Area check box d Click OK to return to the chromatogram cell 7 To set the integration parameters do the following a Right click the chromatogram and choose Peak Detection gt Settings from the shortcut menu The Avalon Peak Detection Settings page appears on the left side of the window see Figure 160 Note The Avalon Peak Detection Settings page appears only when Avalon is selected as the peak algorithm in the Chromatogram Ranges dialog box 252 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Determining Peak Areas Figure 160 Avalon Peak Detection Settings page PBIB E hsl Apply to all plots Auto Cale Initial Events Initial Value Start Threshold 10000 000 Initial Value End Threshold 10000 000 Initial Value Area Threshold 10000 000 Initial Value P P Threshold 1 000 Initial Value Bunch Factor 1 000 Initial Value Negative Peaks Off Initial Value Te
53. Plunger 126 Surveyor Plus User Guide for LC Devices The autosampler uses the inner plunger of the concentric syringe to perform the following tasks e Draw From Sample Transfer From Sample To Sample Transfer From Sample To Reservoir The syringe size determines the default syringe speed and the syringe speed range see Table 34 Use a syringe speed lower than the default for viscous samples Also use a syringe speed lower than the default for samples of very low viscosity or surface tension to prevent the sample bolus from breaking apart during the transport process Note You select the size of the syringe by using the Syringe Type list on the Communication page of the Surveyor AS Configuration dialog box Table 34 Syringe speeds for tasks that use the inner plunger of the concentric syringe Syringe size Minimum speed Maximum speed Default speed uL uL s pL s uL s 100 0 33 13 25 3 250 0 33 33 10 8 500 1 65 66 11 8 Thermo Scientific 4 Sample Preparation Routines Sample Preparation Routine Example Sample Preparation Routine Example The following procedure describes how to create a sample preparation routine to dilute samples tenfold To add a sample preparation routine that dilutes samples tenfold 1 From the Surveyor AS view click the Sample Preparation tab The Sample Preparation page appears 2 Open the meth file that you want to modify In step 3 through step 6 you add the sam
54. Preparation page opening 113 sample rate PDA detector 99 sample trays figure showing conventional trays 204 loading into the tray compartment 210 selecting tray options 47 temperature control 21 vial and microplate well positions 6 Save PDA Display Method dialog box 315 scan threshold 255 screen saver turning off 24 seals piston ruining 77 sequences creating 201 saving 208 turning off the lamps and the solvent flow 213 Snapshot button 169 178 318 solvent composition gradient program linearity 79 instrument method 79 programming for LC pump 72 solvent lines four lines for mobile phase solvents 23 wash bottle 23 solvent platform 23 solvent reservoir bottles 23 spectral light intensity spda file type 315 Thermo Scientific Index S spectrum chromatographic time point 249 cursor actions 226 displaying 238 maximum absorbance 235 speeds flush speed setting 87 loop loading 92 no waste injections 19 stack address or stack number 24 42 63 65 standard syringe single plunger size 14 standby Status page shortcut menu item 154 Start Data button 169 status checking the status of the LC devices 136 LEDs for LC devices 35 Stop Data button 170 switches Ethernet 24 tray compartment door magnetic 6 synchronizing the LC devices 32 syringe valve description and figure 13 syringe autosampler configuring 53 description 14 flushing 196 sample preparation rules for 115 T target port fixture arm cali
55. Start To stop the solvent flow Click Stop To change the global pressure limits Click Pressure Limits The Pressure Limits dialog box appears see Figure 107 Figure 107 Pressure Limits dialog box Pressure Limits Min pressure bar Max pressure bar made For global options In the Min Pressure box type the minimum operating pressure for the pump In the Max Pressure box type the maximum operating pressure for the pump The maximum pressure for the Surveyor MS Pump Plus is 1000 bar 100 MPa or 14504 psi Click OK to accept the settings and close the dialog box Surveyor Plus User Guide for LC Devices 191 6 Direct Controls Autosampler Direct Controls Autosampler Direct Controls The On Off switch is the only manual control provided with the autosampler To perform tasks such as moving the XYZ arm to the back of the tray compartment use the direct control commands in the autosampler view or the tune application for your Thermo Scientific mass spectrometer These topics describe the direct controls for the autosampler e Applying a Direct Command e Direct Control Commands for the Autosampler e Flushing the Autosampler Syringe e Removing and Installing Sample Trays e Controlling the Tray and Oven Compartment Temperatures You can access the direct control commands for the autosampler from the autosampler view of your data system or the tune application for your mass spectrometer
56. TIC chromatogram in the upper cell and a mass range spectrum in the lower cell Follow these topics to change the upper cell to a chromatogram and the lower cell to spectral data acquired by the PDA detector e Specifying the Chromatogram Ranges e Specifying the Spectrum Range Note You can modify the cells in any order Specifying the Chromatogram Ranges Thermo Scientific There are two types of chromatograms for the PDA detector chromatograms acquired from any of the three discrete channels and chromatograms interpolated from the scan data Follow these procedures to display the two types of chromatograms acquired by the PDA detector in the Qual Browser window e Displaying Scan Wavelength Chromatograms e Displaying Discrete Wavelength Chromatograms Displaying Scan Wavelength Chromatograms To display a scan chromatogram for the PDA detector data 1 Open a data file raw that has PDA data and MS data see Opening a Raw Data File in Qual Browser on page 219 The data file opens with the MS TIC chromatogram in the upper cell and a mass range spectrum in the lower cell Surveyor Plus User Guide for LC Devices 233 8 Qual Browser Creating a Layout for PDA Data 2 Pin the chromatogram cell see Active and Pinned Cells on page 225 3 Right click the chromatogram cell 4 From the shortcut menu choose Ranges The Chromatogram Ranges dialog box appears see Figure 141 Figure 141 Chromatogram Ranges
57. To display multiple chromatogram cells 1 Click the chromatogram cell to make it the active cell with a gray border 2 Choose View gt Ranges The Chromatogram Ranges dialog box appears see Figure 125 216 Surveyor Plus User Guide for LC Devices Thermo Scientific 7 Sequence Setup Working with the Real Time Plot View Figure 125 Chromatogram Ranges dialog box Total Scan SE GET z z O o o O O O a Dee ov scan hiter Z Avalon zj Channel B BS E zj oo Hangels Fly scale to 3 For each cell that you want to add do the following a Inthe Type column select its corresponding check box b In the Detector list select a detector c Inthe Plot Type list select a plot type 4 Click OK to close the Chromatogram Ranges dialog box 5 Choose View gt Lock Display to resume monitoring real time data acquisition Thermo Scientific Surveyor Plus User Guide for LC Devices 217 ee i Qual Browser This chapter provides an introduction to the Xcalibur Qual Browser functions that you can use to review the PDA data contained in your raw data files Contents e Opening a Raw Data File in Qual Browser e Working with the Cell Grid e Changing the Font Size of the Display e Viewing a Report of the Instrument Method e Creating a Layout for PDA Data e Viewing the Spectrum for a Specific Time Point e Viewing the Chromatogram for a Specific Wavelength e Determining Peak Areas
58. To open the Inlet Direct Control dialog box from the tune application 1 In the Tune window choose Setup gt Inlet Direct Control The Inlet Direct Control dialog box appears with tabbed pages for each configured LC device 2 Click the Surveyor AS tab The Surveyor AS page appears see Figure 108 192 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 1 6 Direct Controls Autosampler Direct Controls Figure 108 Inlet Direct Control dialog box for the Surveyor pump and autosampler Inlet Direct Control Surveyor MS Pump Plus Command amp Parameters Position arm to access tray Position arm to access tra Flush syringe Flush syringe at Fill position Wash needle Needle removal Set oven temperature J Set tray temperature Turn off oven temperature Turn off tray temperature Inject sample Move needle Set injector position Set to syringe removal position Set syringe to home position Set Arm to Home Position To open the Direct Control dialog box 1 Open the autosampler view 2 From the menu bar choose Surveyor AS gt Direct Control The Direct Control dialog box appears see Figure 109 Figure 109 Direct Control dialog box Instrument Setup window Direct Control Command amp Parameters Position arm to access tray v Surveyor Plus User Guide for LC Devices 193 6 Direct Controls Autosampler Direct Controls Applying a Direct
59. Well bottom distance Ces uo The Arm Calibration wizard appears see Figure 193 The Current Calibration Values area displays the current calibration values for the x axis and y axis position of the XYZ arm over the autosampler injection port Figure 193 Current Calibration Values page Diagnostic Arm Calibration Current calibration values x offset microns 571 00 Y offset microns 1517 00 Press Next to continue lt Back i Cancel Help Note The user interface specifies the x and y axis offsets in microns which is another term for micrometers 1000 micrometers 0 04 inches The diameter of the hole in the center of the target port fixture is 0 047 inches 5 Click Next to proceed to the next page of the wizard Go to the next procedure Moving the Arm to the Needle Removal Position Surveyor Plus User Guide for LC Devices 291 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Moving the Arm to the Needle Removal Position Use this page of the Arm Calibration wizard to move the arm to the needle removal position see Figure 194 Figure 194 Move the Arm to Needle Removal Position button page Diagnostic Arm Calibration Move the arm to needle removal position Press Next when movement stops Cancel Help To move the XYZ arm to the needle removal position 1 Click Move the Arm to Needle Removal Position The XYZ arm moves to
60. When the Verify Door Is Closed check box is selected the autosampler cannot trigger a run when the tray compartment door is open If the tray door is opened during a sequence run the XYZ arm moves to the back of the tray compartment at the end of the current run and the Xcalibur sequence halts Optional To activate the maintenance log select the Enable Maintenance Log check box The maintenance log keeps an internal count of the total injections total valve cycles total needle usage and total syringe cycles When any of the counters exceed the user set scheduled maintenance time SMT the autosampler cannot trigger a run until you perform the scheduled maintenance or you clear the check box In the Vial Bottom Sensing area select the type of vial bottom sensing that is appropriate for your application e To activate vial bottom sensing for every injection in a sequence select the On option e To activate vial bottom sensing for only the first injection in a sequence select the Auto option e To deactivate vial bottom sensing select the Off option Each tray type has a stored value for the distance that the needle must travel to reach the bottom of the vial or well When you activate vial bottom sensing the autosampler performs a search routine to determine the actual location of the vial or well bottom If the search routine determines a new value for the bottom distance it is stored until you modify the tray type I
61. X Time jpa ti S Background Subtraction Filter Type Scan Process Time range 1 po FZ Time range 2 po Raw file c wcalbu data pahs Olraw Isl Cancel Help If you have not already done so modify the layout for the chromatogram cell as described in Specifying the Chromatogram Ranges on page 233 If you have specified the ranges for the chromatogram cell and the spectrum cell go to the next procedure Specifying the Display Options for the Chromatogram and Spectrum Cells Thermo Scientific Surveyor Plus User Guide for LC Devices 239 8 Qual Browser Creating a Layout for PDA Data Specifying the Display Options for the Chromatogram and Spectrum Cells After you specify the chromatogram and spectrum ranges specify the display options for the chromatogram and spectrum cells as described in these topics e Setting the Display Options for the Chromatogram Cell e Setting the Display Options for the Spectrum Cell Setting the Display Options for the Chromatogram Cell To set the display options for the chromatogram cell 1 Pin the chromatogram cell 2 Right click the pinned chromatogram cell 3 From the shortcut menu choose Display Options The Display Options dialog box appears 4 Specify the Normalization parameters a Click the Normalization tab The Normalization page appears see Figure 147 Figure 147 Normalization page in the Display Options dialog box Display Options Style Color
62. about the Wait for Temperature Ready check box see Communication Page on page 52 Not Ready The oven compartment temperature has not reached the set temperature Surveyor Plus User Guide for LC Devices 143 5 Daily Operation Checking the Status of the LC Devices Error Log Autosampler Page Figure 80 shows the Error Log page for the autosampler Figure 80 Error Log page AS Status Oven Tray Error log Application code Table 39 describes the parameters on the Error Log page Table 39 Error Log page parameters Parameter Description Index Lists the order of the error events in increments of 1 The index number for the first error event that occurs after you clear the log is 1 Application code Refer to your autosampler hardware manual for information about the application codes Buttons Refresh Loads the error log messages stored by the autosampler Clear Clears the error log 144 Surveyor Plus User Guide for LC Devices Thermo Scientific 5 Daily Operation Checking the Status of the LC Devices Surveyor MS Pump Plus Thermo Scientific For information about the status of the pump and the degassing unit see these topics e General Page of the Pump Status View e Extended Page of the Pump Status View e Degasser Page of the Pump Status View General Page of the Pump Status View Figure 81 shows the General page of the pump status view Figure 81 General page pump status view
63. allowing you to remove trays or replace vials Opening the tray compartment door while the autosampler is making an injection does not interrupt the current run The XYZ arm moves to the back of the compartment after the current injection is complete The programmed sequence of injections then halts When you close the tray compartment door the sequence resumes Vial and Well Notation Vial Notation You specify the vial or microplate well location where you want the autosampler to withdraw sample in the sequence table or the Inject Sample direct command You also specify the vial or microplate well locations for sample preparation tasks These topics describe the notation for specifying vial and well locations e Vial Notation e 96 Well Microplate Notation e 384 Well Microplate Notation The notation for the location of vials is as follows Tray location in tray compartment Vial location in tray Where Tray location in tray compartment A B C D or E Vial location in tray through 40 A colon separates the tray location in the tray compartment from the vial location in the tray Figure 6 shows the tray locations 6 Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Autosampler Figure 6 Standard trays E 40 Tray A Tray B Tray C Tray D Tray E 96 Well Microplate Notation The notation for the location of 96 well microplates is as follows Plate RowColumn Wher
64. and the compressibility setting which affects the pressure pulsation of the system The alpha setting is factory calibrated to produce an accurate flow rate for water The compressibility setting is set to 0 45 GPa which is the compressibility value for water If you are pumping solvents other than water and your application is sensitive to pressure pulsation you might want to optimize the compressibility setting After you optimize the compressibility setting check the flow rate accuracy If adjusting the compressibility setting has affected the flow rate accuracy adjust the alpha setting In addition to the alpha setting and the compressibility setting the pressure transducer that is attached to the back of the purge manifold assembly is also factory calibrated If you replace the pressure transducer you must update the pressure sensor adjustment setting Even if you never replace the pressure sensor you must occasionally re zero its output as the readout tends to drift under normal usage These topics provide information on calibrating the LC pump e Accessing the Calibration Options for the Surveyor LC Pump Plus e Calibration Options for the Surveyor LC Pump Plus e Calibration Procedures for the Surveyor LC Pump Plus Accessing the Calibration Options for the Surveyor LC Pump Plus 260 You can fine tune the performance of the Surveyor LC Pump from the Calibration Surveyor LC Pump Direct Control dialog box To open the
65. autosampler can deposit draw or transfer during a sample preparation task depends on the syringe type the task requested and the previous step in the sample preparation method Table 28 categorizes the sample preparation tasks into three groups based on whether the task uses the inner bore only the outer bore only or either bore of the dual plunger concentric syringe For information about the dual plunger concentric syringe see Interchangeable Syringe on page 14 Table 28 Sample preparation tasks arranged in groups according to bore usage Inner bore only Outer bore only Inner or outer bore Draw from Sample Mix at Sample Draw from Reservoir Transfer from Mix at Reservoir Deposit Liquid in Sample Sample to Sample Transfer from Wash Needle Deposit Sample in Reservoir Sample to Reservoir Flush to Waste Transfer from Reservoir to Sample Transfer from Reservoir to Reservoir For the 250 pL concentric syringe these rules restrict the arrangement of the tasks in the sample preparation list For tasks performed with the inner bore of the dual concentric syringe the maximum volume sample air bubble that the autosampler can draw deposit or transfer is limited to the nominal size of the syringe 250 pL e For tasks performed with either bore if the sum of the requested volume liquid air bubble plus any volume left in the needle tubing from a previous step is less than the nominal syringe size the dual plunger conc
66. available If the output polarity is Active High the Set Active Low button is available 164 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls PDA Detector Direct Controls 2 Under Analog Outputs see Figure 93 do one of the following e Click Set Active High to change the output polarity from Active Low to Active High or e Click Set Active Low to change the output polarity from Active High to Active Low Figure 93 Analog Outputs area on the Configuration page Analog Outputs Ready Output Turn On Turn Off Output is Active High Set Active Low Event Output Tum On Tum Off Output is Active High Set Active Low Short DACs Output DAC Outputs Active Zero DACs Testing the Analog Outputs Use the Configuration page of the Surveyor PDA Plus Direct Control dialog box to change the polarity of the analog outputs KD To test the analog outputs 1 Open the Configuration page of the Surveyor PDA Plus Direct Control dialog box see Configuration Page on page 171 2 Under Analog Outputs see Figure 93 do the following e Click Turn On or Turn Off to trigger the external device e Click Zero DACs to calibrate external instruments such as an SS420X analog to digital converter When you click Zero DACs the DACs outputs are set to zero for about 20 seconds You can extend this calibration time by clicking the button again Thermo Scientific Surveyor Plus User G
67. control the acquisition choose Actions gt Pause Analysis or Actions gt Stop Analysis Thermo Scientific Surveyor Plus User Guide for LC Devices 213 7 Sequence Setup Working with the Real Time Plot View Working with the Real Time Plot View To view and review data as it is being acquired in the Real Time Plot view follow these procedures e Viewing Data Acquisition e Reviewing Real Time Data e Adding Cells to the Display Viewing Data Acquisition To view the data as it is acquired 1 Choose View gt Real Time Plot View or click the Real Time Plot View button on the Lo ie Home Page toolbar ry 2 If the display is not already locked click the Lock Display button to lock the display Locked Locking the display lets you monitor the real time progress of your run a In the unlocked position you cannot monitor the real time progress of your run but you Unlocked can review your data For example you can display the spectrum for a particular peak that has already eluted Data collection continues off screen as you review your data If you are collecting PDA scan data a view similar to that shown in Figure 124 is displayed The view contains three cells a chromatogram cell a spectrum cell and a Total Scan cell 214 Surveyor Plus User Guide for LC Devices Thermo Scientific 7 Sequence Setup Working with the Real Time Plot View Figure 124 Real Time Plot view showing the acquisition of PDA scan data and one disc
68. dataset en aera en eae ek 210 Starting Data Acquisition 6 ec cc eee 211 Working with the Real Time Plot View s vs c05c2 cesscew seen dee bans 214 Viewing Data Acquisition s s i 0 cu 50 b aeeiaye aide eden bool iow ads Bee 214 Reviewing Real Time Date nieacd apex wee tiek ad web wh op els Sek w he ks 215 Adding Cells to the Display ooon Va ene Maral ae Saranac ad heats 216 Qual BrOwWSEl s cxcwienn inni naa aa wine E E 219 Opening a Raw Data File in Qual Browser 0 0 eee cece eee 219 Working with the Cell Grid s poesia cence aba on one ees 224 Coll States ot rie teehee A tee mae teal Mie tae a rA wats tay 224 CURE ACHORS nu pta Sera be Riga het hook ie AOL se MUR RAA 226 Changing the Font Size of the Display 0 000 ee eee 230 Viewing a Report of the Instrument Method 00000 232 Surveyor Plus User Guide for LC Devices xiii Contents Chapter 9 Chapter 10 Chapter 11 Chapter 12 Creating a Layout for PDA Date won tactics ohh an retin bel eleteee dae 233 Specifying the Chromatogram and Spectrum Ranges 004 233 Specifying the Display Options for the Chromatogram and Spectrum CellSesaa n ie ea a ee eee awe RU a asa R ae Pash a 240 Jiiserting Cells 4 8 ice swmedinisey se Seka i ae PED ES HES Ee RRS 244 Saving the New Layout n meeitetide bose whe oie kee ee 248 Viewing the Spectrum for a Specific Time Point 00000048 249 Viewing the Chromatogram for a Sp
69. detection 251 purity settings 255 polarity active high or active low 164 Post Injection Valve Switch Time box 89 Power LED autosampler 38 LC pump 37 MS pump 36 PDA detector 39 UV Vis detector 40 power turning on off 134 precision injection to injection 89 preheating tubing 21 Prep Operations list 116 pressure minimum for LC pump 69 recorder terminals 264 sensor adjustment 269 units for displaying backpressure 63 pressure recorder terminals scaling the output 268 pressure transducer replacing 265 zeroing 265 269 processing method pmd file type 203 pump See LC pump or MS pump Pump Ready signal 35 Q Qual Browser accessing 219 cell grid 224 cursor actions 226 display options UV chromatograms 240 layout files creating 233 Ready signal pump 77 ready to download message 137 real time data locking 214 reviewing 215 regulatory compliance iii removal position needle 303 report instrument method 232 Reservoir Content page autosampler solvent descriptions 93 Reset Lifetime button 173 Thermo Scientific retention times chromatographic peak displaying 242 effect of temperature control on reproducibility 87 rise time filter for the PDA detector 96 for the UV Vis detector 106 Run LED autosampler 38 LC pump 37 MS Pump 36 PDA detector 39 UV Vis detector 40 S safety interlock lamps 23 safety standards iii sample loop description 18 sample preparation routines creating 113 rules 115 Sample
70. dialog box with the default layout settings Chromatogram Ranges Ranges Automatic processing Range Time range minutes Fixed scale Scan filter Delay min Scale Raw file 0 00 C Scalibur O O g0 0O 0O 0O 0O lt m Plot properties Raw file c xcalibursdataspahs_01 raw a Detector MS Scan filter Peak algorithm ficis Plot type Tic z Delay min 0 00 Rangels Fix scale to 5 In the Range area set the displayed time range of the chromatogram e Fora generic layout file leave an asterisk in the Time Range box When you open a raw data file the x axis of the chromatogram is scaled to the run time for your detector in the instrument setup method used to acquire the data e To specify a specific time range type a beginning time point and an ending time point separated by a dash in the Time Range minutes box 234 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Creating a Layout for PDA Data 6 In the Plot Properties area see Figure 142 make the following selections a In the Detector list select PDA b In the Peak Algorithm list select Avalon c Inthe Plot Type list select a plot type e Select Wavelength to display the chromatogram for a specific wavelength within your scan range or to display the averaged results from a range of wavelengths in your scan range e Select Total Scan to display the average absorbanc
71. displaying 242 arm calibration autosampler 287 attenuators PDA 22 autosampler automated sample preparation 113 busy status message 139 calibrating 274 configuration parameters 45 custom vials or microplates using 305 Direct Inlet Control dialog box 343 instrument method parameters 85 loading trays 210 timed events table parameters 94 transfer tubing 17 vial and well notation 6 autozero function for the UV Vis detector 107 Avalon integration algorithm 237 Thermo Scientific back panels Ethernet port location 24 unit ID location 42 baseline drift reducing 209 noise reducing 187 zeroing absorbance level PDA detector 103 UV Vis detector 23 C cables Ethernet 3 41 RS 232 serial 2 system interconnect 32 calibration arm calibration autosampler 287 column oven 275 dark current 323 LC pump 260 tray temperature 281 wavelength 328 well bottom distance custom vials or microplates 305 calibration curves creating 203 cell grid Qual Browser adding cells to the real time display 216 cell states 224 cursor actions 226 inserting cells 244 channels instrument method 100 chemicals filtering 210 chromatograms cursor actions cell grid 226 labels retention time area and so on 241 peak detection 252 UV data displaying 250 column See LC column column arrangement sequence spreadsheet 205 Surveyor Plus User Guide for LC Devices 345 Index D column oven description 21 direct control 199 temperature calibratio
72. dual light source an optical bench a photodiode array a low voltage power supply several printed circuit boards PCBs and four status light emitting diodes LEDs The dual light source includes a deuterium lamp for detection in the ultraviolet wavelength range 190 to 360 nm and a tungsten halogen lamp for detection in the visible wavelength range 360 to 800 nm The light emitted by the two lamps overlaps in the 300 to 500 nm range A pair of attenuators that you can manually adjust controls the intensity of light reaching the photodiode array The optical bench contains a beam combiner focusing lens filter wheel flow cell beam shaper folding mirror and grating see Figure 19 The beam combiner reflects the light coming from the tungsten halogen lamp so that it is parallel to and coincident with the light from the deuterium lamp The combined beam is then focused on the inlet window of the flow cell through the filter wheel The standard filter wheel has two positions Use position 1 Open which places a clear quartz window in the optical path for normal operation Use position 2 Holmium Oxide which places a sealed quartz cuvette filled with a holmium oxide perchloric acid solution NIST traceable in the optical path for wavelength accuracy verification and calibration Figure 19 Optical bench of the PDA detector Deuterium Beam combiner Flow cell lamp Focusing lens Beam shaper Filter wheel Folding mirror
73. e Calculating the Purity of the Chromatographic Peaks Opening a Raw Data File in Qual Browser Data files containing the raw chromatographic and spectral data have the raw file extension To open a raw file in Qual Browser 1 Click the Qual Browser icon in the Roadmap view of the Homepage window or choose GoTo gt Qual Browser The empty Qual Browser window appears see Figure 126 Thermo Scientific Surveyor Plus User Guide for LC Devices 219 8 Qual Browser Opening a Raw Data File in Qual Browser Figure 126 Empty Qual Browser window M Qual Browser File View Tools Help sels S elo gt etl e 4 E l E m aee 3 SIERAN e e nN 2 Choose File gt Open The Open Raw Data File dialog box appears see Figure 127 Figure 127 Open Raw File dialog box Open Raw File Look in O data e m e a 2 drugx_O05 raw F drugx_11 r raw J drugx_06 raw J drugx_12 J drugx_O1 raw J drugx_07 raw drugx_ 13 1 J drugx_02 raw J drugx_08 raw A drugx_ 14 1 drugx_03 raw drugx_09 raw drugx_15 r A drugx J drugx_ J drugx_ A drugx_04 raw A drugx_10 raw A drugx_16 t lt ii File name Fa Files of type Raw Files raw Cancel r Header Information No file selected O Me selecte E Window C Cell Plot Add Window Plot Default Layout k A 3 Select the raw file that you want to review 220 Survey
74. expected baseline width of your chromatographic peaks For optimal integration acquire a minimum of 20 data points across the baseline width of the narrowest peak For example if the narrowest chromatographic peak has a baseline width of 10 seconds select a data rate of 2 Hz or higher 3 To zero the baseline at a specific time point select the Enable Autozero check box and type a time in the Autozero Time min box The detector resets its output voltage to zero at this time point 4 In the Program Type area select one of the following options e To collect one chromatogram during a run select the Single Wavelength 190 to 800 nm option You can program time wavelength changes in the program table e To collect two chromatograms in the UV range during a run select the Dual Wavelength UV 190 to 450 nm option You can program time wavelength changes in the program table e To collect two chromatograms in the visible range during a run select the Dual Wavelength Vis 366 to 700 nm option You can program time wavelength changes in the program table 5 To zero the baseline when a programmed wavelength change occurs select the Zero on Wavelength Change check box Thermo Scientific Surveyor Plus User Guide for LC Devices 107 3 Instrument Method Setup UV Vis Detector Instrument Method Parameters The detector does not zero the baseline on the first or last rows of a wavelength program If the wavelength program contains three
75. go to Adjusting the Light Throughput to the Diode Array Adjusting the Light Throughput to the Diode Array The PDA Detector has two attenuators that control the light throughput from the lamps Manually adjusting the position of the attenuators increases or decreases the amount of light falling onto the array Adjust the light throughput to the diode array whenever you do the following e Observe an increase in the detector noise level e Move the detector e Replace either lamp or the flowcell The first time that you adjust the attenuators you must create a display method that records light intensities You can identify display methods by their spda file extension After creating the method for adjusting the attenuators save it with a descriptive name such as diagnostics spda and store it for future use to simplify future adjustments of the attenuators Note Before you adjust the attenuators replace the column with a flow restrictor and set the pump to deliver HPLC grade water at a flow rate of 1 mL min through the flowcell To adjust the light output from the lamps follow these procedures in order 1 Preparing the LC System for an Attenuator Adjustment on page 316 2 Adjusting the Attenuators on page 317 3 Adjusting the Attenuators on page 317 Thermo Scientific Surveyor Plus User Guide for LC Devices 315 11 PDA Detector Performance Check and Calibration Verifying the Performance of the PDA
76. in Updating the Flow Rate Adjustment Setting on page 268 Thermo Scientific Surveyor Plus User Guide for LC Devices 267 9 LC Pump Calibration and Record Keeping Calibrating the Surveyor LC Pump Plus Scaling the Output of the Pressure Recorder Terminals For information on using the pressure terminals on the pump s back panel see Pressure Recorder Full Scale on page 264 To set the full scale output of the pressure recorder terminals 1 Open the Calibration page for the Surveyor LC Pump see Accessing the Calibration Options for the Surveyor LC Pump Plus on page 260 2 Enter a value from 1 to 10 in the Pressure Recorder Full Scale box see Figure 168 on page 261 Then click Set For information on scaling the output of the pressure recorder terminals see Pressure Recorder Full Scale on page 264 Updating the Flow Rate Adjustment Setting If you change the compressibility setting for the Surveyor LC Pump you might also need to change its flow rate adjustment setting Changing the flow rate adjustment setting can compensate for minor deviations in the flow rate of approximately 5 percent from the expected value To update the flow rate adjustment setting 1 Open the Calibration page for the Surveyor LC Pump see Accessing the Calibration Options for the Surveyor LC Pump Plus on page 260 2 In the Flow Rate Adjustment alpha box see Figure 168 on page 261 type a new value e Ifthe act
77. in compliance with international regulations the physical handling of this Thermo Fisher Scientific instrument requires a team effort to lift and or move the instrument This instrument is too heavy and or bulky for one person alone to handle safely Notice on the Proper Use of Thermo Scientific Instruments In compliance with international regulations Use of this instrument in a manner not specified by Thermo Fisher Scientific could impair any protection provided by the instrument Notice on the Susceptibility to Electromagnetic Transmissions Your instrument is designed to work in a controlled electromagnetic environment Do not use radio frequency transmitters such as mobile phones in close proximity to the instrument For manufacturing location see the label on the instrument WEEE Compliance This product is required to comply with the European Union s Waste Electrical amp Electronic Equipment WEEE Directive 2002 96 EC It is marked with the following symbol Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union EU Member State and these companies should dispose of or recycle this product See www thermo com WEEERoHS for further information on Thermo Fisher Scientific s compliance with these Directives and the recyclers in your country WEEE Konformitat Dieses Produkt muss die EU Waste Electrical amp Electronic Equipment WEEE Richtlinie 2002 96 E
78. larger than the injection volume Because the accuracy of the nominal size is 20 use an estimate of 80 for the actual size e Consider matching the chemistry of the sample matrix the flush solution and the mobile phase e Inject at least 1 0 UL of sample Tray Temperature Control Enable Tray Temp Control Select this check box to enable temperature control for the tray compartment In the default instrument method this check box is clear temperature control for the tray compartment is not enabled To maintain a stable temperature set the temperature to a value that is a least 10 C above or below the ambient room temperature As a safety feature a thermostat turns off the power to the sample tray if the temperature reaches 65 C Temperature C Specifies the tray temperature Default 30 C Range 0 to 60 C Column Oven Control Enable Tray Temp Control Select this check box to enable temperature control for the column oven In the default instrument method this check box is clear temperature control for the column compartment is not enabled Temperature C Specifies the column oven temperature To maintain a stable temperature set the temperature to a value that is a least 10 C above or below the ambient room temperature As a safety feature a thermostat turns off the power to the column oven if the temperature reaches 110 C Default 30 C Range 5 to 95 C 90
79. mass spectrometer refer to the Getting Started Guide for your mass spectrometer Note You can use the PDA Direct Control dialog box to perform diagnostic tests such as checking the performance of the deuterium lamp To acquire PDA data for a single injection you must run a single row sequence from the Sequence window To inject a single sample from the Tune window 1 Prepare the LC system for operation See Chapter 5 Daily Operation 2 From the Tune window for your Thermo Scientific mass spectrometer choose Setup gt Inlet Direct Control The Inlet Direct Control dialog box that contains tabbed pages for each configured LC device appears 3 Start the solvent flow from the pump as follows e For the Surveyor LC Pump Plus click the Surveyor LC Pump tab In the Method area see Figure 246 enter the appropriate values for the flow rate and the solvent percentages Click Download In the Pump area click Pump On to start the solvent flow Thermo Scientific Surveyor Plus User Guide for LC Devices 341 12 Making a Single Injection from the Tune Window Figure 246 Surveyor LC Pump page of the Inlet Direct Control dialog box m Pump r Method Flow Rate Doo mL min Pump Of Component amp fo Component B fo Component C fo Component D fo Download Purge Time fi min m Error Condition Solvent Valve Clea we ahd Purge x iLL For the Surveyor MS Pump Plus click
80. of the pump status view aay j as Pump 1 Flow rate 0 0 pl min Pressure 0 0 bar Pressure SD 0 0 bar Solvent 100 00 Solvent B 0 00 Solvent C 0 00 Solvent D 0 00 Stroke count 150041 Table 41 describes the status readbacks on the Extended page of the pump status view Table 41 General page of the pump status view Readback Flow Rate Description Displays the user specified flow rate Flow rate changes are linear between time lines in the gradient program Tip You can change the percent composition of solvents A B C and D by running an instrument method or by downloading new solvent conditions from the Inlet Direct Control dialog box Pressure Displays the pressure monitored by the pump Pressure SD Displays the standard deviation of the pressure monitored by the pump Solvent A B C or D Displays the user specified percent composition of solvent A B C or D Stroke Count Thermo Scientific Displays the stroke count for the pump pistons When the stroke count exceeds 1 000 000 the number is displayed in red Surveyor Plus User Guide for LC Devices 147 5 Daily Operation Checking the Status of the LC Devices Degasser Page of the Pump Status View Figure 83 shows the Degasser page of the pump status view Figure 83 Degasser page of the pump status view Accssessonscescssensceseed Pump 1 Degasser status Ready Vacuum level 67 1 mbar
81. options for the autosampler e Column Oven Air Sensor Calibration e Vial Tray Metal Sensor Calibration e Arm Calibration e Well Bottom Distance Calibration The column oven and oven compartment temperature calibrations and the arm calibration are typically performed by a Thermo Fisher Scientific field service representative To perform these calibrations yourself you must have the service kit that contains the temperature test fixtures In addition to calibrate the temperature sensors for the autosampler s temperature controlled zones your Thermo Scientific application must be capable of providing feedback for these sensors Note Typically a Thermo Fisher Scientific field service representative calibrates the controlled temperature zones and the XYZ arm position To perform the temperature calibrations yourself order the Field Service Calibration Kit P N 60053 62001 To calibrate the XYZ arm order the LED light fixture and the non reflective target port fixture If you choose to use custom vials or custom microwell plates you must perform the Well Bottom Distance calibration which determines the depth of the custom vial or microplate well Perform this calibration you select a new custom tray configuration and each time you use a new type of custom vial or custom microwell plate Note If you are controlling the autosampler from a Thermo Scientific data system other than the Xcalibur data system refer to the Help provided w
82. or an error condition has occurred Green The pump pistons are moving but a pump program is not running This state can occur when the pump is under direct control or a pump program has ended Flashing green The pump is running a pump program from a downloaded method Degas Amber The degas unit is building vacuum Flashing amber A failure such as a loss of vacuum has occurred Green Sufficient vacuum has developed to perform Surveyor Plus User Guide for LC Devices chromatography Thermo Scientific Surveyor LC Pump Plus LED States 1 Introduction to the Surveyor Plus LC System Status LEDs Table 2 list the LED states for the Surveyor LC Pump Plus Table 2 Surveyor LC Pump Plus status LEDs and meaning LED Status Meaning Power Green The pump is on and receiving power Comm Amber The pump is not communicating with the data system computer Flashing amber The rotary switches on the back panel of the LC pump are set to 00 for downloading firmware Green The pump is communicating with the data system computer Run Amber The pump is not communicating with the data system computer the pump s motor is stopped the pistons are homing or the pump is stabilizing except during a run Flashing amber The pump is experiencing an error condition Green The pump is in the Ready state Flashing green The pump is performing a run or the pump is stabilizing during a run Degas Amber The pump is powering up
83. reproducibility of the chromatographic retention times Autosampler Method Page Parameters Table 19 describes the parameters on the Surveyor AS Method page The autosampler ships with a 250 pL concentric plunger syringe but you can replace this syringe with a 100 or 500 pL concentric plunger syringe or a 2500 pL single plunger syringe The injection volume range and the syringe speeds depend on the syringe size as described in these topics e Injection Volume Range e Syringe and Loop Loading Speeds for Injections Thermo Scientific Surveyor Plus User Guide for LC Devices 87 3 Instrument Method Setup Autosampler Instrument Method Parameters Table 19 Autosampler Method page parameters Sheet 1 of 3 Parameter Injection Volume pL Description Specifies the sample volume that the autosampler loads into the sample loop The default value and the range depend on the syringe size see Injection Volume Range on page 91 Needle Height from Bottom mm Specifies the height from the bottom of the vial or well where the needle withdraws liquid see Figure 13 on page 15 Range 0 1 to 18 0 mm Default 2 mm Syringe Speed uL s Specifies the rate at which the syringe withdraws liquid from a tray vial or a plate well The default value and the range depend on the syringe size see Syringe and Loop Loading Speeds for Injections on page 91 Flush Volume uL Flush Wash source Specifies th
84. s 82 71 pL s IMPORTANT A flush speed of 250 pL s for the 250 pL concentric syringe is the maximum flush speed for a solvent of low viscosity such as 100 methanol If you are using a solvent of higher viscosity reduce the flush speed accordingly For example because water has approximately twice the viscosity as methanol if you are using water as your flush solvent lower the flush speed to 100 pL s At high flush speeds viscous solvents can cause the autosampler to make a grinding sound Post Injection Valve Switch Time min Loop Loading Speed uL s At the default post injection valve switch time of 0 minutes the injection valve remains in the inject position during the run A time value greater than 0 1 minutes specifies the time when the injection valve switches from the inject position to the load position at the end of an injection cycle To reduce the gradient delay volume for low flow gradient applications consider switching the injection valve from the inject position to the load position during the run by typing a nonzero value in this box Allow enough time for the mobile phase to backflush the sample out of the sample loop Default 0 minutes Range 0 to 999 0 minutes Specifies the rate at which the autosampler meters the sample into the sample loop for no waste injections During a no waste injection the autosampler meters the sample through the transfer tubing to the injection valve at the specified syringe
85. signal to the other LC modules or peripheral devices when the autosampler injects a sample Gradient Start Active Use this check box to set the polarity of the Gradient Start output signal High 2 e When the check box is selected the signal from the autosampler is LO Closed and goes HI Open to trigger the start of the pump s gradient program e When the check box is clear the signal from the autosampler is HI Open and goes LO Closed to trigger the start of the pump s gradient program Note The Grad Start terminal sends a signal to the pump to start the gradient program 58 Surveyor Plus User Guide for LC Devices Thermo Scientific 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Table 10 Signal Polarity page parameters Sheet 3 of 3 Parameter Pump Stop Active High Description Use this check box to set the polarity of the Pump Stop output signal e When the check box is selected the signal from the autosampler is LO CLosed and goes HI Open when the pump is to stop e When the check box is clear the signal from the autosampler is HI Open and goes LO Closed when the pump is to stop Note The Pump Stop terminal sends a signal to the pump to stop The Pump Stop output signal is not active during the injection sequence The computer must make an explicit request to issue the Pump Stop signal Timed Events Active High Thermo Scientific Use this check
86. system 2 In the Thermo Xcalibur Roadmap window click the Instrument Setup icon on the Road Map or choose GoTo gt Instrument Setup The Instrument Setup window appears see Figure 45 The view bar on the left side of the window contains an icon for each configured instrument device Clicking the device icon opens the view for that device Figure 45 Instrument Setup window E9 Untitled Instrument Setup Dataset 6 month content assay File Surveyor 45 Help Da S x cp Surveyor AS Method Sample Preparation Reservoir Content Timed Events Injection Mode o KG oe ls Injection volume ul Partial lop Fullloop Surveyor S M mm Needle height from bottom mm No waste 99 D Syringe speed fuls iw Tray Temperature Control Flush volume ul l Enable tray temperature control le fa C3 KG Surveyor LC Flush Wash source Pump Temperature C Column Oven Control Wash volume ful j Flush speed fuls Post injection valve switch time min Surveyor PDA Plus Jalal Enable column oven control Temperature C o D Loop loading speed ul s J 68 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Surveyor LC Pump Plus Instrument Method Parameters Surveyor LC Pump Plus Instrument Method Parameters Use the Surveyor LC Pump view to set up the instrument method parameters for the pump To s
87. tab The Configuration page appears see Figure 100 Surveyor Plus User Guide for LC Devices 171 6 Direct Controls PDA Detector Direct Controls Display Configuration Information Calibration 172 Figure 100 Configuration page m Lamp Maintenance Deuterium Lamp Lamp is Off Last Lifetime Reset Lifetime Hours Elapsed m Tungsten Lamp Q Lamp is Off Last Lifetime Reset Lifetime Hours Elapsed Analog Outputs M Ready Output Turn On Output is Active High Turn Off Set Active Low m Event Output Turn On Output is Active High Turn Off Short DACs Output DAC Outputs Active EEEE Help Surveyor Plus User Guide for LC Devices Programmed Lamp Startup Lamps will be started automatically at 04 55 PM on weekdays Zero DACs Change l l l l l l l l l l l l l l Set Active Low l l l l l l l l l l l l Thermo Scientific 6 Direct Controls PDA Detector Direct Controls Configuration Page Parameters Table 48 describes the parameters on the Configuration page Table 48 Configuration page of the Direct Control dialog box for the PDA detector Sheet 1 of 4 Parameter Description Lamp Maintenance Use the controls in this area to turn the lamps on and off and to reset the lamp lifetime hours after you replace a lamp Deuterium Lamp Status readback Indicates the status of the deuteriu
88. the Surveyor LC Pump Plus e Compressibility e Pressure Recorder Full Scale e Flow Rate Adjustment Alpha e Pressure Sensor Adjustment Pressure Transducer Zero The compressibility of a liquid is a measure of its resistance to a decrease in volume caused by an increase in pressure Compared to gases most liquids are relatively incompressible Water a commonly used mobile phase solvent is even less compressible than most organic solvents because of its extensive hydrogen bonding and cluster structure For information on updating the compressibility setting see Updating and Optimizing the Compressibility Setting on page 266 Effect of the Compressibility Setting Even though liquids are relatively incompressible the compressibility of the mobile phase can affect your chromatography if you are running the LC pump at the upper limit of its pressure range You can use the compressibility setting for the Surveyor LC Pump to compensate for the compressibility of the mobile phase However changing the compressibility setting simultaneously affects both the pressure pulsation of the Surveyor LC Pump and the flow rate of the mobile phase 262 Surveyor Plus User Guide for LC Devices Thermo Scientific 9 LC Pump Calibration and Record Keeping Calibrating the Surveyor LC Pump Plus The compressibility effect is caused by the portion of the cam cycle where the pistons are compressing the mobile phase The compressibility portion of t
89. the Configuration page whenever you replace the tungsten lamp This resets the Last Lifetime Reset readback to the current date and time and restarts the Lifetime readback to zero 178 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls PDA Detector Direct Controls Table 49 Display page parameters Sheet 3 of 4 Parameter Status bottom left Description Status area Displays the status of the PDA detector and the lamps Connection Displays the communication status of the PDA detector Depending on whether the data system can connect to the PDA detector the status displays Connected or Not Connected If this readback displays Not Connected make sure that the PDA detector is powered on Check the Ethernet connections and the instrument configuration settings for the PDA detector Diode array scan rate Displays the current configuration setting for the diode array scan rate The possible diode array scan rates are 20 40 and 80 Hz PDA status Displays the current state of the PDA detector The possible states are Not Ready for a Run and Ready for a Run This readback displays Not Ready for a Run if both lamps are off or if the deuterium lamp is warming up Wavelength calibration Displays whether the wavelength calibration has been applied Dark current calibration Displays whether the dark current calibration has been applied Method validity Displays whethe
90. the Flow Rate Adjustment Setting on page 268 Pressure Sensor Adjustment Reset the Pressure Sensor Adjustment parameter when you replace the pressure sensor Each pressure sensor is labeled with a data sticker that contains a 0 XXXX value for the pressure sensor adjustment setting Multiply this value by 10 000 and then update the pressure sensor adjustment setting for your Surveyor LC Pump Plus For information on updating the pressure sensor adjustment see Updating the Pressure Sensor Adjustment Setting on page 269 Pressure Transducer Zero Thermo Scientific The pressure readout for the Surveyor LC Pump Plus is produced by a cell type potentiometer This type of device tends to drift by small increments requiring you to occasionally re zero the readout To update the pressure transducer zero value turn off the pump flow and open the drain valve knob Then click the pressure transducer zero button in the data system that operates your pump For information on zeroing the pressure transducer see Zeroing the Pressure Transducer on page 269 Surveyor Plus User Guide for LC Devices 265 9 LC Pump Calibration and Record Keeping Calibrating the Surveyor LC Pump Plus Calibration Procedures for the Surveyor LC Pump Plus You fine tune the performance of the Surveyor LC Pump Plus from the Calibration Surveyor LC Pump Direct Control page Figure 168 on page 261 For instructions on opening the Calibration pag
91. the autosampler Ready to Download The autosampler is ready to start a run Ready to Run This state appears momentarily when the data system is downloading an instrument method for an LC MS system Running The autosampler is making an injection If the instrument method contains a time function for the autosampler this state is displayed until the time function has expired Direct Control The direct control or calibration windows are open Busy The autosampler is performing a direct control operation Error An error condition other than the loss of communication has occurred Off The data system has attempted to connect to the autosampler and failed five times AS Status Page Table 36 describes the readbacks on the AS Status page of the autosampler status view Table 36 Status readbacks for the autosampler Sheet 1 of 3 Readback Target injection Description Vial Position Injection Volume Thermo Scientific Displays the current vial or microplate well position For information about the vial and well notation see Vial and Well Notation on page 6 Displays the injection volume for the current injection Surveyor Plus User Guide for LC Devices 139 5 Daily Operation Checking the Status of the LC Devices Table 36 Status readbacks for the autosampler Sheet 2 of 3 Readback Description Other AS State Displays the following run conditions Waiting for The autosam
92. the column equilibration period you can add an equilibration period to the end of the gradient program and make the gradient program time for the pump longer than the data acquisition time for the detector Figure 52 Example of a pump gradient program Pump General Gradient Program Pump 1 Solvent colors Ha Mis Lic Mp 82 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings Table 17 Gradient program Time min Solvent composition 0 00 to 5 00 Held constant at 90 solvent A 10 solvent B 5 00 to 25 00 Linear ramp from 10 solvent B to 90 solvent B 25 00 to 30 00 Held constant at 10 solvent B 90 solvent B 30 00 to 40 00 Column is equilibrated at the initial solvent composition of 90 solvent A 10 solvent B Thermo Pump Gradient Program Page Parameters Table 18 describes the parameters on the Gradient Program page Table 18 Thermo pump method parameters Parameter Gradient table Description Each row in the gradient table defines the solvent composition and flow rate for a specific time point Between time points the solvent composition changes linearly whereas the flow rate changes as a discontinuous step function The pump program can contain up to 398 time lines Time The time parameter min box specifies at what point in the run the associated solvent composition an
93. tiead cee eked dew 39 UV Vis Detector LED States cis 5 ch cei si treen se cbimens cba Kew cbes 40 Chapter2 Thermo Foundation Instrument Configuration 0eeeee ees 41 Checking the Communication Hardware 0 0 cece cece eee 41 Opening the Thermo Foundation Instrument Configuration Application 43 Adding Devices to the Instrument Configuration 000005 44 Thermo Scientific Surveyor Plus User Guide for LC Devices xi Contents Specifying the Configuration Settings 0 cee cece eee eee 45 Surveyor Autosampler Plus Configuration Settings 04 45 Surveyor MS Pump Plus Configuration Settings 0000 61 Surveyor LC Pump Plus Configuration Settings 0000 63 Surveyor PDA Plus Detector Configuration Settings 0 65 Surveyor UV Vis Plus Detector Configuration Settings 66 Closing the Foundation Application lt a sete rowers Wau doa Monae 66 Chapter3 Instrument Method Setup 0 0 cce eee eee eee e eee eee eee 67 Opening the Instrument Setup Window 0 0 cece eee eee eee 68 Surveyor LC Pump Plus Instrument Method Parameters 69 Surveyor LG Pump Plus General Page s0 5 cae bes sah ioee sds sae eneee 69 Surveyor LC Pump Plus Gradient Program Page 00 0 000 71 Surveyor MS Pump Plus Instrument Method Settings 74 Specifying the Chromatographic Conditions for a
94. time in minutes when the autosampler TF terminal TF1 to TF4 signals an event Time 0 00 is defined as the time when the autosampler issues an INJECT OUT signal The autosampler issues the specified Timed Event signals after issuing the Inject Out signal Default 0 Range 0 to 9999 0 minutes TF1 TF2 TF3 and TF4 Specifies whether the event is on or off at the specified time 94 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup PDA Detector Instrument Method Parameters PDA Detector Instrument Method Parameters Use the Surveyor PDA Plus Method page to specify the data acquisition settings for the detector and to trigger external devices from the detector To program the PDA detector to acquire absorbance data 1 In the view bar click the Surveyor PDA Plus icon The view for the Surveyor PDA Plus Detector appears with the Surveyor PDA Plus Method page displayed see Figure 59 Figure 59 Surveyor PDA Plus Method page with the default settings Surveyor PDA Plus Method Run Run Length min Filter Rise Time sec 1 0 e Help m Spectra m Units MV Collect Spectral Data Wavelength Step nm f Wavelength Start Wavelength nm 200 Sample Rate Hz 5 0 aE C Diode 7 End Wavelength nm eoo Filter Bandwidth nm fi Intensity Channels Channel 4 Cc PEt Wavelength nm 1214 Filter Bandwidth nm C One Channel Channel B Two Channels Wavelength nm
95. trays Slot for tray Tray runner Vial position A 20 Vial position E 40 H Standard 1 8 mL vial Vial position Vial position A E 21 Tray handle For more information about the vial locations for conventional trays and the well locations for microwell plates see Vial and Well Notation on page 6 To select a non contiguous set of sample vials or well locations click Select Vials and then select the vial or well locations by using the Vial Selection dialog box For information about using the Vial Selection dialog box see Selecting the Vial Locations Interactively on page 206 4 In the Injections per Sample box type the number of injections per sample that you want the autosampler to make per vial or well location 5 In the Base Sample ID box type an identifying name for the sample Base sample IDs are optional If you do not enter a sample identification the data system automatically uses the vial position as the sample identification If you enter a sample identification the data system automatically appends the vial position to your entry 6 Click OK to display your sequence spreadsheet see Figure 115 204 Surveyor Plus User Guide for LC Devices Thermo Scientific 7 Sequence Setup Creating a Single Sample Sequence The injection volume displayed in the Inj Vol column matches the injection volume contained in your instrument setup method You can override this injection volume
96. uses to create the mobile phase and operating conditions for the pump see Figure 49 74 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings Figure 49 General page for the Surveyor MS Pump Plus Pump General Gradient Program m Pump 1 Name Comment IV Solvent IV Solvent B M Solvent C V Solvent D Operating mode Start settings Method finalizing Min pressure bar Max pressure bar Pressure stability bar Pressure units bar v Pump 1 Low pressure 0 7000 PSI X Surveyor AS injection logic v First line conditions E 0 0 I 400 0 10 0 oat When you connect two pumps to the data system computer you must specify the general parameters for both pumps The autosampler triggers the gradient program for Pump 1 at the start of a run Pump 1 triggers the gradient program for Pump 2 at a user specified time during the run see Programming the Pumps in a Dual Pump System on page 84 Note You can use a dual pump system to perform two dimensional chromatography or to create a high pressure gradient The Instrument Method report attached to the raw file contains the values that you select or enter on this page You can access this report in the Qual Browser view by choosing View gt Reports gt Instrument Method Thermo Scientific Surveyor Plus User Guide for
97. value 7 To change the injection volume double click the spreadsheet cell containing the injection volume value that you want to change highlight the current value and then type a new value in the cell For full details of all the parameters in the New Sequence Template dialog box refer to the Help or the Xcalibur manual set Figure 115 Sequence Setup view showing newly created one line sequence Thermo Xcalibur Sequence Setup Open File Edit Change Actions View GoTo Help DSa lelo TL Drp elk pmm 2 Sample Type File Name Sample ID Path Inst Meth ProcMeth Position Inj Vol Level Unknown TestMix01 1 C calibur D at C lt calibur methods T estMix For Help press F1 l NUM 9 26 2008 7 43PM NOT SAVED 8 To alter the current column arrangement Fea a Click the Column Arrangement toolbar button The Column Arrangement dialog box appears see Figure 116 Figure 116 Column Arrangement dialog box Column Arrangement Available Columns Displayed Columns Client Sample Type Comment File Name Company sd Sample ID Dil Factor Dea Path ISTD Corr Amt spern Inst Meth Laboratory Remove Proc Meth Phone Position Sample Vol Ei Inj Yol Sample wt Love up Level SampleN ame aa Study OVE OWT Cancel Help Thermo Scientific Surveyor Plus User Guide for LC Devices 205 7 Sequence Setup Creating a Single Sample Sequence b Do one of the following e To add a column to the sequence select the co
98. vial or well that the needle of the autosampler descends to before withdrawing sample from the vial well location The default value is 2 mm and the range is 0 1 to 18 mm Entering a lower value causes the needle to descend closer to the bottom of the vial or well The standard 1 8 mL vials supplied with the autosampler have a depth of approximately 20 mm Figure 13 on page 15 shows the needle descending to a depth of 2 mm from the bottom of a standard 1 8 mL vial 5 In the Syringe Speed L s box keep the syringe speed at its default value 8 pL s for the 250 pL concentric syringe for most applications If you see the sample in the needle tubing break up as the autosampler withdraws sample from a vial or well location into the needle tubing adjust the syringe speed 6 In the Flush Volume pL box type or select a volume from 0 to 6000 pL or keep the value at its default of 400 pL 7 In the Flush Wash Source list select a flush wash solution For most applications select Bottle wash bottle If you select one of the reservoir vial locations as your flush wash source make sure that you load the autosampler with a reservoir vial 86 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Autosampler Instrument Method Parameters For information about the location of the 16 mL reservoir vials see Tray Compartment on page 5 For information about specifying the contents of the reservoir vials a
99. with the wavelength in nanometers on the x axis and the Absorbance absorbance in milli absorbance units mAU on the x axis Default Wavelength Absorbance Select the Wavelength Absorbance option for instrument methods Spectra with Wavelength Absorbance option Collect Spectral Data To collect scans having a specific wavelength range nm bandwidth nm scan rate Hz and step nm select this check box Start Wavelength nm Specifies the first wavelength in nanometers of the scan range Default 200 nm Range 190 to 799 nm End Wavelength nm Wavelength Step Specifies the last wavelength in nanometers of the scan range Default 600 nm Range 191 to 800 nm The end wavelength must be greater than the start wavelength Specifies the wavelength interval between data points across the wavelength range Default 1 nm The maximum step size is the full width of the scan The highest spectral resolution is 1 nm and the lowest resolution is the full width of the scan When you specify a spectral scan from 200 to 300 nm at a step of 10 nm the PDA detector sends 11 scan wavelengths to the data system computer Sample Rate Thermo Scientific Specifies the number of data points per second that the PDA detector sends to the data system for each scan wavelength For optimal integration of the chromatographic peaks acquire 20 points across the baseline width of the peak For the Surveyor PDA Detect
100. you view the plate from the top The autosampler samples wells from left to right and then from top to bottom as you view the plate from the top BREE Surveyor Plus User Guide for LC Devices 51 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Placing objects taller than 1 87 in into the autosampler tray compartment will stall the autosampler arm For custom vials use the appropriate tray insert to ensure correct positioning In addition to trigger the vial sensor position the vials in the tray so that the top of each vial reaches the minimum height of 1 55 in Do not use microtitre plates that exceed the heights listed in Table 8 Table 8 Autosampler tray compartment height limitations Tray type Maximum height Conventional standard 1 8 mL vials N A Custom Vial Setting N A 96 Well Microplate Tall Microwell Carrier 0 77 in 96 Well Microplate Tall Solid Microwell Carrier or 0 77 in 96 Well Microplate Short Microwell Carrier Riser Plate 1 mL or 2 mL Deep Well Plate Short Microwell Carrier 1 80 in 96 Well Microplate Short Microwell Carrier 1 80 in 96 Well PCR Plate Short Microwell Carrier 1 80 in Custom 96 Well Setting 1 80 in 384 Well Microplate Tall Microwell Carrier 0 77 in 384 Well Microplate Tall Solid Microwell Carrier or 0 77 in 384 Well Microplate Short Microwell Carrier Riser Plate Custom 384 Well Setting 0 77 in Communication Page Use the Communic
101. zero between the last two lines in the table To provide a complete spectrum of ultraviolet and visible light the detector uses a deuterium lamp for the UV range 190 to 365 nm and a tungsten lamp for the visible range 366 to 800 nm The lamps are protected by a cover with a special safety interlock to reduce the possibility of human exposure to harmful UV light To control the UV Vis Detector you must first add the detector to the software instrument configuration see Adding Devices to the Instrument Configuration on page 44 After you add the UV Vis detector to the instrument configuration you can set up the data acquisition parameters from the UV Vis detector view of the Thermo Xcalibur Instrument Setup window see UV Vis Detector Instrument Method Parameters on page 106 You can turn the detector lamps on or off and zero the detector output from the Direct Control dialog box see UV Vis Detector Direct Controls on page 183 Solvent Platform The solvent platform located on the top of the LC stack holds four 1 liter solvent reservoir bottles and one 1 liter wash bottle Four 1 8 in OD x 1 16 in ID FEP solvent lines carry solvent from the reservoir bottles down to the vacuum membrane degasser which is built into the analytical pump One 1 8 in OD x 1 16 in ID FEP solvent line carries solvent from the wash bottle to the two position syringe valve of the autosampler Thermo Scientific Surveyor Plus User Guid
102. 0 Time Min Event Value 0 000 Tension z 0 200 Add Delete Change Help RT 1 25 1 80 ie RT 1 57 NL Peak Purity 983 1 55E5 150000 nm 224 5 225 5 PDA 140000 Avalon 130000 Benzene with 120000 imp riy 110000 100000 90000 gt 80000 E 70000 60000 a a threshold a ver 50000 o peax coverage 1 3 14 1 5 1 6 1 7 Time min Thermo Scientific Surveyor Plus User Guide for LC Devices 257 8 Qual Browser Calculating the Purity of the Chromatographic Peaks Figure 166 Effect of scan threshold on peak purity calculation RT 1 57 NL 6 92E5 a Peak Purity 769 nm 238 5 239 5 PDA Avalon 500000 2 3 uAU scan threshold 7 95 peak coverage 13 14 15 16 1 7 Time min RT 1 57 NL 6 92E5 E Peak Purity 997 nm 238 5 239 5 PDA 5000002 200000 uAU scan threshold Avalon 0 k 95 peak coverage 13 14 15 16 1 7 Time min RT 1 57 NL 1 31E6 z J Spectrum Maximum 1000000 nm 220 0 300 0 PDA q Avalon 3 5000004 13 14 15 16 1 7 Time min Figure 167 Effect of peak coverage on peak purity calculations IRT 1 25 1 80 RT 1 57 NL ae ae threshold Peak Purity 898 6 525 _ nm j 6000004 P pea TCOYELAJE PDA Avalon gt 4000004 Peak start Peak stop 2 7 3 4 200000 1 25 1 30 1 35 1 40 1 45 1 50 1 55 1 60 1 65 1 70 1 75 Time min RT 1 25 1 80 l RT 1 57 NL gut ne threshold Peak Purity 998 6 525 NEE nm j soodaa 5
103. 0 to 400 bar 5800 psi with a default value of 0 bar g Inthe Max Pressure bar box type or select the maximum operating pressure for the pump An appropriate maximum pressure setting prevents the pump from operating with a restriction on the outlet side of the pump Excess pressure can damage the HPLC column and any other component between the restriction and the pump Select a value that is well above the typical operating pressure for your application but also below the pressure that can damage your system If the pressure rises above this limit the pump automatically stops and sends an error message to the computer The range is 0 to 400 bar 5800 psi with a default value of 400 bar h In the Pressure Stability bar box type or select an appropriate pressure stability value from 1 to 100 The MS pump sends a Ready signal when the system pressure reaches this limit A lower value requires greater pressure stability before the pump becomes ready A higher value is more forgiving of pressure pulsations i In the Pressure Units list select the pressure units for the pressure readback Note 1 bar 14 5 psi Thermo Pump General Page Parameters Table 16 describes the parameters on the General page Table 16 Thermo pump method parameters Sheet 1 of 3 Parameter Description Name Identifies the pump on the pump view of the Status page of the Info view The text string can consist of up to 16 alphanumeric characters
104. 00 900000999096600990566009 809060990866660000866000 909600999056000900506000 loleletefelelelelelejelefelelelelelelelelelelele 800666998066600000506008 8O0O8G999GO98H9G8H009S6 800006999086066800800008 90G0009990HO009990H66000 900060999066600990566009 899660990856660800560000 90000009905600O900560000 8866609908966690008O6600 900060990056606900566000 lelelefefelelelelelejeleleleleleleleleelelelele 900066609086606800806008 8OOO8G0O980OG8G0G8H00086 elelelefelelelelelelelefeleleleleleelerelelele 8066009000606 O006600 900060999096000900566009 B A1 P 6666666055666 070101010010 606665066056665066556606 A D 1 24 24 1 AAI A 229000099990000999900000 299999099990000999900009 P 01070701010101010101010l0101010 01010101010100 90008699908666G900SO0G00 806060999066600900060000 900060099090600990506009 809060999860660000860000 909600099056606900560009 lolejefefelelelelelele efeleleleleleelelelelele 800060999066600000566008 8O0O9GG998G998G9GSHG09S6 900O8699H08600G900SOG000 90G0009990HH800990066000 9000609990G6000990560009 809060998866660000566000 900900090056000900560000 8O6660O99866666000866000 800600090066606000566000 lelelefofelelelelelejelefelelelelelelelelelelele 806666998080600900866008 8OOG8G6G980O98G0G9H000S8 906086G0908066G90080G600 8990009900H6600000560000 900060099096600900500009 899060990066660000560000 909600999056606000566000 lelelerefelelelelelelelefeleleleleleelelelelele 800006998086000000806008 lelefeleleleteleleleleleleleletelele
105. 01 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Time min PAHs_01 1 RT 0 01 AV 1 NL 135E6 Ez T c sid 8 00 Q1MS 127 60 254 60 253 1 100 Do O 80 wT 5 60 a x g 254 1 20 ce 1282 1292 102 2021 203 2 29414 228 2 2292 9392 252 2 128 129 130 202 203 204 228 229 230 252 253 254 miz miz miz mz Specifying the Spectrum Range To display a spectrum for the PDA data 1 If you have not already done so open a data file raw that has PDA data and MS data see Opening a Raw Data File in Qual Browser on page 219 The data file opens with the MS TIC chromatogram in the upper cell and a mass range spectrum in the lower cell 2 Pin the spectrum cell 3 Right click the spectrum cell 4 From the shortcut menu choose Ranges The Spectrum Ranges dialog box appears see Figure 146 5 In the Plot Properties area select PDA in the Detector list 238 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Creating a Layout for PDA Data 6 For a generic layout file for PDA data keep the other settings in the Spectrum Ranges dialog box at their defaults as shown in Figure 146 Figure 146 Spectrum Ranges dialog box with the PDA detector selected Spectrum Ranges x Ranges Automatic Processing Range Wavelength Range F V Average J Fix scale 1000000 0 Raw File C calibur data PAHs_01 RAW Filter Subtract 1 P Plot properties Detector
106. 01 to 9 999 mL min b In the Component A B C and D boxes type the solvent composition c Click Download Starting and Stopping the Solvent Flow To start or stop the solvent flow 1 Open the Operation Surveyor LC Pump Direct Control dialog box see Surveyor LC Pump Plus Direct Controls on page 185 2 Do one of the following e To start the solvent flow click Pump On e To stop the solvent flow click Pump Off Clearing an Error Condition for the Pump When an error condition occurs the solvent flow from the pump stops Before you can restart the solvent flow you must clear the error condition To clear an error condition for the pump 1 Open the Surveyor LC Pump Plus view 2 From the menu bar choose Surveyor LC Pump gt Direct Control gt Operation The Operation Surveyor LC Pump Direct Control dialog box appears 3 Click Clear Thermo Scientific Surveyor Plus User Guide for LC Devices 189 6 Direct Controls Pump Direct Controls Surveyor MS Pump Plus Direct Controls Use the Direct Control dialog box to download new solvent conditions to the pump start and stop the solvent flow from the pump and change the global pressure limits Tip To open the direct controls for the pump from the Tune window choose Setup gt Inlet Direct Control from the menu bar Then click the pump tab To download new solvent conditions to the pump 1 Turn on the power to the pump Tip When the power
107. 1 Disconnect the LC column from the system and then pump HPLC grade methanol through the flowcell to remove any contaminants 2 Turn on both lamps and wait one hour for the lamps to equilibrate see Turning the Lamps On or Off on page 163 3 Verify that the array is not saturated Adjusting the Light Throughput to the Diode Array on page 315 4 In the Wavelength Calibration area click Calibrate The Wavelength Calibration wizard appears 5 Follow the instructions provided by the wizard For more information click Help at the bottom of the Wavelength Calibration dialog box To reset the wavelength or dark current calibration to the default values To reset the dark current calibration values in the Dark Current Calibration area click Reset Dark Current Calibration To Default Values To reset the wavelength calibration values in the Wavelength Calibration area click Reset Wavelength Calibration To Default Values Thermo Scientific Surveyor Plus User Guide for LC Devices 321 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Calibration Page Parameters Table 63 describes the parameters on the Calibration page for the PDA detector Table 63 Calibration page parameters for the PDA detector Parameter Description Dark Current Calibration Calibrate Starts the dark current calibration Last Calibration Indicates whether or not the PDA detector is currently calibrate
108. 1 NL 6 05E5 microAU io 258 0 600000 Pinned cell 500000 400000 2 300000 200000 100000 0 220 240 260 280 300 320 340 360 380 400 wavelength nm Cursor Actions Within the cells of the grid you can use the cursor in three ways e A click selects a point on the cell A line dragged parallel to any axis selects a range A line dragged in any diagonal direction selects an area The effect of these actions depends on the state of the cell Within an active cell cursor actions rescale the plot see Table 54 Table 54 Effect of cursor action in an active cell Cursor action Effect Drag parallel to x axis Rescales graph showing selected x axis range only same y axis range Drag parallel to y axis Rescales graph showing selected y axis range only same x axis range Dragged area Rescales graph showing both the selected x axis and y axis ranges 226 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Working with the Cell Grid If one of the cells is pinned the cursor action in any of the inactive cells affects the pinned cell see Table 55 Table 55 Effect of cursor action in an inactive cell on the pinned cell Pinned cell Cursor action Effect Spectrum Click in a chromatogram cell The spectrum cell displays the spectrum at that retention time Chromatogram Click in a spectrum cell The chromatogram cell displays the chromatogram for the wavelength selected in the
109. 100 0 O00 0 0 1 00 100 0 0 0 0 0 84 Surveyor Plus User Guide for LC Devices 100 0 0 0 0 0 0 0 2000 D plimin P2 0 0 200 0 0 0 200 0 i8 0 0 0 0 100 0 080 0 0 0 0 oO Thermo Scientific Autosampler Instrument Method Parameters 3 Instrument Method Setup Autosampler Instrument Method Parameters Use these three pages of the Surveyor AS view to specify the injection settings the temperatures of the controlled temperature zones the solvents contained in the wash bottle and the autosampler s 16 mL reservoir bottles and any external events triggered by the autosampler e Surveyor AS Method Page e Reservoir Content Page e Timed Events Page for the Autosampler For information about the Sample Preparation page see Chapter 4 Sample Preparation Routines Surveyor AS Method Page Use the Surveyor AS Method page to set the injection and the temperature control parameters for the autosampler see Figure 54 Figure 54 Surveyor AS Method page Accela AS Method Sample Preparation Reservoir Content Timed Events Injection volume ful Needle height from bottom fram Syringe speed uls Flush volume ul Flush Wash source Wash volume ul Flush speed ul s Post injection valve switch time min Loop loading speed ul s kk le co oOo UEN bottle w o 100 00 0 0 e Injection Mode Partial loop C
110. 2 Making a Single Injection from the Tune Window 6 Start pumping 100 methanol at a flow rate of 1000 pL min 7 Fill the loop completely to expel any air that might be trapped in the dampener loop 8 Set the flow rate to one that is appropriate for your system 9 Close the manual bleeder valve see Figure 87 on page 156 by turning the valve clockwise Always keep the pulse dampener valve closed during normal operation Surveyor Plus User Guide for LC Devices 157 5 Daily Operation Accessing the Direct Controls Accessing the Direct Controls You can access the direct controls for each instrument from the Instrument Setup window You can use the direct controls to start and stop the solvent flow from the LC pump move the autosampler s XYZ arm turn the detector s lamps on and off flush the autosampler s syringe and so on For information about using the direct controls to prepare your LC system for daily operation see the Chapter 6 Direct Controls To access the direct controls 1 Depending on the data system do one of the following e Ifyou are controlling your instrument from the Xcalibur data system do the following Roadmap button in the toolbar a If it is not already open open the Roadmap view by clicking the es ala Click the Instrument Setup button on the toolbar or the larger see Instrument Setup icon in the Roadmap View The Instrument Setup window opens to the first mod
111. 230 240 250 260 270 280 230 300 310 320 330 340 350 360 370 380 330 400 wavelength nm Rette absorbance a o o Q o t A a 8 0 0 0 5 1 0 15 2 0 25 3 0 35 4 0 45 5 0 55 6 0 65 7 0 75 8 0 8 amp 5 3 0 35 10 0 Time min 4 Select the appropriate range options for the map cell as follows a Right click the map cell b From the shortcut menu choose Ranges The Map Ranges dialog box appears see Figure 154 Figure 154 Map Ranges dialog box Map Ranges Detector PDA 7 Wavelength 220 00 400 00 Time 0 00 10 00 Scan filter Cancel Help c Inthe Wavelength box type the wavelength range that you want to display d In the Time box type the time range that you want to display 246 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Creating a Layout for PDA Data 5 Select the appropriate display options for the map cell as follows a Right click the map cell b From the shortcut menu choose Display Options The Display Options dialog box appears c Click the Axis tab The Axis page appears see Figure 151 on page 244 d In the Units area select the Absolute option e Click the Normalization tab The Normalization page appears f In the Normalize Method area select the Auto Range option g Click the Style tab The Style page appears see Figure 155 Figure 155 Style page in the Display Options dialog box for the map cell Display Options Style Color
112. 24 122 Surveyor Plus User Guide for LC Devices Thermo Scientific 4 Sample Preparation Routines Draw Eject and Transfer Volumes for Sample Preparation Tasks Draw Eject and Transfer Volumes for Sample Preparation Tasks The maximum volume that the autosampler can deposit draw or transfer during a sample preparation task depends on the syringe type the task requested and the previous step in the sample preparation method For tasks performed with the inner plunger of the concentric syringe the maximum volume liquid air bubble that the autosampler can draw deposit or transfer is limited to the nominal size of the syringe e For tasks performed with the outer plunger of the concentric syringe the maximum volume liquid air bubble that the autosampler can draw deposit or transfer is limited to 500 pL except for the Wash Needle and Flush to Waste tasks which are limited to a range of 100 to 6000 pL and the Mixing tasks which are limited to a maximum of 490 pL Table 31 lists the maximum volumes by task Table 31 Draw eject and transfer volumes for sample preparation tasks Sheet 1 of 2 Task Maximum volume pL Maximum volume pL with the inner plunger with the outer plunger Draw from Sample Nominal size of the concentric syringe minus the current N A contents liquid air bubble of the needle tubing Transfer from Sample Nominal size of the concentric syringe minus the current N A to Sample cont
113. 969 4 03 12 PM Reset Wavelength Calibration To Default Values Help Before you perform a wavelength calibration verify that the diode array is not saturated see Adjusting the Light Throughput to the Diode Array on page 315 To open the Calibration page 1 From the PDA detector view choose Surveyor PDA Plus gt Direct Controls The Direct Control dialog box appears 2 Click the Calibration tab 320 Surveyor Plus User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Note The diode array used in the PDA detector has a background count level at each diode even when both lamps are off This background count level is called the dark current This background or dark current must be subtracted from the intensity counts before the intensity values are converted to absorbance units AU After you perform a dark current calibration the PDA detector corrects the spectrum intensity values for the dark current To start a dark current calibration 1 Turn on both lamps and wait one hour for the lamps to equilibrate see Turning the Lamps On or Off on page 163 2 In the Dark Current Calibration area click Calibrate The Dark Current Calibration wizard appears 3 Follow the instructions provided by the wizard For more information click Help at the bottom of the Dark Current Calibration dialog box To start a wavelength calibration
114. After you verify the stability of the column oven temperature turn off the column oven using the autosampler direct controls and remove the temperature probe For information about the autosampler direct controls see Controlling the Tray and Oven Compartment Temperatures on page 199 280 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Vial Tray Metal Sensor Calibration Use the Vial Tray Metal Temperature Sensor Calibration wizard and an external temperature sensor to calibrate the vial tray temperature control To perform the vial tray metal sensor calibration procedure you must have the following items provided in the Field Service Calibration Kit P N 60053 62001 e Calibrated Omega 869C RTD thermometer or equivalent e A S vial tray sensor To calibrate the column oven temperature follow these procedures in order 1 Preparing to Calibrate the Tray Compartment Temperature 2 Specifying the Internal Set Target for the Tray Compartment Temperature 3 Adjusting the Tray Temperature Calibration Preparing to Calibrate the Tray Compartment Temperature Thermo Scientific To set up the system to calibrate the temperature of the tray compartment 1 Install the tray temperature sensor as follows a b d Open the door to the tray compartment Install the tray temperature sensor into location E of the tray compartment
115. Bottom Distance Starting the Well Bottom Distance Wizard To start the Well Bottom Distance wizard 1 Open the status view for the autosampler For information about opening the status view from the Xcalibur data system see Checking the Status of the LC Devices on page 136 2 Verify that the autosampler status reads Ready to Download 3 Open the view for the autosampler 4 From the Surveyor AS menu choose Calibration The Calibration dialog box appears see Figure 211 Thermo Scientific Surveyor Plus User Guide for LC Devices 305 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 211 Calibration dialog box with the Well Bottom Distance option selected Calibration Choose the diagnostic item Column oven air sensor calibration Vial tray metal sensor calibration Arm calibration 5 Select the Well Bottom Distance option and then click Next The Select Calibration Method page appears see Figure 212 Figure 212 Select Calibration Method page Select calibration method Current distance value 15000 Calibrate to find value lt Back Cancel Help Go to the next procedure Selecting the Calibration Method for the Well Bottom Distance on page 306 Selecting the Calibration Method for the Well Bottom Distance Use the Select Calibration Method page of the Well Bottom Distance wizard to select a calibration method You can manually enter
116. C 29 9 Adjust Cancel Help d Repeat step la through step 1c until the temperatures on the thermometer and the current temperature readout see Figure 187 agree within 0 2 C 2 When the temperatures on the 869C thermometer and the Current Temperature readout are within 0 2 C of each other click Finish at the bottom of the Diagnostic External Set Target page 3 On the Tray status page verify that the Current Temperature readout is stable at 30 0 C with a maximum temperature drift of 0 2 C 4 After you have verified the stability of the oven tray temperature remove the temperature probe 286 Surveyor Plus User Guide for LC Devices Thermo Scientific Arm Calibration Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler During an injection the XYZ arm moves between the specified vial or well location and the injection port When you move the autosampler you can jar the XYZ arm causing it to lose alignment Performing the arm calibration procedure requires you to visually align the XYZ arm over the injection port To make this visual alignment you must replace the needle with an LED light fixture that shines a small beam of red light onto the port and replace the stainless steel injection port with a non reflective target fixture These test fixtures do not come with the autosampler you must order them from Thermo Fisher Scientific After following the in
117. C Pump Direct Control dialog box appears see Figure 105 Surveyor Plus User Guide for LC Devices 187 6 Direct Controls Pump Direct Controls Figure 105 Operation page of the Surveyor LC Pump Direct Control dialog box Operation Surveyor LC Pump Direct Control Method Flow Rate 0 100 mL min Component A 30 00 Component B Component C Component D Download Error Condition Purge Time 3 0 min Solvent Valve B Help Close 4 In the Purge area do the following a In the Purge Time box type an appropriate purge time The range is 0 1 to 9 9 minutes Each solvent line holds approximately 3 mL of solvent b From the Solvent Valve list select the solvent valve for the solvent line that you want to draw solvent through c Click Purge The pistons of the pump begin to move rapidly increasing the flow rate to 9 99 mL min 5 After drawing fresh solvent through the solvent lines close the drain valve Downloading New Solvent Conditions to the Pump To download new solvent conditions to the pump 1 Open the Surveyor LC Pump Plus view 2 From the menu bar choose Surveyor LC Pump gt Direct Control gt Operation The Operation Surveyor LC Pump Direct Control dialog box appears 188 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls Pump Direct Controls 3 In the Method area do the following a In the Flow rate box type the flow rate The range is 0 0
118. C erf llen Das Produkt ist durch folgendes Symbol gekennzeichnet Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs Entsorgungsfirmen in allen EU Mitgliedsstaaten getroffen damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann Mehr Information ber die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific ber die Verwerter und weitere Hinweise die n tzlich sind um die Produkte zu identifizieren die unter diese ROHS Anweisung fallen finden sie unter www thermo com WEEERoHS Conformit DEEE Ce produit doit tre conforme la directive europ enne 2002 96 EC des D chets d Equipements Electriques et Electroniques DEEE Il est marqu par le symbole suivant Thermo Fisher Scientific s est associ avec une ou plusieurs compagnies de recyclage dans chaque tat membre de Punion europ enne et ce produit devrait tre collect ou recycl par celles ci Davantage d informations sur la conformit de Thermo Fisher Scientific 4 ces directives les recycleurs dans votre pays et les informations sur les produits Thermo Fisher Scientific qui peuvent aider la d tection des substances sujettes 4 la directive RoHS sont disponibles sur www thermo com WEEERoHS a a E Contents Prelate ee ek ee ee ere re ce rere rer ree xv Related Documenon isi0rc0ds dp Ue pratauep ends de pene ss aie ee we xvi Safety and Special Notices pu ioc vascheu un codes nade saeennusaceead xvii Contacting
119. Calibration e Creating and Editing a Custom Wavelength Calibration List To calibrate the wavelength accuracy of the optical bench the PDA detector uses a holmium oxide reference solution one of the four calibration files provided with the Xcalibur data system or your own custom wavelength calibration file IMPORTANT Before you perform a wavelength calibration verify that the diode array is not saturated see Adjusting the Light Throughput to the Diode Array on page 315 Figure 222 shows the holmium oxide spectrum Figure 222 Holmium oxide spectrum Holmium Oxide Bands oO Lo Absorbance 230 270 310 350 390 430 470 510 550 590 630 4670 Wavelength nm Thermo Scientific Surveyor Plus User Guide for LC Devices 319 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Calibration Page for the PDA Detector Use the Calibration page see Figure 223 to perform the dark current and wavelength accuracy calibrations Perform these calibrations on a regular basis and as part of the operation verification procedure Figure 223 Calibration page showing that the detector is not calibrated Display Configuration Information Calibration Dark Current Calibration Currently NOT Calibrated Last Calibration 12 31 1969 4 03 12 PM Reset Dark Current Calibration To Default Yalues Wavelength Calibration Calibrate Currently NOT Calibrated Last Calibration 12 31 1
120. Configuration Specifying the Configuration Settings Surveyor LC Pump Plus Configuration Parameters Table 12 describes the configuration parameters for the Surveyor LC Pump Plus Table 12 Surveyor LC Pump Plus configuration parameters Parameter Description Configuration Pressure Units Specifies the pressure units for the status display The selections are MPa bar and psi To convert psi to bar multiply by 0 0689476 To convert bar to psi multiply by 14 5038 Stack Number Specifies the unit ID value for the Surveyor LC Pump Plus The unit ID on the back panel of the pump consists of two rotary switches Each switch contains ten positions The arrow on the left switch points to the first digit of the unit ID The arrow on the right switch points to the second digit of the unit ID The rotary switches are set to 01 at the factory Error Handling Pause Sequence Select this check box to pause the injection sequence when the following Degasser pump detects a degassing error Error Clear this check box if you do not want the injection sequence to pause when the pump detects a degassing error 64 Surveyor Plus User Guide for LC Devices Thermo Scientific 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Surveyor PDA Plus Detector Configuration Settings The PDA detector communicates with the Xcalibur data system through an Ethernet connection To make this connection connect the Ether
121. Detector Preparing the LC System for an Attenuator Adjustment To prepare the LC system for an attenuator adjustment 1 Ensure that the lamps are on You can view the lamp status from the Configuration page of the Direct Control dialog box or from the PDA detector view of the Status page of the Information view For information about the Configuration page see Configuration Page on page 171 2 Replace the LC column with a flow restrictor 3 Start pumping HPLC grade water at a flow rate of 1 mL min through the flowcell Go to the next procedure Accessing the Attenuators Accessing the Attenuators To access the attenuators 1 Open the front doors of the detector 2 Unscrew the captive screw and then remove the flowcell cover The attenuators are located on the right side of the front panel Two black tabs are attached to the attenuators for manual adjustments see Figure 219 The left tab controls the light throughput from the deuterium lamp UV region and the right tab controls the light throughput from the tungsten lamp Visible region Moving an attenuator tab up increases the light throughput and moving the tab down decreases the light throughput to the diode array Figure 219 Attenuator tabs for the Surveyor PDA Plus Detector Deuterium lamp attenuator tab ige Tungsten lamp attenuator tab Go to the next procedure Adjusting the Attenuators on page 317 316 Surveyor Plus
122. Figure 214 type a vial or well location Note If you are calibrating the bottom distance of a vial verify that you have placed a vial in the selected location Figure 214 Calibrate to find page Well Bottom Distance Current distance value 15000 Note Micro well or vial tray must be installed Calibrate at well vial Set Calibration toed ob 4 Click Set Calibration to activate the autosampler After the XYZ arm moves to the selected location the needle mechanism descends until it detects the bottom of the vial or well After it detects the bottom the XYZ arm moves to the home position In the Well Bottom Distance wizard the new bottom distance calibration value appears at the top of the page 5 Click Finish to accept the calibration 308 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Autosampler Maintenance Information Autosampler Maintenance Information Thermo Scientific Use the Maintenance Information dialog box see Figure 215 to set the scheduled maintenance time SMT for the autosampler maintenance items Injections Valve Cycles Needle Cycles and Syringe Cycles Figure 215 Maintenance Information dialog box Maintenance Information 1 bd 1 Injections Valve Cycles Syringe Cycles Needle Cycles Usage limit 0 Set new limit Current counter Zero counter To open the Maintenance Information dialog box
123. Fullloop C No waste m Tray Temperature Control l Enable tray temperature control Temperature C Column Oven Control Enable column oven control Temperature C a ma ie Thermo Scientific Surveyor Plus User Guide for LC Devices 85 3 Instrument Method Setup Autosampler Instrument Method Parameters To specify the injection and temperature control settings for your instrument method 1 Select the injection mode e Ifyou want to vary the volume of your sample injections select the Partial Loop option e Ifyou want a high degree in injection to injection precision select the Full Loop option When you select Full loop the Injection Volume uL box becomes unavailable e Ifyou have a limited amount of sample select the No Waste option When you select No Waste the Loop Loading Speed L s box becomes available Note For more information about the injection modes see Injection Modes on page 19 2 For the No Waste injection mode type or select a loop loading speed in the Loop Loading Speed box For most applications keep the loop loading speed at its default value 3 For the Partial Loop and No Waste injection modes type or select an injection volume in the Injection Volume box The injection volume range depends on the syringe size see Injection Volume Range on page 91 4 In the Needle Height from Bottom mm box type or select the height from the bottom of the
124. N 61000 3 3 1995 EN 61000 4 6 1996 A1 2001 IEC 61000 3 3 1994 EN 61000 4 11 1994 Al 2001 EN 61326 1 1997 EN 61000 4 2 1995 A1 1998 A2 2001 CISPR 11 1999 A1 1999 A2 2002 FCC Class A CFR 47 Part 15 Subpart B 2004 Low Voltage Safety Compliance Low voltage safety compliance has been evaluated by TUV Rheinland of North America Inc This device complies with Low Voltage Directive 73 23 EEC and harmonized standard EN 61010 1 2001 Surveyor PDA Plus Detector When the Surveyor PDA Plus Detector is delivered to you it meets all pertinent electromagnetic compatibility EMC and safety standards as described below EMC Directive 89 336 EEC amended by 92 31 EEC and 93 68 EEC EMC compliance has been evaluated by Underwriters Laboratories Inc EN 55011 1998 EN 61000 4 3 2002 EN 61000 3 2 1995 Al 1998 A2 1998 A14 2000 EN 61000 4 4 1995 Al 2001 A2 2001 IEC 61000 3 2 2000 EN 61000 4 5 1995 Al 2001 EN 61000 3 3 1995 EN 61000 4 6 1996 A1 2001 IEC 61000 3 3 1994 EN 61000 4 11 1994 Al 2001 EN 61326 1 1997 EN 61000 4 2 1995 A1 1998 A2 2001 CISPR 11 1999 Al 1999 A2 2002 FCC Class A CFR 47 Part 15 Subpart B 2003 Low Voltage Safety Compliance Low voltage safety compliance has been evaluated by TUV Rheinland of North America Inc This device complies with Low Voltage Directive 73 23 EEC and harmonized standard EN 61010 1 2001 Surveyor UV Vis Plus Detector When the Surveyor UV Vis Detector is deli
125. OCOOOOOOOCOOOO0S OQOQOOOOOOOOOOOOOOOOOCOOOOO OQOQOOOOOOOOOOOOOOOOOOOOOO OQOQOQOOOOOOOOOOOOOOOOOOOOO O OQOQOOOOOOOOOOOOOOOOOCOOOOO OQOOOOOOOOOOOOOOOOOOOOOOO OQOQOOOOOOOOOOOOOOOOOCOOOOO OQOQOOOOCOOOOOOOOOOOOOOOOOO OQOQOOOOOOOOOOOOOOOOOOOOOO OOOO 0000 P QOOOCOCOOOOOOOOOOOOCOOO00S8 P1 P24 1 24 2 Place the microplates in each end of the microwell carrier leaving the middle position empty 3 Load the microwell carrier into the tray compartment of the autosampler as follows a From the menu bar choose Surveyor AS gt Direct Control The Direct Control dialog box appears see Figure 209 302 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 209 Direct Control dialog box for the autosampler Direct Control Command amp Parameters Position arm to access tray b Select Position Arm to Access Tray and then click Apply The XYZ arm moves to the back of the tray compartment c Insert the microwell carrier into the tray compartment d Verify that the microwell carrier sits flat and is properly installed 4 Send the XYZ arm to the home position as follows a In the Direct Control dialog box select Go to Home Position b Click Apply The XYZ arm moves to the home position which is above the injection port 5 Make an injection from each corner of the microplate as follows a In the Direct Control dialog bo
126. Open the view for your autosampler The Method page for your autosampler appears In the menu bar choose Surveyor AS gt Maintenance To set a new usage limit Click the tab for the page that contains the maintenance item that you want to change the usage limit for In the Usage Limit box type the usage limit Click Set New Limit To reset the usage counter after performing the scheduled maintenance task Click the tab for the scheduled maintenance task Click Zero Counter Note If you selected the Enable Maintenance Log check box on the Communication page of the Surveyor AS Autosampler dialog box when you configured the Surveyor Autosampler you can set the scheduled maintenance times see Communication Page on page 52 Surveyor Plus User Guide for LC Devices 309 10 Autosampler Calibration and Record Keeping Autosampler Maintenance Information Maintenance Information Parameters Table 61 describes the parameters on the Maintenance Information pages When anyone of these counters on the Maintenance Information pages exceeds the user specified usage limit the Maintenance Due readback displays Yes and the data system prevents the autosampler from making injections To enable the autosampler you must zero the counter or change the usage limit If the usage limit is based on a scheduled maintenance plan perform the scheduled maintenance Table 61 Maintenance Information dialog box pages an
127. P24 Volume For the no waste and partial loop injection modes the minimum injection volume is 0 1 pL The maximum volume depends on the syringe type Syringe Maximum volume 100 pL concentric syringe 20 pL 250 uL concentric syringe 125 uL 500 uL concentric syringe 300 pL 2500 uL standard syringe 1250 pL Injection Full Loop Partial Loop and No Waste Mode Surveyor Plus User Guide for LC Devices 195 6 Direct Controls Autosampler Direct Controls Table 53 Direct control commands for the autosampler Sheet 3 of 3 Command Move Needle Description Moves the XYZ arm to a specific vial or well location Set Injector Position Set Syringe to Removal Position Switches the position of the injection valve The injection valve has two positions fill and inject Sets the syringe to its removal position Set Syringe to Home Position Sets the syringe to its home position Set Arm to Home Position Moves the XYZ arm to its home position which is just above the injection port Button Apply Executes the command Flushing the Autosampler Syringe To ensure the proper performance of the autosampler remove air from the wash bottle tubing and the autosampler syringe before you make your first injection Once you have your system running periodically check the level of solvent in the wash bottle and remove air from the syringe as needed Tip During a flush operation the autosampler draws wash solven
128. PDA Avalon J Benzene J with z 4000007 239 nm scan wavelength impurity 3 J 3uAU scan threshold 200000 7 95 peak coverage 1 25 1 30 1 35 1 40 1 45 1 50 1 55 1 60 1 65 1 70 1 75 Time min 256 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Calculating the Purity of the Chromatographic Peaks Figure 164 Chromatogram for the 225 nm scan wavelength with default integration parameters HIBA E ksl T Apply to all plots Auto Cale Initial Events Start Threshold End Threshold Area Threshold P P Threshold Bunch Factor Negative Peaks Tension 10000 000 10000 000 10000 000 1 000 1 000 Initial Value Initial Value Initial Value Initial Value Initial Value Initial Value Initial Value Time Min Event Value f 480 Tension x 1 000 Add Delete Change Help RT 1 25 1 80 a RT 1 57 NL Peak Purity 988 1 55E5 150000 nm 224 5 225 5 PDA 140000 Avalon 130000 Benzene Benzene with 120000 Impurity 110000 100000 90000 gt 80000 3 70000 60000 50000 400003 Impurity 1 3 14 1 5 1 6 1 7 Time min ZDR A hsl 02 25 2003 11 20 31 AM T Apply to all plots Initial Value Start Threshold 1242 480 Initial Value End Threshold 621 240 Initial Value Area Threshold 12424 805 Initial Value P P Threshold 1 000 Initial Value Bunch Factor 1 000 Initial Value Negative Peaks Off Initial Value Tension 0 20
129. Run time 0 00 min 00 00 00 Flow rate 0 0 plimin Pressure 42 8 bar Pressure SD 0 0 bar Start gradient Pump ready fa Release injection Start 2nd pump Surveyor Plus User Guide for LC Devices 145 5 Daily Operation Checking the Status of the LC Devices Table 40 describes the status readbacks on the General page of the pump status view Table 40 General page of the pump status view Sheet 1 of 2 Readback Description Status Displays the pump status as follows Ready The pump is ready for a run Running Isocratic The solvent flow is on but the pump is not running a gradient program Homing The pump pistons are moving toward the home position Running Gradient The pump is running the solvent conditions specified in the gradient program of an instrument method The gradient program can contain isocratic or gradient solvent conditions Low Pressure Error The system pressure has fallen below the minimum pressure setting for more than one minute If you are controlling the pump from the Direct Control dialog box the status returns to Ready after the pump stops pumping The error is posted to the pump s event log High Pressure Error The system pressure has risen above the maximum pressure setting Note When a pressure error occurs one of the following occurs e Ifyou are controlling the pump from the Direct Control dialog box the status returns to Ready after the pump stops pumping The
130. Single Pump System 74 Programming the Pumps in a Dual Pump System 84 Autosampler Instrument Method Parameters 0 0000s eee 85 Surveyor AS Method Page seis orbs se 2 adem Sales Aa keds ahs cre es 85 Reservoir Content Page 6 ec ee eee ees 92 Timed Events Page for the Autosampler ssesees wiens ee idan vad ees 93 PDA Detector Instrument Method Parameters 00000 e sees 95 Triggering an External Device with the PDA Detector 104 UV Vis Detector Instrument Method Parameters 000 200005 106 Saving the Instrument Method iiss cae Piee a pate tie is eae he eae 109 Chapter4 Sample Preparation Routines 0 0 ee cece eee e eee eee eee 113 Opening the Sample Preparation Pages sere scss dts deat see 113 Sample Preparation les re SY reat te Ohh ts wet Re A thon AS 115 Building the Sample Preparation Routine 000 e eee eee eee 116 Sample Locations for the Sample Preparation Tasks 0004 122 Draw Eject and Transfer Volumes for Sample Preparation Tasks 123 Syringe Speed Range for Sample Preparation Tasks 00004 124 Syringe Speed for Tasks that Can Use Either Plunger 125 Syringe Speed for Tasks that Use the Inner Plunger 126 Sample Preparation Routine Poampless stave ode veoh onus eats 127 Chapter5 Daily Operation 00 c cece eect eee eaee 133 Turn
131. Surveyor PDA Plus Wavelength Calibration txt Save as type Text X Cancel b Type a name in the File Name box and then click Save After you save the file with a name of your choice you can view or print the contents of the file using any text editing program see Figure 242 Figure 242 Wavelength Calibration file viewed in Microsoft Notepad P Holmium12 txt Notepad File Edit Format View Help Wavelength Calibration Report Printed Wavelength Calibration File Window Target MANMANM wnan 241 249 278 287 333 345 361 416 451 485 536 640 08 98 03 47 40 49 16 Found 240 250 277 287 333 345 361 416 451 485 536 640 Difference o f 0 0 i y D 23 14 04 05 12 02 07 D D 0 D D Regression Coefficients a 162 729 p 0 870 Wavelength Calibration Table Diode A Surveyor Plus User Guide for LC Devices Diode AnoOseUNrRPOoOW Fr ooooocooco oF act A 000000 162295 324590 486885 649180 811475 973770 136066 Peak 243 252 281 290 337 349 365 421 455 489 540 643 c 0 0000425 Fract oooccc 00 B Diagnostic 34 79 16 84 45 55 27 000000 837705 675410 513115 350820 188525 026230 863934 Tue Dec 28 13 08 26 2004 Diode Array offset 2 2 3 3 4 4 4 4 4 3 3 2 Interpolation
132. Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Autosampler Instrument Method Parameters Injection Volume Range The injection volume for full loop injections is automatically set to the value in the Sample Loop Volume box on the Communication page of the Surveyor Autosampler dialog box see Communication Page on page 52 For partial loop and no waste injections the minimum injection volume is 0 1 pL The maximum injection volume depends on the syringe size see Table 20 For optimal performance follow these guidelines e For no waste injections do not inject less than 1 0 pL and limit the maximum injection volume to 80 of the nominal loop size minus an additional 5 uL e For partial loop injections limit the maximum injection volume to 40 of the nominal loop size For the standard 25 pL sample loop limit the maximum injection volume to 10 uL Table 20 Maximum injection volume Syringe size pL Maximum injection volume pL 100 20 250 125 500 300 2500 1250 Syringe and Loop Loading Speeds for Injections During an injection sequence the inner plunger of the concentric syringe descends pulling liquid from a sample vial or well into the needle tubing After the autosampler withdraws sample the XYZ arm moves the needle to the injection port The inner plunger of the concentric syringe ascends pushing liquid through the transfer tubing and into the sample loop A stepper
133. The deuterium lamp is off Q Deuterium Lamp is Of The deuterium lamp is starting up which requires about Q Lamp is Starting 1 5 min The deuterium lamp is on Q Deuterium Lamp is On Tungsten Lamp The tungsten lamp states are as follows The tungsten lamp is on Q Tungsten Lamp is On Q Lamp is Off The tungsten lamp is off 152 Surveyor Plus User Guide for LC Devices Thermo Scientific 5 Daily Operation Checking the Status of the LC Devices Figure 86 shows the Status view for the Surveyor UV Vis Plus Detector You can view the absorbance level of the chromatographic baseline from this view Figure 86 Surveyor UV Vis Plus Detector Status view Status Acquisition Queue Run Manager Ready To Download Sequence Sample Name Working On Position Raw File Inst Method Surveyor AS Ready to Download Surveyor LC Pump Ready to Download Surveyor UV IS Ready to Download Current status State Ready for run Run time min 0 Data type Dual U D2 Lambda 1 nm 254 Lambda 2 nm 280 Absorbance 1 AU 2 0206e 005 Absorbance 2 AU 0 00010741 Table 45 describes the status readbacks for the Surveyor UV Vis Plus Detector Table 45 UV Vis detector status readbacks Readback Description State Displays the following states Ready for Run and Off Run Time Displays the elapsed run time Data Type Displays the program type specified in the current instrument method
134. The tray temperature sensor is a standard tray with a temperature sensor cemented into a middle vial location of the tray Route the cable of the sensor through the notch at the top on the tray compartment so that it does not interfere with the door closure Close the door to the tray compartment 2 Open the status page for the tray temperature To open the Tray page from the Xcalibur data system do the following a If the Information view is closed click the Information View button open the view The Information view opens with the Status page displayed Verify that the status reads Ready to Download For more information see Checking the Status of the LC Devices on page 136 Click the listing for the autosampler in the directory tree The status pages for the autosampler appear at the bottom of the Status window Surveyor Plus User Guide for LC Devices 281 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler 3 Click the Tray tab The Tray page appears see Figure 182 Figure 182 Tray page AS Status Oven Tray Eror lag Tray Control on No Current temperature C 21 7 Set temperature C 25 0 Ready status Ready 4 Open the Calibration dialog box for the autosampler see Calibrating the Autosampler on page 274 5 Select the Vial Tray Metal Sensor Calibration option see Figure 183 Figure 183 Calibration dialog box Calibration Choose the diagno
135. Transfer Volumes for Sample Preparation Tasks on page 123 Syringe Speed Syringe Speed for Tasks that Can Use Either Plunger on page 125 Needle Height Default 2 mm Range 0 to 18 mm Deposit Liquid in Deposit liquids in a reservoir vial Reservoir Parameter Reference range or selections Volume Draw Eject and Transfer Volumes for Sample Preparation Tasks on page 123 Destination RV1 RV2 RV3 or RV4 Reservoir Syringe Speed Syringe Speed for Tasks that Can Use Either Plunger on page 125 Thermo Scientific Surveyor Plus User Guide for LC Devices 117 4 Sample Preparation Routines Building the Sample Preparation Routine Table 29 Sample Preparation page Sheet 2 of 5 Parameter Draw from Reservoir Description Draws liquid from a reservoir vial or the wash bottle Draw from Sample Flush to Waste Parameter Reference range or selections Volume Draw Eject and Transfer Volumes for Sample Preparation Tasks on page 123 Source Reservoir RV1 RV2 RV3 RV4 or Bottle Syringe Speed Syringe Speed for Tasks that Can Use Either Plunger on page 125 Air Bubble Range 0 to 10 pL Draws liquid from a vial or well Parameter Reference range or selections Sample Location Sample Locations for the Sample Preparation Tasks on page 122 Volume Draw Eject and Transfer Volumes for Sample Preparation Tasks on page 123 Syringe Speed Syringe Spe
136. Type 0 Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector 13 To apply the calibration results to the detector click Apply on the Delta Values page see Figure 240 on page 335 The success confirmation page appears see Figure 243 Figure 243 Success confirmation page for a wavelength calibration Wavelength Calibration FW calibration has been successfully applied 14 Click Finish to complete the wavelength calibration The calibration is saved The date and time of the calibration are displayed in the Wavelength Calibration area of the Calibration page see Figure 231 on page 329 Creating and Editing a Custom Wavelength Calibration List Use the Custom List Name dialog box to name a custom wavelength calibration list WCL file To open the Custom List Name dialog box and the Edit Peak List area 1 Start the Wavelength Calibration wizard see Performing a Wavelength Calibration on page 328 2 Verify that the PDA detector meets the preconditions for a wavelength calibration and click Next The wavelength list page appears see Figure 233 on page 331 3 Click Save As Custom List The Custom List Name dialog box appears see Figure 244 Thermo Scientific Surveyor Plus User Guide for LC Devices 337 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Figure 244 Custom List Name dialog box Custom List Name Us
137. US os deco cet a innia ba wea tae ce eeaw een E eed xviii Chapter 1 Introduction to the Surveyor Plus LC System cece eeeeees 1 Anal ptical Pump 0d hotscw side ceambanhwlevssouie de a 2 Surveyor MS Pump Plus siss cooks enya eee dee eseedbareee eben een 2 Surveyor LC Pump Plus 5 isctow ces aoe cde pe daa wee Ree Rew ee 3 Aut sampler seesi sana on ee di E Ea E A E E Le eet 5 Tray Compartment conte tiea nin brea EdE E ARE A 5 Vial and Well Notation ia ede a e e E a eae oe 6 Injection Systemi succeded iit a Gea toa edd OINERA Eades 11 Injection Modes si rscra ces tetg kines doses ceay Get cee certo 19 Temp rature Control s acute eee newer owes Mew Eee Peek eee ates 21 Detector prekenen cea a Ganda Oe eee es eae 21 PDA D tectOb lt a c ch eg cad ennwnd iii deled doe Dew Ewe RE Eee 22 UV Vis Del co cemsrcenay ehh rae bee dba a babs phases RRS 23 Solvent Plafon cit ic2t a koe bead erst chan ubee saree ee A 23 Communication with the Data System Computer 0005 24 Turning Off the Computer s Energy Saving Features 004 24 Synchronization of the LC Devices eich ise cioel vee egos be anedcowneey 32 Status LEDS 024 ac ieee hitep rie divdida EE E S 35 Surveyor MS Pump Plus LED States o a doionw aces a nen coweue sien 36 Surveyor LC Pump Plus LED States a a dceceaddstoven cena secede 37 Antosampler LED States iis vidio din eheses nee eh eke eee oe 38 PDA Detector LED States pet co eke cee bas ce
138. User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Verifying the Performance of the PDA Detector Adjusting the Attenuators To adjust the attenuators 1 If you have not already done so create a display method to view the light intensity from the lamps see Creating a Display Method on page 313 2 Load the display method to the detector as follows a In the Direct Control dialog box for the PDA detector click the Display tab The Display page appears b In the Control area click Load Method The Open Display Method dialog box appears see Figure 220 Figure 220 Open Display Method dialog box for the PDA detector Open Display Method Look in methods x f e EE E shutdown meth startup meth E test2 meth E Test3 meth intensity spda lt File name lintensity spda Files of type PDA Display Method spda meth i Open as read only c Choose your display method file spda d Click Open The file name of the display method appears in the Current Method readback on the Display page see Figure 221 on page 318 3 Start the data stream and adjust the attenuators as follows a Inthe Control area click Start Data The spectrum of light intensities appears in the top window see Figure 221 For the UV region the diode of maximum intensity is between diode 10 and diode 50 For the Visible region the diode of maximum intensity is be
139. a bottom distance value for your custom vials or microplates or you can use the autosampler s needle sensor feature to determine the correct distance value 306 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler To select the calibration method for the well bottom distance Do one of the following e Select the Enter Value Manually option if you want to enter a previously determined value for the well bottom distance Click Next Then go to the next procedure Manually Entering the Well Bottom Distance or e Select the Calibrate to Find Value option to perform an active calibration Click Next Then go to Using the Needle Sensor to Determine the Well Bottom Distance on page 308 Note The autosampler stores only one well bottom distance value for custom tray configurations The number at the top of this dialog box is the current value for the distance Manually Entering the Well Bottom Distance To manually enter a new value for the well bottom distance 1 In the Enter New Value microns box type the new value in micrometers see Figure 213 The range is 15 000 to 46 990 micrometers 15 to 46 9 mm Note The user interface specifies the bottom distance in microns which is another term for micrometers Figure 213 Manual calibration page Well Bottom Distance Current distance value 15000 Enter new v
140. a ees 313 Adjusting the Light Throughput to the Diode Array 315 Calibrating the PDA Detector sewed sg wh Chae os ob oe ek wee wh we 319 Calibration Page for the PDA Detector 6 cjsce g6 oiace ace oe Seesaw ae arose 320 Performing a Dark Current Calibration i uae oan ius Pia eee ws 323 Performing a Wavelength Calibration 00 00 cee eee eee 328 Creating and Editing a Custom Wavelength Calibration List 337 Making a Single Injection from the Tune Window 5 341 NOK ass iene aana EEE nana taanea wade ERE sane a eRe 345 xiv Surveyor Plus User Guide for LC Devices Thermo Scientific M Preface This guide describes how to use your Thermo Scientific mass spectrometry application to control the Surveyor Plus high performance liquid chromatography HPLC system Contents e Related Documentation e Safety and Special Notices Contacting Us Tip Use the Lamp Startup Time feature to preserve the useful lifetime of the deuterium lamp The default lamp startup time for the PDA detector is 4 55 PM For optimal system performance reset the lamp startup time to approximately two hours before you plan to start data acquisition For information about changing the lamp startup time see Setting the Lamp Startup Time on page 166 Tip The default setting for the autosampler maintenance counters is 0 If you turn on the autosampler maintenance log see Communication Page
141. a system 2 Click the Sample Preparation tab The Sample Preparation page appears see Figure 69 For a new method in the Prep Operations list the Deposit Liquid in Sample task is highlighted and its parameters are listed below the Add To Task List button Thermo Scientific Surveyor Plus User Guide for LC Devices 113 4 Sample Preparation Routines Opening the Sample Preparation Page Figure 69 Sample Preparation page of the Surveyor Autosampler view Surveyor AS Method Sample Preparation Reservoir Content Timed Events Prep Operations YAAOo amp g a Method A Deposit liquid in sample Deposit liquid in reservoir Draw from reservoir Draw from sample Flush to waste Mix at sample Mix at reservoir Transfer from reservoir to reservoir Transfer from reservoir to sample Transfer from sample to reservoir Transfer from sample to sample Wait time Wash needle zi Add To Task List gt gt Sample Location Absolute location ea Relative location Cutent Volume ful joo Syringe speed ulrs 250 0 Remove Task Clear All Tasks Needle height mm 20 File name Import Sample Preparation Help Deposit liquid in sample task parameters Empty task list 114 Surveyor Plus User Guide for LC Devices Thermo Scientific 4 Sample Preparation Routines Sample Preparation Rules Sample Preparation Rules Thermo Scientific The maximum volume that the
142. ach device displayed on a separate page see Figure 140 2 Click KI D Show Previous and Show Next to move through the pages of your Instrument Method Figure 140 Instrument Method Report PDA page in the Qual Browser view w PAHs_01 RAW C Xcaliburidata PAHs_01 PAHs O1 PDA Run Time min Rise Time Scan scan scan scan Rate Step Channel sample rate Hz Channel Channel Channel Channel Channel Channel Surveyor Plus User Guide for LC Devices Wavelength nm Bandwidth mm 1 15 00 sec 1 00 200 400 Hz 1 000000 mm 1 10 000000 wavelength nm 239 bandwidth nm 9 wavelength nm bandwidth fnm 9 wavelength nm bandwidth nm 9 266 295 Thermo Scientific 8 Qual Browser Creating a Layout for PDA Data Creating a Layout for PDA Data This section describes how to view chromatograms and spectral information acquired by the PDA detector In addition it describes how to save the range and display settings for the PDA data in a layout file To create a layout file for PDA data follow these procedures in order 1 Specifying the Chromatogram and Spectrum Ranges 2 Specifying the Display Options for the Chromatogram and Spectrum Cells 3 Optional Inserting Cells 4 Saving the New Layout Specifying the Chromatogram and Spectrum Ranges When you open a raw data file in the Qual Browser application using the default layout the data file opens with the MS
143. ack panels of Surveyor devices showing the 7 connector system interconnect cable Solvent platform Detector back panel To MS detector Pump connector Pump connector of adapter cable Surveyor MS Pump connector Autosampler back panel LC pump back panel Figure 30 shows the cable assembly with five green combicon connectors The assembly has two pump connectors one is labeled MS PUMP and one is labeled LC Pump You can identify the connectors for the autosampler detector and MS detector by the small tags on their adjacent cables To connect the MSQ Plus Mass Detector you must modify the wiring connections inside the MS detector connector Surveyor Plus User Guide for LC Devices 33 1 Introduction to the Surveyor Plus LC System Synchronization of the LC Devices 34 Figure 30 5 connector system interconnect cable P N F5049 010 To Detector M S F5049 010 To To WS K MS Detector Autosampler To z S LC Pump MS Pump 5 dNNd 91 Figure 31 shows the interconnect cable connections for a Surveyor LC system Figure 31 Back panels of the Surveyor devices showing the 5 connector interconnect cable MS i Detector Detector Autosampler Siete S
144. age Wavelength Calibration Wavelength calibration has completed successfully Crest nm Found t nm Delta nm 241 08 241 06 0 02 333 40 333 47 0 07 361 16 361 11 0 05 451 30 451 28 0 02 Export Results 536 97 536 98 0 01 Click the Apply button to accept the calibration Cancel Help Click to export the Click to accept calibration results the calibration to a text file see see step 13 step 12 11 Verify that the delta values are within 1 nm e Ifthe Delta values are acceptable go to step 12 e Ifthe delta values are not within the range of 1 nm do not export the results Complete the calibration procedure Then repeat the wavelength calibration After applying a second calibration if the Delta values are still not within the range of 1 nm call your Thermo Fisher Scientific service representative for assistance 12 Optional To print a report of the calibration results do the following a Click Export Results to print the results to a file The Save As dialog box appears see Figure 241 Thermo Scientific Surveyor Plus User Guide for LC Devices 335 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector 336 Figure 241 Save As dialog box Save in e data e aE E D12_2 txt E D12_28 txt D 1 10 txt D_1 18 txt E LampCal txt E NewHOS txt E NewHOs txt E NewHO txt W13 txt W13_1_16 txt E wHOS txt File name
145. al order You can add modify and remove events by double clicking the event setting you want to modify or by using the New Delete and Delete All buttons 102 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup PDA Detector Instrument Method Parameters Table 26 Timed events table on the Surveyor PDA Plus Method page Sheet 2 of 2 Parameter Time Description Specifies the time in minutes when the detector triggers the event The maximum time is the data acquisition time specified in the Run Length box see Figure 59 on page 95 Default 0 00 minutes Type Specifies an event type Event Off Event On Zero Data or Level Trigger Use a Level Trigger event to specify the absorbance threshold level for triggering an event When you select a Level type event you must specify the channel of the event the absorbance level that is to trigger the event and the delay time that the event is to occur after the absorbance level trigger event Use a Zero event to zero the absorbance from the detector Channel Note This list is available if you select Level Trigger in the Event Type list Specifies the discrete wavelength channel Channel A Channel B or Channel C that the PDA detector monitors to activate the external event Level Note This box is available if you select Level Trigger in the Event Type list Specifies the absorbance level that triggers the external eve
146. alue microns Pemi Set Calibration coe toe 2 Click Set Calibration The new bottom distance value in microns appears at the top of the dialog box and the Finish button becomes available 1 micron 1 micrometer 3 Click Finish to close the Well Bottom Distance dialog box Thermo Scientific Surveyor Plus User Guide for LC Devices 307 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Using the Needle Sensor to Determine the Well Bottom Distance The autosampler has a needle sensor that can determine the bottom distance of custom vials or microplate wells To determine the well bottom distance with the autosampler s needle sensor 1 Remove the cap or lid from your vial or well plate IMPORTANT Remove vial caps or well plate lids before performing an active well bottom distance calibration As the needle pierces a vial cap or a well plate lid the spring in the needle mechanism is compressed which can cause premature activation of the needle sensor IMPORTANT Before placing a custom tray into the autosampler tray compartment check the height limitations for 96 well and 384 well plates listed in the hardware manual for your autosampler Tall objects will stall the autosampler arm 2 Place the vial into a tray or the well plate into a carrier and then place the tray or carrier into the tray compartment of the autosampler 3 In the Calibrate at Well Vial position box see
147. and the degas unit is building vacuum Flashing amber The degas unit is experiencing a failure such as a loss of vacuum Green The degas unit has developed sufficient vacuum to Thermo Scientific degas the mobile phase solvents when the pump flow is set to a typical flow rate for chromatography Surveyor Plus User Guide for LC Devices 37 1 Introduction to the Surveyor Plus LC System Status LEDs Autosampler LED States Table 3 lists the LED states for the autosampler Tip To ensure that the controlled temperature zones are in equilibrium at the set temperature before the autosampler makes an injection select the Wait for Temperature Ready check box when you add the autosampler to the data system instrument configuration When you select this check box the autosampler waits until the controlled temperature zones are in equilibrium at the set temperature before it makes an injection While the temperature zones are equilibrating to the set temperature the Temp LED remains amber When you do not select this check box the autosampler does not wait for the temperature zones to equilibrate to the set temperature before making an injection and the Temp LED remains green Table 3 Surveyor Autosampler status LEDs and their meaning LED State Meaning Power Green The autosampler is on and receiving power Comm Amber Communication with the data system has not been established Green Communicatio
148. are securely fastened onto the vials Before you start a sequence run ensure that you have samples in the locations specified in your sequence Note To trigger the vial sensor make sure to position custom vials in the tray so that the top of the vial reaches the minimum height of 1 55 inches If you place vials that fall below this minimum height in the tray the vial sensor does not detect them When the sequence reaches a vial that is below the minimum height the sequence halts and the Vial Not Found message appears To load a conventional tray into the autosampler 1 Open the left door of the autosampler If you configured the Surveyor AS device driver to verify that the tray compartment door is closed the XYZ arm automatically moves to the back of the tray compartment Figure 37 on page 53 shows the location of the Verify Door Is Closed check box available in the Instrument Configuration window 2 If necessary use the direct controls to move the XYZ arm to the back of the tray compartment see Autosampler Direct Controls on page 192 3 Hold the tray handle tilting the back end of the tray down Insert the tray runner into the slot at the rear of the tray compartment Lower the front of the tray into place Then press down firmly to seat the tray 210 Surveyor Plus User Guide for LC Devices Thermo Scientific 7 Sequence Setup Starting Data Acquisition Starting Data Acquisition 1 To inject a sam
149. arget temperature C Start calibration The default temperature for the calibration of the column oven temperature is 50 0 C 3 In the Calibration Target Temperature C box type 30 see Figure 177 Figure 177 Diagnostic Internal Set Target page of the Column Oven Air Sensor Calibration wizard with the user setting of 30 C Diagnostic Internal Set Target Calibration target temperature C Ei Start calibration Ney Sancel Help User setting The range is 5 to 95 C 4 Click Start Calibration The data system turns on the column oven and downloads the target temperature The Next button becomes available 5 Click Next Thermo Scientific Surveyor Plus User Guide for LC Devices 277 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler The Diagnostic External Standard page of the Column Oven Air Sensor Calibration wizard appears see Figure 178 The default calibration temperature for the external standard is 50 C Figure 178 Oven page and the Diagnostic External Standard page of the Column Oven Air Sensor Calibration wizard Diagnostic External Standard AS Status Oven Tray Error log Oven Control on Yes External standard temperature C 50 0 Current temperature C 24 4 ae Set temperature C 30 0 Ready status Ready The oven control is on and the set temperature is 30 C The default temperature for the cali
150. as follows a Click the Labels tab The Labels page appears see Figure 149 Thermo Scientific Surveyor Plus User Guide for LC Devices 241 8 Qual Browser Creating a Layout for PDA Data Figure 149 Labels page in the Display Options dialog box Display Options Style Color Labels Axis Normalization m Label with NL I Retention time Flags 1 02E6 I Scannumber M Area nm 238 0 239 0 PDA Base peak I Height Test Mixture Signal to noise A01 Label Styles IV Offset Size 35 I Rotated Il Boxed 10 Time min Label threshold o o Cancel Help b Select the check boxes associated with the labels that you want to display such as retention time area height and name 7 Click OK to accept the settings and close the Display Options dialog box Setting the Display Options for the Spectrum Cell To set the display options for the spectrum cell 1 Pin the spectrum cell 2 Right click the pinned spectrum cell 3 From the shortcut menu choose Display Options The Display Options dialog box appears 4 Specify the Normalization parameters as follows a Click the Normalization tab The Normalization page appears see Figure 150 242 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Creating a Layout for PDA Data Figure 150 Normalization page in the Display Options dialog box Display Options b In the Normalize Method area
151. ated Last Calibration 12 31 1969 4 03 12 PM Reset Wavelength Calibration To Default Values Help b In the Wavelength Calibration area click Calibrate Page 1 of the wizard appears This page lists the preconditions required to perform a wavelength calibration see Figure 232 Thermo Scientific Surveyor Plus User Guide for LC Devices 329 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Figure 232 Preconditions page Wavelength Calibration Before proceeding with wavelength calibration make sure that 1 The filter wheel is in the OPEN position position 1 2 Both lamps have been on for an hour or more 3 The flow cell is filled with MeOH 4 The MeOH is being pumped at 1 mL min To begin calibration click the Next button To abort calibration click the Cancel button c Read the preconditions and determine if the detector meets these preconditions e Ifthe detector meets all of the preconditions click Next to proceed to the next page of the wizard where you are prompted to select a wavelength file e Ifthe detector does not meet all the preconditions click Cancel to exit the wizard and prepare the PDA detector for calibration Note On any page of the wavelength calibration wizard you can click Cancel to exit the procedure 330 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibra
152. atic gradient program the two time lines specify the same solvent composition and flow rate To set up the gradient program for the Surveyor MS Pump Plus 1 Open the view for your pump 2 Specify the general pump parameters see Specifying the Chromatographic Conditions for a Single Pump System on page 74 Surveyor Plus User Guide for LC Devices 79 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings 3 Click the Gradient Program tab The Gradient Program page appears see Figure 50 The columns that represent the solvents selected on the Pump General page are available for editing Figure 50 Gradient Program page Pump General Gradient Program Solvent colors ia Mis Lic Mp 100 Type of view Solvent Gradient v 4 For time 0 00 do the following a Type the initial solvent composition in the A B C and D columns For each solvent after you type the percent composition press ENTER or click another box in the gradient program table The first row in the gradient program table is set to 0 00 min and is uneditable As you change the percent composition for each solvent the data system maintains a total solvent composition of 100 b Type the initial flow rate in the pL min column and then press ENTER or click another box in the gradient program table The minimum flow rate setting depends on the start setting
153. ation page to specify these options e The autosampler s stack address e The syringe size and the sample loop size e The dead volume of the transfer tubing that connects the autosampler injection port to the injection valve e Whether the controlled temperature zones must be at their set temperature the tray compartment door must be closed or both before the autosampler makes an injection e Whether the autosampler uses the bottom distance for the configured tray type or the stored custom value or determines the bottom distance of sample vials or wells for each injection or at the start of a sequence e Whether the maintenance log is enabled 52 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings To specify the configuration settings on the Communication page 1 Open the Surveyor Autosampler Configuration dialog box see Surveyor Autosampler Plus Configuration Settings on page 45 2 Click the Communication tab The Communication page appears see Figure 37 Figure 37 Communication page Tray Communication Signal polarity Firmware Stack Address aa Syringe Type Concentric 250ul v P wait for temperature ready V Verify door is closed _HHH4 _______ When this option is selected the XYZ arm moves to the back of the Enable maintenance log tray compartment when you open Vial bottom se
154. avelengths that you set in the Peak Purity Settings dialog box To display the purity values for the integrated peaks 1 Select a chromatogram for a scan wavelength see Displaying Scan Wavelength Chromatograms on page 233 2 Set the integration parameters for the chromatogram see Determining Peak Areas on page 251 3 Right click the chromatogram cell and choose Peak Purity from the shortcut menu The Peak Purity Settings dialog box appears see Figure 162 254 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Calculating the Purity of the Chromatographic Peaks Figure 162 Peak Purity Settings dialog box Peak Purity Settings OK IV Enable Scan Threshold u U 3 Peak Coverage 95 Cancel Help I Limit Scan Wavelength Wavelength Range nml I Apply To All Traces 4 Select the Enable check box 5 In the Scan Threshold AU box type an appropriate scan threshold The scan threshold limits the portion of the peak included in the analysis to spectral slices that have a lambda max above the scan threshold You can set this limit to eliminate noise from the analysis The limits for this box are 0 to 2 000 000 HAU 6 In the Peak Coverage box type an appropriate value for your application The limits for this parameter are 1 to 100 coverage At a setting of 100 the data system compares all the spectral slices that fall within the beginning and ending tick ma
155. bes the readbacks on the Oven page of the autosampler status view Table 37 Oven page readbacks Readback Description Control On Displays Yes or No You can turn off the oven temperature control by doing one of the following e Using the Turn Off Oven Temperature command see Controlling the Tray and Oven Compartment Temperatures on page 199 e Running an instrument method that has the Enable Column Oven Control check box cleared Current Temperature C Displays the temperature monitored by the autosampler s internal temperature sensor Set Temperature C Displays the user specified temperature You can change the set temperature by doing one of the following e Using the Set Oven Temperature command see Controlling the Tray and Oven Compartment Temperatures on page 199 e Running an instrument method that has a temperature setting for the column oven Ready Status Displays one of the following Ready The oven compartment temperature has reached the set temperature you did not select the Wait for Temperature Ready check box when you specified the configuration settings for the autosampler or both For information about the Wait for Temperature Ready check box see Communication Page on page 52 Not Ready The oven compartment temperature has not reached the set temperature Tray Page Figure 79 shows the Tray page of the autosampler status view Figure 79 Tray page AS Status Oven Tray E
156. box to set the polarity of the Timed Events output signals e When the check box is selected the signal from the autosampler is LO Closed and goes HI Open when the timed events program is to start e When the check box is clear the signal from the autosampler is HI Open and goes LO Closed when the timed events program is to start Note The TF terminals send signals for events entered in the timed events table of the instrument method For information about setting up the timed events table for the autosampler see Timed Events Page for the Autosampler on page 93 Surveyor Plus User Guide for LC Devices 59 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Firmware Page Use the Firmware page to check the firmware version of the autosampler To check the firmware version of the autosampler 1 Open the Surveyor Autosampler Configuration dialog box see Surveyor Autosampler Plus Configuration Settings on page 45 2 Click the Firmware tab The Firmware page appears see Figure 40 Figure 40 Firmware page Tray Communication Signal polarity Firmware Upload the firmware version from the Autosampler to ensure that user interface is consistent Current version 2 15 Oven Temperature Controller Installed Tray Temperature Controller Installed OK Cancel Help 3 If you have upgraded your autosampler upload the firmware version as follows a Cli
157. bration 299 Temp LED 38 temperature control tray and LC column compartments 21 Wait for Temperature Ready check box 54 terminals output signals 164 Timed Events page autosampler 94 timed events PDA detector 104 total scan 235 tray compartment door magnetic switch 210 Verify Door Is Closed check box 54 tray compartment temperature calibration 281 control 21 tray temperature sensor installing 281 trays See sample trays Surveyor Plus User Guide for LC Devices 349 Index U tubing behind column oven 21 degasser 2 needle tubing 13 solvent lines 23 wash bottle 13 Turn Device On command 154 U unit ID description 42 relation to communication protocols 24 unpinned cells Qual Browser 225 UV Vis detector configuring 66 direct controls 183 instrument method parameters 108 lamp controls 183 parameters in method report 232 wavelength modes 23 V valves six port injection valve 18 syringe two position rotary valve 13 variable volume injections types 20 Verify Door Is Closed check box 6 54 290 vial bottom sensing 54 Vial Not Found message 210 vial trays notation 6 viscous flush solvents 89 volume flush 197 full loop injections 20 gradient delay pulse dampener in LC pump 3 no waste injections 19 90 partial loop injections 20 preheat tubing 21 sample loops 18 sample preparation operations 115 standard needle tubing and needle tubing extension 13 tubing in chambers of vacuum degassing unit 2 W Wait f
158. bration of the column oven temperature is 50 0 C Adjusting the Temperature Calibration for the Column Oven To adjust the temperature calibration for the column oven 1 Specify the calibration temperature and start the Column Oven Air Sensor Calibration wizard see Specifying the Internal Set Target for the Column Oven Calibration Temperature on page 276 2 Wait for the current temperature readback on the Oven page to reach 30 0 C see Figure 179 The Current temperature readback displays the temperature recorded by the autosampler s internal temperature sensor 278 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 179 Oven page showing that the current temperature has reached the set temperature AS Status Oven Tray Error log Oven Control on Yes Current temperature C 30 0 _ The current temperature is 30 C Set temperature C 30 0 Ready status Ready 3 When the current temperature readback on the Oven page autosampler view on the Status page of the Information view reaches exactly 30 0 C see Figure 179 do the following a Type the reading from the 869C thermometer in the External Standard Temperature C box see Figure 180 For example if the thermometer reading is 29 8 C type 29 8 in the External Standard Temperature C box The range is 0 t
159. calibration and then repeat the alignment test with the second A microplate located at the front of the tray compartment 304 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Well Bottom Distance Calibration The autosampler supports custom vials and well plates in addition to the standard 1 8 mL vials 96 well plates and 384 well plates However to use custom vials or well plates you must first determine how far the autosampler needle must travel to reach the bottom of the vials or wells Use the Well Bottom Distance wizard to determine the distance that the needle must travel to reach the bottom of a vial or well The XYZ arm uses this value when you select one of the custom tray configurations IMPORTANT Because the autosampler stores only one value for the custom well bottom distance you must perform a well bottom distance calibration each time you select a new custom tray type configuration and each time you use a different type of custom vial or custom microwell plate To perform a well bottom distance calibration follow these procedures in order 1 Starting the Well Bottom Distance Wizard 2 Selecting the Calibration Method for the Well Bottom Distance 3 Depending on the selected calibration method follow one of these procedures e Manually Entering the Well Bottom Distance or e Using the Needle Sensor to Determine the Well
160. ce Template dialog box appears see Figure 113 Go to the next topic Creating the Sequence on page 203 Figure 113 New Sequence Template dialog box New Sequence Template General Base File Name Co Starting Number fi Path Co Browse Instrument Method FO O O Browse Processing Method Browse Calibration Fil Samples Number of Samples f Tray Type 1 8 ml Vial 5 trays 40 vials each v Injections per Sample f Initial Vial Position a V Re Use Vial Positions Base Sample ID Select Vials Cancel Selection m Bracket Type C None Open Non Overlapped Overlapped m Calibration Qc Add Standards M Add OCs Number of brackets fi After First Calibration Only After Every Calibration Injections per Level fi iar Sisy Colston iz Add Blanks je Add Blant V Fillin Sample ID for Standards IV Fillin Sample ID for OCs OK Cancel Save As Default Help Cancel SaveAsDefaut Heb 202 Surveyor Plus User Guide for LC Devices Thermo Scientific Creating the Sequence Thermo Scientific 7 Sequence Setup Creating a Single Sample Sequence To create anew sequence 1 If it is not already open open the New Sequence Template dialog box see Opening the Sequence Setup Window on page 201 2 In the General area make the following entries and selections a b In the Base File Name box type a name for the raw data file Browse to t
161. cell 3 Click a time point in the chromatogram cell The spectrum for the selected time point appears in the spectrum cell see Figure 157 Figure 157 Qual Browser window with a chromatogram of the PDA test mixture and a spectrum for the 7 42 minute time point C XcaliburidataiTest Mixture A01 0212 2003 06 03 30 PM FT 0 00 10 00 1 NL a 1 02E6 nm 238 5 233 5 PDA Test Mixture A01 3 28 4 13 4 65 3 03 3 45 5 Time min 239 351 356 362 300 320 wavelength nm Thermo Scientific Surveyor Plus User Guide for LC Devices 249 8 Qual Browser Viewing the Chromatogram for a Specific Wavelength Viewing the Chromatogram for a Specific Wavelength To view the scan chromatogram for a specific wavelength 1 Open a raw data file with PDA data and apply an appropriate layout file see Opening a Raw Data File in Qual Browser on page 219 2 Pin the chromatogram cell 3 Click a wavelength in the spectrum cell The scan chromatogram for the selected wavelength appears in the chromatogram cell as shown in Figure 158 Figure 158 Qual Browser window displaying a chromatogram cell and a spectrum cell 334 nm scan wavelength C Xcaliburdata PAHs_01 03 04 2003 05 50 29 PM RT 0 00 15 00 9 453 NL 6 44E5 nm 333 5 334 6 PDA PAHS 01 6 85 7 37 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Time min PAHs_01 274 RT 4 55 AV 1 NL 1 01E6 microAU a 239 0 351 0 362
162. cells are not highlighted with a gray border and the pin icon in their upper right corners is gray The cell in the lower portion of Figure 131 is inactive as indicated by the absence of a gray border Menu commands toolbar buttons and cursor actions do not affect inactive cells To zoom in on the contents of a cell or access its shortcut menu you must make the cell active 224 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Working with the Cell Grid Figure 131 Qual Browser window displaying an active chromatogram cell and an inactive PDA spectrum cell Gray border Test Mixture A01 RAW CAXcaliburidatatTest Mixture A01 02 12 2003 06 03 30 PM RT 0 00 10 00 l 107 View Ha J Active cell Plot Total Seon 300000 Peak Detection gt Miura ot 2 200000 Library 4 Export gt 1 i Unpinned 100000 AutoFilter 3 30 3 77 413 4 63 4 38 5 32 6 15 6 38 6 87 2 3 45 3 72 0 Ranges 0 0 05 1 0 15 2 0 as 3 0 35 4 0 45 5 0 55 6 0 65 7 0 Display Options Time min rs Test Mixture A01 447 RT 7 43 AV 1 NL 3 04E5 microAU 233 0 300000 1 Inactive cell Shortcut 200000 272 0 menu for 2 150000 chromatogram 100000 cell 351 0 356 0 362 0 220 230 240 250 260 270 280 230 300 310 320 330 340 350 360 370 380 330 400 wavelength nm Active but Unpinned Cells An active but unpinned cell is highlighted with a gray border and the pin icon in its upper right corn
163. ch device from the menu bar of the device view as follows Device Menu Reference Surveyor LC Pump Plus Choose gt Surveyor LC Pump gt Surveyor LC Pump Plus Direct Direct Control gt Operation Controls on page 185 Surveyor MS Pump Plus Choose Surveyor MS Pump gt Surveyor MS Pump Plus Direct Direct Control Controls on page 190 Surveyor PDA Plus Detector Choose Surveyor PDA Plus gt PDA Detector Direct Controls on Direct Control Then click the page 162 Configuration tab Surveyor UV Vis Plus Detector Choose Surveyor UV Vis gt UV Vis Detector Direct Controls on Direct Control page 183 Surveyor Autosampler Plus Choose Surveyor AS gt Direct Control Autosampler Direct Controls on page 192 Thermo Scientific Surveyor Plus User Guide for LC Devices 159 Direct Controls You can control some device features without downloading an instrument method For example you can turn the lamps on or off set the solvent conditions for the pump start and stop the solvent flow from the pump and control the autosampler s temperature zones and its XYZ arm by using the direct controls provided by the data system For information about accessing the direct controls for each device see Accessing the Direct Controls on page 158 Contents e PDA Detector Direct Controls e UV Vis Detector Direct Controls e Pump Direct Controls e Autosampler Direct Controls Note For instructions on loading samples into th
164. cientific Surveyor Plus User Guide for LC Devices 263 9 LC Pump Calibration and Record Keeping Calibrating the Surveyor LC Pump Plus Table 57 Measured flow rate and pressure pulsation versus compressibility setting erg feo sete ee rate Rel diff 0 45 GPa 0 2 3 01 0 3 1 25 GPa 0 4 3 05 1 8 3 0 GPa 1 3 18 5 9 Compressibility Ratios for Common Solvents Because most mobile phases are made up of a mixture of solvents you must determine the correct compressibility setting for a given mobile phase empirically Table 58 lists the compressibility ratios for a few common solvents Table 58 Measured flow rate and pressure pulsation versus compressibility setting Solvent Compressibility ratio GPa Water 0 45 Acetonitrile 1 20 Methanol 1 25 Hexane 1 60 Pressure Recorder Full Scale 264 The pressure recorder full scale calibration option sets the scaling factor for the pressure trace if you choose to monitor the pressure with a chart recorder The pressure recorder terminals are located on the back of the Surveyor LC Pump Plus see Figure 170 Integer values from 1 to 10 are within the allowable range Full scale Set value x 4 9 MPa 50 kgf cm2 full scale voltage 1 mV For example When the set value 1 the full scale is 4 9 MPa 50 kgf cm2 When the set value 10 the full scale is 49 0 MPa 500 kgf cm2 4 9 MPa 50 kgf cm2 49 bar 711 psi Note The value for the scaling factor i
165. cified injection volume V dead dead volume held by the transfer tubing injection port and rotor slot This equation is valid until the syringe reaches its maximum capacity when only the maximum capacity of the syringe is withdrawn The maximum capacity of the 250 pL concentric syringe is 265 pL 20 Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Detector Temperature Control The full featured Surveyor Autosampler Plus has two built in temperature control features e Tray Temperature Control e Column Oven Control Tray Temperature Control Column Oven Control Detector Thermo Scientific The tray temperature control feature provides temperature control of the samples in the range from 0 to 60 C A Peltier device maintains the tray temperature The built in column oven controls the temperature of the air surrounding the chromatographic column Isothermal temperature control is achieved using a Peltier device The Peltier device is a solid state heat transferring assembly used to heat or cool the column oven The range of temperature control is 5 to 95 C CAUTION The column oven can reach temperatures as high as 95 C 203 F To prevent personal injury before installing the LC column or connecting the pump to the autosampler make sure that the column oven compartment is at room temperature Between the analytical pump and the autosampler injection valve the m
166. cifying the Configuration Settings Table 7 Tray page parameters Sheet 2 of 2 Parameter A1 Well Position for the microplate trays Description Use the options in the Al Well Position area to select the orientation of the microplate when it is mounted in the autosampler plate holder You can mount the plate in the plate holder so that the Al well is located at the top left or located at the bottom right of the plate Top Specifies that the A1 well is located at the top left of the microplate Left QQOQQQOQQQO0O0O000000 QQOOQOOO000OO00000 QQQQ mronmnmmoouwp p QOOOOOOOOOOOO Jedd L OOOO QQQQQQQOQQOOOOQQOQQ000000O QQOQQQQOQOOOOOOOOQOO000000O QQQOOOOOOOOOQOOOOOOOO0OQ QIIE QQOQOQQQQ QQOQOQQQQQ Poono mmm E 1211109 8765 43 2 1 24 1 Well Ordering for the microplate trays Thermo Scientific Use the buttons in the Well Ordering area to select the sampling path that the autosampler follows during a sequence run The sampling path you select is independent of the A1 well position The path options are shown below Description The autosampler samples wells from bottom to top and then from left to right as you view the plate from the top The autosampler samples wells from left to right and then from bottom to top as you view the plate from the top The autosampler samples wells from top to bottom and then from left to right as
167. ck Upload Firmware Version The firmware version of the autosampler appears next to Current Version b Click OK to save the settings and close the dialog box If you have finished configuring all of your LC devices go to Closing the Foundation Application on page 66 60 Surveyor Plus User Guide for LC Devices Thermo Scientific 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Surveyor MS Pump Plus Configuration Settings During normal operation the Surveyor MS Pump Plus communicates with the data system computer through an RS 232 link Before you configure the pump device driver connect the pump to the data system computer If your LC system contains two pumps connect both pumps to the data system computer To specify the configuration settings for the Surveyor MS Pump Plus 1 Ensure that the pump is connected to the data system computer and powered on 2 For a dual pump system ensure that pump 2 is powered off 3 In the Configured Devices list double click the Surveyor MS Pump Plus icon The Surveyor MS Pump Plus dialog box appears see Figure 41 Figure 41 Surveyor MS Pump Plus dialog box Surveyor MS Pump Plus Pump Communication Pump 1 Pump 2 Serial number 14126 v Serial number Status Connected Status Connected Communication port COMZ Communication port COMS Stroke count 797166 Stroke count 1267375 Pump type Thermo Pump Pump type Thermo Pump Configurat
168. ctor that the mobile phase passes through Attached to the side leg of the T connector is a 2 mL loop of stainless steel tubing The loop terminates with a priming valve pulse dampener flush valve When the priming valve is open you can flush or fill the dampening loop with an appropriate solvent such as methanol or isopropanol When the priming valve is closed the loop is shut off from the flow path and absorbs pump pulsations Because the 2 mL loop is shut off from the flow path it adds no gradient delay volume to the LC system The priming solvent in the loop does not interfere with the purity of the mobile phase and its composition does not need to match the mobile phase The data system remotely controls the pump with an RS 232 communication link from the data system computer The only manual control is the power switch located on the front of the pump in the lower left corner below the door Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Analytical Pump Surveyor LC Pump Plus The Surveyor LC Pump Plus is a dual piston quaternary low pressure mixing pump with a built in vacuum degasser and pulse dampener The pumping system provides flow rates from 0 001 to 9 999 mL min which is the range needed to perform high performance liquid chromatography You can run precise gradients from 0 200 to 2 000 mL min The Surveyor LC Pump Plus is a bench top unit for inclusion in the Surve
169. current temperature readback on the Tray page reaches exactly 30 0 C see Figure 187 do the following a Inthe External Standard Temperature C box see Figure 187 on the External Set Target page type the reading from the thermometer Figure 187 Tray page status view and the Diagnostic External Standard page of the Vial Tray Metal Sensor Calibration wizard External Standard AS Status Oven Tray Error log Diagnostic Tray Control on Yes External standard temperature C 29 9 Current temperature C 30 0 ean Set temperature C 30 0 Ready status Ready lt Back Cincel Help _ cpe Heb Type the temperature reading For Hells press F1 Current temperature has from the test fixture that you reached the set temporarily installed in the temperature of 30 0 C tray compartment b On the Tray page verify that the Current Temperature readback still displays 30 0 C c On the Diagnostic External Standard page see Figure 187 click Adjust The data system downloads the calibration to the autosampler and the Finish button becomes available see Figure 188 Thermo Scientific Surveyor Plus User Guide for LC Devices 285 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 188 Diagnostic External Standard page of the Vial Tray Metal Sensor Calibration wizard with an available Finish button Diagnostic External Standard External standard temperature
170. d air being transported is less than or equal to the nominal syringe size Table 32 Tasks that can use either syringe plunger Task Draw from Reservoir Deposit Liquid in Sample Deposit Sample in Reservoir Transfer from Reservoir to Sample Transfer from Reservoir to Reservoir Table 33 lists the speed range for the sample preparation tasks that can use either plunger of the concentric syringe Note The ToolTips for the speed parameters list a range of allowable speeds The minimum speed listed is valid for only the inner plunger and the maximum speed listed is valid for only the outer plunger of the configured syringe If you enter a volume that triggers the use of the outer plunger and a speed that is valid for only the inner plunger an error message appears when you attempt to add the task to the sample preparation list Surveyor Plus User Guide for LC Devices 125 4 Sample Preparation Routines Syringe Speed Range for Sample Preparation Tasks Table 33 Syringe speed ranges for tasks that can use either syringe plunger Syringe size Volume Minimum speed Maximum speed Default speed uL liquid air pL s pL s pL s 100 lt 100 0 33 13 25 3 0 100 gt 100 1 65 661 38 250 250 lt 250 0 83 33 09 8 0 250 gt 250 1 65 661 38 250 500 lt 500 1 65 66 10 8 0 500 gt 500 1 65 661 38 250 2500 0 to 1500 0 83 331 25 0 standard Syringe Speed for Tasks that Use the Inner
171. d If the detector has not been calibrated the readback is Not Calibrated If the detector has been calibrated the date and time of the last calibration are displayed Reset Dark Reloads the default instrument dark current calibration values When you perform a dark Current Calibration To current calibration the Xcalibur data system compares the results to the last saved Default Values calibration file This can cause successive calibrations to deviate from the default Occasionally you must reset to the default calibration values before performing a new dark current calibration to get calibration values as close to the default as possible Wavelength Calibration Calibrate Starts the wavelength calibration Last Calibration Indicates whether the PDA detector is calibrated If the detector has not been calibrated Wavelength this readback displays Not Calibrated If the detector has been calibrated this readback displays the date and time of the last calibration Reset Wavelength Reloads the default instrument wavelength calibration values When you perform a Calibration To Default wavelength calibration the Xcalibur data system compares the results to the last saved Values calibration file This can cause successive calibrations to deviate from the default Occasionally you must reset to the default calibration values before performing a new wavelength calibration to get calibration values as close as possible to the default
172. d a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Software version Thermo Fisher Scientific provides the Surveyor device drivers on the LC Devices software CD This manual describes Surveyor devices available on the LC Devices 2 2 0 software CD or later These drivers are compatible with Xcalibur 2 0 or later and Thermo Foundation 1 0 x or later Firmware versions Installing the Surveyor device drivers also installs the Surveyor Firmware Upgrade Utility and the firmware files for the Surveyor devices For the Surveyor PDA Plus Detector ensure that the firmware version is 2 02 or later Revision history Revision A January 2009 Revision B April 2010 Revision C March 2011 For Research Use Only Not for use in diagnostic procedures Regulatory Compliance Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with applicable domestic and international regulations When the system is delivered to you it meets all pertinent electromagnetic compatibility EMC and safety standards as described in the next section or sections by product name Changes that you make to your system may void compliance with one or more of these EMC and safety standards Changes to your system include replacing a part or adding components options or peripherals no
173. d flow rate become effective The first time line remains set to 0 min A B C and D The solvent composition parameters A B C and D columns work interactively with each other and specify the mobile phase composition at the time point specified in the associated Min box The mobile phase composition changes linearly between two consecutive time points Default 100 A pL min The pL min box specifies the flow rate of the mobile phase at the time specified in the associated Time box Default 10 pL min P2 Dual pump system For a dual pump system the time line position of the ball in the P2 column specifies the time when Pump 1 triggers Pump 2 Graph view Type of View Thermo Scientific Select Solvent Gradient to view the solvent gradient profile created by the pump program Select Flow Gradient to view the flow rate changes created by the pump program The Gradient Profile area graphically displays the values entered in the pump program The y axis represents percent composition or flow rate and the x axis represents time in minutes Each solvent is color coded for better visualization of the programmed gradient Surveyor Plus User Guide for LC Devices 83 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings Programming the Pumps in a Dual Pump System To program the pumps in a dual pump system 1 On the Pump General page do the following a Follow the
174. d parameters Page or Parameter Description Page Injections Use this page to set the scheduled maintenance time for the number of user defined injections excluding any cancelled injections Valve Cycles Use this page to set the scheduled maintenance time for the number of user defined valve cycles for the injection valve from Fill to Inject Needle Cycles Use this page to set the scheduled maintenance time SMT for the number of user defined needle cycles when the needle is inserted into a septum injection port or wash station Syringe Cycles Use this page to set the scheduled maintenance time SMT for the number of user defined syringe cycles where the syringe is put in the Ready position Parameter Usage Limit Use this box to specify the new usage limit for the selected maintenance item Note When a counter exceeds the usage limit the autosampler cannot start a run until you reset the counter to zero change the usage limit or clear the Enable Maintenance Log check box on the Communication page of the Surveyor Autosampler Configuration dialog box see Communication Page on page 52 Set New Limit Downloads the new usage limit to the autosampler Current Counter and Zero Counter Displays the current count When the counter exceeds the usage limit scheduled maintenance time the autosampler cannot start a run until you perform the scheduled maintenance or clear the Enable Main
175. detector and a spectrum cell displaying the spectral data from the PDA detector for time 0 C Xcaliburidata PAHs_01 03 04 2003 05 50 29 PM RT 0 00 15 00 oe es 200000 6 85 11 42 Total Scan 150000 Ts U 765 828 905 10 33 12 55 13 52 0 1 2 3 4 5 6 7 8 9 10 11 12 143 w4 45 Time min PAHs_01 1 RT 0 00 AV 1 NL 0 microAU G 100 80 60 Spectrum for time 0 minutes 3 40 20 0 200 220 240 260 280 300 320 340 360 380 400 wavelength nm Thermo Scientific Surveyor Plus User Guide for LC Devices 223 8 Qual Browser Working with the Cell Grid Working with the Cell Grid Cell States Inactive Cells 9 To use the Qual Browser facility you must understand the concept of cell states and the effect of cursor actions in a cell This section contains the following topics e Cell States e Cursor Actions When you open a raw data file in the Qual Browser window the information within the data file is displayed as a grid of cells There are three hierarchal states for a cell within the grid e Inactive Cells e Active but Unpinned Cells e Active and Pinned Cells The grid always contains either one active but unpinned cell or one pinned cell If the grid contains more than one cell only one cell can be active and the rest of the cells are inactive An unpinned cell has a gray pin icon in its upper right corner A pinned cell has a green pin icon in its upper right corner Inactive
176. diluent to the current 1 vial location 5 Add a task that homes the position of the concentric syringe plungers as follows Note The syringe cannot switch between bores without first homing the position of the two syringe plungers The Transfer from Reservoir to Sample task that you added in step 4 uses the inner syringe bore The Mix at Sample task that you add in step 6 uses the outer syringe bore The Wash Needle task that you add in this step homes the position of the two syringe plungers a Inthe Prep Operations list select Wash Needle The task parameters appear below the Add To Task List button b Keep all the default parameter settings for the Wash Needle task see Figure 72 Figure 72 Default parameter settings for the Wash Needle task Prep Operations Deposit liquid in reservoir Draw from reservoir Draw from sample Flush to waste Mix at sample Mix at reservoir Transfer from reservoir to reservoir Transfer from reservoir to sample Transfer from sample to reservoir Transfer from sample to sample Wait time Add To Task List gt gt Volume ul 400 0 Reservoir battle Default settings c Click Add To Task List to add this task to the sample preparation routine 130 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 4 Sample Preparation Routines Sample Preparation Routine Example 6 Add a task that mixes the solution in the
177. diluted samples create a ten line sequence that lists all the vial locations A1 to A10 Ensure that you use the method that contains the sample preparation routine on the odd rows only Rows 1 3 5 7 and 9 132 Surveyor Plus User Guide for LC Devices Thermo Scientific ee Daily Operation During the initial installation of the Surveyor Plus LC system a Thermo Fisher Scientific field service engineer sets up the solvent lines primes the pulse dampener of the Surveyor MS Pump Plus and calibrates the PDA detector Note The pulse dampener of the Surveyor LC Pump Plus does not require priming To prepare the system for daily operation check the status of the devices warm up the detector s lamps and remove air from the solvent lines To maintain optimal performance of the system calibrate the PDA detector on a monthly basis or whenever you move the detector and check the light throughput to the diode array whenever you move the detector observe an increase in detector noise or replace the flowcell or lamps see Verifying the Performance of the PDA Detector on page 313 Prime the pulse dampener of the Surveyor MS Pump Plus on a monthly basis or when you notice an increase in pump pulsation Contents e Turning On the Power to Each LC Device e Initiating Communication with the Data System e Checking the Status of the LC Devices e Turning Devices On Off or into Standby from the Info View e Filling the Solv
178. ding Maintenance Information for the Surveyor LC Pump Plus To reset the solvent volumes or the pump operating time Perform the following tasks as specified e Every time you install a new piston seal click the appropriate Reset button Clicking Reset sets the readback for the volume of liquid pumped by the respective pump head assembly to zero e Ifyou install a new motor click the Reset button under Pump Operating Time Clicking Reset sets the recorded hours for the pump operating time to zero To set the pistons to the maintenance position before removing the pump heads Click Maintenance Position Maintenance Surveyor LC Pump Direct Control Parameters Table 59 describes the parameters in the Maintenance dialog box for the Surveyor LC Pump Plus Table 59 Maintenance dialog box for the Surveyor LC Pump Plus Parameter Left Seal Volume Description Reset Zeros the recorded volume of mobile phase pumped by the left pump head Every time you install a new piston seal in the left pump head click Reset in the Left Seal Volume area to set the recorded volume of liquid pumped by the left pump head assembly back to zero Right Seal Volume Reset Zeros the recorded volume of mobile phase pumped by the right pump head Every time you install a new piston seal in the right pump head click Reset in the Right Seal Volume area to set the recorded volume of liquid pumped by the right pump head assembly back to zer
179. dow layout to the Qual Browser view do the following a Choose File gt Layout gt Apply The Open Layout File dialog box appears see Figure 129 Thermo Scientific Surveyor Plus User Guide for LC Devices 221 8 Qual Browser Opening a Raw Data File in Qual Browser Figure 129 Open Layout File dialog box Open Layout File Look in methods ee templates File name PDA Ipt __ Caneel Files of type Layout Files lyt v Cancel Header Information Created Thursday August 31 2006 3 49 59 PM By alison cook Number of saves Not changed Comment Layout for Raw Data View in Qual Browser Application b Select a layout file from the list Layout files have the lyt file extension c Click Open to apply the layout to the raw data file Figure 130 shows a custom layout file applied to a raw data file containing both MS data and PDA data The custom layout replaces the MS TIC chromatogram with a Total Scan chromatogram for the PDA data It also replaces the mass range spectrum data from the MS detector with the spectral data from the PDA detector For instructions on how to create a Layout file for your PDA data see Creating a Layout for PDA Data on page 233 222 Surveyor Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Opening a Raw Data File in Qual Browser Figure 130 Qual Browser view with a chromatogram cell displaying a Total Scan from the PDA
180. e Plate A B or C Row A through H Column 1 through 12 Thermo Scientific Surveyor Plus User Guide for LC Devices 7 1 Introduction to the Surveyor Plus LC System Autosampler Figure 7 shows the notation for 96 well microplates when you select the top left orientation Figure 7 Notation for 96 well plates Top left orientation Plate C C A1 Plate B B A1 Plate A A A1 8 Surveyor Plus User Guide for LC Devices SOOOOOGOOSSS OOOOOOGOOsSS eS OOOOOOGOOSSs S OOOOOOGOOSSS OOOOOOGOOSS S OOOOOOGOODSS OSOOOooqgoosss OOOOGCoogoodsss SBOOOOOGOOSSS OOOOOOGOOSS S OOOOOOGOOSSS OOOOOOOOOSSS OO6060G00339 OOOOOOGO000SS OOOOooooodsss OOOOGCOGOOsss SOOOOOGOOSSS OOOOOOGOOsSSs S OOOOOOGOOSSS OOOOOOGOOSSS OO6060G00939 OOOO OO0G0033S OOOOooogoosss OOOOSOGOOss Thermo Scientific 1 Introduction to the Surveyor Plus LC System Autosampler ion for 96 well microplates when you select the bottom right Figure 8 shows the notat Figure 8 Notation for 96 well plates Bottom right orientation Plate C C A1 600000080 00000000 00000000 00000000 00000000 00000000 60606000 090000000 00000000 80000000 806000080 80000000 80000000 80000000 9 Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Autosampler 384 Well Microplate Notation The notation for the location of 384 well microplates is as follows Plate Row Column Where Plate
181. e 0 to 18 mm Air Bubble 0 to 10 pL Destination Vial Needle Height 120 Surveyor Plus User Guide for LC Devices Default 2 mm Range 0 to 18 mm Thermo Scientific 4 Sample Preparation Routines Building the Sample Preparation Routine Table 29 Sample Preparation page Sheet 5 of 5 Parameter Description Wait Time Pauses the sample preparation routine for a period of time for example for a reaction to occur Range 0 to 1000 minutes Wash Needle Washes the exterior of the needle with the solvent in a reservoir vial or the wash bottle Parameter Reference range or selections Volume Range 100 to 6000 pL Reservoir bottle RV1 RV2 RV3 or RV4 Button Add To Task List Use the Add To Task List button to add a task to the sample preparation routine Method Use the Method area to display the parameters of a task remove a task clear all tasks in the task list or import the sample preparation routine from a stored instrument method The Method area consists of the sample preparation task list the Remove Task button the Clear All Tasks button and the File Name read only box and Import method button File Name box Displays the name of the selected instrument method that contains the sample preparation routine that you want to import into the current instrument method Buttons Remove Task Use this button to remove a task from the task list in the Method area Clear All Tasks
182. e see Accessing the Calibration Options for the Surveyor LC Pump Plus on page 260 To fine tune the performance of the Surveyor LC Pump Plus follow these procedures Updating and Optimizing the Compressibility Setting Scaling the Output of the Pressure Recorder Terminals Updating the Flow Rate Adjustment Setting Updating the Pressure Sensor Adjustment Setting Zeroing the Pressure Transducer Updating and Optimizing the Compressibility Setting 266 If you have already determined the best compressibility setting for your application update the compressibility setting of the Surveyor LC Pump Plus For information on compressibility see Compressibility on page 262 To update the compressibility setting Open the Calibration page for the Surveyor LC Pump see Accessing the Calibration Options for the Surveyor LC Pump Plus on page 260 Type a new value into the Compressibility setting box Then click Set To optimize the compressibility setting for your application Set up your system a Set up a device to record the pressure output from the back panel pressure terminals See Pressure Recorder Full Scale on page 264 b Scale the output of the pressure terminals as described in Scaling the Output of the Pressure Recorder Terminals on page 268 Download the mobile phase parameters specified in your application a If it is not already on turn on the power to the Surveyor LC Pump Plus
183. e alignment can become offset if the detector is sharply jolted in shipping for example Such bumps and jars can slightly change the wavelength of light reaching the photodiode array The automated wavelength calibration procedure determines the detector s wavelength accuracy and adjusts the detector s wavelength algorithm to correct for any misalignment To perform a wavelength calibration 1 Pump HPLC grade methanol at 1 mL min through the flowcell 2 Turn on both lamps and wait one hour for the lamps to equilibrate as follows a From the PDA detector view choose Surveyor PDA Plus gt Direct Controls The Direct Control dialog box appears b Click the Configuration tab The Configuration page appears c Inthe Deuterium Lamp area click Lamp On to turn on the deuterium lamp d Inthe Tungsten Lamp area click Lamp On to turn on the tungsten lamp 3 Start the Wavelength Calibration wizard as follows a Click the Calibration tab The Calibration page appears see Figure 231 328 Surveyor Plus User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Figure 231 Calibration page for the PDA detector Display Configuration Information Calibration Dark Current Calibration Currently NOT Calibrated Last Calibration 12 31 1969 4 03 12 PM Reset Dark Current Calibration To Default Values Wavelength Calibration Calibrate Currently NOT Calibr
184. e autosampler see Loading the Autosampler on page 210 Thermo Scientific Surveyor Plus User Guide for LC Devices 161 6 Direct Controls PDA Detector Direct Controls PDA Detector Direct Controls The Direct Control dialog box for the PDA detector contains the following pages Display Configuration Information and Calibration To open the Direct Control dialog box for the PDA detector 1 Open the PDA detector view 2 From the menu bar choose Surveyor PDA Plus gt Direct Control see Figure 90 Figure 90 Surveyor PDA Plus menu 9 Untitled Thermo Xcalibur Instrument Setup File Emed TE Help Direct Control i D a Surveyor PDA Plus Method Surveyor PDA Plus Run Run Length min 110 00 Spectra The Surveyor PDA Plus Direct Control dialog box opens to the Display page see Figure 91 Figure 91 Surveyor PDA Plus Control dialog box tabs Surveyor PDA Plus Direct Control Display Configuration Information Calibration Control Current method Unknown Help Load Method Start Data Ea Spectrum ae 162 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls PDA Detector Direct Controls Table 46 lists the direct control procedures by the page where they are performed Table 46 Direct control procedures Page Procedure Display Page Checking the Chromatographic Baseline on page 168 Verifying the Performance of t
185. e column prior to the next run the solvent composition is held at the initial solvent composition for a period of 15 minutes Note When you are performing a sequence of gradient runs add an equilibration step at the end of the Gradient Program 72 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Surveyor LC Pump Plus Instrument Method Parameters Figure 48 Example of a gradient program for the Surveyor LC Pump Plus General Gradient Program Placeholder line Surveyor LC Pump Gradient Program Page Parameters Table 15 describes the parameters on the Gradient Program page Table 15 Gradient Program page parameters for the Surveyor LC Pump Plus Sheet 1 of 2 Parameter Description Graph Displays the percent composition of solvents A B C and D as a function of time Table Specifies the gradient steps The table can contain up to 80 rows The solvent composition boxes are interactive After you type a value in column A and press ENTER or click another box the value in column B changes to maintain a total of 100 and so on The solvent composition changes linearly between time points Time min Specifies the time duration for each gradient step The initial time is always 0 minutes Range 0 to 655 35 minutes Thermo Scientific Surveyor Plus User Guide for LC Devices 73 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings Table 15 Gradi
186. e energy Make a plan active by Choose what the power button selecting it or choose a plan and customize it by changing does its power settings Tell me more about power plans Create a power plan 2 Choose when to turn off the display Balanced Change plan settings recommended Automatically balances performance with energy consumption on capable hardware Preferred plans Change when the computer sleeps Power saver Change plan settings Saves energy by reducing your computer s See also performance where possible Personalization User Accounts Show additional plans v b Select the Balanced option c Click Change Plan Settings for the Balanced option The Edit Plan Settings dialog box appears see Figure 26 Figure 26 Edit Plan Settings dialog box gt lt D E Power Options Edit Plan Settings v 4 Search Control Panel P Change settings for the plan Balanced Choose the sleep and display settings that you want your computer to use 2 Turn off the display 10 minutes Change advanced power settings Restore default settings for this plan Save changes Cancel 30 Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Turning Off the Computer s Energy Saving Features d Click Change Advanced Power Settings The Advanced Settings page of the Power Options dialog box appears see Figure 27 Figure 27 Advanced Settings page of t
187. e extension 5 To collect a wavelength scan select the Collect Spectra Data check box and then make the following entries and selections a In the Start Wavelength nm box type a starting wavelength from 190 to 799 nm b In the End Wavelength nm box type an ending wavelength from 191 to 800 nm The ending wavelength must be greater than the starting wavelength 96 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 3 Instrument Method Setup PDA Detector Instrument Method Parameters In the Wavelength Step nm box type a value for the wavelength interval The default value is 1 nm The maximum step size depends on the wavelength range defined by the starting and ending wavelengths The range is 1 to 610 nm for a scan from 190 to 800 nm If you are collecting spectral data for a spectral library use a wavelength step of 1 nm In the Sample Rate Hz list select a sample rate For optimal integration of the chromatographic peaks select a sample rate that acquires a minimum of 20 points across the baseline width of the narrowest peak of interest For example if the baseline width of the narrowest peak is 20 seconds select a sample rate of 1 Hz or higher Increasing the sampling rate increases the data file size In the Filter Bandwidth nm box type a bandwidth Depending on the wavelength range defined by the starting and ending wavelengths the range is the subset of odd integers from 1 t
188. e for LC Devices 23 1 Introduction to the Surveyor Plus LC System Communication with the Data System Computer Communication with the Data System Computer The Surveyor Autosampler Plus Surveyor LC Pump Plus Surveyor PDA Plus Detector and the Surveyor UV Vis Plus Detector use an Ethernet link to communicate with the data system computer To establish communication with these devices you connect one end of an Ethernet cable to the Ethernet port on the back panel of the device and the other end of the cable to an Ethernet switch You use a second Ethernet cable to connect the Ethernet switch to the computer that has the data system installed The accessory kits include a shielded Category 5 RJ 45 7 ft length Ethernet cable with ferrite The Surveyor MS Pump Plus uses an RS 232 serial link to communicate with the data system computer The accessory kit for the Surveyor MS Pump Plus includes a USB cable In addition to connecting the communication cables you must enter the appropriate stack addresses for the Surveyor Autosampler Plus Surveyor PDA Plus Detector Surveyor UV Vis Plus Detector and Surveyor LC Pump Plus when you configure the device drivers The stack address or stack number that you enter when you add one of these devices to the configuration for your instrument must match the unit ID setting on the back panel of the device For more information about configuring the Surveyor Plus device drivers see Chapter 2 Thermo Foundati
189. e for each time point of all the wavelengths in your scan range e Select Spectrum Maximum to display a plot of the maximum absorbance values in your scan range for each time point d Select a wavelength range if you selected the Total Scan plot type this box is unavailable e To display the chromatogram for a specific scan wavelength type the wavelength number in the Range s box e To display a plot of the average absorbance values for a range of wavelengths type the beginning wavelength number and the ending wavelength number separated by a dash in the Range s box For example type 200 300 to display a plot of the average absorbance values for the scanned wavelengths from 200 to 300 nm Figure 142 Plot Properties area of the Chromatogram Ranges dialog box Plot properties Raw file c xcalibur data pahs_01 raw E Detector PDA Scan filter Peak algorithm Avalon Plot type Total Scan Delay min 0 00 7 Click OK to close the dialog box and view your scan chromatogram Figure 143 shows a chromatogram for a wavelength in the PDA scan To modify the layout for the spectrum cell go to Specifying the Spectrum Range on page 238 Thermo Scientific Surveyor Plus User Guide for LC Devices 235 8 Qual Browser Creating a Layout for PDA Data Figure 143 Chromatogram view with a chromatogram for a PDA scan wavelength 220 nm scan wavelength C XcaliburidatalPAHs_01 03 04 2003 05
190. e last task in the list click Remove Task e To remove a specific task select the task and then click Remove Task e To clear the entire task list click Clear All Tasks Tip To save an instrument method the sample preparation routine must conform to the rules described in Sample Preparation Rules on page 115 Sample Preparation Parameters Table 29 Sample Preparation page Sheet 1 of 5 Parameter Description Prep Operations Use this area to select and add tasks to the task list in the Method area You can add up to 512 tasks to a sample preparation routine however the arrangement of the tasks in the task list must follow a logical order or you will not be able to save the instrument method For example a draw task must precede a deposit task In addition if you are using the 250 pL concentric syringe that comes with the autosampler you must follow an additional set of rules that allow for the proper positioning of the inner and outer plungers of the syringe See Sample Preparation Rules on page 115 If you are using the 2500 pL single plunger syringe to transfer volumes larger than 500 pL add an optional tubing extension assembly to the needle tubing Task List Description Deposit Liquid in Deposits liquid in a sample vial or well Sample Parameter Reference range or selections Sample Location Sample Locations for the Sample Preparation Tasks on page 122 Volume Draw Eject and
191. e positive pin on the external device input and connect one of the PDA GND terminals either of pins 1 or 7 to the external device negative pin If the external device is triggered using a TTL signal connect the PDA 5V output pin 2 to the positive Input terminal of the external device and connect the PDA EVENT output pin 8 to the negative Input terminal of the external device Turn On and Turn Off Indicates whether the Event output state is On or Off If the Event output state is On the buttons Turn Off button is available If the Event output state is Off the Turn On button is available Event Output readback Indicates whether the Event output polarity is Active High or Active Low If the Event output polarity is Active Low the Set Active High button is available If the Event output polarity is Active High the Set Active Low button is available Set Active Low or Set Set the polarity of the Event Output signal Active High buttons Note The output polarity must match the polarity either Active High or Active Low of the instrument connected to the Event output connection on the back panel of the PDA detector The signal terminal is the high connection and the GND Terminal is the low connection Short DACs Output Zero DACs button To calibrate external instruments such as an SS420X analog to digital converter use the controls in this area to short the DACs outputs to zero for about 20 seconds Thermo Scienti
192. e stepper motor for the outer plunger Parameter Setting Autosampler action Source reservoir RV1 Draws solvent from reservoir vial 1 Destination Sample Location Relative Location Deposits solvent in the current 1 vial location listed in Location Current 1 the sequence table Volume 225 Transfers 225 uL of solvent Figure 71 Settings for the Transfer from Reservoir to Sample task Prep Operations Deposit liquid in reservoir Draw from reservoir Draw from sample Flush to waste Mix at sample Mix at reservoir Transfer from reservoir to reservoir Transfer from reservoir to sample Transfer from sample to reservoir Transfer from sample to sample Wait time Wash needle Add To Task List gt gt m Sample Location Absolute location Relative location fas Curent 1 Volume ful 225 0 Syringe speed uls 8 00 Needle height mm 2 9 Source reservoir Evi Default settings leat Surveyor Plus User Guide for LC Devices 129 4 Sample Preparation Routines Sample Preparation Routine Example c To add this task to the sample preparation routine twice click Add To Task List twice When the autosampler performs this task it uses the inner syringe plunger to withdraw 225 uL of diluent from the reservoir vial 1 and deposit the diluent in the current 1 vial location Performing this task twice transfers a total of 450 pL of
193. e that tells you the wavelength file is being downloaded see Figure 234 Figure 234 Download status for the selected peak list page Instruction to click Next Wavelength Calibration Click the Next button to proceed with calibration Checking lamp states Checking Filter wheel position Retrieving current method Retrieving current calibration Downloading calibration method Click the Next button to proceed with calibration Cancel Help b After you see the message Click the Next button to proceed with the wavelength calibration click Next The next page of the Wavelength Calibration wizard appears see Figure 235 This page instructs you to place the filter wheel in position 2 Figure 235 Request to rotate the filter wheel to position 2 page Wavelength Calibration Please turn the filter wheel to the HOLMIUM OXIDE position position 2 6 Rotate the Holmium Oxide filter wheel to position 2 as directed After you turn the wheel the Next button becomes available see Figure 236 332 Surveyor Plus User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Figure 236 Available Next button Wavelength Calibration Click the Next button to proceed with calibration 7 Click Next The calibration status page of the wizard appears see Figure 237 Figure 237 Calibration status page Wavelength Calibration Click the Next button
194. e volume of liquid that the autosampler flushes through the inside of the needle the injection port and the transfer tube During a flush cycle the injection valve is in the inject position to prevent the flush solvent from entering the sample loop To reduce carryover increase the flush volume When the specified flush volume exceeds the syringe capacity the autosampler takes multiple draws from the reservoir or bottle Range 0 0 to 6000 0 pL Default 400 pL Specifies the flush wash source Selections bottle RV1 RV2 RV3 or RV4 Default bottle wash bottle Wash Volume pL Specifies the volume of liquid used to wash the internal and external surfaces of the needle During a wash cycle the autosampler lowers the needle into the wash port When the specified wash volume exceeds the syringe capacity the autosampler takes multiple draws from the reservoir vial or wash bottle Range 0 0 to 6000 0 pL Default 0 pL 88 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Autosampler Instrument Method Parameters Table 19 Autosampler Method page parameters Sheet 2 of 3 Parameter Flush Speed L s Description Specifies the rate at which the syringe draws flush solvent into its chamber and expels flush solvent through the needle during a flush cycle Syringe type Default Range Concentric dual plunger 1 65 to 661 38 pL s 100 0 pL s Standard single plunger 8 27 to 330 85 pL
195. eating a Layout for PDA Data Figure 152 Qual Browser window with three cells Test Mixture 401 RAW C Xcaliburidata Test Mixture 4 01 02 2 2003 06 03 30 PM 1 07 NL Chromatogram cell Bes a FDA Ter 7 43 3 30 3 77 413 4 63 4 38 5 32 6 15 6 38 8 23 8 58 6 72 3 45 3 72 0 0 Os 1 0 15 2 0 25 3 0 3 5 4 0 45 5 0 5 5 6 0 65 7 0 5 6 0 65 3 0 3 5 10 0 Time min 6 87 233 0 Spectrum cell 334 0 351 0 357 0 362 0 220 230 240 250 260 270 280 230 300 310 320 330 340 350 360 370 380 330 400 wavelength nm 233 0 Spectrum cell 2 334 0 351 0 357 0 362 0 220 230 240 250 260 270 280 230 300 310 320 330 340 350 360 370 380 330 400 wavelength nm 3 Change the lower cell so that it displays the Map view see Figure 153 as follows a Pin the cell by clicking its pin button b Click the View Map button in the toolbar Thermo Scientific Surveyor Plus User Guide for LC Devices 245 8 Qual Browser Creating a Layout for PDA Data Figure 153 Qual Browser window with a chromatogram cell spectrum cell and map cell Test Mixture A01 RAW l apixi C XcaliburidatalTest Mixture A01 02 1 2 2003 06 03 30 PM tor ML 3 93E5 a Tatal Scan PDA Tort Mixture A01 7 43 3 30 3 77 413 4 63 4 38 6 87 5 92 6 15 6 38 0 0 Os 1 0 15 2 0 25 3 0 3 5 4 0 45 5 0 5 5 6 0 65 7 0 7 5 6 0 65 3 0 3 5 10 0 Time min 233 0 4a 23 658 6 72 3 45 3 72 351 0 357 0 362 0 220
196. ecific Wavelength 250 Determining Peak Areas coa 5 Ble Satin lus to seh eee 251 Calculating the Purity of the Chromatographic Peaks 0 254 LC Pump Calibration and Record Keeping 0 0 eeeeeeeeeee 259 Calibrating the Surveyor LC Pump Plus s a cs accsa sg teeace ye ee ak 260 Accessing the Calibration Options for the Surveyor LC Pump Plus 260 Calibration Options for the Surveyor LC Pump Plus 262 Calibration Procedures for the Surveyor LC Pump Plus 266 Recording Maintenance Information for the Surveyor LC Pump Plus 270 Firmware Version Information for the Surveyor LC Pump Plus 272 Autosampler Calibration and Record Keeping 0 2eeeeeee 273 Calibrating the Aumtosamiplet sit iven ieee acti Sale Gal ee ae ei lls 274 Column Oven Air Sensor Calibrations 2i00ciSesavie ohne Ake 275 Vial Tray Metal Sensor Calibration 4 54 ant dyotpheyeanttye gi aant eq canee Aen 281 Arm Calibrations seee stan E ate G aoe a eines ee 287 Well Bottom Distance Calibration 0 0 eee eee eee 305 Autosampler Maintenance Information 0454004 5 vba e pause cepa 309 Autosampler Validation Information es c a csie cea eee eae eo eas eee 311 PDA Detector Performance Check and Calibration 05 313 Verifying the Performance of the PDA Detector 00002004 313 Creating a Display Method sss bee beeches bet Gis hh
197. ecting data in the spectral range of the deuterium lamp Thermo Scientific Surveyor Plus User Guide for LC Devices 163 6 Direct Controls PDA Detector Direct Controls Resetting the Lamp Usage Hours Use the Configuration page of the Surveyor PDA Direct Control dialog box to reset the lamp usage hours To reset the lamp usage hours lifetime hours elapsed 1 Open the Configuration page of the Surveyor PDA Direct Control dialog box see Configuration Page on page 171 2 Click Reset Lifetime for the associated lamp The stored total run time for the associated lamp resets to zero and the Last Lifetime Reset readback is updated to the current date and time Tip Avoid indiscriminately clicking the Reset buttons Click Reset only after you replace the associated lamp with a new one Changing the Polarity of the Analog Outputs Use the Configuration page of the Surveyor PDA Direct Control dialog box to change the polarity of the analog outputs There are two output signal terminals on the back panel of the PDA detector Event and Ready see Figure 92 Figure 92 Event and Ready terminals on the back panel of the PDA detector Ready terminal Event terminal UNIT ID ENET To change the polarity of the analog outputs 1 Open the Configuration page of the Surveyor PDA Direct Control dialog box see Configuration Page on page 171 If the output polarity is Active Low the Set Active High button is
198. ector see Figure 64 Figure 64 Instrument Setup view for the UV Vis detector Method Ae Program type Rise time sec 11 0 Z C Single wavelength UY Zis 190 800 nm Datarate Hz J10 Fl Dual wavelength UY 190 450 nm V Enable autozero Dual wavelenath Vis 366 700 nm Autozero time min 10 00 V Zero on wavelength change Time min Wavelength 1 nm Wavelength 2 nm 254 280 254 280 254 280 To open the UV Vis Detector view Click the Surveyor UV Vis icon on the view bar To set up the instrument method parameters for the UV Vis detector 1 In the Rise Time sec list select a rise time from 0 to 10 0 seconds Rise time is the response time of the detector in seconds to the signal Increasing the rise time decreases the baseline noise however setting the rise time to a value greater than one tenth the width of the chromatographic peak at half height results in peak broadening The one second default value is appropriate for most LC applications Figure 65 shows the effect of rise time on peak tailing 106 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup UV Vis Detector Instrument Method Parameters Figure 65 Effect of rise time on band broadening 0 1 s rise time 2 0 s rise time 5 0 s rise time mAU 2 0 24 22 23 24 25 26 27 Minutes 2 In the Data Rate Hz list select a data rate from 4 to 20 points per second The optimal data rate depends on the
199. ed average from 190 to 210 nm A value greater than 21 nm would be outside the lower range limit of the detector which is 190 nm For information about the Method page parameters see these topics e PDA Detector Instrument Method Parameters e Display Method Parameters e Timed Events Table for the PDA Detector For information about adding timed events to trigger external devices see Triggering an External Device with the PDA Detector on page 104 PDA Detector Instrument Method Parameters Table 24 describes the parameters for an instrument method These parameters are available when you select the Wavelength Absorbance option in the Units area Table 24 PDA detector Method page parameters for an instrument method Sheet 1 of 3 Parameter Description Run Run Length Specifies the time in minutes that the PDA detector acquires data Default 10 00 minutes Range 0 00 to 600 00 minutes At the end of the run time the PDA detector goes to the Ready for Download state Filter Rise Time Specifies the detector s response time to the signal in seconds The selections are 0 00 0 10 0 20 0 50 1 00 2 00 5 00 and 10 00 seconds 98 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup PDA Detector Instrument Method Parameters Table 24 PDA detector Method page parameters for an instrument method Sheet 2 of 3 Parameter Description Units Wavelength Displays absorbance spectra
200. ed for Tasks that Can Use Either Plunger on page 125 Needle Height Default 2 mm Range 0 to 18 mm Air Bubble Range 0 to 10 pL Flushes the needle tubing and homes the syringe When the concentric syringe plungers are in the home position and the needle tubing is flushed the autosampler can next perform any of the sample preparation tasks with the exception of the deposit tasks Parameter Reference range or selections Volume Range 100 to 6000 pL Reservoir bottle RV1 RV2 RV3 or RV4 Syringe Speed 1 65 to 661 38 pL s for the concentric syringes 0 83 to 330 85 pL s for the 2500 pL standard syringe 118 Surveyor Plus User Guide for LC Devices Thermo Scientific 4 Sample Preparation Routines Building the Sample Preparation Routine Table 29 Sample Preparation page Sheet 3 of 5 Parameter Mix at Sample Description Mixes the contents of a vial or well To mix a sample the autosampler draws a specified volume of the sample into the needle tubing at a specified speed and then ejects the sample back into the same location at a specified speed Parameter Reference range or selections Sample Location Sample Locations for the Sample Preparation Tasks on page 122 Volume The maximum volume is 490 pL for the concentric syringes and 1490 uL for the standard 2500 uL syringe Draw Speed The draw or delivery speed range is from 1 65 to 661 38 pL s for the Daves Speed concentric syringe
201. ength is displayed Ad 2 62 318 355 413 4 63 i i 7 43 8 18 8 60 8 92 3 45 Time min Test Mixture A018319 RT 5 30 AY 1 NL 8 50E5 microAU 250 0 In the spectrum cell the pointer is set to 251 nm 310 0 324 0 340 0 357 0 300 320 wavelength nm Clicking Full Size in the toolbar sizes the active or pinned cell to the full width and height of the window as shown in Figure 135 228 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 8 Qual Browser Working with the Cell Grid Figure 135 Spectrum cell sized to full size of window C XcaliburidataiTest Mixture A01 02 12 2003 06 03 30 PM Test Mixture A01 319 RT 5 30 AV 1 NL 8 90E5 microAU ie 250 0 waveleng h nm Dragging across a region in the active or pinned cell zooms in on that region as shown in Figure 136 Figure 136 Full size view of the spectrum cell zoomed in on the 320 to 380 nm region C iXcaliburidatalTest Mixture A01 02 12 2003 06 03 30 PM Test Mixture A01 319 RT 5 30 AV 1 NL 4 33E4 microAU 340 350 360 wavelength nm Surveyor Plus User Guide for LC Devices 229 8 Qual Browser Changing the Font Size of the Display Changing the Font Size of the Display Occasionally you might want to change the font size of the data displayed in the Xcalibur ata system For example you might want to increase the font size for screen captures that you data system F ple y ght want t the font s
202. ent Program page parameters for the Surveyor LC Pump Plus Sheet 2 of 2 Parameter Description Flow mL min Specifies the flow rate Range 0 000 to 9 999 mL min A Specifies the percent composition of solvent A for each time point B Specifies the percent composition of solvent B for each time point C Specifies the percent composition of solvent C for each time point D Specifies the percent composition of solvent D for each time point Surveyor MS Pump Plus Instrument Method Settings Use the Surveyor MS Pump Plus view in the Instrument Setup window to specify the chromatographic conditions for your instrument method To open the Surveyor MS Pump Plus view click the Surveyor MS Pump Plus icon in the view bar of the Instrument Setup window To set up the chromatographic conditions see these topics e Specifying the Chromatographic Conditions for a Single Pump System e Programming the Pumps in a Dual Pump System Specifying the Chromatographic Conditions for a Single Pump System To specify the chromatographic conditions for a single pump system follow these procedures in order 1 Setting Up the Pump General Parameters 2 Setting Up the Gradient Program Tip After you specify the solvents that make up the mobile phase you can switch back and forth between the Pump General and Gradient Program pages Setting Up the Pump General Parameters Use the Pump General page to specify the solvents that the pump
203. ent Reservoir Lines with Fresh Solvent e Priming the Pulse Dampener of the Surveyor MS Pump Plus e Accessing the Direct Controls Thermo Scientific Surveyor Plus User Guide for LC Devices 133 5 Daily Operation Turning On the Power to Each LC Device Turning On the Power to Each LC Device To turn on the power to the LC devices 1 Depress the power switch on each device 2 Observe the status LEDs for each device Shortly after you turn on the power all the LEDs except the Comm LEDs turn green In addition the autosampler syringe goes through its initialization process 3 Verify that the Power LEDs the Lamp LED and the Degas LED turn green e Ifany of the Power LEDs remain amber make sure that the power line to the affected device or devices is connected Ifthe Degas LED on the pump is flashing amber the degas unit has failed to produce a vacuum Call your local Thermo Fisher Scientific representative for repairs e Ifthe Lamp LED remains amber both of the lamps are turned off If the lamps are off turn them on when you check the detector s status from the data system 134 Surveyor Plus User Guide for LC Devices Thermo Scientific 5 Daily Operation Initiating Communication with the Data System Initiating Communication with the Data System You control the LC devices from your Thermo Scientific mass spectrometry application The only manual control for the autosampler and UV Vis detector are their ON OFF power
204. entric syringe uses the small bore If this volume is greater than the nominal syringe size the syringe uses the outer bore e For tasks performed with the outer bore of the dual plunger concentric syringe the maximum volume sample air bubble that you can draw deposit or transfer is limited to 500 pL except for the Wash Needle and Flush to Waste tasks e Crossover between bores is not allowed This means that you cannot add a task that uses the outer syringe bore immediately following a task that uses the inner syringe bore To switch from the inner bore to the outer bore of the syringe you must insert a Flush to Waste step or a Wash Needle step These tasks home the position of the syringe plungers Surveyor Plus User Guide for LC Devices 115 4 Sample Preparation Routines Building the Sample Preparation Routine Building the Sample Preparation Routine Sample preparation routines are part of the instrument method see Autosampler Instrument Method Parameters on page 85 A sample preparation routine consists of a list of tasks performed in order by the autosampler before it makes an injection To build a sample preparation routine Do one of the following e To modify an existing sample preparation routine go to step 2 e To create a new sample preparation routine go to step 3 Import the sample preparation routine from a stored instrument method as follows a Click Import The Open files dialog box appear
205. ents liquid air bubble of the needle tubing Transfer from Sample Nominal size of the concentric syringe minus the current N A to Reservoir contents liquid air bubble of the needle tubing Mix at Sample N A 490 Mix at Reservoir N A 490 Tip If the ToolTip specifies a range of 0 0 to 0 0 the contents of the needle tubing already equals 500 pL or the previous task used the inner plunger of the syringe If the previous task used the inner plunger insert a Flush to Waste or a Needle Wash task to home the syringe Thermo Scientific Surveyor Plus User Guide for LC Devices 123 4 Sample Preparation Routines Syringe Speed Range for Sample Preparation Tasks Table 31 Draw eject and transfer volumes for sample preparation tasks Sheet 2 of 2 Task Maximum volume pL Maximum volume pL with the inner plunger with the outer plunger Wash Needle N A 6000 Flush to Waste N A 6000 Draw from Reservoir Nominal size of the concentric syringe minus the current 500 uL minus the current contents liquid air bubble of the needle tubing contents of the needle tubing Deposit Liquid in Total contents liquid air bubble of the needle tubing Total contents Sample from previous steps liquid air bubble of the needle tubing from previous steps Deposit Sample in Total contents liquid air bubble of the needle tubing Total contents Reservoir from previous steps liquid air bubble of the needle tubing from previous steps Transfer fro
206. er Peak List 1 Cancel Help Type a name for the list in the box and then click OK to add the name to the Choose Calibration Peak List and close the dialog box The name of the custom list appears in the Choose Calibration Peak List box In the Choose Calibration Peak List box click the custom list name The wavelength list becomes available In the wavelength list click a wavelength that you want to edit The Edit Peak List area appears to the right of the wavelength list To create a custom wavelength calibration list Start the Wavelength Calibration wizard see Performing a Wavelength Calibration on page 328 Click Save As Custom List The Custom List Name dialog box appears In the box type a name Click OK The name of the new wavelength calibration list appears in the Choose Calibration Peak List box To edit the wavelength calibration list Click the Crest Window pane The Edit Peak List area appears To add a wavelength type a wavelength in the Peak Crest box and a window in the Peak Window box and then click Add To delete a wavelength select the wavelength and then click Delete 338 Surveyor Plus User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector 4 Click Save As Custom List to save the edited list The Custom List Name dialog box appears 5 Type the name of the custom list in
207. er is gray The cell in the upper portion of Figure 131 is active but unpinned Menu commands toolbar buttons and cursor actions affect the active cell If the grid does not contain a pinned cell clicking an inactive cell in the grid makes it the active cell Active and Pinned Cells Clicking the pin in the upper right corner of a cell makes it the pinned cell within the grid A pinned cell is an active cell that cannot be made inactive by clicking in another cell Instead actions performed in the inactive cells affect the pinned cell as described in the next topic Cursor Actions on page 226 The lower cell in Figure 132 is a pinned cell To automatically change the range of a cell by clicking in the grid you must pin the cell For example to display the spectrum for the 1 minute time point without opening the Spectrum Ranges dialog box pin the spectrum cell and then click the 1 minute time point in the inactive chromatogram cell Thermo Scientific Surveyor Plus User Guide for LC Devices 225 8 Qual Browser Working with the Cell Grid Figure 132 Qual Browser window displaying an inactive cell and a pinned cell C Xcaliburidata Test Mixture A01 02 12 2003 06 03 30 PM RT 0 00 10 00 1 07 NL Inactive cell 3 93E5 Total Scan PDA Test 300000 Mixture A01 2 200000 180 2 23 100000 5 30 2 62 3 30 3 77 4 13 463 6 15 643 8 23 858 945 0 1 2 3 4 5 6 7 8 9 10 Time min Test Mixture A01 61 RT 1 00 AV
208. error is posted to the pump s event log e Ifyou are controlling the pump from the Sequence Setup window the Acquisition Server dialog box appears Run Time Displays the elapsed time since the last instrument method downloaded you turned the device on from the Status page of the Information view or you started the pump from the Direct Control dialog box Flow Rate Displays the user specified flow rate For an instrument method the flow rate changes linearly between time lines Pressure Displays the pressure monitored by the pump Pressure SD Displays the standard deviation of the pressure monitored by the pump Start Gradient A check appears in this box when the pump receives the Start gradient signal from the autosampler Pump Ready A check appears in this box when the pressure monitored by the pump reaches the stability level specified in the instrument method 146 Surveyor Plus User Guide for LC Devices Thermo Scientific 5 Daily Operation Checking the Status of the LC Devices Table 40 General page of the pump status view Sheet 2 of 2 Readback Release Injection Description A check appears in this box when the pump sends the Release Injection signal to the autosampler Start 2nd Pump A check appears in this box when Pump 1 triggers Pump 2 to start its pump program Extended Page of the Pump Status View Figure 82 shows the Extended page of the pump status view Figure 82 Extended page
209. esponds to wavelength 190 nm and diode 511 corresponds to 800 nm This gives a spacing of 611 nm 510 diodes 1 2 nm diode The PDA detector interpolates the data to give integer values Spectra with Diode Intensity option Collect Spectral Data Select this check box to scan a range of diodes Start Diode diode num Specifies the first diode in the scan range Default 2 Range 2 to 510 in increments of 1 Diode 2 corresponds to 190 nm End Diode diode num Specifies the last diode in the scan range Default 511 Range 3 to 511 in increments of 1 Diode 511 corresponds to 800 nm Diode Step Specifies the interval between data points across the range of diode numbers The selections are 1 2 4 5 or 10 diodes Sample Rate Not applicable Thermo Scientific Surveyor Plus User Guide for LC Devices 101 3 Instrument Method Setup PDA Detector Instrument Method Parameters Table 25 PDA Method page parameters for a display method Sheet 2 of 2 Parameter Description Channels with Intensity Units No Channels Specifies that no discrete channel measurements are to be acquired When you select this option the parameters in the Channels area are unavailable One Channel Specifies the acquisition of one discrete channel The data for Channel A is displayed in the bottom view of the Display page in black Two Channels Specifies the acquisition of two discrete channels The data
210. et up the instrument method parameters for the Surveyor LC Pump Plus see these topics e Surveyor LC Pump Plus General Page e Surveyor LC Pump Plus Gradient Program Page Surveyor LC Pump Plus General Page Use the General page for the Surveyor LC Pump Plus to identify the mobile phase solvents the LC column and the operation pressure limits for the pump see Figure 46 Figure 46 General page for the Surveyor LC Pump Plus General Gradient Program m Solvents Pressure Limits Solvent name iti wt B Solvent name Po Min pressure poo MPa C Solvent name OoOO Max pressure Booo MPa D Solvent name Po Column Description Help To specify the instrument method settings on the General page 1 In the Solvent Name boxes in the Solvents area type the solvent names 2 In the Description box in the Column area type a description of the LC column 3 In the Pressure Limits area do the following a Inthe Min Pressure box type the minimum operating pressure Note Pressure drops can indicate the following problems e Mobile phase in the solvent reservoir bottles has run out e A leak has occurred in the flow line or lines e An excessive amount of air has entered the pump head assemblies Thermo Scientific Surveyor Plus User Guide for LC Devices 69 3 Instrument Method Setup Surveyor LC Pump Plus Instrument Method Parameters 70 b In the Max Pressure box type the max
211. eter Description Purge Draws the specified solvent at a speed of approximately 10 mL min through the pump for the specified purge time CAUTION Before you click the Purge button open the drain valve by turning the drain valve knob 180 counterclockwise Stop Purge Stops the solvent flow from the pump Tip After you finish purging the pump close the drain valve by gently turning the drain valve knob clockwise until you feel resistance Removing Air from the Solvent Lines Connected to the Surveyor LC Pump Plus Thermo Scientific Use the purge feature to remove air bubbles from the solvent lines or the pump heads If the solvent line connecting the solvent reservoir bottle to the degassing assembly is completely dry attach a syringe to the drain line and open the drain valve Make sure that the pump power is on and then draw the syringe barrel back pulling solvent into the line Tip Cyclical baseline noise can be an indication of air in the pump heads To remove air from the solvent lines or the pump head assemblies 1 Open the drain valve by turning it counterclockwise 180 to the purge position Look for the word DRAIN to appear upside down on the knob see Figure 104 Figure 104 Drain valve knob in the closed and open positions Closed position Open position 2 Open the view for the Surveyor LC Pump Plus 3 From the menu bar choose Surveyor LC Pump gt Direct Control gt Operation The Operation Surveyor L
212. f the Event and Ready outputs include the following Output state Output polarity Vdc Off Active High 5 174 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls PDA Detector Direct Controls Table 48 Configuration page of the Direct Control dialog box for the PDA detector Sheet 3 of 4 Parameter Description Ready Output Turn On and Turn Off Indicates whether the Ready output state is On or Off If the Ready output state is On the buttons Turn Off button is available If the Ready output state is Off the Turn On button is available Ready Output Indicates whether the Ready output polarity is Active High or Active Low If the Ready readback output polarity is Active Low the Set Active High button is available If the Ready output polarity is Active High the Set Active Low button is available Set Active Low or Set Set the polarity of the Ready Output signal Active High buttons Note The output polarity must match the polarity either Active High or Active Low of the instrument connected to the Ready output connection on the back panel of the PDA detector The signal terminal is the high connection and the ground GND terminal is the low connection The autosampler requires active low remote inputs Event Output Use the controls in this area to specify the parameters for output events If the external device is triggered by a contact closure connect the PDA EVENT terminal pin 8 to th
213. f you do not want the needle to touch the bottom of a vial or well deactivate vial bottom sensing In the Dead Volume uL box type the value specified on the label attached to the transfer tube assembly Tip When you use the No Waste injection mode for best results calibrate the transfer tube volume and then type the empirically determined value in the Dead Volume box To calibrate the transfer tube volume refer to the hardware manual for the autosampler In the Sample Loop Volume pL box type the nominal size of the sample loop attached to the injection valve The autosampler ships with a 25 uL sample loop 54 Surveyor Plus User Guide for LC Devices Thermo Scientific 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Autosampler Communication Page Parameters Table 9 describes the parameters on the Communication page Table 9 Communication page parameters Sheet 1 of 2 Parameter Communication Description Stack Address Specifies the stack address of the autosampler The stack address must match the unit ID setting The unit ID setting is specified by two rotary switches on the back panel of the autosampler The rotary switches are set to 01 at the factory Syringe Specifies the syringe type The selections are 100 250 500 and 2500 pL Wait for Temperature Ready Selecting this check box specifies that the autosampler waits for the column oven temperature and t
214. fic Surveyor Plus User Guide for LC Devices 175 6 Direct Controls PDA Detector Direct Controls Table 48 Configuration page of the Direct Control dialog box for the PDA detector Sheet 4 of 4 Parameter Description Programmed Lamp Startup Programmed Lamp Displays the current lamp startup program and provides controls to create a lamp startup Startup program that automatically turns on the lamps for operation at a specified time and day never weekdays every day Change Opens the Lamp Startup Time dialog box where you can specify a lamp startup time see Setting the Lamp Startup Time on page 166 Display Page Use the Display page to perform these procedures e Checking the Chromatographic Baseline on page 168 e Adjusting the Light Throughput to the Diode Array on page 315 To open the Display page 1 Open the Surveyor PDA Direct Control dialog box see PDA Detector Direct Controls on page 162 2 Click the Display tab The Display page appears see Figure 101 176 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls PDA Detector Direct Controls Figure 101 Display page Surveyor PDA Plus Direct Control Display Configuration Information Calibration Control Current method Unknown Load Method Start Data Spectrum Zero Data Stop Data Levels Counts Channel Level 759386 Channel B Level 474119 Channel C Level 759744 Lamp Lifetimes hour
215. for Channel B is displayed in the bottom view of the Display page in red Three Channels Specifies the acquisition of three discrete channels The data for Channel C is displayed in the bottom view of the Display page in green Sample Rate Not applicable Ch A B C Specifies the diode that you want the detector to monitor Diode Number Channel A default 40 Channel B default 55 Channel C default 450 Range 2 to 511 in increments of 1 Timed Events Table for the PDA Detector Table 26 describes the timed events area at the bottom of the Surveyor PDA Plus Method page Use the Timed Events area to program actuation of a back panel contact closure as a function of either time or the absorbance level from one of the discrete wavelength channels You can use this feature to trigger an external device such as a fraction collector and to zero the absorbance level during an acquisition run For information about connecting an external device to the PDA detector refer to the Surveyor PDA Plus Detector Hardware Manual Table 26 Timed events table on the Surveyor PDA Plus Method page Sheet 1 of 2 Parameter Description Timed Events Use this area to add modify and remove timed events You can specify the time when the event occurs the event type the channel the absorbance level mAU and the delay settings Click New to open the Timed Events dialog box Timed Events table This table lists all the events in chronologic
216. for LC Devices Thermo Scientific 8 Qual Browser Changing the Font Size of the Display Figure 138 Proportional pitch font size 8 C Xcaliburidata T est Mixture A01 02 12 2003 06 03 30 PM RT 0 00 10 00 q 380000 J 360000 J 3400004 J 3200004 3000004 J 2800004 J 2600004 J 2400004 J 2200004 J 2 2000004 S J 1800007 1600004 1400004 1200004 1000004 800005 J 600004 J 400004 J 200004 0 25 0 65 oo 0 5 10 1 80 16 2 0 25 3 0 3 5 40 45 60 5 5 60 65 70 75 8 0 8 5 90 9 5 u E 3 93E5 Total Scan PDA Test Mixture Ant 2 23 3 30 377 413 Time min Figure 139 Proportional pitch font size 16 C Xcalibur data Test Mixture A01 02 12 2003 06 03 30 PM RT 0 00 10 00 Thermo Scientific 1 07 a NL 3 93E5 Total Scan PDA Test Mixture A01 1 80 2 23 2 62 413 4 63 8 23 8 58 10 Time min Surveyor Plus User Guide for LC Devices 231 8 Qual Browser Viewing a Report of the Instrument Method Viewing a Report of the Instrument Method 232 After you open a data file you might want to check the instrument parameters that were used to acquire it To view a report that lists the instrument control parameters 1 Choose View gt Report gt Instrument Method The instrument method is displayed in the top cell of the window The instrument method is divided by device with the parameters for e
217. for ordering information Phone 800 532 4752 Fax 561 688 8731 E mail us customer support analyze thermofisher com Web site www thermo com ms To get local contact information for sales or service Go to www thermoscientific com wps portal ts contactus To copy manuals from the Internet Go to mssupport thermo com agree to the Terms and Conditions and then click Customer Manuals in the left margin of the window To suggest changes to documentation or to Help e Fill out a reader survey online at www surveymonkey com s PQM6P62 e Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com xviii Surveyor Plus User Guide for LC Devices Thermo Scientific ee i Introduction to the Surveyor Plus LC System The Surveyor Plus high performance liquid chromatography system see Figure 1 which integrates with the Thermo Scientific family of mass spectrometers consists of an analytical pump an autosampler an optional PDA detector or UV Vis detector and a solvent platform Figure 1 Surveyor Plus LC instrument Solvent oo latform SN b p An Detector Autosampler Analytical pump Contents e Analytical Pump e Autosampler e Detector e Solvent Platform e Communication with the Data System Computer e Turning Off the Computers Energy Saving Features e Synchronization of the LC Devices e Status LEDs Thermo Scientific Surveyor Plus User Guide for LC Devices 1
218. for the gradient program as follows e When you select Surveyor AS Injection Logic or Manual and the Home Before Run check box the minimum flow rate is 10 0 pL min e When you select Manual and leave the Home Before Run check box cleared the minimum flow rate is 0 0 pL min The maximum flow rate setting is 2000 pL min for the Surveyor MS Pump Plus 80 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings 5 For an isocratic separation method do the following on the Gradient Program page for the Surveyor MS Pump Plus a Double click the Time column in the second row of the gradient program table and then type a time value in this cell The time range is 0 01 to 655 00 minutes If the time value for the second time point is longer than the data acquisition time for the PDA detector or the MS detector the data system waits for the gradient program to finish before proceeding to the next row in the acquisition sequence Type the same values for the solvent composition and the flow rate that you specified for the initial time point Press ENTER to accept the values IMPORTANT You must specify the flow rate and solvent composition for at least two time lines Verify the gradient program in the Solvent Gradient view see Figure 51 Figure 51 socratic gradient program Pump General Gradient Program Pump 1
219. ger a run when the autosampler makes an injection select Surveyor AS Autosampler Injection Logic e In the Method Finalizing list select the ending conditions for the run e Fora gradient method do one of the following Select First Line Conditions to return the mobile phase conditions to the first line of the gradient program following the last time line in the gradient program table Select Last Line Conditions so that the mobile phase conditions remain at those of the last time line in the gradient program e Fora shutdown method that turns off the solvent flow at the end of a run select Stop after the End Note The Idle Settings list is available for a dual pump system in the Pump 2 area of the Pump General page f In the Min Pressure bar box type or select the minimum operating pressure for the pump 76 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings An appropriate minimum pressure setting prevents the pump from operating when the solvent reservoirs have run dry or the system plumbing has developed a leak Running the pump without solvent quickly ruins the piston seals Select a value that is well below the typical operating pressure for your application In the event that the pressure falls below this limit for more than one minute the pump automatically stops and sends an error message to the computer The range is
220. gh check box e Ifthe signal from the pump is HI Open and goes LO Closed when the pump is ready clear the Injection Hold Release Active High check box Output These check boxes are clear in the default instrument method For a Thermo Scientific LC MS system leave these check boxes clear Autosampler Ready Use this check box to set the polarity of the A S Ready output signal Active High TE e When this check box is selected the signal from the autosampler is LO Closed and goes HI Open when the autosampler is ready e When this check box is clear the signal from the autosampler is HI Open and goes LO Closed when the autosampler is ready Note The A S Ready terminal sends a signal that indicates that the autosampler is in the Ready state The autosampler is ready when it meets the selected ready conditions The ready conditions you select include sample tray temperature column oven temperature door is closed maintenance log and vial bottom sensing see Communication Page on page 52 Injection Out Active Use this check box to set the polarity of the Inject Out output signal High e When this check box is selected the signal from the autosampler is LO Closed and goes HI Open when the autosampler injects a sample e When this check box is clear the signal from the autosampler is HI Open and goes LO Closed when the autosampler injects a sample Note The Injection Out terminal sends a
221. h station b Align the retention clip with the slot located in front of the wash station c Using the retention clip to push the injection port down align the circular cutout in the retention clip over the alignment screw d Insert the end of the retention clip into the wash station slot as far as it will go Figure 207 shows the installation of the retention clip 300 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 207 Retention clip installation Retention clip installed 5 Reinstall the needle assembly as follows a b G d Remount the syringe drive assembly Slide the needle into the needle mount on the XYZ arm Turn the latch to the right Reconnect the needle tubing assembly to the needle assembly Leave the autosampler view of the Instrument Setup view open and go to the next procedure Testing the Alignment of the XYZ Arm Surveyor Plus User Guide for LC Devices 301 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Testing the Alignment of the XYZ Arm To test the alignment of the XYZ arm make injections from the four corners of two 384 well microplates To test the alignment of the XYZ arm 1 Cover columns 1 2 23 and 24 of two 384 well microplates with tape see Figure 208 Figure 208 384 well microplate positions Al A24 A OQOOOOOOOOO
222. he PDA Detector on page 313 Configuration Page Turning the Lamps On or Off on page 163 Resetting the Lamp Usage Hours on page 164 Changing the Polarity of the Analog Outputs on page 164 Testing the Analog Outputs on page 165 Setting the Lamp Startup Time on page 166 Information Page Viewing Exporting and Clearing the Error Log for the PDA Detector on page 171 Checking the Firmware Version of the PDA Detector on page 171 For information about using the Calibration page to determine the wavelength accuracy of the detector and the dark current produced by the diode array see Calibrating the PDA Detector on page 319 Turning the Lamps On or Off Use the Configuration page of the Surveyor PDA Plus Direct Control dialog box to turn each lamp on or off To turn the lamps on or off 1 Open the Configuration page of the Surveyor PDA Plus Direct Control dialog box see Configuration Page on page 171 2 Click Turn On for the associated lamp When you turn on the deuterium lamp its Status readback reads Starting during the 30 second ignition period and then it changes to On If there is a problem with either lamp its Status readback reads Failed Note The intensity of the deuterium lamp falls off very slightly over a period of time after the lamp is turned on Plan to wait at least one hour for the lamp to stabilize after a cold start before coll
223. he Power Options dialog box i 3 Power Options Advanced settings a Select the power plan that you want to customize and B then choose settings that reflect how you want your computer to manage power Change settings that are currently unavailable Balanced B Hard disk Turn off hard disk after Setting Never Desktop background settings Wireless Adapter Settings Sleep after Allow hybrid sleep Hibernate after rr e Set the Turn Off Hard Disk After option to Never as follows i Click the icon to the left of Hard Disk ii Click the icon to the left of Turn Off Hard Disk After iii If the setting is not set to Never click the setting and select Never f Set the Hibernate After option to Never as follows i Click the icon to the left of Sleep ii Click the icon to the left of Hibernate After iii If the setting is not set to Never click the setting and select Never g Click Apply to accept these settings h Click OK to close the Advanced Settings page 7 Close the Control Panel window Thermo Scientific Surveyor Plus User Guide for LC Devices 31 1 Introduction to the Surveyor Plus LC System Synchronization of the LC Devices Synchronization of the LC Devices A system interconnect cable contact closure provided in the Surveyor System Kit coordinates the run control signals between the Surveyor Plus devices Figure 28 shows the cable a
224. he cam cycle extends from the time when the primary piston starts discharging until the time the secondary piston reaches full intake approximately 80 of the cam cycle To minimize the pressure pulsation and maintain a constant flow rate the on board CPU compensates for this compression by making fine adjustments to the speed of the stepping motor If the compressibility setting is incorrect the LC pump cannot effectively minimize the pressure pulsation Figure 169 shows the overlaid pressure traces for three runs of water pumped at a nominal flow rate of 3 mL min The compressibility settings for the three runs were 0 45 GPa 1 25 GPar and 3 0 GPa as labeled The compressibility of water is 0 45 GPa Figure 169 Overlaid LC pump pressure traces showing the effect of the compressibility setting EE LC Pump Pressure Time 2 33873 Minutes Amplitude O psi 2450 wee y ray ee 70 9 AEE EE RL aea Oe IE R 4 Se 2250 fogs GPat J 4 i lt i i J p i maer r ae Aa r a AT A T A eee ELTETE ETITI TETET f 2 0 2 5 Minutes Table 57 lists the calculated pressure pulsation and the empirically determined flow rates for the three different compressibility settings The pressure pulsation as well as the actual flow rate increased as the compressibility setting increased Thermo S
225. he data file directory where you want to store your raw data files The data system adds the raw file extension to the data files that contain the chromatographic and spectral data Browse to the instrument method that you want to use to acquire your raw data files Instrument methods have a meth file extension The Instrument Setup view for the Surveyor Plus devices is described in Chapter 3 Instrument Method Setup If you have not yet created a processing method that contains the information needed to quantitate your unknowns do not select a processing method You can create a processing method and reprocess your stored data files at a later date Processing methods have a pmd file extension For information about performing tests to determine the suitability of your chromatographic method and on creating calibration curves to quantitate your unknowns refer to the Thermo Xcalibur Quantitative Analysis User Guide 3 In the Samples area specify the vial locations by doing one of the following e To specify a contiguous set of sample vials or well locations Inthe Number of Samples box type the number of samples that you want to analyze In the Initial Vial Position box type the vial position The vial positions for the conventional trays are shown in Figure 114 Surveyor Plus User Guide for LC Devices 203 7 Sequence Setup Creating a Single Sample Sequence Figure 114 Vial positions for conventional sample
226. he following e Use a sample loop that is at least 5 pL larger than the injection volume Because the accuracy of the nominal size is 20 use an estimate of 80 for the actual size For example use 20 uL as an estimate for the actual volume of a 25 uL loop and inject no more than 15 pL with this loop size e Consider matching the chemistry of the sample matrix the flush solution and the mobile phase For no waste injections the autosampler loads approximately 2 pL of flush solvent and 3 pL of air into the sample loop regardless of the requested injection volume e Inject at least 1 0 uL of sample Surveyor Plus User Guide for LC Devices 19 1 Introduction to the Surveyor Plus LC System Autosampler Partial Loop Injection Mode The partial loop injection mode is a technique that withdraws 22 pL of excess sample from the vial in addition to the requested injection volume Approximately one half of the excess volume is expelled to waste before the center of the sample bolus is metered into the front of the sample loop The second portion of excess sample is expelled to waste after the sample bolus is backflushed onto the column Partial loop injections are useful when you have a limited volume of sample Using the partial loop injection mode you can inject variable amounts of sample ranging from a minimum of 0 1 pL to a working maximum of one half the volume of your sample loop This maximum volume limitation is caused by the lami
227. he scan plot shows absorbance mAU normalized to 100 percent on the y axis and time on the x axis Each discrete channel is color coded Channel A is yellow Channel B is purple and Channel C is blue 180 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls PDA Detector Direct Controls Information Page Use the Information page to monitor the chronological run log instrument version and system date and time The error log is an ongoing record of critical and non critical errors in the PDA detector The log is generated and stored in the detector This data is useful for troubleshooting hardware and software problems To open the Information page 1 Open the Direct Control dialog box for the PDA detector see PDA Detector Direct Controls on page 162 2 Click the Information tab The Information page appears see Figure 102 Figure 102 Information page Surveyor PDA Plus Direct Control Display Configuration Information Calibration Date Time Sev File Information pErolLo Clear Log Export Log Versions Detector ROM 2 0 2 Date and Time 02 27 05 15 43 32 Help Thermo Scientific Surveyor Plus User Guide for LC Devices 181 6 Direct Controls PDA Detector Direct Controls Information Page Parameters Table 50 describes the parameters on the Information page Table 50 Information page parameters
228. he tray compartment temperature to reach their set temperatures before going to the Ready state Select this check box if you want the heated zones to reach their setpoint before the autosampler makes an injection Verify Door Is Closed Selecting this check box specifies that the autosampler waits for the door to be closed before starting a run and that the XYZ arm moves to the back of the tray compartment when you open the tray compartment door Select this check box if you want the autosampler to pause a sequence and send the XYZ arm to the back of the tray compartment when you open the tray compartment door Enable Maintenance Log Selecting this check box activates the maintenance log The maintenance log keeps an internal count of the total injections total valve cycles total needle usage and total syringe cycles When any of the counters exceed the user set scheduled maintenance time SMT the autosampler cannot trigger a run until you perform the scheduled maintenance or you clear the check box For information about setting up the scheduled maintenance time for the autosampler s hardware components see Autosampler Maintenance Information on page 309 Tip When you select the Enable maintenance log check box check the maintenance schedule and make sure that the settings are appropriate for your autosampler Vial Bottom Sensing Thermo Scientific Specifies whether the vial bottom sensing feature is tu
229. ic Internal Set Target page of the Vial Tray Metal Sensor Calibration wizard Diagnostic Internal Set Target Calibration target temperature C 30 Start calibration lowest ee User setting The data system turns on the tray temperature control and downloads the set temperature of 30 0 C The Next button becomes available 3 Click Next The Diagnostic External Standard page appears see Figure 186 The default external standard temperature is 40 0 C The range is 0 to 110 0 C Figure 186 Tray page and the Diagnostic External Standard page of the Vial Tray Metal Sensor Calibration wizard Diagnostic External Standard AS Status Oven Tray Eror lag External standard temperature C 40 0 Adjust Control on Yes Current temperature C 21 7 Tray Set temperature C 30 0 Ready status Ready femes e Tray temperature control is on The set temperature is 30 0 C Default setting 284 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Adjusting the Tray Temperature Calibration Use the Diagnostic External Standard page of the Vial Tray Metal Sensor Calibration wizard the status readout on the Tray page and the external temperature sensor to adjust the temperature calibration of the tray compartment To adjust the calibration temperature of the tray compartment 1 When the
230. ientific The tray compartment see Figure 5 can hold up to five conventional sample trays or one carrier that holds three microwell plates The tray compartment also holds up to four 16 mL capacity reservoir vials that you can use to hold solvent reagent or diluent The reservoir vials are located behind the wash station and are designated RV1 RV2 RV3 and RV4 Figure 5 Tray compartment XYZ arm mechanism Wash station Injection port Surveyor Plus User Guide for LC Devices 5 1 Introduction to the Surveyor Plus LC System Autosampler The five conventional sample trays from the left side to the right side of the tray compartment are designated A B C D and E Each sample tray holds up to 40 standard 1 8 mL vials for a total capacity of 200 samples Overlays allow the sample trays to accommodate different vial sizes The microwell carrier can hold up to three low density 96 well microplates or up to three high density 384 well microplates The microplates are designated A B and C The tray compartment door contains a magnetic switch The magnet is located in the door and the switch is attached to the chassis When you open the door the switch signals the autosampler that the door is open When you configure the autosampler from the data system to verify whether the tray compartment door is open or closed the XYZ arm automatically moves to the back of the tray compartment when you open the door
231. imum operating pressure Note The maximum pressure setting is 43 10 MPa 431 00 bar or 6258 00 psi Reduce the maximum pressure setting for PEEK fittings to 28 MPa 276 bar or 4000 psi 1 bar 14 5 psi 10 MPa Surveyor LC Pump Plus General Page Parameters Table 13 describes the parameters on the General page Table 13 General page parameters for the Surveyor LC Pump Plus Parameter Description Solvents A Solvent Name Specifies the solvent contained in the solvent A reservoir bottle B Solvent Name Specifies the solvent contained in the solvent B reservoir bottle C Solvent Name Specifies the solvent contained in the solvent C reservoir bottle D Solvent Name Specifies the solvent contained in the solvent D reservoir bottle Column Description User specified description for the LC column Pressure Limits Min Pressure Specifies the minimum operating pressure for the pump If the system pressure falls below this limit the data system turns off the solvent flow from the pump Pressure units Minimum Maximum MPa 0 00 43 10 bar 0 00 431 00 psi 0 00 6258 00 Max Pressure Specifies the maximum operating pressure for the pump If the system pressure rises above this limit the data system turns off the solvent flow from the pump The maximum pressure setting must be greater than the minimum pressure setting Pressure units Minimum Maximum MPa 1 00 43 10 bar 10 00 431 00
232. ine the available injection volume range In addition to offering three sizes of concentric syringes Thermo Scientific also offers a 2500 pL standard single plunger syringe The XYZ arm mechanism moves the needle along the x y plane to the requested vial or well location After it positions the needle above the vial or well the XYZ arm mechanism lowers the needle along the z axis to the requested needle height Figure 13 shows the needle descending to a depth of 2 mm from the bottom of a standard 1 8 mL vial 14 Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Autosampler Figure 13 Autosampler needle positioned 2 mm from the bottom of a vial Needle height from bottom Bottom of vial a 2mm mae Wash solvent t fim Sample After the autosampler withdraws the sample from the sample vial or well into the needle tubing the XYZ arm mechanism moves along the x y plane back to the home position which is above the injection port of autosampler and then lowers the needle into the injection port where it expels the sample The sample travels through transfer tubing and into the sample loop of the injection valve IMPORTANT Because the XYZ arm moves to the sample position to withdraw sample do not place objects taller than 1 8 inches into the tray compartment as they will stall the XYZ arm Do not move the XYZ arm manually Instead use the following co
233. ing On the Power to Each LC Device orvcdca in teas ees mks 134 Initiating Communication with the Data System 0 0 000005 135 Checking the Status of the LC Devices ood ise pink ees oes wie ken atie ds 136 Opening the Status Page of the Information View 0 136 Viewing the Status of Each Device 4 oes ee oue ete ei Ian eas 137 Turning Devices On Off or into Standby from the Info View 154 Filling the Solvent Reservoir Lines with Fresh Solvent 155 Priming the Pulse Dampener of the Surveyor MS Pump Plus 156 Accessing the Direct Controls cea oi eee ee ee cae 158 xii Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific Chapter 6 Chapter 7 Chapter 8 Contents Direct Contr ls s secina E a er wranard a a Wis A ae aa 161 PDA Detector Direct Controls se c 8 d ykesey tb ay honcative dem aderashoecle oe nCantye cok a 162 Turning the Lamps On or Off eats tiuates unane 163 Resetting the Lamp Usage Hours 00 0 cee eee eee eee ee 164 Changing the Polarity of the Analog Outputs 0000005 164 Testing the Analog Outputs ion tae saa ahead ee ahs ia Sees 165 Setting the Lamp Startup tine sinc asta wes Sone anu nein tt 166 Checking the Chromatographic Baseliti s sscia es ecinda ean iedn ee 168 Viewing Exporting and Clearing the Error Log for the PDA Detector 171 Checking the Firmware Version of the PDA Detect
234. ing for equilibration 5 sec FW calibration started Restoring saved method Restoring lamp states Calibration complete 324 Surveyor Plus User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector 7 When the calibration is complete click Next The next page of the wizard appears see Figure 226 You can export the results of the calibration from this page Figure 226 Export results page Dark Current Calibration Dark current calibration has completed successfully Click the Apply button to accept the calibration Click the Cancel button to discard the calibration Export Results Cancel Help 8 Optional To print a record of the dark current calibration do the following a Click Export Results The Save As dialog box appears see Figure 227 Figure 227 Save As dialog box showing the file extension for a text file Save in lo data e ae E D12_2 txt E NewHOs txt E D12_28 txt E NewHO txt E D 1 10 txt W13 txt E D_1 18 txt E w13_1_18 txt E Lampcal txt E wHOS txt E NewHOS txt Filename EOEMUENSISE TET Save as type Text Files txt Cancel b Type a name in the File Name box and then click Save Once you have saved the file with a name of your choice you can view or print the contents of the file using any text editing program see Figure 228 Thermo Scientific Surveyor P
235. instructions in Setting Up the Pump General Parameters on page 74 b In the Pump 2 area select the Idle settings for the pump that you configured as the sample pump Pump 2 as follows In the Idle Settings list select the solvent conditions for Pump 2 before it starts its gradient program If you want Pump 2 to remain idle until Pump 1 sends the start signal select Standby If you want Pump 2 to pump solvent at the solvent composition and flow rate specified in the first line of its gradient program until Pump 1 sends the start signal select First Line If you want Pump 2 to pump solvent at the solvent composition and flow rate specified in the last line of its gradient program until Pump 1 sends the start signal select Last Line c Specify the remaining parameters for Pump 2 2 On the Gradient Program page see Figure 53 do the following a To specify the gradient programs for both pumps follow the instructions in Setting Up the Gradient Program on page 79 b Inthe Pump 1 area in the P2 column select the time line that corresponds to the time that you want the start pump to trigger the sample pump To select the trigger time for Pump 2 click the appropriate row in the P2 column besssead Figure 53 Gradient page for a dual pump system Pump General Gradient Program Pump 1 At 1 00 minute into the run Pump 1 triggers the start of the Pump 2 gradient program Time A B C 0 00
236. instrument that triggers the run Manual At the start of a run the pump program starts immediately When you use this injection logic set up the pump as the start instrument Min Pressure Specifies the minimum operating pressure of the pump If the system pressure falls below this level for more than one minute the data system triggers turns off the mobile phase flow Default 0 bar Max pressure Specifies the maximum operating pressure of the pump If the system backpressure rises above this level for more than one minute the data system triggers the pump to turn off the mobile phase flow Default 400 bar Pressure Stability Specifies the stability condition required for the pump to go into a Ready state A lower value requires greater pressure stability before the pump state goes to Ready A higher value is more forgiving of pressure pulsations Default 10 The range depends on the pressure units selection Units Range psi 1 to 1450 MPa 1 to 10 bar 1 to 100 78 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Surveyor MS Pump Plus Instrument Method Settings Table 16 Thermo pump method parameters Sheet 3 of 3 Parameter Pressure Units Description Specifies the units for the pressure readout Selections PSI and MPa 1 00 MPa 10 0 bar 145 psi Idle Settings Pump 2 of a dual pump system Specifies the conditions for Pump 2 while it
237. ion Quaternary Configuration Quaternary Firmware version 12 47a Firmware version 12 47a 4 If two pumps are connected to the data system computer make sure that the appropriate pumps are selected in the Pump 1 and Pump 2 area Thermo Scientific Surveyor Plus User Guide for LC Devices 61 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings You can use two pumps of the same pump type to perform two dimensional chromatography or high pressure gradient mixing 5 Click OK to close the dialog box Surveyor MS Pump Configuration Parameters Table 11 provides descriptions of the parameters in the Surveyor MS Pump Configuration dialog box Table 11 Surveyor MS Pump Plus Configuration dialog box parameters Parameter Description Serial number Lists the serial number stored by the Surveyor MS Pump Plus Status Displays the pump s status The states are Not Connected or Connected Communication Port Displays the type of communication port on the data system computer where the pump is connected Stroke Count Displays the total stroke counts for the pump s pistons Pump Type Displays the pump type Thermo Pump Configuration Displays Quaternary Firmware Version Displays the firmware version Use Leak Sensor When this check box is selected the leak sensor is in use 62 Surveyor Plus User Guide for LC Devices Thermo Scientific 2 Thermo Foundation Instrument Configura
238. ion 19 injection valve description 18 injection volume full loop injections 20 no waste injections 19 90 partial loop injections 20 instrument methods adding a sample preparation routine 113 autosampler parameters 85 creating 67 LC pump parameters 69 MS pump parameters 74 parameters report data file 232 Thermo Scientific Index G PDA detector parameters 98 saving 109 UV Vis detector parameters 108 Instrument Setup window opening 68 integration auto calculation 253 Avalon integration algorithm 252 intensity counts maximum light throughput 318 data recording 318 intensity display 178 isocratic pump program creating for LC pump 71 creating for MS pump 81 L Labels page Display Options dialog box 241 Lamp Startup Time dialog box 166 lamps controls on the PDA detector Configuration page 163 deuterium 22 23 Information view Turn Device On command 154 lamp warm up message 137 safety interlock 23 timed startup for PDA detector 166 tungsten 22 23 turning on UV Vis detector 183 usage hours resetting for the PDA detector 164 wavelength range for the PDA detector 22 Lamps LED PDA detector 39 UV Vis detector 40 layout files for PDA data creating 233 saving 248 LC column damaging 77 equilibrating 209 LC pump components 3 in line filter frit 4 instrument method parameters 69 LED states 37 purging 4 187 LEDs device status 35 level trigger 103 light fixture arm calibration 287 294 light through
239. irect controls for the Surveyor LC Pump Plus see these topics e Opening the Direct Control Dialog Box for the Surveyor LC Pump Plus e Operation Surveyor LC Pump Direct Control Parameters e Removing Air from the Solvent Lines Connected to the Surveyor LC Pump Plus e Downloading New Solvent Conditions to the Pump e Starting and Stopping the Solvent Flow e Clearing an Error Condition for the Pump Opening the Direct Control Dialog Box for the Surveyor LC Pump Plus In the pump view the direct controls are on the Operation Surveyor LC Pump Direct Control dialog box In the Tune window for your Thermo Scientific mass spectrometer the direct controls for the pump are on the pump page of the Inlet Direct Control dialog box To open the Operation Surveyor LC Pump Direct Control dialog box 1 Open the pump view 2 From the menu bar choose Surveyor LC Pump gt Direct Control gt Operation The Operation Surveyor LC Pump Direct Control dialog box appears Thermo Scientific Surveyor Plus User Guide for LC Devices 185 6 Direct Controls Pump Direct Controls To access the direct controls for the pump from the Tune window 1 Open the Tune window for your Thermo Scientific mass spectrometer 2 Choose Setup gt Inlet Direct Control The Inlet Direct Control dialog box that contains tabbed pages for each configured LC device appears 3 Click the Surveyor LC Pump tab Operation Surveyor LC Pump Direct Control Parameters
240. is degradation in light intensity Date the printout and add it to your maintenance records To save the data to a file click SNAPSHOT The data system saves a comma separated values file named PDASnapshot csv to the following folder on the data system computer drive Xcalibur data A date and time stamp are appended to the file name The format of the date and time stamp is MMDDYYHHMMSS MM is the month DD is the day of the month YY is the last two digits of the year HH is the hour in military time MM are minutes SS are seconds You can open this file with the Excel application 318 Surveyor Plus User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector For a wavelength absorbance method the file contains the absorbance values for the spectral scan and the discrete channel wavelengths at the moment that you clicked Snapshot For an intensity diode method the file contains the intensity values for the scan of the diode array and the intensity values for up to three individual diodes 5 After you finish adjusting the attenuators replace the flowcell access cover close the front doors of the detector and replace the flow restrictor with your LC column Calibrating the PDA Detector For information about calibrating the PDA detector see these topics e Calibration Page for the PDA Detector e Performing a Dark Current Calibration e Performing a Wavelength
241. is waiting to be triggered by Pump 1 Default Standby Selections Standby First Line Conditions and Last Line Conditions In the Standby mode the pump remains in the Idle state Setting Up the Gradient Program Thermo Scientific The pump contains a built in solvent proportioning assembly that is capable of proportioning up to four solvents to create binary tertiary and quaternary mobile phases This capability reduces the need to make premixed mobile phases You can run the pump in either the isocratic mode or the gradient mode In the isocratic mode you maintain the same proportions of solvent throughout the run Use the Gradient Program page to specify the solvent composition and flow rate for your chromatographic method The Gradient Program page contains a gradient table with time lines for the solvent composition and flow rate and an interactive view that displays a graphical profile of the solvent gradient or flow rate gradient Each row in the gradient table defines the solvent composition and flow rate for a specific time point The solvent composition columns A B C and D work interactively with each other maintaining a total solvent composition of 100 Between time points the solvent composition changes linearly whereas the flow rate changes as a discontinuous step function The gradient table can contain 2 to 398 time lines IMPORTANT The gradient table must contain at least two time lines For an isocr
242. isition of three discrete channels The data for Channel C is displayed in the bottom view of the Display page in green Sample Rate Specifies the sample rate in Hz for all of the discrete channels selected see sample rate in the Spectra area Ch A B C Specifies the discrete channel wavelength to be acquired Wavelength Channel A default 214 Channel B default 254 Channel C default 280 Range 190 to 800 nm Ch A B C Specifies the bandwidth for the corresponding discrete channel Bandwidth values are Filter Bandwidth limited to the subset of odd integers from 1 to 49 Default 9 nm 100 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup PDA Detector Instrument Method Parameters Display Method Parameters Table 25 describes the parameters for a display method These parameters are available when you select the Diode Intensity option in the Units area Table 25 PDA Method page parameters for a display method Sheet 1 of 2 Parameter Description Run Run Length Not applicable Filter Rise Time Not applicable Units Units Diode Intensity Specifies the display units for the spectrum plots When you select the Diode Intensity option you can view the light intensity detected by the photo diodes of the diode array The x axis corresponds to the photo diode number 2 to 511 There are 512 diodes in the diode array Diodes 0 and 1 are not used Diode 2 corr
243. ith your data system for information about accessing the Calibration dialog box for the autosampler To open the Calibration dialog box for the autosampler 1 Open the view for your autosampler 2 In the menu bar choose Surveyor AS gt Calibration The Calibration dialog box appears see Figure 175 274 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 175 Calibration dialog box for the autosampler Calibration Choose the diagnostic item Vial tray metal sensor calibration C Arm calibration C Well bottom distance toed He Column Oven Air Sensor Calibration To calibrate the column oven temperature you must have the oven sensor test fixture provided in the Field Service Calibration Kit P N 60053 62001 for the autosampler CAUTION Because the column oven compartment can reach temperatures as high as 95 C 203 F ensure that the column oven is off and that the column oven compartment is at room temperature before you install the oven sensor test fixture To calibrate the column oven temperature follow these procedures in order 1 Preparing to Calibrate the Column Oven Temperature 2 Specifying the Internal Set Target for the Column Oven Calibration Temperature 3 Adjusting the Temperature Calibration for the Column Oven Preparing to Calibrate the Column Oven Temperature To set up the system for a temperatu
244. ius inner diameter 2 L column length in cm To equilibrate your LC column 1 From the Thermo Xcalibur Roadmap menu choose GoTo gt Instrument Setup to display the Instrument Setup window 2 Download the same solvent percentages and flow rate as those contained in your method to the pump e For information on downloading new solvent conditions to the Surveyor LC Pump Plus and starting the solvent flow see Surveyor LC Pump Plus Direct Controls on page 185 e For information on downloading new solvent conditions to the Surveyor MS Pump Plus and starting the solvent flow see Surveyor MS Pump Plus Direct Controls on page 190 3 In the status view for your pump available on the Status page of Info View monitor the readings in the Pressure Status area to ensure that the pressure is appropriate for your application See Viewing the Status of Each Device on page 137 Thermo Scientific Surveyor Plus User Guide for LC Devices 209 7 Sequence Setup Loading the Autosampler Loading the Autosampler Before you load your samples into the autosampler ensure that your samples are completely soluble in the mobile phase and that you have filtered your samples through a 0 5 ym filter if necessary These techniques minimize sample precipitation in the lines and remove particulate matter that could obstruct the flow through the autosampler s injection valve or the LC column In addition make sure that the vial caps
245. ize fi ptures that y plan to use for presentations To increase the font size 1 From the Thermo Xcalibur Roadmap window choose Tools gt Configuration The Thermo Xcalibur Configuration dialog box appears 2 Click the Fonts tab The Fonts page appears see Figure 137 Figure 137 Fonts page in the Thermo Xcalibur Configuration dialog box Thermo Xcalibur Configuration Labeling and Scaling Intelligent Shutdown Error Handling Dataset List Folders Customer Info Fonts Peak Detection Mass Options Fixed Pitch Font Proportional Pitch Font Font Min Font 8 A 10 11 12 4 Arial monospaced for SAF Courier Courier New Fixedsys Lucida Console Lucida Sans Typewriter Japanese Gothic Adobe Garamond Pro Adobe Garamond Pro Agency FB Algerian Preview Preview Fixed Pitch Proportional Fixed Pitch Proportional 3 To increase the font size of the chromatogram spectrum and map axis labels in the Proportional Pitch Font area select a larger font size from the Max list and select a larger font size from the Min list 4 To increase the font size for the Spectrum List Scan Header Scan Filters or Report in the Fixed Pitch Font area select a larger font size from the Max list and select a larger font size from the Min list Figure 138 shows the chromatogram axes labeled with a font size of 8 Figure 139 shows the chromatogram axes labeled with a font size of 16 230 Surveyor Plus User Guide
246. jeleleleleje 900006999086060900800008 MAM P 0066666600666666600666660 000666600066660000566008 AA 1 24 24 lt _________ __ 1 10 Surveyor Plus User Guide for LC Devices Thermo Scientific Injection System 1 Introduction to the Surveyor Plus LC System Autosampler The main components of the injection system include the following Syringe Drive Assembly and Syringe Valve Wash Bottle Reservoir and Tubing Interchangeable Syringe XYZ Arm Mechanism Needle Assembly and Needle Tubing Assembly Injection Port and Transfer Tubing Assembly Injection Valve and Sample Loop Syringe Drive Assembly and Syringe Valve Thermo Scientific The syringe drive assembly holds the autosampler syringe There are three holes with grommets on the back of the syringe drive assembly You mount the syringe drive assembly to the front of the autosampler by matching these holes to one vertical mounting pin and two horizontal mounting pins located in front of the autosampler injection port The rubber grommets minimize the effects of vibration but also cause the connection between the syringe drive assembly and the body of the autosampler to feel slack see Figure 10 Surveyor Plus User Guide for LC Devices 11 1 Introduction to the Surveyor Plus LC System Autosampler Figure 10 Syringe drive assembly for the Surveyor Autosampler Plus showing the front and the back of assembly Two way syringe valve 10 pin connector Wa
247. k for the word DRAIN to appear upside down on the knob Figure 3 Drain valve positions Closed position Open position Figure 4 shows the line body fitting removed from the top of the purge manifold assembly The line body fitting contains an inline filter frit that captures particulate matter shed by the pump seals This prevents particulate matter from contaminating the tubing that connects the pump to the autosampler As this filter frit becomes clogged the system backpressure rises Replace this filter frit when the system backpressure rises above its typical operating limits Figure 4 Line body and filter frit Surveyor Plus User Guide for LC Devices Thermo Scientific Autosampler 1 Introduction to the Surveyor Plus LC System Autosampler Thermo Fisher Scientific offers two autosampler models in the Surveyor Plus product line the full featured Surveyor Autosampler Plus and the Surveyor Autosampler Plus Lite The full featured autosampler includes a built in column oven 5 to 95 C and a temperature controlled tray sample compartment 0 to 60 C Both models let you inject samples and perform sample preparation tasks automatically Note To convert from C to F use the following equation F 1 8 x C 32 For more information about the autosampler see these topics e Tray Compartment e Vial and Well Notation e Injection System e Injection Modes e Temperature Control Tray Compartment Thermo Sc
248. k the light throughput to the diode array 170 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls PDA Detector Direct Controls Viewing Exporting and Clearing the Error Log for the PDA Detector You can access an error log for the PDA detector from the Xcalibur data system 1 bd To view the error log Open the Information page of the Surveyor PDA Direct Control dialog box see Information Page on page 181 Click Request Log To export the log to a Microsoft Excel Spreadsheet Click Export Log To clear the error log Click Clear Log Checking the Firmware Version of the PDA Detector KD bd Configuration Page Thermo Scientific To check the firmware version of the PDA detector Open the Information page of the Direct Control dialog box for the PDA detector see Information Page on page 181 The firmware version of the PDA detector is displayed in the lower right portion of the Information page Use the Configuration page of the Surveyor PDA Plus Direct Control dialog box to perform these procedures Turning the Lamps On or Off Resetting the Lamp Usage Hours Changing the Polarity of the Analog Outputs Testing the Analog Outputs Setting the Lamp Startup Time To open the Configuration page of the Direct Control dialog box Open the Surveyor PDA Direct Control dialog box see PDA Detector Direct Controls on page 162 Click the Configuration
249. l Partial or No Waste For more information see Injection Modes on page 19 f Click Apply The autosampler loads the sample into the sample loop connected to the injection valve as follows The XYZ arm of the autosampler moves to the sample location and then lowers the needle into the sample vial The syringe plunger descends drawing sample into the needle tubing The XYZ arm moves back to the injection port and then lowers the needle into the injection port The syringe plunger ascends pushing sample into the injection port through the transfer tubing and into the sample loop of the injection valve 5 On the Surveyor MS Pump Plus page select the Release Injection check box The injection valve switches to the inject position allowing mobile phase to backflush the sample out of the sample loop and into the LC column Thermo Scientific Surveyor Plus User Guide for LC Devices 343 ee ie Index Numerics 384 well microplates well positions 10 302 96 well microplates well positions 7 A absorbance level zeroing for the PDA detector during a run 105 zeroing for the UV Vis detector 23 zeroing on the Display page 178 accessories reservoir vials 5 solvent lines 23 standard vials 6 wash bottle assembly 13 active and pinned cells Qual Browser 225 air bubbles loaded into the sample loop 19 alpha values for flow rate adjustment 265 268 analog outputs changing the polarity 164 testing 165 areas of peaks
250. l scan and the discrete channel wavelengths at the moment that you clicked Snapshot For an intensity diode method the file contains the intensity values for the scan of the diode array and the intensity values for up to three individual diodes Note The Snapshot button is available only after you click the Start Data button and the graphical display has started updating Zero Data Zeros the absorbance data After you click Zero Data the Current Method status box displays the message Zeroed Data Display Note This button is only available in the wavelength absorbance mode Stop Data Stops the updating of the graphical display After you click Stop Data the Current Method status box displays the message Stopped Data Display Levels mAU Channel A B C level This graphical display shows the intensity or absorbance level of each discrete channel A B or C specified in the method Lamp Lifetimes hours Deuterium Displays the cumulative time in hours that the Deuterium lamp has been in the On state since you clicked the Reset button Note Click Reset Lifetime on the Configuration page whenever you replace the deuterium lamp This resets the Last Reset readback to the current date and time and sets the Lifetime readback to zero Tungsten Displays the cumulative time in hours that the tungsten lamp has been in the On state since you clicked Reset Lifetime Note Click the Reset Lifetime button on
251. le loop with mobile phase the injection valve remains in the inject position during the entire run Figure 18 Injection valve in the inject position Transfer tubing p To column Mobile phase From mm Wash solvent pump 18 Surveyor Plus User Guide for LC Devices Thermo Scientific Injection Modes 1 Introduction to the Surveyor Plus LC System Autosampler The autosampler can operate in any of the following three modes e No Waste Injection Mode e Partial Loop Injection Mode e Full Loop Injection Mode The optimum injection mode depends on the amount of sample that you have and the degree of precision that your application requires No Waste Injection Mode Thermo Scientific The no waste injection mode is a technique that withdraws only the exact amount of sample requested from the sample vial Of the three injection modes the no waste injection mode uses the least amount of sample but it is also the least precise Use this injection mode to conserve sample Approximately 0 25 pL of the sample is lost as it travels from the injection port through the transfer tubing and into the injection valve Because of this loss the minimum recommended injection volume is 1 0 pL The quantity of lost sample depends on the syringe rate Decreasing the syringe rate decreases the sample loss For best results use a syringe rate no greater than 4 piL s for the no waste injection mode IMPORTANT For no waste injections do t
252. length channels in the visible range 366 700 nm The acquisition wavelengths are time programmable Other options Zero on Wavelength Change When this check box is selected the detector zeros the absorbance data at the times specified in the Time column for rows 2 through the last time line Programmable wavelength table Time Specifies the time when the detector is to start monitoring the wavelength or wavelengths listed in the Wavelength 1 and Wavelength 2 columns 108 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Saving the Instrument Method Table 27 UV Vis detector method parameters Sheet 2 of 2 Parameter Description Wavelength 1 Specifies the wavelength that the detector is to start monitoring at the time specified in the Time column To view the chromatogram for this wavelength in Qual Browser select Wavelength 1 in the Range list for the Chromatogram window Wavelength 2 Specifies the wavelength that the detector is to start monitoring at the time specified in the Time column To view the chromatogram for this wavelength in Qual Browser select Wavelength 2 in the Range list for the Chromatogram window Saving the Instrument Method The following procedure applies only to the Xcalibur data system For other Thermo Scientific mass spectrometry applications refer to the Help To save the instrument method 1 Choose File gt Save As The Save As dialog bo
253. lumn from the Available Columns list and click Add To remove a column from the sequence select the column from the Displayed Columns list and click Remove To alter the position of the columns in the sequence select the column from the Displayed Columns list and click either Move Up or Move Down as appropriate Selecting the Vial Locations Interactively Use the Vial Selection dialog box to select specific vials for the sequence template 1M To interactively select vial or well locations for the sequence list 1 In the Sequence Setup window choose File gt New The New Sequence Template dialog box appears 2 In the Samples area click Select Vials The Vial Selection dialog box appears see Figure 117 206 Surveyor Plus User Guide for LC Devices Thermo Scientific 7 Sequence Setup Creating a Single Sample Sequence Figure 117 Vial Selection dialog box Vial Selection 0 selected 3 Click on a vial position to add it to the sequence template 4 When you have finished making your selection click OK The vial or well locations appear in the position column in the order that you selected them Thermo Scientific Surveyor Plus User Guide for LC Devices 207 7 Sequence Setup Creating a Single Sample Sequence Saving the Sequence To save the sequence 1 Choose File gt Save As The File Summary Information dialog box appears see Figure 118 Figure 118 File Summary Information dialog box
254. lus User Guide for LC Devices 325 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Figure 228 PDA dark current calibration text file PD PDA Plus Dark Calibration txt Notepad File Edit Format wiew Help PDA Dark Current Count Printed Fri Jan 28 10 57 33 2005 Dark Current Count List Diode Count 5313 7361 7261 7159 7065 6948 6855 6660 6587 6418 6361 ovo nAoO BR WNP OO he 9 Click Apply to download the calibration results to the detector The wizard proceeds to the success confirmation page see Figure 229 Figure 229 Success confirmation page Dark Current Calibration FW calibration has been successfully applied Cancel Help 10 Click Finish to close the wizard The calibration is saved and the date and time of calibration are displayed in the Dark Current Calibration area of the Calibration page as the Last Calibration see Figure 230 326 Surveyor Plus User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Figure 230 Calibration page showing the Currently Calibrated status Thermo Scientific Surveyor Plus User Guide for LC Devices 327 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Performing a Wavelength Calibration The alignment of the spectrum on the diode array depends on the physical alignment of various components of the optical bench Th
255. m Nominal size of the concentric syringe minus the current 500 pL Reservoir to Sample contents liquid air bubble of the needle tubing Transfer from Nominal size of the concentric syringe minus the current 500 pL Reservoir to Reservoir contents liquid air bubble of the needle tubing Syringe Speed Range for Sample Preparation Tasks The syringe speed range for sample preparation tasks depends on whether the task can use either syringe plunger or only the inner plunger If you enter a speed that is invalid for the volume you are transferring an error message appears For information about the syringe speed range for the sample preparation tasks see these topics e Syringe Speed for Tasks that Can Use Either Plunger e Syringe Speed for Tasks that Use the Inner Plunger 124 Surveyor Plus User Guide for LC Devices Thermo Scientific 4 Sample Preparation Routines Syringe Speed Range for Sample Preparation Tasks Syringe Speed for Tasks that Can Use Either Plunger Thermo Scientific The syringe speed range is determined by the type of syringe and the volume requested For a concentric syringe the autosampler can use either the outer or inner plunger to draw liquid into or expel liquid from the needle tubing For the tasks listed in Table 32 the autosampler uses the following The outer plunger if the volume of liquid air being transported is greater than the nominal syringe size e The inner plunger if the volume of liqui
256. m lamp Graphic Text Meaning ff Th ium lamp is off Q Deuterium Lamp is Off a a i Starting The deuterium lamp is starting up 9 iha ite which requires about 1 5 min On The deuterium lamp is on When the status is On the Turn Off button is available When the status is Off the Turn On button is available Deuterium Lamp is On Last Lifetime Reset Displays the date and time that the deuterium lamp was last reset readback Lifetime Hours Elapsed Displays the cumulative time in hours that the deuterium lamp has been in the On state since you clicked the Reset Lifetime button Turn On Off button 3 Turns on the deuterium lamp if its current status is Off Q Deuterium Lamp is Off A Turns off the deuterium lamp if its current status is On 9 Deuterium Lamp is On Reset Lifetime button Resets the date and time monitored by the Last Reset readback and the Lifetime readback Note Click Reset Lifetime whenever you replace the deuterium lamp This resets the Last Reset readback to the current date and time and restarts the Lifetime readback at zero Thermo Scientific Surveyor Plus User Guide for LC Devices 173 6 Direct Controls PDA Detector Direct Controls Table 48 Configuration page of the Direct Control dialog box for the PDA detector Sheet 2 of 4 Parameter Description Tungsten Lamp Status readback Indicates the status of the tungsten lamp as follows Graphic Test Meaning i On The t
257. mation dialog box Table 62 Validation Information dialog box parameters Parameter Time Description To change the date that the validation was performed click the arrows to increase or decrease the value and then click Set Initial Name To change the name of the person who performed the validation type the new value in the Initial Name box and then click Set Current Values This readback displays the current time and initial name Button Set 312 Surveyor Plus User Guide for LC Devices Enter the appropriate values in the Time box and the Initial Name box and then click Set to set the values Thermo Scientific ee i PDA Detector Performance Check and Calibration This chapter describes the performance verification and calibration procedures for the PDA detector Contents e Verifying the Performance of the PDA Detector e Calibrating the PDA Detector The PDA detector is factory tested for linearity noise and drift Because of the sensitivity of its optical bench adjust the light throughput to the diode array and recalibrate the PDA detector after you install it and each time you move it change its flow cell or replace either of the lamps Verifying the Performance of the PDA Detector Before you perform either calibration procedure turn on both lamps see Turning the Lamps On or Off on page 163 let the temperature of the detector stabilize for approximately one hour and adj
258. mmands and options provided by the data system to control the position of the XYZ arm To make the XYZ arm automatically move to the back of the tray compartment when you open the tray door select the Verify Door is Closed option which is available when you configure the autosampler device driver see Communication Page on page 52 e To move the XYZ arm to the back of the tray compartment use the Position Arm to Access Tray direct command see Removing and Installing Sample Trays on page 199 e To move the XYZ arm mechanism to its home position above the injection port use the Set Arm to Home Position direct command To move the XYZ arm mechanism to the middle front of the tray compartment allowing easy access to the needle use the Remove Needle direct command Thermo Scientific Surveyor Plus User Guide for LC Devices 15 1 Introduction to the Surveyor Plus LC System Autosampler Needle Assembly and Needle Tubing Assembly The needle assembly consists of a blunt tip needle a latch nut a flag a compression spring and a 10 32 fitting that connects to the needle tube assembly The needle fits into the needle mount on the XYZ arm The needle tube assembly connects the solvent path between the needle and the syringe valve and consists of low pressure tubing an internally threaded fitting that connects to the needle assembly fitting a sleeve a black or red PVC cap a needle tube guide that attaches to the x axis p
259. motor controls the speed of the plunger You can specify how fast in microliters per second the syringe withdraws liquid from a tray vial or plate well and then expels liquid into the autosampler injection port The default syringe speed and the syringe speed range depend on the syringe size see able 21 The appropriate syringe speed depends on the sample For viscous samples use a syringe speed lower than the default value to avoid stalling the syringe For samples of low viscosity or surface tension use a lower syringe speed to prevent the sample bolus from breaking apart during the transport process Tip Select the syringe size on the Communication page of the Surveyor Autosampler Configuration dialog box The autosampler ships with a 250 pL concentric syringe Thermo Scientific Surveyor Plus User Guide for LC Devices 91 3 Instrument Method Setup Autosampler Instrument Method Parameters Table 21 Syringe speeds for injections Syringe size Minimum speed Maximum speed Default speed uL uL s pL s uL s 100 0 3 13 2 3 00 250 0 8 33 0 8 0 500 1 6 66 1 8 0 2500 8 2 330 8 25 0 For no waste injections you can use a higher syringe speed to push the sample from the autosampler injection port to the injection valve and a lower loop loading speed to meter the sample into the sample loop The range for the loop loading speed depends on the syringe size see Table 22 Table 22 Loop loading speeds
260. mple Location Sample Locations for the Sample Preparation Tasks on page 122 Volume Draw Eject and Transfer Volumes for Sample Preparation Tasks on page 123 Syringe Speed Syringe Speed for Tasks that Can Use Either Plunger on page 125 Needle Height Default 2 mm Range 0 to 18 mm Source Reservoir bottle RV1 RV2 RV3 or RV4 Transfer from Sample to Reservoir Transfers liquid from a vial or well to a reservoir vial Parameter Sample Location Reference range or selections Sample Locations for the Sample Preparation Tasks on page 122 Volume Draw Eject and Transfer Volumes for Sample Preparation Tasks on page 123 Destination RV1 RV2 RV3 or RV4 Reservoir Syringe Speed Syringe Speed for Tasks that Can Use Either Plunger on page 125 Needle Height Default 2 mm Range 0 to 18 mm Air Bubble 0 to 10 pL Transfer from Sample to Sample Transfers liquid from one vial or well to another vial or well Parameter Source Sample Reference range or selections Sample Locations for the Sample Preparation Tasks on page 122 Destination Sample Locations for the Sample Preparation Tasks on page 122 Sample Volume Draw Eject and Transfer Volumes for Sample Preparation Tasks on page 123 Syringe Speed Syringe Speed for Tasks that Can Use Either Plunger on page 125 Source Vial Needle Default 2 mm Height Rang
261. n 275 test fixture installing 276 Comm LED autosampler 38 LC pump 37 MS pump 36 PDA detector 39 UV Vis detector 40 communication Xcalibur data system 41 compliance FCC vii regulatory iii WEEE ix compressibility defined 262 updating 266 values 264 concentric syringe See syringe autosampler configuration options autosampler 45 LC pump 63 MS pump 61 PDA detector 65 UV Vis detector 66 contact closure cable 32 conventional vial trays 6 Custom List Name dialog box 337 custom vials and microplates calibrating the bottom distance of 305 selecting tray options 47 dark current calibration 323 data acquisition analyzing acquired data 219 starting 211 viewing real time 214 data files naming 203 opening 219 dead volume for transfer tubing configuring 54 Degas LED LC pump 37 MS pump 36 degassing unit built in 2 23 delay volume LC pump 3 delay PDA detector timed event 103 346 Surveyor Plus User Guide for LC Devices delta values PDA calibration 335 Description box LC column 69 detectors See PDA detector or UV Vis detector devices adding to the instrument configuration 44 start instrument 213 status viewing 137 turning into Standby mode 154 turning on off 154 dilutions sample preparation example for automating 127 diode numbers 102 diode voltage leakage 323 Direct Control dialog box autosampler 197 LC pump 188 MS pump 190 PDA detector 162 UV Vis detector 183 discrete channel wavelengths in
262. n valve switches to the inject position the autosampler sends a signal to the detector to begin data acquisition 6 Set up how the run is started as follows To start the run automatically select the Start When Ready check box After you complete the entries and selections in the Run Sequence dialog box and click OK the run begins after the pump sends a pump ready signal to the autosampler The pump does not indicate the Ready state until it monitors a stable backpressure as defined in your instrument method To start the run manually clear the Start When Ready check box 7 In the After Sequence Set System area select one of these three options e To keep the devices in the On state select the On option e To automatically turn off the solvent flow from the pump and the detector s lamps at the end of the sequence run select the Off option e To turn off the solvent flow from the pump but keep the lamps at the end of the sequence run select the Standby option 8 Keep the parameters in the other areas at their defaults You can use the Instrument Method and Programs areas in the Run Sequence dialog box to specify particular acquisition or processing requirements For full details of these features refer to the Xcalibur Help 9 Start the run as follows For automated runs click OK to start the run e For manual runs click OK and then choose Actions gt Start Analysis from the Sequence Setup menu To subsequently
263. n with the data system has been established Run Flashing Amber An error condition such as an XYZ arm jam or initialization startup error has occurred Green The autosampler is in the Ready state Flashing Green An injection or timed event is in progress Temp Amber A temperature change within the column oven or tray temperature zones is in progress Green The column oven and tray temperature zones are in 38 Surveyor Plus User Guide for LC Devices equilibrium at the set temperature The Wait for Temperature Ready check box on the Communication page of the Instrument Configuration application is not selected Thermo Scientific 1 Introduction to the Surveyor Plus LC System Status LEDs PDA Detector LED States Table 4 lists the LED states for the PDA detector Table 4 PDA detector LED states and their meaning LED State Amber Power Green The detector is turned on and receiving power Comm Amber There is no communication with the data system Flashing amber The rotary switches are set to 00 and firmware is being downloaded to the CPU of the detector Green Communication to the data system computer has been established Run Amber The PDA detector is not ready to start a run for one of the following reasons e You have not downloaded a valid instrument method since the last time you powered on the detector Both lamps are off or one of the lamps is failing to turn on e The lamp or wavelength calibration is
264. nar flow of fluid within the stainless steel sample loop IMPORTANT To make precise partial loop injections use a sample loop that is at least twice the size of the injection volume The accuracy of the nominal sample loop volume is 20 Because the actual volume of the 25 pL sample loop provided with the autosampler is anywhere from 20 to 30 pL limit the maximum injection volume with this loop to 10 uL To inject more sample use a larger sample loop Full Loop Injection Mode The full loop injection mode is a technique that withdraws a sample volume from the vial sufficient to overfill the sample loop by a minimum factor of two Because the physical size of the sample loop determines the actual injection volume not the metering action of the stepper motor a full loop injection is very reproducible However because the intent of the full loop injection mode is to completely fill the sample loop you cannot inject variable amounts of sample Full loop injection is useful when you want maximum precision and have unlimited sample To change the injection volume you must change the sample loop size Note Full loop injections are limited to the size of the configured sample loop In the full loop injection mode the autosampler withdraws a large excess of solution from the sample vial according to the following equation Amty 3 x Vinj Vdead 7 5 pL Where Amt sample volume withdrawn by the autosampler Vinj user spe
265. nd the wash bottle see Reservoir Content Page on page 92 8 In the Wash Volume pL box keep the wash volume at its default value of 0 pL To wash the exterior of the needle after each injection type a value from 1 to 6000 pL in the Wash Volume box 9 In the Flush Speed uL s box set a flush speed appropriate for the flush solvent e Ifyou are using a flush solvent of low viscosity such as methanol keep the flush speed at its default 100 pL s for the 250 pL concentric syringe e Ifyou are using water or a methanol water mixture as the flush solvent reduce the flush speed Tip If you hear a grinding noise from the autosampler as it performs a flush lower the flush speed 10 In the Post Injection Valve Switch Time min box keep the time value at its default of 0 minutes for most applications This leaves the sample loop in the inject position during the entire run allowing ample rinsing of the sample loop between injections 11 In the Tray Temperature Control area to control the temperature of the tray compartment select the Enable Tray Temperature Control check box Then type an appropriate temperature from 0 to 60 C in the Temperature box 12 In the Column Oven Control area to control the temperature of the LC column select the Enable Column Oven Control check box Then type an appropriate temperature from 5 to 95 C in the Temperature box Controlling the temperature of the LC column increases the
266. net cable to the Ethernet port on the back of the detector and to the Ethernet switch The unit ID setting on the back panel of the detector must match the configured stack number To specify the configuration options for the PDA detector 1 In the Configured Devices list double click the Surveyor PDA Plus icon Surveyor PDA Plus The Surveyor PDA Plus Configuration dialog box appears see Figure 43 Figure 43 Surveyor PDA Plus Configuration dialog box Surveyor PDA Plus Configuration Stack Number zz Please enter the stack number for the Surveyor PDA Plus Cancel Help 2 In the Stack Number box type the appropriate number unit ID 3 Click OK to close the Surveyor PDA Plus Configuration dialog box When you have finished configuring the instrument devices go to the next topic Closing the Foundation Application Thermo Scientific Surveyor Plus User Guide for LC Devices 65 2 Thermo Foundation Instrument Configuration Closing the Foundation Application Surveyor UV Vis Plus Detector Configuration Settings The UV Vis Detector communicates with the data system computer through an Ethernet connection To specify the configuration settings for the UV Vis detector 1 In the Configured Devices list double click the Surveyor UV Vis icon Surveyor UY AVIS The Surveyor UV Vis Configuration dialog box appears see Figure 44 Figure 44 Surveyor UV Vis Configuration dialog box Surveyor UV VIS Configuration
267. new sample location a In the Prep Operations list select Mix at Sample The task parameters appear below the Add To Task List button Keep all the default parameter settings for the Mix at Sample task except those listed below see Figure 73 Parameter Setting Sample Location Autosampler action Aspirates and expunges 250 uL sample from the current 1 vial location listed in the sequence table 10 times Location Relative Location Location Current 1 Volume 250 Cycles 10 Click Add To Task List to add this task to the sample preparation routine When the autosampler performs this task it aspirates and expunges 250 pL of the sample solution in the current 1 vial location 10 times Figure 73 Settings for the Mix at Sample task Prep Operations Deposit liquid in reservoir Draw from reservoir Draw from sample Flush to waste Mix at reservoir Transfer from reservoir to reservoir Transfer from reservoir to sample Transfer from sample to reservoir Transfer from sample to sample Wait time Wash needle Add To Task List gt gt Sample Location Absolute location Current 1 z 250 0 Relative location Volume ful Draw speed ul s 250 00 Delivery speed fuls dhl 250 00 at Cycles 10 0 Needle height mm 20 4 JH Default setting Default settings Surveyor Plus User Guide for LC Devices 131
268. ng e Use the up or down arrow to the left of the time entry to scroll to the time value that you want or Press the UP or DOWN key on your computer keyboard to scroll to the time value that you want e Type the numeric value that you want 3 To change AM to PM or the reverse highlight the current setting and then type AM or PM 4 To change the day of the week or to turn off the lamp startup feature in the On These Days list select Never Weekdays or Everyday 5 Click OK to apply the new lamp startup time Lamp Startup Time Parameters Table 47 describes the parameters in the Lamp Startup Time dialog box Table 47 Lamp Startup Time dialog box parameters Parameter Description Xcalibur Should Start the Lamps At Specifies the time that the Xcalibur data system automatically turns the lamps on Default 4 55 PM On These Days Specifies the days that the Xcalibur data system automatically turns the lamps on The selections are Never Weekdays and Every Day Default Weekdays Buttons OK Applies the settings and closes the dialog box Cancel Cancels the applied time value or date Thermo Scientific Surveyor Plus User Guide for LC Devices 167 6 Direct Controls PDA Detector Direct Controls Checking the Chromatographic Baseline Use the Display page of the Direct Control dialog box to check the chromatographic baseline see Display Page on page 176 gt bX To check the stabili
269. not valid Flashing amber The PDA detector is in an error state while in the Run mode Green The detector is ready for a run Flashing green A run is in progress and the detector is sending data to the data system computer Lamps Amber The lamps are off or the D2 lamp is starting It takes approximately 10 seconds for the D2 lamp to turn on Green One or both lamps are turned on Thermo Scientific Surveyor Plus User Guide for LC Devices 39 1 Introduction to the Surveyor Plus LC System Status LEDs UV Vis Detector LED States 40 Table 5 lists the LED states for the UV Vis detector Table 5 UV Vis detector LED states and their meaning LED State Meaning Power Green The detector is on Comm Green Communication to the data system computer has been established Amber There is no communication with the data system Run Green The detector is ready for a run Flashing green A run is in progress and the detector is sending data to the data system computer Flashing Amber An error has occurred during a run Lamps Green One or both lamps are turned on Amber The lamps are off Surveyor Plus User Guide for LC Devices Thermo Scientific ee i Thermo Foundation Instrument Configuration This chapter provides information about configuring the LC device drivers Contents e Checking the Communication Hardware e Opening the Thermo Foundation Instrument Configuration Application e Adding Device
270. nsing the tray compartment door Off C On Auto Dead Volume ul 17 0 _ Type the value specified on the label attached to the transfer tube Sample Loop Volume ul 25 0 assembly 3 In the Stack Address box type the appropriate stack address or use the up and down arrows to select the appropriate stack address The stack address must match the unit ID setting located on the back panel of the autosampler The rotary switches of the unit ID are factory set to 01 and the default Stack Address is 1 The value of 00 is reserved for service functions Under Syringe in the Type list select the size of the syringe that is attached to the autosampler The default is Concentric 250 pL the syringe that ships with the autosampler Optional To prevent the autosampler from making an injection when the temperature zones are not equilibrated at the set temperature select the Wait for Temperature Ready check box When the Wait for Temperature Ready check box is selected the autosampler does not trigger a run until the column oven temperature the sample tray temperature or both have reached their setpoint values Surveyor Plus User Guide for LC Devices 53 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings 6 10 Optional To prevent the autosampler from making an injection when the tray compartment door is open select the Verify Door Is Closed check box
271. nsion 1 000 Time Min Event Value 0 000 Tension 7 1 000 Add Delete Change Help b Click Auto Calc Initial Events to force the Avalon peak integration algorithm to determine the best values for the following initial events Start Threshold End Threshold Peak Threshold P P Threshold Bunch Factor Negative Peaks and Tension Figure 161 shows a chromatogram for the 239 nm scan wavelength that is integrated with the best initial integration values as determined by the Avalon peak integration algorithm The peaks areas are shown above the apexes of the integrated peaks Thermo Scientific Surveyor Plus User Guide for LC Devices 253 8 Qual Browser Calculating the Purity of the Chromatographic Peaks Figure 161 Avalon Peak Detection Settings page displaying a chromatogram acquired with the PDA detector C Xcaliburidata Test Mixture A01 RT 0 00 10 00 9 AA 6667672 NL 1000000 1 02E6 nm 238 5 900000 239 5 PDA Avalon 800000 Test Mixture A01 uAU oa Oo Oo oO oO Oo AA 1592426 AA 3335200 AA 3890122 AA 859596 Time min Calculating the Purity of the Chromatographic Peaks The data system can calculate the spectral purity of your chromatographic peaks by comparing the similarity of the spectra across the peak to a spectrum from the peak apex The calculation is affected by the integration of the scan chromatogram and by the scan threshold peak coverage and scan w
272. nstrument devices you must close the Instrument Configuration application before you can open the Thermo Scientific data system Note The Accela UV Vis Detector driver is provided with LC Devices 2 5 0 or later Surveyor Autosampler Plus Configuration Settings Use the Surveyor Autosampler Configuration dialog box to specify the configuration settings for the autosampler For information about specifying the configuration settings for the autosampler see these topics e Tray Page e Communication Page e Signal Polarity Page e Firmware Page To open the Surveyor Autosampler Configuration dialog box 1 If it is not already open open the Thermo Foundation Instrument Configuration window see Opening the Thermo Foundation Instrument Configuration Application on page 43 2 In the Configured Devices list double click the Surveyor AS icon Surveyor 4S Thermo Scientific Surveyor Plus User Guide for LC Devices 45 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings The Surveyor Autosampler Configuration dialog box appears with the Tray page displayed see Figure 35 Figure 35 Tray page of the Surveyor Autosampler Configuration dialog box Surveyor Autosampler Configuration Tray Communication Signal polarity Firmware Cancel Help 46 Surveyor Plus User Guide for LC Devices Thermo Scientific 2 Thermo Foundation Instrument Configuration Specifying the C
273. nt Range 2000 to 4000 milli absorbance units mAU Delay Note This box is available if you select Level Trigger in the Event Type list Specifies the delay time in seconds that is to occur between the activation of the event by the preset absorbance level being exceeded and the actual change of the event output state at the back panel terminals of the PDA detector This delay compensates for the time interval between for example when a compound leaves the detector and when it reaches a fraction collector Default 0 seconds Range 0 to 65 535 in increments of 1 Buttons New Click this button to open the Timed Event dialog box where you can add external events to the external events table Delete Click this button to remove an external event from the external events table Select the external event that you want to remove and then click Delete Delete All Thermo Scientific Click this button to remove all external events from the external events table To remove all events click Delete All Surveyor Plus User Guide for LC Devices 103 3 Instrument Method Setup Triggering an External Device with the PDA Detector Triggering an External Device with the PDA Detector The PDA detector can trigger an external device during a chromatographic run For example you can program the PDA detector to trigger a fraction collector as an analyte begins to elute from the LC column Note You can al
274. o Pump Operating Time Reset Position Pistons Maintenance Position Thermo Scientific Resets the recorded operating time for the Surveyor LC Pump Plus to zero If you install a new motor click Reset in the Pump Operating Time area to set the recorded Pump Operating Time back to zero Sets the pistons to the maintenance position Set the pump pistons to the maintenance position before removing the pump heads To set the pistons to the maintenance position click Maintenance Position Surveyor Plus User Guide for LC Devices 271 9 LC Pump Calibration and Record Keeping Firmware Version Information for the Surveyor LC Pump Plus Firmware Version Information for the Surveyor LC Pump Plus Use the Configuration Surveyor LC Pump Direct Control dialog box see Figure 174 to view the firmware versions of the pump s Main board and Pump Converter board Figure 174 Configuration Surveyor LC Pump Direct Control dialog box Configuration Surveyor LC Pump Direct Control Firmware Versions Pump Main Board 1 10 Pump Converter Board 1 14 To view the firmware version of your Surveyor LC Pump Plus 1 Open the pump view 2 From the menu bar choose Surveyor LC Pump gt Direct Control gt Configuration The Configuration Surveyor LC Pump Direct Control page appears Configuration Page Parameters Table 60 describes the parameters on the Firmware page Table 60 Configuration Surveyor LC Pump Direct Con
275. o 110 0 C Note The external standard is the thermometer Figure 180 Diagnostic External Standard page of the Column Oven Air Sensor Calibration wizard Diagnostic External Standard External standard temperature C j2a q Adjust Type the temperature reading from the thermometer that you temporarily installed in the column oven compartment b Verify that the current temperature on the Oven page is still displaying 30 0 C c On the Diagnostic External Set Target page see Figure 180 click Adjust Thermo Scientific Surveyor Plus User Guide for LC Devices 279 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler The data system downloads the temperature calibration to the autosampler and the Finish button becomes available see Figure 181 Figure 181 Diagnostic External Standard page of the Column Oven Air Sensor Calibration wizard Diagnostic External Standard External standard temperature C 29 8 Adjust Cancel Help Finish button d Repeat step 3a through step 3c until the readings from the 869C thermometer and the current temperature readout agree within 0 2 C 4 When the temperatures on the 869C thermometer and the Current Temperature readback are within 0 2 C of each other click Finish see Figure 181 5 On the Oven page verify that the Current Temperature readback is stable at 30 0 C with a maximum temperature drift of 0 2 C 6
276. o 49 nm The maximum scan range for a particular bandwidth is limited as follows e Start Wavelength minimum 190 nm bandwidth 1 2 e End Wavelength maximum 800 nm bandwidth 1 2 Increasing the bandwidth decreases the spectral resolution see Figure 61 Figure 61 Spectra of toluene effect of bandwidth on spectral resolution soo 2 20 Min 500 Toluene 1 nm bandwidth 400 400 300 ann 11 nm bandwidth 5 x 200 200 100 100 0 0 230 240 250 260 270 280 nm Surveyor Plus User Guide for LC Devices 97 3 Instrument Method Setup PDA Detector Instrument Method Parameters 6 To collect discrete channel data select one of the options in the Channels area and then make the following entries a Inthe Sample Rate list select a sampling rate in data points per second Higher data rates for discrete channels do not add significantly to the data file size b For each discrete channel A B and C type a wavelength from 190 to 800 nm in the Wavelength nm box and a filter bandwidth in the Filter Bandwidth nm box Depending on the discrete wavelength the acceptable bandwidth range is 1 to 49 nm in odd number increments with 1 nm meaning no filtering Bandwidth values outside the range of the detector are not allowed For example for the discrete wavelength of 200 nm the maximum bandwidth setting is 21 nm At a bandwidth setting of 21 nm the reported absorbance value for 200 nm is a weight
277. obile phase is diverted through a heat exchanger located behind the column oven As it passes through the heat exchanger the mobile phase equilibrates to the temperature of the column oven before it reaches the injection valve The heat exchanger adds only 3 uL of gradient delay volume to the LC system The Surveyor Plus product line includes two detectors that you can control from your Thermo Scientific data system a PDA detector and a UV Vis detector The PDA detector in combination with the 5 or 1 cm LightPipe flowcell provides the highest level of sensitivity available in photodiode array detection for HPLC The UV Vis detector can monitor two wavelength channels Both detectors have a dual lamp optical bench that covers the UV visible spectrum from 190 to 800 nm For more information about the Surveyor Plus detectors see these topics e PDA Detector e UV Vis Detector Surveyor Plus User Guide for LC Devices 21 1 Introduction to the Surveyor Plus LC System Detector PDA Detector The PDA detector is a full featured time programmable photodiode array detector that can scan the full ultraviolet visible range from 190 to 800 nm The detector can acquire data at a rate of up to 20 Hz with a 20 bit digital conversion The optimal location for the PDA detector is above the autosampler and below the solvent platform The data system computer controls the PDA detector through an Ethernet communication link The PDA detector consists of a
278. of the clamp d Verify that the sensor is between the upper and lower column clamps and that it is not touching any metal e Tighten the thumbscrew on the sensor route the cable of the sensor so as not to interfere with the door and then close the column oven door 5 Open the Calibration dialog box for the autosampler For information about accessing the Calibration dialog box from the Xcalibur data system see Calibrating the Autosampler on page 274 Specifying the Internal Set Target for the Column Oven Calibration Temperature 276 Use the Internal Set Target page of the Column Oven Air Sensor Calibration wizard to specify the calibration temperature To specify the internal set target for the calibration temperature 1 Set up the system to perform the column oven calibration see Preparing to Calibrate the Column Oven Temperature on page 275 2 Select the Column Oven Air Sensor Calibration option and then click Next The Diagnostic Internal Set Target page of the Column Oven Air Sensor Calibration wizard appears see Figure 176 The default calibration temperature is 50 0 C Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 176 Diagnostic Internal Set Target page of the Column Oven Air Sensor Calibration wizard with the default temperature setting of 50 0 C Diagnostic Internal Set Target Calibration t
279. olvent platform MS Pump Detector Interconnect cable back panel To gt MS detector Autosampler back panel Surveyor MS Pump Plus back panel Not drawn to scale Not used For more information about connecting the interconnect cable to the devices of your LC system refer to the Surveyor Plus LC System Getting Connected Guide Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Status LEDs During a run the system issues the following sequence of run control signals l 2 Status LEDs The data system computer issues a request to perform an injection When the autosampler becomes ready it issues the A S Ready signal The autosampler goes into the Ready state when all the configuration and instrument method conditions are met including the closing of the tray compartment door and the sample tray and column oven temperature zone readings showing they are within tolerance of their setpoints When the pump pressure stabilizes the pump issues the Pump Ready signal to the autosampler The autosampler injection valve switches to the fill position and then the autosampler pushes sample into the sample loop The autosampler issues the Gradient Start signal to the pump This signal commands the pump to start its gradient program When its piston cam reaches the home position the pump issues the Inject Hold release signal to the autosampler
280. on 1 Click Move the Arm to the Home Position The XYZ arm moves to the home position The Next button becomes available 2 Click Next to proceed to the next page of the Arm Calibration wizard Go to the next procedure Aligning the Light Beam with the Target 296 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Aligning the Light Beam with the Target Use this page of the Arm Calibration wizard see Figure 202 to adjust the fine position of the XYZ arm Two lead screws and two stepper motors control the x axis and y axis position of the XYZ arm see Figure 203 The Left and Right buttons move the XYZ arm along the x axis The Forward and Backward buttons move the XYZ arm along the y axis Figure 202 Alignment buttons page Diagnostic Arm Calibration Please align the light beam directly over the injector port Control the needle movement with direction buttons Step Left fix 61 75 microns Right gt 5x 158 75 microns Backward gt 10 317 5 microns 25x 793 75 microns 50x 1587 5 microns Down Y toed ue Thermo Scientific Surveyor Plus User Guide for LC Devices 297 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 203 XYZ arm of the Surveyor Autosampler Plus X axis stepper motor XYZ arm X axis axis lead screw y lead screw
281. on Instrument Configuration Turning Off the Computer s Energy Saving Features 24 The Surveyor PDA Plus Detector Surveyor UV Vis Detector Surveyor LC Pump Plus and the Surveyor Autosampler Plus communicate with the data system computer through an Ethernet link To ensure communication between the data system computer and the LC system turn off the data system computer s screen saver and energy saving features To turn off the screen saver and energy saving features for the Windows XP operating system 1 From the Windows XP desktop choose Start gt Control Panel Tip Ifyou selected the Classic Start Menu option for the Start menu properties choose Start gt Settings gt Control Panel 2 Double click Display The Display Properties dialog box appears Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Turning Off the Computer s Energy Saving Features 3 Click the Screen Saver tab The Screen Saver page appears see Figure 20 Figure 20 Screen Saver page of the Display Properties dialog box Windows XP Display Properties Themes Desktop Screen Saver Appearance Settings Screen saver CE vy Settings Preview Wait 15 minutes v On resume password protect Monitor power To adjust monitor power settings and save energy click Power 4 In the Screen Saver list select None 5 Click Apply to accept this setting 6
282. on and the no waste injection modes draw transfer solution from the wash bottle If the wash bottle runs dry the wash bottle tubing and the syringe barrel fill with air If the syringe runs dry the autosampler cannot draw sample into the needle tubing Figure 11 shows the syringe valve in the wash bottle position Figure 11 Drawing wash solvent from the wash bottle Two way syringe valve Needle tubing assembly Wash tubing gas Wash solvent Surveyor Plus User Guide for LC Devices 13 1 Introduction to the Surveyor Plus LC System Autosampler Interchangeable Syringe XYZ Arm Mechanism The standard configuration for the autosampler consists of a 250 pL dual concentric syringe The dual concentric syringe consists of a small inner plunger and a larger outer plunger see Figure 12 Figure 12 Dual concentric syringe Inner plunger Outer plunger The syringe uses its inner plunger to draw and deliver sample amounts equal to or less than its maximum capacity which is 265 pL for the 250 pL concentric syringe The syringe uses its outer plunger to draw and expel large volumes of solvent for example during a flush or wash cycle Dual concentric syringes are available in 100 250 and 500 pL sizes The volume of the outer plunger region 565 pL is the same for all three dual concentric syringes The size of the inner plunger and the injection mode determ
283. on port and transfer tube Wash station Injection port Transfer tube assembly label specifying the dead volume Transfer tube Surveyor Plus User Guide for LC Devices 17 1 Introduction to the Surveyor Plus LC System Autosampler Injection Valve and Sample Loop The injection valve is a two position six port valve that introduces sample onto the column by way of the sample loop The sample loop is a section of stainless steel tubing with end fittings It is an interchangeable part that is attached to ports 1 and 4 of the injection valve The autosampler comes with a 25 pL sample loop There are two positions for the six port injection valve fill and inject In the fill position see Figure 17 the sample loop is isolated from the mobile phase stream As the mobile phase bypasses the sample loop the upward movement of the autosampler syringe plunger pushes sample into the front of the sample loop connected to port 1 of the injection valve Once the sample loop is filled excess solution exits the injection valve through port 3 to waste Figure 17 Injection valve in the fill position Transfer tubing To column t Mobile phase From m Wash solvent pump In the inject position see Figure 18 mobile phase enters the sample loop from the back backflushing the contents of the sample loop onto the column Excess sample left in the transfer tube is expelled directly to waste To allow ample rinsing of the samp
284. onfiguration Settings Tray Page The autosampler accessory kit contains several tray types including trays that hold 1 8 mL vials trays that hold 96 well microplates and trays that hold 384 well microplates Use the Tray page see Figure 36 to specify the tray type that you are using To select the tray type and orientation 1 In the list of tray types select the tray type Table 6 lists the available selections For the three custom selections you must calibrate the well bottom distance before you use the trays Note The Autosampler Accessory Kit contains the vial trays and microplate carriers The current version of the accessory kit contains a standard tray a short microwell carrier and a tall microwell carrier with a solid metal bottom Previous versions of the accessory kit contained a riser plate that you could use in combination with the short microwell carrier to load standard depth 96 well or 384 well microplates into the autosampler tray compartment Thermo Fisher Scientific has replaced the short microwell carrier and riser plate option with a tall microplate carrier that has a solid metal bottom for thermal conduction Thermo Scientific Surveyor Plus User Guide for LC Devices 47 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings 48 Table 6 Tray type selections Tray type Requires well bottom distance calibration 1 1 8 mL Vial 5 trays 40
285. or 171 Configuration Page 5 sis sieata sia tacks Wa seh aebi0 0 oarelaetiet ante we aes 171 Display Pag irens ote eiernite e a e a dobar d wink hora ann aigh 176 Information Paves ken an ee wean cea eens eee nae E OER 181 UV Vis Detector Direct Controls ay 24 5556 PROS DAES PRS 183 Pump Direct Controls apas cola ei sl risee ek cro Re ak eeaee done Mees 185 Surveyor LC Pump Plus Direct Controls 0000 ee eee 185 Surveyor MS Pump Plus Direct Controls is 44 ss ones desde witeaues 190 Autosampler Direct Controls coe doe a saree awa are 192 Applying a Direct Command ict caururba crates dat rnrn eera 194 Direct Control Commands for the Autosampler 00000004 194 Flushing the Autosampler Syringe 1 2 0 ee cee ee eee 196 Removing and Installing Sample Trays iw i ccocus ai auewd wea ee ws weds 199 Controlling the Tray and Oven Compartment Temperatures 199 Seguent SOUP win cscs cond a a E eae eN eae 201 Creating a Single Sample Sequence n u Lhe stwase kde sie ealantina eels 201 Opening the Sequence Setup Window 0 c eee eee eee eee 201 Creating the Sequences ty oid Pee eas ce A E Loe Se 203 Selecting the Vial Locations Interactively prs ti ok ae epaeen wai 206 Saving the Sequence el Gaus he anes arate aes ce was Rena aes 208 Equilibrating the Chromatographic Column 000000005 209 Loading the Avitosatnip letra casters wa aeashesrn s aintape bso
286. or Plus the sample rates are 0 5 1 0 2 0 4 0 5 0 10 0 and 20 Hz Surveyor Plus User Guide for LC Devices 99 3 Instrument Method Setup PDA Detector Instrument Method Parameters Table 24 PDA detector Method page parameters for an instrument method Sheet 3 of 3 Parameter Description Filter Bandwidth Specifies the bandwidth for the scan wavelengths Bandwidth values are limited to the subset of odd integers from 1 to 49 In addition the maximum scan range for a particular bandwidth is limited as follows Lower range 190 nm bandwidth 1 2 Upper range 800 nm bandwidth 1 2 The maximum scan range for a bandwidth of 49 nm is 214 to 776 nm Note Wider bandwidths decrease both spectral noise and the resolution of the spectra In general the detector bandwidth should not exceed 10 percent of the bandwidth at half height of the narrowest spectral feature of interest Channels with Wavelength Absorbance Units No Channels Specifies that no discrete channel measurements are to be acquired When you select this option the parameters in the Channels area are unavailable One Channel Specifies the acquisition of one discrete channel The data for Channel A is displayed in the bottom view of the Display page in black Two Channels Specifies the acquisition of two discrete channels The data for Channel B is displayed in the bottom view of the Display page in red Three Channels Specifies the acqu
287. or Plus User Guide for LC Devices Thermo Scientific 8 Qual Browser Opening a Raw Data File in Qual Browser 4 Select the layout from the list at the bottom of the dialog box The available selections are Default Layout and Current Layout Select Current Layout if the current layout for the Qual Browser window is different from the default layout and you want to apply it to your data file 5 Click Open If the default layout has not been modified and your raw file contains MS data in addition to PDA or UV data the data file opens with the MS TIC chromatogram in the upper cell and a mass range spectrum in the lower cell For an explanation of cells see Working with the Cell Grid on page 224 The y axis for these cells is set to relative absorbance see Figure 128 Figure 128 Qual Browser view with a chromatogram cell displaying MS TIC data and a spectrum cell displaying mass range data C Xcaliburidata PAHs_01 03 04 2003 05 50 29 PM RT 0 00 15 00 al NL 100 2 13E7 g 80 TIC MS c 463 PAHs 01 T 5 60 a xt g 40 w 204042 148 207 3 25 4 06 517 5 71 S 723 855 9 18 10 68 0 1 2 3 4 5 6 T 8 9 10 11 12 13 14 Time min PAHs_01 1 RT 0 01 AV 1 NL 135E6 io T c Sid 8 00 Q1MS 127 60 254 60 406 253 1 Do 80 gej 5 60 a tl oe 254 1 3 20 130 2 203 2 amp 128 2 129 2 i 202 1 2 304 1 228 2 2292 2302 252 2 128 129 130 202 203 204 228 229 230 252 253 254 miz miz miz miz 6 To apply a custom win
288. or Sounds Screen Saver Background Sky Windows Default Bubbles Ease of Access Center Harmony 4 Click the Screen Saver icon on the bottom right side of the window The Screen Saver Settings dialog box appears see Figure 24 28 Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Turning Off the Computer s Energy Saving Features 5 Change the screen saver setting as follows a In the Screen Saver list select None Figure 24 Screen Saver Settings dialog box Windows 7 operating system Screen saver Wait 1 minutes E On resume display logon screen Power management Conserve energy or maximize performance by adjusting display brightness and other power settings Change power settings ox cae a b Click Apply to accept this setting 6 Change the power settings as follows a Click Change Power Settings The Select a Power Plan page of the Power Options dialog box appears see Figure 25 Thermo Scientific Surveyor Plus User Guide for LC Devices 29 1 Introduction to the Surveyor Plus LC System Turning Off the Computer s Energy Saving Features Figure 25 Select a Power Plan page of the Power Options dialog box All Control Panel Items Power Options Search Control Panel D Control Panel Ho ae Select a power plan Require a password on wakeup Power plans can help you maximize your computer s performance or conserv
289. or Temperature Ready check box 54 wash bottle location 13 350 Surveyor Plus User Guide for LC Devices wavelength accuracy calibrating 328 calibration list editing 338 data acquisition range PDA detector 99 UV Vis detector 108 WEEE compliance ix well bottom distance calibration 305 well position and well ordering selecting 49 X x and y axis offset values arm calibration 300 Xcalibur data system Instrument Setup Window opening 68 Qual Browser opening 219 Roadmap view 135 Sequence Setup window opening 201 XYZ arm description 15 home position 296 moving to the back of the tray compartment 303 position calibrating 287 Z Zero DACs button 175 Zero Data button on Display page 170 event type PDA detector 105 zeroing absorbance level PDA detector 103 UV Vis detector 23 107 Thermo Scientific
290. or more rows the detector zeroes the baseline on the second row and all successive rows until it reaches the last row The detector zeroes its output signal even if the same wavelength is listed in the second through second to last rows of the table UV Vis Detector Instrument Method Parameters Table 27 describes the parameters on the Method page for the UV Vis detector Table 27 UV Vis detector method parameters Sheet 1 of 2 Parameter Description Rise Time Specifies the filtering in the time domain Default 2 0 seconds Selections 0 0 0 01 0 1 0 2 0 5 1 0 2 0 3 0 4 0 and 5 0 seconds Data Rate Specifies the number of points per second acquired per wavelength Default 10 Hz Selections 20 10 6 67 5 and 4 Hz Enable Autozero Enable Autozero When this check box is selected the detector zeros the absorbance data at the specified time Autozero Time min Specifies the time when the detector zeros the absorbance data Default 0 minutes Range 0 minutes to the run length Program Type Single Wavelength Specifies that the detector is to acquire data on one wavelength channel The acquisition UV Vis 190 800 nm wavelength is time programmable Dual Wavelength UV Specifies that the detector is to acquire data on two wavelength channels in the UV range 190 365 nm The acquisition wavelengths are time programmable Dual Wavelength Vis Specifies that the detector is to acquire data on two wave
291. or the lamps to equilibrate 3 Open the Calibration page for the PDA detector 4 To start the wizard for the dark current calibration click Calibrate in the Dark Current Calibration area The preconditions page appears see Figure 224 Thermo Scientific Surveyor Plus User Guide for LC Devices 323 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Figure 224 Preconditions page Dark Current Calibration Before proceeding with dark current calibration make sure that 1 The filter wheel is in the OPEN position position 1 2 Both lamps have been on for an hour or more 3 The flow cell is filled with MeOH 4 The MeDH is being pumped at 1 mL min To begin calibration click the Next button To abort calibration click the Cancel button Cancel Help 5 Read the list of preconditions and determine if the PDA detector is ready e Ifthe detector meets all the preconditions click Next to proceed with the calibration The status page appears e Ifthe detector does not meet all the preconditions click Cancel to exit the wizard Then prepare the PDA detector for calibration and begin this wizard again 6 Observe the status pane as the calibration proceeds see Figure 225 Figure 225 Calibration status page Dark Current Calibration Calibration complete Click Next to continue Checking lamp states Saving current method Downloading calibration method Shutting off lamps Wait
292. ort fixture 1 Remove the needle assembly from the needle mount as follows a Unscrew the needle tubing assembly from the needle assembly b For the Surveyor Autosampler Plus remove the syringe drive assembly refer to the instructions in the Surveyor Autosampler Plus Hardware Manual c Pull the latch nut of the needle assembly forward d Pull the needle up from the needle mount on the XYZ arm 2 Install the LED light fixture as follows a Connect the 8 pin connector of the light fixture cable to the timed events connector on the back panel of the autosampler see Figure 197 The red wire with the resistor connects to the 5V autosampler pin and the black wire connects to the autosampler ground pin Thermo Scientific Surveyor Plus User Guide for LC Devices 293 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 197 Cable connection for the light fixture Resistor Light fixture connector 8 pin connector on the back panel of the autosampler ele ENET b Verify that the LED is brightly lit c Insert the LED holder into the needle mount see Figure 198 294 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 198 Inserting the LED holder into the needle mount LED holder Needle mount
293. ositioning frame and an externally threaded fitting with a flangeless ferrule that connects to the right side of the syringe valve IMPORTANT To prevent damage to the needle tubing take care when you connect the needle tubing guide to the back of the syringe drive assembly Pinched tubing causes performance problems Figure 14 shows the needle assembly and the needle tubing assembly Figure 14 Needle assembly and needle tubing assembly Needle assembly Latch nut Compression spring Flag Needle tubing assembly 10 32 A fitting N Externally threaded nut and flangeless ferrule that connect to E the right side of the syringe valve v S is B Blunt tip needle PEEK fitting Sleeve Two pronged Black or red that connects to the needle guide PVC cap needle assembly 16 Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Autosampler Injection Port and Transfer Tubing Assembly Thermo Scientific Figure 15 shows the autosampler injection port Figure 15 Autosampler injection port Injection port Figure 16 shows the 0 012 in ID transfer tube that connects the autosampler injection port to port 2 of the injection valve IMPORTANT The label attached to the transfer tube assembly specifies its internal volume You must enter this value when you specify the configuration settings for the autosampler Figure 16 Injecti
294. ow open the Information view by doing one of the following e Choose View gt Info View or e Click the Information view icon 5 in the toolbar 136 Surveyor Plus User Guide for LC Devices Thermo Scientific 5 Daily Operation Checking the Status of the LC Devices 2 Click the Status tab The Status page appears see Figure 76 Figure 76 Status page of the Information View Status Acquisition Queue Run Manager Check Devices Sequence Sample Name Working On Position Raw File Inst Method E Surveyor 4S Ready to Download E Surveyor MS Pump Ready to Download Surveyor PDA Plus Ready to Download If you have just recycled the power and have not yet downloaded a method you see the following status readouts on the Status page e Initializing is displayed while the data system attempts to connect to an instrument module e Lamp Warm up is displayed for the detector while the deuterium lamp is igniting e Ready to Download is displayed after the data system establishes communication with an instrument device and after each run has ended Viewing the Status of Each Device Thermo Scientific The Surveyor Plus LC system contains an autosampler and an analytical pump In addition your system might contain an optional detector Check the status of each device by clicking its name in the device tree list The status information for a specific device is displayed in the lower po
295. ple and start data acquisition 1 Open the sequence file containing the information for the sample that you want to inject a From the Sequence Setup view choose File gt Open The Open dialog box appears see Figure 120 Figure 120 Open dialog box showing the selection of a sequence file Look in GQmetheds o y oE templates iy test sld File name test sld Files of type calibur Sequences sld Cancel Help Header Information Created Saturday August 26 2006 7 01 22 PM Modified Saturday August 26 2006 7 01 22 PM Last saved by alison cook Number of saves 1 Comment b Browse to the appropriate folder c Select the sequence that contains the sample you want to run You can identify sequence files by their sld file extension d Click Open The selected sequence appears 2 Highlight the sequence row that you want to run Do this even if the sequence contains just one row Figure 121 shows a highlighted sequence row Thermo Scientific Surveyor Plus User Guide for LC Devices 211 7 Sequence Setup Starting Data Acquisition Figure 121 Sequence Setup view showing the first row selected Thermo Xcalibur Sequence Setup Test Mix Sequence sld Open File Edit Change Actions View GoTo Help Cy cam bal S Bess 00 gt gt gt ine 2 File Name Sample ID Path Inst Meth Proc Meth Position Inj Vol Level For Help press F1 9 26 2008 7 49PM
296. ple preparation tasks to the task list 3 Add a task that transfers an aliquot of sample solution from the original sample location to another sample location a In the Prep Operations list select Transfer from Sample to Sample The task parameters appear below the Add To Task List button b Keep all the default parameter settings for the Transfer from Sample to Sample task except those that are shown below see Figure 70 Parameter Setting Autosampler action Source Sample Location Relative Location Withdraws sample from the current vial location listed in the Location Current sequence table Destination Sample Location Relative Location Deposits sample in the current 1 vial location listed in Location Current 1 the sequence table Volume 50 Transfers 50 uL of sample Thermo Scientific Surveyor Plus User Guide for LC Devices 127 4 Sample Preparation Routines Sample Preparation Routine Example Figure 70 Settings for the Transfer from Sample to Sample task Prep Operations Deposit liquid in sample Deposit liquid in reservoir Draw from reservoir Draw from sample Flush to waste Mix at sample Mix at reservoir Transfer from reservoir to reservoir Transfer from reservoir to sample Transfer from sample to reservoir Wash needle z Add To Task List gt gt Source Sample C Absolute location fan Relative Location Curent x Destination Sample
297. pler is waiting for the data system to download an Download instrument method Waiting for Door The Verify Door Is Closed check box is selected see Communication Close Page on page 52 and the tray compartment door is open Waiting for The Wait for Temperature Ready check box is selected see Temperature Communication Page on page 52 and the tray compartment temperature column oven temperature or both have not yet reached the set temperature This state remains until the temperature controlled areas are equilibrated to the set temperature Injecting The autosampler is making an injection Waiting for Pump The autosampler has loaded the sample loop and is waiting for the Inject Hold Release signal from the pump Ready The autosampler is ready to make an injection Error An error condition other than the loss of communication has occurred For example if you enable the maintenance log and you attempt to start a run when one or more of the maintenance counters has exceeded its limit an error condition occurs Door State Displays one of the following Open The Verify Door Is Closed check box on the Communication page of the Surveyor Autosampler Configuration dialog box in the Instrument Communication window is selected and the tray compartment door is open For information about selecting the Verify Door Is Closed check box see Communication Page on page 52 Closed The Door State displays Closed for these conditions
298. psi 143 00 6258 00 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Surveyor LC Pump Plus Instrument Method Parameters Surveyor LC Pump Plus Gradient Program Page Use the Gradient Program page see Figure 47 to specify the solvent composition and flow rate for your chromatographic method Figure 47 Example of an isocratic pump program for the Surveyor LC Pump Plus General Gradient Program 100 ae A B S ao C 5 60 D oO 2 40 5 amp 20 0 0 0 02 04 06 08 1 0 Time rin Time min Flow ml min Methanol Water 0 00 1 000 80 00 20 00 1 00 1 000 80 00 20 00 1 00 1 000 80 00 20 00 Placeholder line To specify the solvent conditions for the Surveyor LC Pump Plus 1 Click the Gradient Program tab The Gradient Program page appears see Figure 47 2 Type the initial flow rate and the initial solvent composition for your pump program in the first time line of the time program table and then press ENTER If you are not creating a gradient program skip the next step Note If you set the limit for the maximum pressure to less than 21 MPa the allowable flow rate range is 0 000 to 9 999 mL min If you set the maximum pressure limit to 21 MPa 215 bar 3129 psi or higher the maximum allowable flow rate is 5 000 mL min Thermo Scientific Surveyor Plus User Guide for LC Devices 71 3 Instrument Method Setup Surveyor LC Pump Plus Instrument Method Parameters
299. pump in Standby mode it stops pumping e When you place the detector in Standby mode nothing happens e When you place the autosampler in Standby mode nothing happens To turn a device off Right click the device listing on the Status page and choose Turn Device Off Depending on the device the following actions occur e When you turn off the pump it stops pumping e When you turn off the detector the lamps turn off e When you turn off the autosampler nothing happens 154 Surveyor Plus User Guide for LC Devices Thermo Scientific 5 Daily Operation Filling the Solvent Reservoir Lines with Fresh Solvent Filling the Solvent Reservoir Lines with Fresh Solvent Thermo Scientific After filling the solvent bottles connecting the solvent lines to the degasser and configuring the pump to communicate with the data system prepare the pump for operation by removing the air from the solvent lines that connect the solvent reservoir bottles to the pump s degassing unit For information about using the direct controls to start the solvent flow from the Surveyor MS Pump Plus see Pump Direct Controls on page 185 To quickly draw fresh solvent into the solvent reservoir lines 1 For any solvent line that you want to pull solvent through disconnect the tubing that is connected to the corresponding degasser outlet port 2 Connect a Luer Lok fitting to the degasser outlet port 3 Connect a 10 mL syringe to the Luer Lok fit
300. put to the diode array adjusting 315 Load Method button 177 317 Lock Display button 214 Surveyor Plus User Guide for LC Devices 347 Index M maintenance log autosampler 54 manuals accessing xvi methods See instrument methods or display methods microplates 384 well 10 96 well 7 description 6 selecting tray options 47 MS pump instrument method parameters 74 operating without solvent 77 pressure settings minimum and maximum 77 pressure stability 77 priming the pulse dampener 156 Ready signal 77 names chromatographic peaks 242 needle and needle tubing assemblies description 16 New Sequence Template dialog box 202 no waste injection description 19 injection volume recommendation 91 instrument method parameter 90 noise detector 170 Normalization page Display Options dialog box 240 0 On Off Standby shortcut menu 154 On Off switches for LC devices 135 output signal terminals 164 Oven page readbacks autosampler 142 P partial loop injection description 20 instrument method parameter 89 PCR plate configuring 48 PDA detector dark current calibration 323 data acquisition parameters 95 display method parameters 101 functional description 22 instrument method parameters 98 light throughput adjusting 315 parameters in method report 232 timed events parameters 102 wavelength calibration 328 348 Surveyor Plus User Guide for LC Devices PDASnapshot csv 318 peaks chromatographic areas displaying 251 peak
301. r a method has been downloaded to the PDA detector Filter wheel position Displays the position of the filter wheel The filter wheel has two positions 1 and 2 When the filter wheel is in position 1 the readout displays Run Position When the filter wheel is in position 2 the readout displays Calibration Position Deuterium lamp Displays whether the deuterium lamp is on or off Tungsten lamp Displays whether the tungsten lamp is on or off Current method top right Current method Displays the status of the current method Spectrum Spectrum Plot Thermo Scientific Depending on the method type meth or spda these scan plots are displayed e For display methods spda the scan plot shows intensity counts normalized to 100 percent on the y axis and diode number 2 to 511 on the x axis e For instrument methods meth the scan plot shows absorbance mAU normalized to 100 percent on the y axis and wavelength nanometers on the x axis Surveyor Plus User Guide for LC Devices 179 6 Direct Controls PDA Detector Direct Controls Table 49 Display page parameters Sheet 4 of 4 Parameter Description Channels Channels Plot Depending on the method type meth or spda these discrete channel plots are displayed e For display methods spda the plot shows intensity counts normalized to 100 percent on the y axis and time on the x axis e For instrument methods meth t
302. rameter Selections or range Reservoir RV1 RV2 RV3 RV4 or Bottle Volume 0 to 6000 pL 194 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls Autosampler Direct Controls Table 53 Direct control commands for the autosampler Sheet 2 of 3 Command Needle Removal Description Sets the needle to the needle removal position Apply this command before you remove the needle from the XYZ arm Set Oven Temperature Sets the temperature of the column oven compartment without downloading an instrument method Parameter Range Temperature 5 to 95 C IMPORTANT Avoid setting the temperature above the boiling point of the mobile phase Set Tray Temperature Sets the temperature of the tray compartment without downloading an instrument method The temperature range is 0 to 60 C Parameter Range Temperature 0 to 60 C Turn Off Turns off the oven temperature control allowing the temperature of the column oven Oven Temperature compartment to return to ambient Turn Off Turns off the tray temperature control allowing the temperature of the tray compartment to Tray Temperature return to ambient Inject Sample Thermo Scientific Injects a sample Parameter Vial The vial or well entries depend on the tray configuration Tray type Vial locations Conventional trays A 01 to E 40 96 well plates A A1 to C H12 384 well plates A A1 to C
303. ray 3 Click Apply The XYZ arm moves to the back of the tray compartment Controlling the Tray and Oven Compartment Temperatures Thermo Scientific The autosampler has two controlled temperature zones the tray compartment and the column oven compartment Before you start a sequence run equilibrate the controlled temperature zones at the temperature specified in the instrument method Use the direct commands in the Direct Control dialog box or the Inlet Direct Control dialog box to control the oven and tray compartment temperatures For information about opening the Direct Control and Inlet Direct Control dialog boxes see Autosampler Direct Controls on page 192 To download a new column oven temperature 1 Select Set Oven Temperature from the list of commands 2 In the Temperature box type an appropriate value for the column oven temperature The range is 5 to 95 C IMPORTANT Do not set the oven temperature above the boiling point for the mobile phase solvent 3 Click Apply To turn the column oven off 1 Select Turn Off Oven Temperature from the list of commands 2 Click Apply Surveyor Plus User Guide for LC Devices 199 6 Direct Controls Autosampler Direct Controls To download a new tray compartment temperature 1 Select Set Tray Temperature from the list of commands 2 In the Temperature box type an appropriate value for the tray compartment temperature The range is 0 to 60 C 3
304. re calibration 1 Open the status view for the autosampler s oven temperature To open the Oven page from the Xcalibur data system do the following E a Ifthe Information view is closed click the Information View button open the view to The Information view opens with the Status page displayed Thermo Scientific Surveyor Plus User Guide for LC Devices 275 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler b Verify that the status reads Ready to Download For information about checking the status see Checking the Status of the LC Devices on page 136 c Click Surveyor AS in the directory tree The status pages for the autosampler appear at the bottom of the Status page d Click the Oven tab The Oven status page appears 2 On the Oven page check the column oven status 3 If the column oven is on and set to a high temperature turn the column oven off open the column oven door and wait for the column oven to cool to room temperature For information about using the direct controls to turn the column oven on or off see Controlling the Tray and Oven Compartment Temperatures on page 199 4 Install the oven sensor test fixture 869C thermometer or equivalent as follows a If it is not already open open the column oven door b Loosen the top thumbscrew that holds the column clamp c With the sensor facing down slide the metal cable protector under the right side
305. rete channel File Actions View GoTo Help Lock display button LT lal bimn 21S zeje Aka RT 0 00 10 00 106 NL A Status Acquisition Queue Run Manager Acquiring Sequence C TempSequence sid Sample Name Working On Seq Row 1 Position 4 1 Raw File D calibur Data T est Mix Test Mixture 1C Inst Method D xcalibur T est Mix methods T est Mis E Surveyor AS Ready to Download Surveyor LC Pump Ready to Download Surveyor PDA Running Status M Degasser Run Time 0 00 min Time Remaining 0 00 min Flow 1 00 mL min Pressure 1429 31 psi A 80 B 20 Cc 0 D 0 Channel A UY Test Mixture 10103021 2175216 2 63 2 85 3 31 3 78 4 14 6 20 6 61 o 1 2 3 4 5 6 7 6 3 10 Time min Test Mixture 101_030212175216 453 RT 7 53 NL 2 32E5 microAU al 239 00 200000 150000 231 00 3 100000 50000 351 00 357 00 T T T a T TT T T 220 240 260 280 300 320 340 360 380 400 start dec wavelength nm RT 0 00 10 00 1 07 NL ma 3 93E5 350000 Total Scan PDA Test 200000 Mixture 250000 101 03021 2175216 180 2 23 0 32 0 65 2 63 2 83 3 25 3 77 413 Time min Mon 2 12 2003 6 00 PM NOT SAVED 6 00 PM X amp 1 Real Time Plot 48 Reviewing Real Time Data You can review the data as it is being collected
306. rks of the integrated peak To limit the peak purity calculation to a specific range of wavelengths in the scan select the Limit Scan Wavelength check box and then enter a wavelength range in the Wavelength Range box 7 Click OK to close the Peak Purity Settings dialog box and then view the effect of your peak purity settings The following figures show the effect of various settings on peak purity e Figure 163 shows the effect of the scan wavelength on peak purity e A comparison of Figure 164 and Figure 165 on page 257 demonstrates the effect of integration on peak purity e Figure 166 on page 258 shows the effect of the scan threshold setting on peak purity e Figure 167 on page 258 shows the effect of the peak coverage setting on peak purity Thermo Scientific Surveyor Plus User Guide for LC Devices 255 8 Qual Browser Calculating the Purity of the Chromatographic Peaks Figure 163 Comparison of peak purity results for two different scan wavelengths 02 25 2003 11 20 31 AM RT 1 25 1 80 be RT 1 57 NL Peak Purity 983 es er 150000 nm 224 5 225 225 nm scan wavelength BDA Avalon J 3uAU scan threshold 100000 95 peak coverage a 2 4 Impurity 500004 RT 1 45 7 Peak Purity 802 0 TT TT Trrtrt ypttttytt ete ty rt tt 1 25 1 30 1 35 1 40 1 45 1 50 1 55 1 60 1 65 1 70 1 75 Time min RT 1 25 1 80 a RT 1 57 NL Peak Purity 769 6 92E5 J nm 238 5 239 5 600000
307. rm position turn off the feature that prevents control of the autosampler when the tray compartment door is open To modify the instrument configuration for the autosampler 1 Open the Surveyor Autosampler Configuration dialog box The dialog box opens with the Tray page displayed see Figure 190 288 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 190 Tray page with the 384 well microplate tray type selected Tray Communication Signal polarity Firmware 41 well position Top left Bottom right Well ordering 2 Select the 384 well plate tray type 3 In the Al Well Position area select the Top Left option 4 Click the Communication tab The Communication page appears 5 Clear the Verify Door Is Closed check box see Figure 191 Surveyor Plus User Guide for LC Devices 289 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 191 Communication page with the Verify Door Is Closed check box cleared Tray Communication Signal polarity Firmware Stack Address 1 Syringe Type Concentric 250ul X P wait for temperature ready Merify door is closed ___________ Clear this check box Reccoseonestencteseccvesescoesvenceessosesccoces Enable maintenance log When the Verify Door Is Closed check box is
308. rned on or off or is set to determine the distance to the bottom of the first vial or well in a sequence of injections The selections are as follows e Off Deactivates the vial bottom sensing feature e On Activates the vial bottom sensing feature for every injection e Auto Activates the vial bottom sensing feature for the first injection of a sequence Surveyor Plus User Guide for LC Devices 55 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Table 9 Communication page parameters Sheet 2 of 2 Parameter Dead Volume uL Description Specifies the volume of the transfer tubing that connects the autosampler s injection port to the autosampler s injection valve The transfer tubing has a label that specifies its dead volume Sample Loop Volume Signal Polarity Page Specifies the nominal size of the sample loop that is connected to the injection valve The autosampler cannot detect the sample loop size it uses the sample loop size that you type in this box During a run the autosampler receives a Pump Ready signal and an Injection Hold release signal from the pump When the autosampler switches its injection valve to the inject position it sends an Inject Out signal to the detector Figure 38 shows the signal terminals on the autosampler s back panel Figure 38 Signal terminals on the autosampler s back panel From pump To detector S us Se
309. rror log Tray Control on No Current temperature C 21 7 Set temperature C 25 0 Ready status Ready 142 Surveyor Plus User Guide for LC Devices Thermo Scientific 5 Daily Operation Checking the Status of the LC Devices Table 38 describes the readbacks on the Tray page of the autosampler status view Table 38 Tray page parameters Readback Control On Description Display Yes or No You can turn off the tray temperature control by doing one of the following e Using the Turn Off Tray Temperature command see Controlling the Tray and Oven Compartment Temperatures on page 199 e Running an instrument method that has the Enable Column Oven Control check box cleared Current Temperature C Displays the temperature monitored by the autosampler s internal temperature sensor Set Temperature C Displays the user specified temperature You can change the set temperature by doing one of the following e Using the Set Tray Temperature command see Controlling the Tray and Oven Compartment Temperatures on page 199 e Running an instrument method that has a temperature setting for the column oven Ready Status Thermo Scientific Displays one of the following Ready The oven compartment temperature has reached the set temperature you did not select the Wait for Temperature Ready check box when you specified the configuration settings for the autosampler or both For information
310. rs on the Tray page Table 7 Tray page parameters Sheet 1 of 2 Parameter Tray Type Description The Tray Type list displays pictures of the 11 sample tray configurations When you choose 96 well plates or 384 well plates two additional options appear Al Well Position and Well Ordering The conventional autosampler tray holds 40 standard 1 8 mL vials For other types of vials select the custom vial setting and the appropriate tray adapter The autosampler accommodates a variety of microwell plates You can use the tall or short microwell carriers to accurately position the various microwell plates at an appropriate location in the autosampler tray compartment The tall microwell carrier with a solid metal bottom provides the same height as the short microwell carrier and riser plate combination The distance that the needle travels to reach the bottom of the vial is pre calibrated for the eight standard configurations You must perform a Well Bottom Distance calibration see Well Bottom Distance Calibration on page 305 to use one of the three custom configurations For information about the height limitations for the various tray selections see Table 8 Note Do not use the short microwell carrier to hold the 384 well high density microtitre plates Do not use the tall microwell carrier to hold PCR plates 50 Surveyor Plus User Guide for LC Devices Thermo Scientific 2 Thermo Foundation Instrument Configuration Spe
311. rtion of the Status page These topics describe the status views for the LC devices e Autosampler Status View e Surveyor MS Pump Plus e Surveyor LC Pump Plus e Surveyor PDA Plus Detector Status View e Surveyor UV Vis Plus Detector Status View Surveyor Plus User Guide for LC Devices 137 5 Daily Operation Checking the Status of the LC Devices Autosampler Status View The Status view for the autosampler see Figure 77 contains four pages e AS Status Page e Oven Page e Tray Page e Error Log Autosampler Page Figure 77 Status page showing the AS Status page for the Surveyor Autosampler Status Acquisition Queue El Run Manager Ready To Download Sequence Sample Name Working On Position Raw File Inst Method Surveyor AS Ready to Download 44 _____ See Table 35 Surveyor LC Pump Ready to Download Surveyor PDA Plus Ready to Download AS Status Oven Tray Error lag Target injection Vial position Injection volume pL AS state Waiting for download Door state Close Maintenance due No Firmware version 2 15 For Help press F1 Table 35 describes the states that might appear below the Surveyor AS listing 138 Surveyor Plus User Guide for LC Devices Thermo Scientific 5 Daily Operation Checking the Status of the LC Devices Table 35 Autosampler states State Meaning Initializing The data system is attempting to establish communication with
312. rveyor LC Pump Plus are connected to the Ethernet switch and that the Ethernet switch is connected to the data system computer Verify that the RS 232 cable for the Surveyor MS Pump Plus is connected to the data system computer e Verify that the stack addresses in the configuration for the Surveyor Autosampler Plus Surveyor PDA Plus Detector or Surveyor UV Vis Plus Detector and Surveyor LC Pump Plus are correct For information about configuring your instrument devices see Chapter 2 Thermo Foundation Instrument Configuration Checking the Status of the LC Devices After you turn on the power to the LC devices and open the Xcalibur data system check the status of each device Tip You can also view the system pressure on the pump page of the Inlet Direct Control dialog box in the Tune window for your Thermo Scientific mass spectrometer To check the status of the LC devices follow these procedures 1 Opening the Status Page of the Information View 2 Viewing the Status of Each Device Opening the Status Page of the Information View You can monitor the status of the LC devices from the Information view of the Xcalibur data system This view is normally displayed on the left side of the Home Page window If this view is not displayed the view has been closed From the Home Page window choose View gt Info View to open the Information view To display the Status page of the Information view 1 In the Home Page wind
313. s b Browse through your Methods folder and select the appropriate instrument method Then click Open Only the sample preparation task list contained in the stored instrument method is imported into the current instrument method For each task that you want to add to the sample preparation routine do the following a In the Prep Operations list select a task Table 29 lists the thirteen tasks that you can use to create a sample preparation routine When you select a task the parameters available for the task appear below the Add to Task List button Tip The syringe position and nominal volume limit the task order and transfer volume e Ifthe previous task used the small bore of the syringe you must add a Flush to Waste or a Wash Needle task before you can add a task that requires the use of the large bore of the syringe These tasks home the concentric syringe plungers e Ifthe previous task used the small bore of the syringe the transfer volume of the current task is limited to the nominal syringe size or less See Sample Preparation Rules on page 115 for more information b Make the appropriate selections and entries for each task parameter c Click Add To Task List The task appears in the task list in the Method area 116 Surveyor Plus User Guide for LC Devices Thermo Scientific 4 Sample Preparation Routines Building the Sample Preparation Routine 4 Edit the task list as needed To remove th
314. s on page 260 2 In the Pressure Sensor Adjustment box see Figure 168 on page 261 type the value on the data sticker O XXXX multiplied by 10 000 3 Click Set Zeroing the Pressure Transducer Thermo Scientific The offset error of the pressure transducer is the value that is displayed when it should be zero such as when the purge manifold knob is set to the open position You can correct for this offset error by re zeroing the pressure readout of the pressure transducer when the purge manifold knob is open To re zero the output of the pressure transducer 1 Stop the flow of solvent from the LC pump a From the Instrument Setup window choose Surveyor LC Pump gt Direct Control gt Operation b Click Pump Off 2 Open the drain valve to ensure that the transducer is actually sensing zero system pressure see Figure 172 When the drain valve is in the open position look for the word DRAIN to appear upside down on the knob Figure 172 Drain valve in closed and open positions Closed position Open position Surveyor Plus User Guide for LC Devices 269 9 LC Pump Calibration and Record Keeping Recording Maintenance Information for the Surveyor LC Pump Plus 3 Open the Calibration page of the Direct Control dialog box by choosing Surveyor LC Pump gt Direct Control gt Calibration 4 Click Zero in the Pressure Transducer area see Figure 168 on page 261 5 When you are finished zeroing the pres
315. s Deuterium 10 Tungsten 10 Status aF Surveyor PDAPlus is Connected Ready to Start Run Wavelength Calibration is Valid Dark Current Calibration is Valid Method is Valid Filter Wheel in Run Position Q Deuterium Lamp is On 9 Tungsten Lamp is On Display Page Parameters Table 49 describes the parameters on the Display page Table 49 Display page parameters Sheet 1 of 4 Parameter Description Control Control The buttons in this area provide control of the display method spda Load Method Loads the display method or the data acquisition parameters of an instrument method to the detector Start Data Initiates the graphical display of the intensity data or the wavelength data Thermo Scientific Surveyor Plus User Guide for LC Devices 177 6 Direct Controls PDA Detector Direct Controls Table 49 Display page parameters Sheet 2 of 4 Parameter Description Snapshot Saves a comma separated values file named PDASnapshot csv to the following folder on the data system computer drive Xcalibur data A date and time stamp are appended to the file name The format of the date and time stamp is MMDDYYHHMMSS MM is the month DD is the day of the month YY are the last two digits of the year HH is the hour in military time MM are minutes SS are seconds You can open this file with the Excel application For a wavelength absorbance method the file contains the absorbance values for the spectra
316. s and from 0 83 to 330 85 uL s for the standard i 2500 pL syringe Cycles Range 1 to 10 Needle Height Default 2 mm Range 0 to 18 mm Mix at Reservoir Mixes the contents of a reservoir vial Parameter Reference range or selections Volume The maximum volume is 490 pL for the concentric syringes and 1490 uL for the standard 2500 uL syringe Destination RV1 RV2 RV3 or RV4 Reservoir Draw Speed The draw or delivery speed range is from 1 65 to 661 38 pL s for the Tiy a concentric syringes and from 0 83 to 330 85 uL s for the standard 2500 pL syringe Cycles Range 1 to 10 Needle Height Default 2 mm Range 0 to 18 mm Transfer from Reservoir to Reservoir Thermo Scientific Transfers liquid from one reservoir to another Parameter Reference range or selections Volume Draw Eject and Transfer Volumes for Sample Preparation Tasks on page 123 Source Reservoir bottle RV1 RV2 RV3 or RV4 Destination RV1 RV2 RV3 or RV4 Reservoir Syringe Speed Syringe Speed for Tasks that Can Use Either Plunger on page 125 Surveyor Plus User Guide for LC Devices 119 4 Sample Preparation Routines Building the Sample Preparation Routine Table 29 Sample Preparation page Sheet 4 of 5 Parameter Description Transfer from Reservoir Transfers liquid from a reservoir vial or the wash bottle to a vial or well to Sample Parameter Reference range or selections Sa
317. s Detector Direct Controls Use the Direct Control dialog box for the UV Vis detector to turn the lamps on or off and to zero the chromatographic baseline To turn the UV Vis detector s lamps on or off 1 Open the Surveyor UV Vis Instrument Setup view 2 From the menu bar choose Surveyor UV Vis gt Direct Control The Direct Control dialog box for the UV Vis Detector appears see Figure 103 Figure 103 Direct Control dialog box for the UV Vis Detector Direct Control Deuterium Lamp ero Help Lamp Off Tungsten Lamp Lamp On Lamp Off AU 0 000025 AU2 0 000133 3 In the Deuterium Lamp area click Lamp On To zero the absorbance Click Zero UV Vis Direct Control Parameters Table 51 describes the buttons and readbacks in the Direct Control dialog box for the UV Vis detector Table 51 Direct control parameters for the UV Vis detector Sheet 1 of 2 Parameter Description Deuterium Lamp Lamp On Turns the deuterium lamp on Lamp Off Turns the deuterium lamp off Surveyor Plus User Guide for LC Devices 183 6 Direct Controls UV Vis Detector Direct Controls Table 51 Direct control parameters for the UV Vis detector Sheet 2 of 2 Parameter Tungsten Lamp Description Lamp On Turns the tungsten lamp on Lamp Off Turns the tungsten lamp off Other Options Zero Zeros the absorbance reading from the detector Readbacks Status AU1
318. s stored until you change it or until you turn off the power to the Surveyor LC Pump Surveyor Plus User Guide for LC Devices Thermo Scientific 9 LC Pump Calibration and Record Keeping Calibrating the Surveyor LC Pump Plus Figure 170 Terminals located on the back of the Surveyor LC Pump Plus Pressure terminals VE L il i PesEQs LTS RS232 1234567 8 910111213141516 UNITID ENET gage 222 2855 TEL TG I BaD oal o ccs BBG 8 A AE gt 4226 z 7 19 o For information on setting the scaling factor for the pressure recorder see Scaling the Output of the Pressure Recorder Terminals on page 268 Flow Rate Adjustment Alpha The alpha value for your Surveyor LC Pump Plus is factory calibrated based on a flow rate of 1 000 mL min for distilled water A sticker containing the factory calibration value is located inside the pump on the motor casing You can optimize the alpha value for your application by updating the alpha setting The range for alpha values is 1 to 9 9 If you are pumping water decreasing the alpha value by 1 decreases the flow rate by 1 percent Increasing the alpha value by 1 however increases the flow rate by 1 percent For information on setting the alpha value see Updating
319. s to the Instrument Configuration e Specifying the Configuration Settings e Closing the Foundation Application To set up the software instrument configuration for your LC system 1 Open the Thermo Foundation application 2 Add the devices of your LC system to the instrument configuration 3 Specify the configuration settings for each device 4 Close the Foundation application Checking the Communication Hardware The autosampler and detector communicate with your Thermo Scientific data system through an Ethernet connection Each device has an Ethernet port on its back panel A shielded Category 5 Ethernet cable with ferrite connects each device to an Ethernet switch which in turn connects by way of an Ethernet cable to the data system computer The unit ID setting on the back panel of the autosampler and PDA detector must match the stack number in the configuration Thermo Scientific Surveyor Plus User Guide for LC Devices m 2 Thermo Foundation Instrument Configuration Checking the Communication Hardware Before you specify the configuration settings check the unit ID setting on the back panels of the autosampler LC pump UV Vis detector and PDA detector The unit ID consists of two rotary switches that are factory set to 01 see Figure 32 Figure 32 Unit ID with a stack address of 01 Set to 0 Set to 1 Unlike the other Surveyor Plus devices the Surveyor MS Pump Plus communicates with the data system through an RS
320. selected the data system prevents you from starting an injection sequence or using some of the direct control commands for the autosampler when the tray compartment door is open 6 Click OK at the bottom of the dialog box to accept the settings and close the dialog box 7 Click Done to close the Thermo Foundation Instrument Configuration window Go to the next procedure Starting the Arm Calibration Wizard Starting the Arm Calibration Wizard Use the Arm Calibration wizard to adjust the home position of the XYZ arm For information about the LED light and non reflective needle port fixtures that you must have to perform the Arm Calibration wizard see Arm Calibration on page 287 To start the Arm Calibration wizard 1 If you have not already done so modify the autosampler instrument configuration as described in Modifying the Autosampler Instrument Configuration on page 288 2 Open the view for the autosampler 3 From the Surveyor AS menu choose Calibration The Calibration dialog box appears see Figure 192 4 Select the Arm Calibration option 290 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 192 Calibration dialog box with the Arm Calibration option selected Calibration Choose the diagnostic item Column oven air sensor calibration Vial tray metal sensor calibration C
321. sh bottle tubing Needle s tubing NE Syringe ming Mounting hole with grommet to vertical mounting stud Mounting holes with grommets to horizontal mounting studs Front view Back view A ll 2 NY fre Vertical mounting stud 6 NTT Horizontal mounting studs S NR 12 Surveyor Plus User Guide for LC Devices Thermo Scientific 1 Introduction to the Surveyor Plus LC System Autosampler The syringe valve is a two position rotary valve In the wash bottle position the syringe draws wash solvent into its syringe barrel as its plunger descends In the needle position the syringe draws sample solution into the needle tubing as its plunger descends and pushes sample solution out of the needle tubing as its plunger ascends The syringe never draws sample solution into its barrel Note The needle tubing holds approximately 560 pL of solvent If you installed the 2500 pL standard syringe which must be special ordered and you plan to make large volume injections install the 1 mL needle tubing extension that comes with this syringe Wash Bottle Reservoir and Tubing Thermo Scientific The wash bottle rests in the solvent platform on the top of the LC stack It is connected to the syringe valve by way of the wash bottle tube Both of the direct commands Flush from bottle and Wash Needle from bottle draw solvent from the wash bottle In addition both the partial loop injecti
322. so zero the absorbance level for a discrete channel during an acquisition run by adding a zero event to the Timed Events table To add a timed event to the instrument method 1 In the Timed Events area of the Surveyor PDA Plus Method page see Figure 62 click New Figure 62 Timed Events area of the Method page Timed Events Time min Type Channel Level m l Delay sec New ik The Timed Event dialog box appears see Figure 63 Figure 63 Timed Event dialog box Timed Eyent Type Event Off i a Time min 0 00 Cancel Channel Help Level m4U Delay sec 2 In the Type list select an event type The selections are Event Off Event On Zero Data or Level Trigger 104 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Triggering an External Device with the PDA Detector 3 In the Time min box type the length of time after the chromatographic run starts that the event is to occur The range is 0 00 to the run length time for the detector The Event Off Event On and Zero Data event types occur at this time Because the Level Trigger event type occurs after this time is exceeded do not enter a time value that exceeds the expected time for example the expected retention time of the analyte that you want a fraction collector to collect of the triggering event The Channel list Level box and Delay box are available for the Level Trigger event
323. spectrum cell In Figure 133 the spectrum cell on the bottom of the view is pinned Clicking the 1 8 minute time point in the unpinned chromatogram cell causes the spectrum of benzene which elutes at 1 8 minutes to appear in the pinned spectrum cell Figure 133 Qual Browser window with a pinned spectrum cell and an unpinned chromatogram cell In the chromatogram cell the pointer is set to 1 8 minutes the peak apex for benzene C XcaliburidataiTest Mixture 401 02 12 2003 06 03 30 PM RT 0 00 10 00 m Al 3 93E5 Total Scan PDA Tort Mixture A01 2 62 3 30 3 77 4 13 4 63 5 92 6 15 6 43 6 87 6 23 8 58 3 45 300 0 306 0 322 0 323 0 300 320 wavelength nm In the spectrum cell the spectrum of benzene which elutes at 1 8 minutes under the chromatographic conditions used is displayed Thermo Scientific Surveyor Plus User Guide for LC Devices 227 8 Qual Browser Working with the Cell Grid In Figure 134 the chromatogram cell on the top of the view is pinned Clicking a specific wavelength in the unpinned spectrum cell displays the chromatogram of the scan wavelength in the pinned chromatogram cell Figure 134 Qual Browser window with a pinned chromatogram cell and an unpinned spectrum cell C XcaliburidataiTest Mixture A01 02 12 2003 06 03 30 PM RT 0 00 10 00 i w NL 3 In the chromatogram cell 4 82E6 the chromatogram of the 251 nm 50 6 PDA Tort Mixture scan wavel
324. speed The injection valve then switches to the load position and the autosampler meters the sample into the sample loop at the specified loop loading speed This parameter is only available in the No Waste injection mode The default value and range depend on the syringe size see Syringe and Loop Loading Speeds for Injections on page 91 Injection Mode Partial Loop Thermo Scientific Select this option if you want to inject variable volumes IMPORTANT To make precise partial loop injections limit the maximum injection volume to less than half the nominal sample loop size Because the accuracy of the nominal volume of the sample loop is 20 which means that the actual volume of the standard 25 uL sample loop is between 20 and 30 pL for best results limit the maximum injection volume to 10 pL for the standard 25 pL sample loop Surveyor Plus User Guide for LC Devices 89 3 Instrument Method Setup Autosampler Instrument Method Parameters Table 19 Autosampler Method page parameters Sheet 3 of 3 Parameter Description Full Loop Select this option when you need a high degree of accuracy The Injection Volume box is unavailable with this selection No Waste Select this option when you have a limited amount of sample IMPORTANT For no waste injections follow these suggestions to optimize injection to injection reproducibility and minimize baseline disturbances e Use a sample loop that is at least 5 pL
325. ssembly with seven green combicon connectors two are labeled PUMP three are labeled DETECTOR and two are unlabeled You can identify the connector for the autosampler by the small A S tag on its adjacent cable You can identify the M S connector by its shape and by the small M S tag on its adjacent cable Figure 28 7 connector system interconnect cable To detector To To MS detector detector S To pump To detector WAL Y0193130 Y0193130 To autosampler m Using the 7 connector cable with the Surveyor MS Pump Plus requires an additional adapter cable Figure 29 shows the interconnect cable connections for a Surveyor LC system 32 Surveyor Plus User Guide for LC Devices Thermo Scientific MS Detector Autosampler MS pump connection PUMP Detector Figure 29 fA a _ a Detector 3 Detector Pump Detector back panel To MS detector dAWNd SW MS pump adapter cable Maa aes Scenics Some ce Sema eet s ciel eee Thermo Scientific Autosampler back panel Surveyor MS Pump back panel 1 Introduction to the Surveyor Plus LC System Synchronization of the LC Devices B
326. state Hibernate Disk space for hibernation Free disk space 404 868 MB Disk space required to hibernate 3 582 MB b Ifthe Enable Hibernation check box is selected clear it c Click Apply to accept the setting 9 Click OK to close the Power Options Properties dialog box 10 Click OK to close the Display Properties dialog box 11 Close the Control Panel window To turn off the screen saver an energy saving features for the Windows 7 operating system 1 From the Windows 7 desktop choose Start gt Control Panel 2 Choose Large Icons from the View By menu View by Category Y Category Large icons Small icons 3 Click the Personalization icon me Personalization The Personalization window appears see Figure 23 Thermo Scientific Surveyor Plus User Guide for LC Devices 27 1 Introduction to the Surveyor Plus LC System Turning Off the Computer s Energy Saving Features Figure 23 Personalization window l S eS a gt Control Panel All Control Panel Items Personalization v Search Control Panel P Control Panel Ho an Change the visuals and sounds on your computer Change desktop icons Click a theme to change the desktop background window color sounds and screen saver all at once Change mouse pointers Change your account picture My Themes 1 Unsaved Theme Savetheme Get more themes online Aero Themes 7 See also 2 DS kA Display lt th ee Maa cree Window Col
327. stic item Column oven air sensor calibration ial tray metal sensor calibrations Arm calibration C Well bottom distance toed He _ 6 Click Next The Diagnostic Internal Set Target page of the Vial Tray Metal Sensor Calibration wizard appears see Figure 184 The default external standard temperature is 40 0 C 282 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Specifying the Internal Set Target for the Tray Compartment Temperature Use the Diagnostic Internal Set Target page see Figure 184 of the Vial Tray Metal Sensor Calibration wizard to specify the calibration temperature Figure 184 Diagnostic Internal Set Target page of the Vial Tray Metal Sensor Calibration wizard Diagnostic Internal Set Target Calibration target temperature C poo Start calibration levee e Default temperature 1M To specify the target calibration temperature for the tray compartment and start the calibration 1 Prepare the system for the temperature calibration see Preparing to Calibrate the Tray Compartment Temperature on page 281 2 In the Calibration Target Temperature box type 30 0 and then click Start Calibration see Figure 185 Thermo Scientific Surveyor Plus User Guide for LC Devices 283 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Figure 185 Diagnost
328. structions in the Arm Calibration wizard to adjust the XYZ arm alignment test the alignment by making a set of injections from one or two 384 well microplates The microplate carrier and the 384 well microwell plates are provided in the Autosampler Accessory Kit To calibrate the XY position of the XYZ arm you must have these items e LED light fixture P N 60357 60021 e Target port fixture P N 60357 20021 e Microplate carrier e One or two 384 well microtitre plates e Masking tape Figure 189 shows the LED light and the target port fixtures Figure 189 Arm calibration fixtures available by special order 8 pin connector LED holder _ w wW Target port fixture Surveyor Plus User Guide for LC Devices 287 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler To calibrate XY position of the XYZ arm and verify the calibration follow these procedures 1 Modifying the Autosampler Instrument Configuration 2 Starting the Arm Calibration Wizard Moving the Arm to the Needle Removal Position A Installing the LED Light Fixture and the Target Port Fixture Moving the XYZ Arm to the Home Position Aligning the Light Beam with the Target N A WN Applying the Arm Calibration Setting 8 Checking the Arm Calibration Offset Values 9 Testing the Alignment of the XYZ Arm Modifying the Autosampler Instrument Configuration To calibrate the a
329. strument method 100 display methods creating 313 saving 314 display options chromatogram cell 240 map cell 247 spectrum cell 242 drain valve knob for LC pump 4 187 269 dual wavelength program UV Vis detector 107 E electromagnetic compatibility vii error log autosampler 144 PDA detector 182 event types PDA detector timed event 103 external devices triggering 102 F FCC compliance vii file types comma separated values file csv 318 data file raw 219 display method spda 315 layout file lyt 222 processing method pmd 203 sequence sld 208 fill position injection valve 18 filter frit LC pump 4 filter wheel PDA detector 22 Thermo Scientific firmware upload version 60 fixed loop injection See full loop injection flow rate adjustment setting 268 gradient program changes 79 range LC pump 3 MS pump 2 flush bottle location 13 flush speeds 87 89 font size of display changing 230 fraction collector triggering 102 full loop injection description 20 instrument method parameter 90 G gradient delay volume autosampler preheat tubing 21 LC pump pulse dampener 3 MS pump 2 gradient program LC pump 71 MS pump 79 Gradient Start signal pump 35 grinding sound caused by high flush speeds 89 H heights chromatographic peak 242 inactive cells Qual Browser 224 initialization process for syringe 134 Initializing status message 137 inject position injection valve 18 injection mode descript
330. sure transducer close the drain valve by gently turning the knob clockwise until you feel resistance Note Applying excessive force to the drain valve knob reduces the life span of its O ring Recording Maintenance Information for the Surveyor LC Pump Plus Use the Direct Control Maintenance dialog box to update the maintenance information for the Surveyor LC Pump Plus and to set the pistons to the maintenance position Each pump head assembly contains a piston seal The two seals can wear at different rates causing leaks to occur in one or both pump heads Before dismantling the pump head assemblies attempt to determine the source of the leakage To save time and materials replace only the piston seal in the pump head assembly that is leaking Or as a preventive measure replace the piston seals after pumping 120 L of mobile phase To open the Direct Control Maintenance dialog box From the menu bar of the Surveyor LC Pump Plus view choose Surveyor LC Pump gt Direct Control gt Maintenance The Maintenance Surveyor LC Pump Direct Control page appears see Figure 173 Figure 173 Direct Control Maintenance dialog box Maintenance Surveyor LC Pump Direct Control Left Seal Volume Right Seal Volume 0 00 0 00 L Reset Pump Operating Time Position Pistons 0 00 hrs Reset Maintenance Position 270 Surveyor Plus User Guide for LC Devices Thermo Scientific 9 LC Pump Calibration and Record Keeping Recor
331. switches The PDA detector has two additional manual controls the filter wheel and the attenuators The filter wheel controls the position of the holmium oxide calibration solution The attenuators control the light throughput to the diode array The pump has a purge valve The following procedure describes how to verify instrument communications from the Thermo Xcalibur data system To open the data system and verify instrument communications 1 From your computer desktop choose Start gt Programs gt Thermo Xcalibur gt Xcalibur The Thermo Xcalibur Roadmap window appears see Figure 75 Figure 75 Thermo Xcalibur Homepage window with the Roadmap and Info view displayed Information view Roadmap Thermo Xcalibur Roadmap File Actions view Tools GoTo Help Status Acquisition Queue Run Manager No Devices Sequence Sample Name Working On Pasition Raw File Inst Method Sequence Setup Resul Re vie i KER pec Thermo Scientific Surveyor Plus User Guide for LC Devices 135 5 Daily Operation Checking the Status of the LC Devices Shortly after you open the data system the Comm LEDs on the front panels of the LC devices turn green if the devices are powered on and connected to the data system computer 2 If the Comm LEDs remain amber do the following e Verify that the Ethernet communication cables for the Surveyor PDA Plus Detector or Surveyor UV Vis Plus Detector Surveyor Autosampler Plus and Su
332. t into the syringe and then pushes wash solvent through the needle tubing and the injection port to waste If you want to remove residual sample from the sample loop use the Flush Syringe at Fill Position command To flush air out of the wash bottle tubing and the autosampler syringe 1 Open the view for the autosampler 2 From the menu bar choose Surveyor AS gt Direct Control The Direct Control dialog box for the Surveyor Autosampler Plus appears see Figure 110 196 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 6 Direct Controls Autosampler Direct Controls Figure 110 Flush syringe direct control command Direct Control Command amp Parameters Flush syringe v Reservoir Flush bottle Volume ul 400 Flush Speed fuls f 00 00 e 3 Initiate the Flush Syringe command a Select Flush Syringe from the list of commands The parameters for the command appear below the list b In the Reservoir list select Flush Bottle c Inthe Volume box type an appropriate flush volume The maximum flush volume is 6000 pL d Click Apply to download the command to the autosampler 4 Verify that the wash bottle tubing and syringe are free of air see Figure 111 5 Close the Direct Control dialog box Surveyor Plus User Guide for LC Devices 197 6 Direct Controls Autosampler Direct Controls Figure 111 Solvent path for flushing the syringe 2 way syringe valve
333. t specifically authorized and qualified by Thermo Fisher Scientific To ensure continued compliance with EMC and safety standards replacement parts and additional components options and peripherals must be ordered from Thermo Fisher Scientific or one of its authorized representatives This section contains regulatory compliance information for the following devices of the Surveyor Plus family of LC instruments e Surveyor LC Pump Plus e Surveyor PDA Plus Detector e Surveyor MS Pump Plus e Surveyor UV Vis Plus Detector e Surveyor Autosampler Plus Surveyor LC Pump Plus When the Surveyor LC Pump Plus is delivered to you it meets all pertinent electromagnetic compatibility EMC and safety standards as described below EMC Directive 89 336 EEC amended by 92 31 EEC and 93 68 EEC EMC compliance has been evaluated by Underwriters Laboratories Inc EN 55011 1998 EN 61000 4 3 2002 EN 61000 3 2 1995 Al 1998 A2 1998 A14 2000 EN 61000 4 4 1995 Al 2001 A2 2001 IEC 61000 3 2 2000 EN 61000 4 5 1995 Al 2001 EN 61000 3 3 1995 EN 61000 4 6 1996 A1 2001 IEC 61000 3 3 1994 EN 61000 4 11 1994 Al 2001 EN 61326 1 1997 EN 61000 4 2 1995 A1 1998 A2 2001 CISPR 11 1999 A1 1999 A2 2002 FCC Class A CFR 47 Part 15 Subpart B 2004 Thermo SCIENTIFIC Low Voltage Safety Compliance Low voltage safety compliance has been evaluated by TUV Rheinland of North America Inc This device complies with Low Voltage Directive 73 23
334. t the data system does not control The TF terminal output signal is LO Closed by default To change the polarity of the TF output signal to HI Open select the Timed Events Active High check box on the Signal Polarity page of the Surveyor Autosampler Configuration dialog box see Signal Polarity Page on page 56 Figure 57 Time function event terminals on the back panel of the autosampler UNIT ID ENET 6 7 ZZ Ea Es m m OQO 44 IO OC 4 0 TF terminals Surveyor Plus User Guide for LC Devices 93 3 Instrument Method Setup Autosampler Instrument Method Parameters Use the Timed Events page see Figure 58 to specify the timed events for the time function terminals TF1 to TF4 Figure 58 Timed Events page for the autosampler Timed Events imei Off Off Off Off 100 Off Off Off Off To control external devices not controlled by your Thermo Scientific MS application 1 Click the Timed Events tab The Timed Events page appears see Figure 58 2 Specify the appropriate timed events in the table 3 Make the appropriate hardwire connections between the TF terminals on the back panel of the autosampler and the external device Autosampler Timed Events Page Parameters Table 23 describes the columns in the timed events table for the autosampler Table 23 Autosampler timed events table Parameter Description Table of timed events Use this table to set up timed events Time Specifies the
335. tenance Log check box on the Communication page of the Autosampler Configuration dialog box Zero Counter 310 Surveyor Plus User Guide for LC Devices Zeros the counter for the selected maintenance item Thermo Scientific 10 Autosampler Calibration and Record Keeping Autosampler Validation Information Autosampler Validation Information Use the Validation Information dialog box see Figure 216 to enter the validation date for the indicated parameter and the name of the person who performed the validation Figure 216 Validation Information dialog box Validation Information Sample Tray Low Temp Sample Tray High Temp Inject Reproducibility Dilution Reproducibility Column Oven Low Temp Column Oven High Temp Set values Current values Time 03717 2010 Initial name e To open the Validation Information dialog box 1 Open the view for your autosampler The Method page for your autosampler appears 2 In the menu bar choose Surveyor AS gt Validation The Validation Information dialog box appears To specify your user name and the validation date 1 In the Time box type or select the validation date 2 In the Initial Name box type your initials 3 Click Set Thermo Scientific Surveyor Plus User Guide for LC Devices 311 10 Autosampler Calibration and Record Keeping Autosampler Validation Information Validation Information Parameters Table 62 describes the parameters on the Validation Infor
336. that the following parameters are specified on the Surveyor PDA Method page in the Spectra area e Start Diode diode num 2 End Diode diode num 511 e Diode Step diode num 1 Note For a display method the following parameters are not downloaded to the PDA detector run length filter rise time and sample rate 4 Choose File gt Save to save the display method An error message appears see Figure 218 Figure 218 Error message that appears when you attempt to save a display method Current Method can only be saved under Direct Control because Units are set to Intensity To open or save a method in this window select Wavelength Absorbance Units Surveyor Plus User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Verifying the Performance of the PDA Detector 5 Click OK 6 From the menu bar choose Surveyor PDA gt Direct Control 7 Click Yes The Save PDA Display Method dialog box appears 8 Save the display method The data system saves the method with a spda file extension Note The spda file extension is a special file extension used for all method files based on Diode Intensity units When you create a file with an spda file extension you can only load and use it in the Direct Control dialog box After you save the method the Direct Control dialog box appears with the Display page open 9 To adjust light throughput to the diode array
337. the Surveyor MS Pump Plus tab Select the Take Pump Under Control check box see Figure 247 Type the appropriate flow rate in the Flow box Type the appropriate solvent proportions in the Inlet boxes Select the Pump Ready check box Click gt Start to start the solvent flow Figure 247 Direct Control dialog box for the pump Pump 1 pump 2 Take pump under control Flow 0 0 0 0 plimin ial Time 0 00 min 00 00 00 Inlet A 100 00 100 00 InletB 0 00 0 00 Inletc 0 00 0 00 Inlet 0 00 0 00 Pressure 0 0 bar ressure Limits 4 Start the injection as follows a In the Inlet Direct Control dialog box click the Surveyor AS tab The Surveyor AS page appears see Figure 248 342 Surveyor Plus User Guide for LC Devices Thermo Scientific 12 Making a Single Injection from the Tune Window b In the list of commands select Inject Sample The Inject sample parameters appear see Figure 248 Figure 248 Surveyor AS page of the Direct Inlet Control dialog box sesgesssesesssssesssesesosoeseeog Command amp Parameters lt Vial a1 Volume ful 10 0 Ful Partial No Waste Heo c Inthe Vial box type the location of the sample Ensure that you have placed a sample in this location For information about the vial and well notation see Vial and Well Notation on page 6 d Inthe Volume pL box type the volume that you want to inject e Select the injection mode Ful
338. the box The Save As Custom dialog box appears see Figure 245 Figure 245 Save As Custom dialog box Save As Custom Name exists overwrite 6 Click Yes to save the wavelength calibration list Edit Peak List Area Table 64 describes the parameters in the Edit Peak List area on the Choose Calibration Peak list page of the Wavelength Calibration wizard Table 64 Edit Peak List area of the Wavelength Calibration wizard for the PDA detector Parameter Description Peak Crest Specifies a spectral band The holmium oxide wheel contains a solution of holmium oxide in perchloric acid Range 190 to 800 nm Peak Window Specifies the search window for the peak crest Start wavelength peak crest peak window 2 End wavelength peak crest peak window 2 Range 0 1 to 611 0 Buttons Modify Modifies the selected spectral band Add Adds a spectral band Delete Deletes a spectral band Thermo Scientific Surveyor Plus User Guide for LC Devices 339 es i Making a Single Injection from the Tune Window If you are using the Surveyor Plus LC system as an inlet to a Thermo Scientific mass spectrometer you can use the direct control dialog boxes available from the Tune window to make a single injection and acquire data For information about setting up the LC MS system refer to the Getting Connected Guide for your mass spectrometer For information about acquiring raw data files from the tune program for your
339. the center front of the tray compartment and the needle holder moves down 1 inch 2 Click Next to proceed to the next page of the wizard Go to the next procedure Installing the LED Light Fixture and the Target Port Fixture Installing the LED Light Fixture and the Target Port Fixture This page of the Arm Calibration wizard instructs you to remove the needle and install the calibration light source see Figure 195 Figure 195 Request to install the LED light fixture page Diagnostic Arm Calibration Please remove needle from Z Axis assembly Please install the arm calibration light source Connect to rear panel Press Next when done 292 Surveyor Plus User Guide for LC Devices Thermo Scientific 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler The needle assembly is a welded piece of 0 012 in ID stainless steel tubing with an externally threaded fitting a needle flag a latch and a compression spring see Figure 196 It slides into the needle mount on the XYZ arm and is secured with the latch The needle tubing assembly has an internally threaded fitting that connects to the 10 32 externally threaded fitting of the needle assembly Figure 196 Needle assembly Latch 10 32 fitting ia Compression spring Needle flag Needle mount on j the XYZ arm To install the light fixture and the target p
340. then specify the instrument method to be used for each run in an acquisition sequence from the Sequence Setup window Instrument methods contain the analysis wavelengths the chromatographic conditions and the autosampler injection parameters such as the injection mode required for data acquisition To create an instrument method 1 Open the Instrument Setup window Xcalibur data system or equivalent window for your Thermo Scientific mass spectrometry application 2 Specify the instrument method settings for each device 3 Save the instrument method Contents e Opening the Instrument Setup Window e Surveyor LC Pump Plus Instrument Method Parameters e Surveyor MS Pump Plus Instrument Method Settings e Autosampler Instrument Method Parameters e PDA Detector Instrument Method Parameters e Triggering an External Device with the PDA Detector e UV Vis Detector Instrument Method Parameters e Saving the Instrument Method Surveyor Plus User Guide for LC Devices 67 3 Instrument Method Setup Opening the Instrument Setup Window Opening the Instrument Setup Window The Instrument Setup window of the Xcalibur data system is where you create instrument methods and access the direct control commands for your instrument devices If you are controlling your LC MS instrument from another Thermo Scientific mass spectrometry application open the equivalent window To open the Instrument Setup window 1 Start the Xcalibur data
341. ting and pull solvent through the line 4 Remove the Luer Lok fitting from the outlet port 5 Reconnect the solvent line to the degasser outlet port Surveyor Plus User Guide for LC Devices 155 5 Daily Operation Priming the Pulse Dampener of the Surveyor MS Pump Plus Priming the Pulse Dampener of the Surveyor MS Pump Plus Before you can operate the Surveyor MS Pump Plus you must prime its built in pulse dampener Priming the pulse dampener involves filling the dampening coil see Figure 87 with a solvent such as methanol or isopropanol After the coil is filled with solvent it effectively dampens pressure pulsations from the rest of your system Closing the pulse dampener flush valve after you fill the coil shuts the dampening coil off from the mobile phase stream Because a permeable membrane separates the mobile phase stream from the dampening coil the solvent in the coil slowly diffuses into the mobile phase stream When the pump is in continuous or frequent use prime the pulse dampener on a monthly basis Note Do not fill the pulse dampener with an aggressive acid or a buffered solution The recommended filling solvents are methanol acetonitrile or isopropyl alcohol If you accidentally fill the pulse dampener with an acidic or buffered solvent flush the loop with a miscible solvent and then refill it with methanol acetonitrile or isopropyl alcohol Figure 87 Pulse dampening assembly of the Surveyor MS Pump Plus
342. ting the PDA Detector 4 Do the following a Select a peak set from the list The peak set should span the wavelengths you use under normal operating conditions Figure 233 shows the selection of the Holmium Oxide 5 peak set This wavelength list instructs the program to calibrate the detector at each of the five wavelengths shown Note The data system has four calibration files to select from For example the Holmium Oxide UV file contains five wavelengths in the UV region while the other files use sets of wavelengths from both the UV and visible wavelength regions The holmium oxide absorbance maxima are selected from a spectrum published in Holmium Oxide Solution Wavelength Standard from 240 to 640 nm SRM 2034 NIST Special Publication 260 54 Figure 233 Choose Calibration Peak List page Wavelength Calibration Choose Calibration Peak List Holmium Oxide 12 3 Holmi giada i Holmium Oxide 7 Holmium Oxide UY Save as custom list Delete tristis Next gt Cancel Help Click to create a custom peak list Note For information about creating a custom peak list see Creating and Editing a Custom Wavelength Calibration List on page 337 Surveyor Plus User Guide for LC Devices 331 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector b Click Next The next page of the wizard appears see Figure 234 5 Do the following a Observe the status pan
343. tion Specifying the Configuration Settings Surveyor LC Pump Plus Configuration Settings The Surveyor LC Pump communicates with the data system by way of an Ethernet connection To make this connection connect the Ethernet cable to the Ethernet port on the back of the pump and to the Ethernet switch The unit ID setting on the back panel of the pump must match the stack address in the configuration To specify the configuration options for the Surveyor LC Pump Plus 1 In the Configured Devices list double click the Surveyor LC Pump icon Surveyor LC Pump The Surveyor LC Pump dialog box appears see Figure 42 Figure 42 Surveyor LC Pump dialog box Surveyor LC Pump Configuration Pressure Units MPa X Cancel Stack Number f Help Error Handling V Pause Sequence following Degasser Error 2 Make the following entries and selections From the Pressure Units list select the unit of measurement that you want to use to display the backpressure of your system Note 1 MPa 10 bar 145 psi e In the Stack Number box type an appropriate value The value must match the Unit ID setting on the back panel of the Surveyor LC Pump e Ifyou want sequence runs to pause following a degasser error select the Pause Sequence Following Degasser Error check box 3 Click OK to exit the Surveyor LC Pump dialog box Thermo Scientific Surveyor Plus User Guide for LC Devices 63 2 Thermo Foundation Instrument
344. tive High check boxes are selected see Figure 39 These check boxes are selected in the default instrument method 4 In the Output area if your instrument consists entirely of Surveyor Plus devices do not select the check boxes Autosampler Signal Polarity Page Parameters Table 10 describes the parameters on the Signal Polarity page Table 10 Signal Polarity page parameters Sheet 1 of 3 Parameter Description Input The Pump Ready Active High and the Injection Hold Release check boxes are selected in the default instrument method Leave these check boxes selected for a Surveyor Plus pump Pump Ready Active Use this check box to specify the polarity of the input signal from the pump High e Ifthe signal from the pump is LO Closed and goes HI Open when the pump is ready select the Pump Ready Active High check box e Ifthe signal from the pump is HI Open and goes LO Closed when the pump is ready clear the Pump Ready Active High check box Thermo Scientific Surveyor Plus User Guide for LC Devices 57 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Table 10 Signal Polarity page parameters Sheet 2 of 3 Parameter Description Injection Hold Release Use this check box to specify the polarity of the input signal from the pump Active High vere e Ifthe signal from the pump is LO Closed and goes HI Open when the pump is ready select the Injection Hold Release Active Hi
345. to proceed with calibration Waiting for equilibration 5 sec Starting FW calibration please wait Fw calibration started Restoring saved method Click the Next button to proceed with calibration Cancel Help Instruction to click Next 8 Do the following a Observe the status pane see Figure 237 The diagnostics program waits a few seconds for the rise time filter to equilibrate and then the detector takes a holmium oxide scan b When you see the message Click the Next button to proceed with calibration click Next The next page of the wizard appears see Figure 238 Thermo Scientific Surveyor Plus User Guide for LC Devices 333 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Figure 238 Request to rotate the filter wheel to position 1 page Wavelength Calibration Please turn the filter wheel to the OPEN position position 1 9 Rotate the wheel back to position 1 Open as instructed After you rotate the wheel the Next button becomes available see Figure 239 Figure 239 Available Next button Wavelength Calibration Click the Next button to proceed with calibration Cancel Help 10 Click Next to proceed The results page for the wavelength calibration appears see Figure 240 334 Surveyor Plus User Guide for LC Devices Thermo Scientific 11 PDA Detector Performance Check and Calibration Calibrating the PDA Detector Figure 240 Delta values p
346. to the pump is off the proportioning valves are closed Before you take the LDA apart to perform maintenance turn off the power to the pump to prevent solvent from leaking out of the proportioning assembly 2 To open the Direct Control dialog box from the pump view do the following a From the menu bar of the pump view choose Surveyor MS Pump Plus gt Direct Control The Direct Control dialog box for the pump appears see Figure 106 Figure 106 Direct Control dialog box for the Surveyor MS Pump Plus Direct Control Pump 1 Take pump under control Flow 1000 0 0 0 pl min gt m Time 0 00 min 00 00 00 Inlet A 100 00 100 00 Inlet B 0 00 0 00 InletC 0 00 0 00 Inlet D 0 00 0 00 Pressure 42 7 bar Pump ready C Release injection 3 In the Direct Control dialog box do the following a Select the Take Pump Under Control check box b In the Flow box type an appropriate flow rate for the pump If you are drawing fresh solvent through the lines and the liquid displacement assembly type the maximum flow rate for the pump 190 Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 6 Direct Controls Pump Direct Controls The maximum flow rate for the Surveyor MS Pump Plus is 1000 pL min c Type percentages for the solvent lines that you want to draw solvent through in the Inlet boxes A B C and D To start the solvent flow Click L gt
347. trol page parameters Parameter Description Firmware Versions Pump Main Board Displays the firmware version of the Pump Main printed circuit board Pump Converter Displays the firmware version of the Pump Converter printed Board circuit board 272 Surveyor Plus User Guide for LC Devices Thermo Scientific Autosampler Calibration and Record Keeping This chapter describes the calibration and record keeping procedures for the autosampler Contents e Calibrating the Autosampler e Autosampler Maintenance Information e Autosampler Validation Information The autosampler does not require calibration upon arrival at its shipping destination However if you use custom vials or custom microplates you must perform the Well Bottom Distance calibration which determines the actual depth of a vial or microplate well see Well Bottom Distance Calibration on page 305 If problems occur with the column oven control the tray temperature control or the arm positioning contact a Thermo Fisher Scientific service representative This appendix includes calibration procedures for these items however to calibrate the autosampler s temperature zones and XYZ arm position you must have the kit that contains the necessary test fixtures Thermo Scientific Surveyor Plus User Guide for LC Devices 273 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Calibrating the Autosampler There are four calibration
348. tween diode 400 and diode 500 Ignore the spike at approximately diode number 380 This spike is due to the deuterium lamp Thermo Scientific Surveyor Plus User Guide for LC Devices 317 11 PDA Detector Performance Check and Calibration Verifying the Performance of the PDA Detector Figure 221 Display page for the PDA detector with an intensity spectrum Start Data or Display method file name SNAPSHOT button Display Configuration Infomation Calibration Control SNAPSHOT Current method intensity spda_ Started data display Help Spectrum Stop Data Levels Counts Channel Level 759386 Channel B Level 474119 Channel C Level 759744 Lamp Lifetimes hours Deuterium 10 Tungsten 10 Status b Adjust the attenuators see Figure 219 on page 316 as follows e Adjust the attenuator with the left tab on the PDA UV range attenuation to achieve a maximum value from 400 000 to 900 000 intensity counts in the region between diode number 10 and diode number 40 e Adjust the attenuator with the right tab Visible range attenuation to achieve a maximum value from 400 000 to 900 000 intensity counts in the region between diode number 400 and diode number 500 4 To record the light intensities do the following e To save a picture of the scan to the Clipboard press ALT PRINT SCREEN Paste this picture into a text editor such as Microsoft Word Keep this scan for future comparisons to see if there
349. ty of the chromatographic baseline before starting a sequence run 1 Open the Instrument Setup window of the Xcalibur data system 2 In the view bar click the icon for the LC pump and then open the Direct Control dialog box for the LC pump 3 Start the solvent flow from the LC pump Use the chromatographic conditions specified on first line pump program in the instrument method For information about starting the solvent flow from the LC pump refer to the Help for the pump 4 In the view bar of the Instrument Setup window click the icon for your PDA detector The PDA detector view of the Instrument Setup window appears with the Method page displayed 5 From the menu bar choose Surveyor PDA Plus gt Direct Control The Direct Control dialog box appears 6 Click the Display tab The Display page appears see Figure 96 Figure 96 Control area buttons on the Display page Display Configuration Information Calibration Control Load Method Start Data _Ze0Data_ _ StopDate_ 7 In the Control area click Load Method The Open Display Method dialog box appears see Figure 97 168 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls PDA Detector Direct Controls Figure 97 Open Display Method dialog box Open Display Method Look in B methods e e le shutdown meth E startup meth le Test3 meth lt File name Files of type PDA Displa
350. type For more information about the Level trigger type see the next procedure 4 To trigger an external device when the absorbance for a discrete channel reaches a specific level do the following a In the Type list select Level Trigger b In the Channel list select the discrete wavelength channel to be used to trigger the event The available selections are A B or C c In the Level mAU box type a value for the absorbance value that triggers the event The default value is 0 00 mAU and the range is 2000 to 4000 00 mAU d In the Delay sec box type a time in seconds The delay time compensates for the time interval between for example when a compound leaves the detector and when it reaches a fraction collector The default value is 0 and the range is the set of integers from 0 to 65 535 5 To zero the absorbance level for all the wavelength channels that the detector is monitoring at a particular time in the run do the following a Inthe Type list select Zero Data b In the Time box type the time that you want the absorbance level to be zeroed 6 Click OK to accept the new event and close the Timed Event dialog box Thermo Scientific Surveyor Plus User Guide for LC Devices 105 3 Instrument Method Setup UV Vis Detector Instrument Method Parameters UV Vis Detector Instrument Method Parameters In the UV Vis detector view use the Method page to set up the instrument method parameters for the UV Vis det
351. ual flow rate is below the set value increase the alpha value If you are pumping water increasing the alpha value by lincreases the flow rate by 1 For example if the pump is set to deliver a flow rate of 1 mL min and the actual flow rate is 0 96 mL min which is 4 percent below the set rate raise the current setting by 4 If the current setting is 5 0 enter a new setting of 9 0 e Ifthe actual flow rate is above the set value decrease the alpha value If you are pumping water decreasing the alpha value by 1 decreases the flow rate by 1 For example if the pump is set to deliver a flow rate of 1 mL min and the actual flow rate is 1 04 mL min which is 4 percent above the set rate lower the current setting by 4 If the current setting is 5 0 enter a new setting of 1 0 3 Click Set 268 Surveyor Plus User Guide for LC Devices Thermo Scientific 9 LC Pump Calibration and Record Keeping Calibrating the Surveyor LC Pump Plus Updating the Pressure Sensor Adjustment Setting Reset this parameter when you replace the pressure sensor Each pressure sensor is labeled with a data sticker that contains a O XXXX value for the pressure sensor adjustment setting Multiply this value by 10 000 and enter the result in the Pressure Sensor Adjustment setting box To update the pressure sensor adjustment setting 1 Open the Calibration page for the Surveyor LC Pump see Accessing the Calibration Options for the Surveyor LC Pump Plu
352. uide for LC Devices 165 6 Direct Controls PDA Detector Direct Controls Setting the Lamp Startup Time Use the Lamp Startup Time dialog box to set the startup time for the lamps If you do not change the lamp startup time the data system automatically turns the lamps on at 4 55 PM on weekdays To open the Lamp Startup Time dialog box 1 Open the Configuration page of the Surveyor PDA Plus Direct Control dialog box see Configuration Page on page 171 2 In the Programmed Lamp Startup area click Change see Figure 94 Figure 94 Programmed Lamp Startup area of the Configuration page Programmed Lamp Startup Lamps will be started automatically Change at 04 55 PM on weekdays The Lamp Startup Time dialog box appears see Figure 95 Figure 95 Lamp Startup Time dialog box Lamp Startup Time calibur should start the lamps at 4 55 23PM on these days weekdays E Cancel Help To set the startup time for the lamps 1 In the Xcalibur Should Start the Lamps At box click the hours or minutes text to highlight it Tip To change both the hours and the minutes change one time field and then click OK to accept the setting and close the dialog box Then open the dialog box a second time and change the other time field 166 Surveyor Plus User Guide for LC Devices Thermo Scientific 6 Direct Controls PDA Detector Direct Controls 2 To change the numeric values do one of the followi
353. ule displayed in the view bar see Figure 89 The view bar is a vertical bar on the left side of the Instrument Setup window It contains an icon for each configured device When you click a device icon a green triangle appears in the lower right corner of the icon and the device view appears e Ifyou are controlling your instrument from a Thermo Scientific data system other than Xcalibur open the instrument control area The instrument control area opens to the first module displayed in the view bar on the left side of the window 158 Surveyor Plus User Guide for LC Devices Thermo Scientific 5 Daily Operation Accessing the Direct Controls Figure 89 Instrument Setup window open to the Surveyor AS Method page of the Surveyor AS view 9 Untitled Instrument Setup Dataset 6 month content assay File Surveyor AS Help osla amp x 2 Surveyor AS Method Sample Preparation Reservoir Content Timed Events Injection Mode Injection volume ful 10 0 Partial loop Surveyor 4S Needle height from bottom mm 20 4 C Full loop A C No waste Syringe speed ul s 80 Er 2 rT Tray Temperature Control 5 Flush volume ull Enable tray temperature control ie UE Flush Wash source bottle X Temperature C foo 4 2 To open the view for the device of interest click its corresponding icon in the view bar The view for the specific device appears 3 Access the direct controls for ea
354. ungsten lamp is on Q Tungsten Lamp is On Off The tungsten lamp is off Q Lamp is Off When the status is On the Turn Off button is available When the status is Off the Turn On button is available Last Lifetime Reset Displays the date and time that the tungsten lamp was last reset readback Lifetime Hours Elapsed Displays the cumulative time in hours that the tungsten lamp has been in the On state since you clicked the Reset Lifetime button Turns on the tungsten lamp if its current status is Off Turn On Off button Q Lamp is Off Turns off the tungsten lamp if its current status is On Q Tungsten Lamp is On Reset Lifetime button Resets the date and time monitored by the Last Reset readback and the Lifetime readback Note Click Reset Lifetime whenever you replace the tungsten lamp This resets the Last Reset readback to the current date and time and restarts the Lifetime readback at zero Analog Outputs Use the controls in this area to configure and test the Event and Ready outputs Determine if the external device is triggered by contact closure or a TTL transistor transistor logic signal If the external device requires a TTL signal determine the polarity of the signal active high or active low Note For TTL connections e Logic level zero 0 is less than 0 8 Vdc reading from Ground e Logic level one 5 is approximately 5 Vdc 2 4 Vdc minimum from Ground Possible configurations o
355. ust the light throughput to the diode array detector To adjust the light throughput to the diode array follow these procedures e Creating a Display Method e Adjusting the Light Throughput to the Diode Array Creating a Display Method Methods that display a plot of integrated light intensity versus diode number have a spda file extension To create a display method for the PDA detector 1 In the view bar of the Instrument Setup window click the Surveyor PDA Plus button The view for the PDA detector appears 2 In the Units area select the Diode Intensity option see Figure 217 Thermo Scientific Surveyor Plus User Guide for LC Devices 313 11 PDA Detector Performance Check and Calibration Verifying the Performance of the PDA Detector 314 Figure 217 Surveyor PDA Plus Method page with the Diode Intensity option selected Surveyor PDA Plus Method Run Run Length min 110 00 Filter Rise Time sec 1 0 z Help Spectra Units V Collect Spectral Data Diode Step diode num f C Wavelength Start Diode diode num 2 Sample Rate Hz 5 0 Saudati Diode End Diode diode num 511 Filter Bandwidth nm f Intensity Channels reece Channel re Diode diode num 40 Fiter Bandwidth rm One Channel Channel B Two Channels Three Channels Channel C Diode diode num 55 Filter Bandwidth nm i Sample Rate Hz j10 0 Diode diode num 450 Filter Bandwidth nm i 3 Verify
356. vered to you it meets all pertinent electromagnetic compatibility EMC and safety standards as described below EMC Directive 89 336 EEC amended by 92 31 EEC and 93 68 EEC EMC compliance has been evaluated by Underwriters Laboratories Inc EN 55011 1998 EN 61000 4 3 2002 EN 61000 3 2 1995 Al 1998 A2 1998 A14 2000 EN 61000 4 4 1995 Al 2001 A2 2001 IEC 61000 3 2 2000 EN 61000 4 5 1995 Al 2001 EN 61000 3 3 1995 EN 61000 4 6 1996 A1 2001 IEC 61000 3 3 1994 EN 61000 4 11 1994 Al 2001 EN 61326 1 1997 EN 61000 4 2 1995 A1 1998 A2 2001 CISPR 11 1999 A1 1999 A2 2002 FCC Class A CFR 47 Part 15 Subpart B 2004 Low Voltage Safety Compliance Low voltage safety compliance has been evaluated by TUV Rheinland of North America Inc This device complies with Low Voltage Directive 73 23 EEC and harmonized standard EN 61010 1 2001 FCC Compliance Statement THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES OPERATION IS SUBJECT TO THE FOLLOWING TWO CONDITIONS 1 THIS DEVICE MAY NOT CAUSE HARMFUL INTERFERENCE AND 2 THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION CAUTION Read and understand the various precautionary notes signs and symbols contained inside this manual pertaining to the safe use and operation of this product before using the device Notice on Lifting and Handling of Thermo Scientific Instruments For your safety and
357. veyor 4S Ready to Download El Surveyor LC Pump Ready to Download Surveyor PDA Plus Lamp Warmup aD Surveyor PDA is Connected Ready to Start Run Wavelength Calibration is Valid Dark Current Calibration is Valid Method is Not Valid Filter Wheel in Run Position Q Deuterium Lamp is Starting Q Tungsten Lamp is On Thermo Scientific Surveyor Plus User Guide for LC Devices 151 5 Daily Operation Checking the Status of the LC Devices Table 44 describes the readbacks for the PDA detector Surveyor UV Vis Plus Detector Status View Table 44 PDA detector status readbacks Readback Connection status Description Displays whether the PDA detector is communicating with the data system computer The connection states are Connected or Not Connected Ready or Not Ready to Ready to Start Run The detector is ready to start a run or is currently Start Run acquiring data Not Ready to Start Run The deuterium lamp is warming up Wavelength The wavelength calibration is valid or invalid Calibration Dark Current The dark current calibration is valid or invalid Calibration Method is Valid N A Filter Wheel Position The filter wheel has two positions Position 1 Run Light passes through the flowcell onto the diode array Position 2 Closed Light passes through the holmium oxide filter onto the diode array Deuterium Lamp The deuterium lamp states are as follows
358. vials each No 2 Custom Vial Setting Yes 3 96 Well Microplate Tall Microwell Carrier No 4 96 Well Microplate Tall Solid Microwell Carrier No 96 Well Microplate Short Microwell Carrier Riser Plate 5 1mLor2 mL Deep Well Plate Short Microwell Carrier No 6 96 Well Microplate Short Microwell Carrier No 7 96 Well PCR Plate Cooling Adapter Short Microwell Carrier No 8 Custom 96 Well Setting Yes 9 384 Well Microplate Tall Microwell Carrier No 10 384 Well Microplate Tall Solid Microwell Carrier No 384 Well Microplate Short Microwell Carrier Riser Plate 11 Custom 384 Well Setting Yes Surveyor Plus User Guide for LC Devices Thermo Scientific Thermo Scientific 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings 2 For a microplate tray type do the following a In the Al Well Position area select either the Top Left or the Bottom Right option see Figure 36 Figure 36 Tray page with a 96 well plate selection Tray Communication Signal polarity Firmware mAT well position Top lett C Bottom right Well ordering b In the Well Ordering area click the button that represents your preference for the order of sequence injections Surveyor Plus User Guide for LC Devices 49 2 Thermo Foundation Instrument Configuration Specifying the Configuration Settings Autosampler Tray Page Parameters Table 7 describes the configuration paramete
359. x select Inject Sample The sample injection parameters appear see Figure 210 Figure 210 Direct Control dialog box with the Inject Sample command selected Direct Control Command amp Parameters Inject sample v Vial Ica 1 Volume ful 10 Ful Partial No Waste ue b In the Vial box type C A1 Thermo Scientific Surveyor Plus User Guide for LC Devices 303 10 Autosampler Calibration and Record Keeping Calibrating the Autosampler Prj 8 h i a Click Apply and wait for the injection to finish The XYZ arm moves to the location of the A 1 well of the C microplate at the back of the tray compartment and then lowers the needle through the masking tape and into the well In the Vial box type C A24 Click Apply and wait for the injection to finish In the Vial box type C P1 Click Apply and wait for the injection to finish In the Vial box type C P24 Click Apply and wait for the injection to finish Remove the microplate and check the location of the injections as follows In the Direct Control dialog box select Position Arm to Access Tray The XYZ arm moves to the back of the tray compartment Remove the tray from the tray compartment and inspect the holes in the tape Verify that the holes are at or near the center of the microplate wells Each hole must be at least 0 05 cm 0 02 inches from the edge of the well If the results are not satisfactory repeat the arm
360. x appears see Figure 66 Figure 66 Save As dialog box showing the file extension for an instrument method Save As Save in methods ti tst s ex Ee File name Instrument Control meth Save as type Methods meth Ez Cancel Help Header Information Thermo Scientific Surveyor Plus User Guide for LC Devices 109 3 Instrument Method Setup Saving the Instrument Method 2 Browse to the following folder drive Xcalibur methods 3 In the File Name box type a file name 4 Click Save The File Summary Information dialog box appears see Figure 67 Figure 67 File Summary Information dialog box File Summary Information User Finn Header File ID Finn Created Monday January 05 2004 1 46 36 PM User ID Finn Logon ID Finn Not changed Description New Method Cancel Help 5 In the Description box type a description of the method file 6 Click OK If the Authorization Manager Comment check box is selected the File Save Audit Trail dialog box appears see Figure 68 110 Surveyor Plus User Guide for LC Devices Thermo Scientific 3 Instrument Method Setup Saving the Instrument Method Figure 68 File Save Audit Trail dialog box File Saye Audit Trail User Finn Comment i Method What changed New Instrument Method e 7 In the Comment box type a comment concerning the changes you made to the instrument method 8
361. y Method spda meth Open as read only 8 Select the instrument method that you plan to use in your acquisition sequence 9 Click Open to download the method to the PDA detector and close the dialog box 10 In the Control area click Start Data The graphical display begins to update The spectral scan appears in the top pane and the chromatographic data for the discrete channel wavelengths appears in the bottom pane When you click Start Data the Start Data button changes to the SNAPSHOT button and the Zero Data button is available see Figure 98 Figure 98 Display page with data displaying for an instrument method Instrument method with a meth file extension Display Configuration Information Calibration Control Current method UY scan meth Started data display Spectrun Zero Data Stop Data Levels m U Channel 4 Level Channel B Level Channel C Level 0 4303 0 0000 0 0000 Lamp Lifetimes hours Deuterium 1980 Tungsten 2142 Thermo Scientific Surveyor Plus User Guide for LC Devices 169 6 Direct Controls PDA Detector Direct Controls 11 To zero the absorbance level click Zero Data The Current method readback displays Zeroed Data Display see Figure 99 Figure 99 Effect of clicking the Zero Data button Current method UY scan meth Zeroed data display Help Spectrum 12 To stop data acquisition click Stop Data If the noise level is too high chec
362. yor Plus high performance liquid chromatograph HPLC The Xcalibur data system controls the pump through an Ethernet communication link with the data system computer The only manual controls are the power switch located on the front of the pump in the lower left corner below the door and the drain valve The Surveyor LC Pump Plus has five major components the vacuum degassing assembly the solvent proportioning assembly the pump head assemblies the purge manifold assembly and the pulse dampening assembly see Figure 2 The pulse dampening assembly adds 400 pL of gradient delay volume to the system The Surveyor LC Pump Plus has status LEDs on the front door and a low voltage power supply Figure 2 Front view of the Surveyor LC Pump Plus Solvent lines entering Pump head Line body containing and exiting the assemblies filter frit degassing assembly es On Off switch Thermo Scientific Solvent Pulse dampening Purge proportioning assembly behind the manifold assembly front panel assembly Surveyor Plus User Guide for LC Devices 3 1 Introduction to the Surveyor Plus LC System Analytical Pump 4 You can use the Purge command from the data system to draw solvent at a rate of 10 mL min through the solvent lines connected to the pump after you open the purge valve To open the purge valve turn the knob on the front of the purge manifold assembly counterclockwise see Figure 3 When the valve is in the open position loo

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