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Thermo PAL User Guide Version C

1. Thermo PAL User Guide 63 5 Using Dynamic Load and Wash DLW Installing Cycle Composer Macros or ICC Cycles General Considerations You must establish the duration of the wash steps for each configuration and application Consider factors such as the viscosity and surface tension of the individual wash solvent composition and the backpressure of the system Be aware that a higher backpressure builds up if the valve bore size standard valve bore 0 25 mm or the installed loop internal diameter is lower Standard loop internal diameter ID for Thermo defined loops with a volume of 5 10 and 20 pL is 0 25 mm The loop with 2 pL content volume has an ID of 0 125 mm Keep the tubing internal diameters of the tubing in line with the valve dimensions loop ID and flow rate For details see Tips amp Hints for HPLC Technique Priming the Solvent Lines Wash1 and Wash2 This macro is used at installation to prime the entire system Set the wash time to approximately 120 seconds for each solvent After installation for best results prime the system before activating the first run For daily preparation of the system the wash time can be much shorter approximately 20 seconds The goal is an entire liquid system free of any air bubbles Macro Name Priming Accela Open AS_Rev01 Table 15 Macro Priming Accela Open AS Sheet 1 of 2 Macro description Macro variable The injection unit moves to the DLW Wash Clean Time solven
2. 2010 Thermo Fisher Scientific Inc All rights reserved Xcalibur is a registered trademark of Thermo Fisher Scientific Inc in the United States The following are registered trademarks in the United States and other countries Microsoft and Windows are registered trademarks of Microsoft Corporation Teflon is a registered trademark of E I du Pont de Nemours amp Company Unimetrics is a registered trademark of Unimetrics Company Tycoon is a registered trade mark of Saint Gobain Performance Plastics Company Redone and the Redone logo are registered trademarks of Redone L P PAL is a trademark of CTC Analytics AG Agilent is a registered trademark of Agilent Technologies Inc 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 erro
3. 4 To complete the definition of a numeric variable e f In the Variable Name box type an appropriate name In the Variable Units list select a unit of measure In the Default Value box type a default value for the variable In the Lower Limit box type a lower limit for the variable In the Upper Limit box type an upper limit for the variable Click OK to save the variable and close the Variable Definition dialog box 5 To complete the definition of an object variable as b c In the Variable Name box type an appropriate name Select the appropriate objects see Figure 30 Click OK to save the variable and close the Variable Definition dialog box Figure 30 Object variable selections Variable Definition Variable Type C A Numeric Value Variable Name Please check what objects this variable may be SYRINGE T VIAL j TRAY_TYPE M TRAY_HOLDER M TRAY P WASH_STATION INJECTOR VALVE AGITATOR M MOTOR_DRIVE J HEATER POSITION PATH M SYNC_SIGNAL M QUT_SIGNAL M IN_EVENT M OUT_EVENT J SW_EVENT M PwR_EVENT M RS232 M MOTOR_X M MOTOR_Y M MOTOR_Z M CHKMOTOR M USER M DILUTOR M SER_VALVE j QUT_EXP Thermo PAL User Guide 49 3 Creating Custom Templates and Macros Defining Variables Variable Definition Dialog Box Use the Variable Definition dialog box to specify the details of a numerical or object Macro Variable that you want to add or edit in the Macro Variables box Table 10 Variable De
4. cycle This is only a sample method for short runs For analytical work the method parameters must be set according to the specific needs Injectors 1 fic Viv x 2 fic via z Syringe a injections Per Vial f100ul fi porom Ready To Download i Hel lal neip 7 Make the following selections and entries e Under Vial Index type the location of the sample vial e Under Trays select the tray where the sample vial is located e Under Volume type the volume that you want the autosampler to inject 8 Click the tab for the configured LC pump and start the solvent flow from the LC pump Note Thermo PAL only downloads the method parameters for the autosampler It ignores the method parameters for the LC pump and the MS detector 9 Return to the Methods page for the Thermo Pal and click Run 54 Thermo PAL User Guide Thermo Scientific Direct Control Methods Page Thermo Scientific 4 Using the Direct Controls to Operate the Autosampler Making Single Injections from the Tune Window The Methods page of the Inlet Direct Control dialog box has the following parameters Table 11 Methods page parameters Parameter Description Method Use this list to select a method file Description This box contains a description of the selected method Syringe This box displays the configured syringe Device Status This box displays the status of the PAL Status states Vial
5. DLW Cycle Step by Step Figure 45 Standard Step 11 Valve is switched to INJECT position start chromatographic process Solenoid Actuator Valve Column 80 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 46 Standard Step 12 Rear sample volume and air segment are dispensed to waste Solenoid p Jl Actuator Valve uuu Thermo Scientific Thermo PAL User Guide 81 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 47 Standard Steps 13 14 Valve clean with Wash Solvent 2 Solenoid Actuator Valve Column 82 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 48 Standard Steps 15 16 Active syringe needle wash with Wash Solvent 2 Solenoid Actuator Valve Column Thermo Scientific Thermo PAL User Guide 83 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 49 Standard Steps 17 18 Valve clean with Wash Solvent 1 Solenoid Actuator Valve Pump gt Pump2 gt E E Column z 84 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 50 Standard Steps 19 20 Active syringe needle wash with Wash Solvent 1 Solenoid Actuator Valve Column Thermo Scientific Thermo PAL User Guide 85 5 Using Dynamic Load and Wash DLW DLW Cycle Ste
6. Terminal settings To change the tray configuration 1 Open the Direct Control dialog box see Opening the Direct Control Dialog Box on page 51 2 Click the Tray Configuration tab The Tray Configuration page appears see Figure 33 Figure 33 Tray Configuration page Direct Control Methods Tray Configuration Direct Control Configuration Tray E Tray Holder Type Vials In amp Direction Vials In Y Direction Help 3 In the Tray list select the tray that you want to modify 4 In the Type list select the tray type 56 Thermo PAL User Guide Thermo Scientific 4 Using the Direct Controls to Operate the Autosampler Specifying the Location of the Direct Control Methods Direct Control Tray Configuration Page Use the Tray Configuration page in the Direct Control dialog box to enter the Tray Configuration information required for the autosampler to carry out autosampling Table 12 Tray Configuration page parameters Parameter Description Tray From this list select the tray location in the three drawer deep drawer configuration tray 1 amp 2 drawer 1 tray 3 amp 4 drawer 2 tray 5 amp 6 drawer 3 Up to six drawers and twelve trays are possible with the shallow drawer configuration Type From this list select the tray type Tray Holder Stack 1 and Stack 2 are the allowed values Tray holders can hold one or more trays A Stack is a tray holder that is designed to hold
7. WASH POWER ien suzzen SER3 SER2 SERI lt Ae ao i C able y nl a i I To LC pump Byuod auis ows y 1 149 RS232 I O UNIT ID ENET 3 a Q 2 A 4 gt D 9 aN9 N JHYL1S GVHD ON ON an9 l dWnd w G10H LOAN dOLs dNNd LYVLS dVeS AGVAY dWNd o G10H LOAPNI SYNSSAYd ano vwo ASH N Agvay NO dnd SUNSSAYd 3YNSSIYd QYOINMOG Md C Accela Pump Surveyor MS Pump Plus Surveyor LC Pump Plus 6 Thermo PAL User Guide Thermo Scientific Figure 4 TSO Series te ck ene eee become eee 30V Max Start In A ie a Sa eee a ee te To MS detector To LC pump Byuod ajBuig oway 1 14d D 7 Q Zz iw 8 3 D m D Q a m dOLs dWNd 1YY1S GVYeD 56 22 EE Zm z9 az 5e 265 Accela Pump 1 Getting Connected Connecting the Contact Closure Cables Contact closure connections to a Thermo Scientific LC pump and an MS detector firmware 4 1 2 Surveyor MSQ Plus LTO Series Start In Start In Autosampler AUX2 POWER FUSE lt O 2 INTERFACE 1 INTERFACE 2 y TERMINAL SER LAN MODBUS Buzzer wasn E samo o a
8. a solvent change you must prime the solvent lines properly until air bubbles are no longer visible Solvent degassing is recommended In order to make the initial and daily priming efficient and controllable the Open Autosampler comes with a Cycle Composer macro or ICC cycle io To prime the solvent lines 1 Load the macros and methods into the folder N Start the corresponding macro for initial or daily priming 3 Check the solvent lines and prime until air bubbles are no longer visible 4 Press F4 forHome Location of Solvent and Waste Bottles The DLW option contains self priming membrane pumps The solvent bottles can be placed either in the fast wash station holder or on the lab bench 70 Thermo PAL User Guide Thermo Scientific DLW Pumps 5 Using Dynamic Load and Wash DLW Operating Dynamic Load and Wash DLW You must place the Waste bottle must be placed gt 30 cm in below the injection valve Make sure that the waste liquid can flow into the waste bottle without restriction Place the waste tubing above the level of the liquid Ideally the tube is fixed at the neck of the waste bottle Note Use good lab practice to avoid contaminating the wash solvents and the wash bottles Avoid biological growth in pure water by either replacing it regularly or adding a small percentage of organic solvents such as methanol or acetonitrile Certain buffer solutions can decompose at room temperature when ex
9. applications Thermo Pal one of the device drivers provided on the LC Devices software CD is the device driver that enables Xcalibur control of the autosampler This user guide provides you with information on how to connect the Thermo PAL autosampler to other devices in the LC MS system and how to operate it from the Xcalibur data system This manual is provided in electronic format only You can access this manual by choosing the following from the computer desktop Start gt All Programs gt Thermo Instruments gt Manuals gt LC Devices gt CTC gt Thermo PAL To provide us with comments about this document click the link below Thank you in advance for your help SURVEY Related Documentation The Thermo PAL autosampler includes Help and this manual as a PDF file e Thermo PAL Autosampler User Guide 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 Thermo Scientific Thermo PAL User Guide ix Preface 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 info
10. list see below is placed below the macro selected in the Macro Sequence box highlighted in blue Replace Replaces the macro highlighted in blue in the Macro Sequence box with the macro that is in the Macro list see explanation below Delete Deletes the macro that is selected highlighted in blue in the Macro Sequence box Run Step Automatically executes the macros that constitute the Method Macro Sequence Executes the Method Macro Sequence in a stepwise manner Macro Individual PAL macros are chosen in this list When you select a macro it is highlighted in blue Displayed at the top of the Macro list is the sequence number x of the chosen macro and the total number of macros y in the Macro Sequence pane Macro x of y The chosen macro may be placed in the Macro Sequence box see explanation above by using the Insert Above Insert Below or Replace buttons as appropriate see corresponding explanations above Default All 36 Thermo PAL User Guide Changes all of the Method Template Editor variables to their default values Thermo Scientific 3 Creating Custom Templates and Macros Testing a Custom Template Table 7 Template Editor page parameters Sheet 3 of 3 Parameter Description Variables The variables that make up the macro in the Macro list are displayed in this area Variables with specific allowed values discrete variables are displayed in lists Continuous
11. long enough so that the entire system is flushed out by both wash solvents Consider the entire delay volume to determine the second valve switch The DLW internal volumes are Manifold 90 pL Holding Loop 108 pL Syringe Needle Gauge 22 6 7 pL Installed Injection Loop Total delay volume 205 pL Loop content volume Do the second valve toggle back to starting condition before the system equilibration time has started The Loop content is ideally a solvent of a low elution power when switched back If isocratic chromatography is applied the remaining contaminants might be washed into the system and can build up higher background noise for the column the detector or both over a longer period of time 88 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Additional Cleaning Step Stator Wash or Valve Toggle Step by Step Figure 53 to Figure 58 illustrate additional cleaning steps for Stator Wash Stator Wash End of Standard Injection Cycle Figure 53 Start for additional cleaning step Valve Toggle Solenoid Actuator Valve Pump 1 lt gt Column Pump Thermo Scientific Thermo PAL User Guide 89 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 54 Stator Wash Step 1 2 Valve switched to Load Position toggle valve clean with Wash Solvent 1 Solenoid Actuator Valve Column Pump 90 Thermo PAL User Guide The
12. microplates The autosampler firmware determines the type and number Vials in X Direction Vials in Y Determined by choice of tray type Direction Specifying the Location of the Direct Control Methods Use the Direct Control Configuration dialog box to specify the location of the methods that you can open in the Methods page of the Direct Control dialog box To specify the method folders 1 Open the Direct Control dialog box see Opening the Direct Control Dialog Box on page 51 2 Click the Direct Control Configuration tab The Direct Control Configuration page appears see Figure 34 By default the methods that appear in the Method list on the Method page are located in the following directory C Xcalibur Methods Thermo Scientific Thermo PAL User Guide 57 4 Using the Direct Controls to Operate the Autosampler Specifying the Location of the Direct Control Methods Figure 34 Direct Control Configuration page Direct Control Methods Tray Configuration Direct Control Configuration Wrap each direct control method run with the following macros V Sequence Entry Exit IV Method Entry Exit Method Search Paths Path Browse Add Delete Reset C Xcalibur Methods 3 To add additional file locations a In the Path box type the folder location or click Browse and browse to the appropriate folder to select it b Click Add The new folder location appears in the box below the row of butto
13. on the back panel of the Thermo Scientific LC pump Table 4 4 Thermo PAL User Guide Thermo Scientific 1 Getting Connected Connecting the Contact Closure Cables Table 4 Contact closure cable connection to Thermo Scientific pump Pump type Clear wire Black wire Surveyor LC Pump Plus PROG START pin 4 GND Surveyor MS Pump Plus GRAD START pin 8 GND Accela Pump GRAD START pin 4 GND 3 Using a 2 pin combicon connector connect the other leg of the contact closure cable to the Start in pins of the Thermo Scientific MS detector Figure 3 and Figure 4 show the contact closure connection between the Thermo PAL and a Thermo Scientific LC pump and the contact closure connection between the autosampler and a Thermo Scientific MS detector Figure 3 is for firmware 2 5 2 and Figure 4 is for firmware 4 1 0 Thermo Scientific Thermo PAL User Guide 5 1 Getting Connected Connecting the Contact Closure Cables Figure 3 Contact closure connections to a Thermo Scientific LC pump and an MS detector firmware 2 5 2 Surveyor MSQ Plus TSO Series LTO Series OR OR te ee eee eee ee nnn ee ee eee eee een ene eens SMS SSS boc See eee Se Start In _ 30V Max in Startin i Start In i f i l l To MS detector Autosample I i 1 kal i M
14. pushing the inner knob button The screen now shows the Tray Type Make the Tray Type active by pushing the inner knob button The Tray Type is highlighted Rotate the outer knob to select the tray type Select NONE if no tray is present rotate the outer knob until NONE appears as the Tray Type Push the inner knob button to select this tray type 4 Repeat step 3 for all the trays to be used 5 Return to the Job Queue screen by pushing the F4 key Home Changing the Pulse Time Setting 22 Thermo PAL User Guide To control LC systems with a Thermo Scientific LC pump and an autosampler from the Xcalibur data system you must change the default pulse time setting for the autosampler from 2 seconds to 4 seconds The pulse time is the length of time that the autosampler sends an output signal after it makes an injection The LC pump receives this output signal through the contact closure cable IMPORTANT If your LC system contains a Thermo Scientific LC pump and an autosampler you must change the autosampler s default pulse time setting If you leave the default pulse time set to 2 seconds the status of the LC pump remains at waiting for contact closure after you make an injection Thermo Scientific 2 Getting Started Using the Autosampler Control Terminal Change the pulse time setting to 4 0 seconds from the Injected screen see Figure 16 Figure 16 Menu path to Injector screen L Menu Ther
15. self priming 62 Recommended Injection Volume box 28 regulatory compliance iii S safety information 1 safety standards iii self priming micro pumps 62 solvent lines priming 64 solvent lnes priming 70 syringe size specifying 28 T Template Editor enabling 17 opening 33 templates editing 33 Single Step LC Injection 26 testing 37 Thermo PAL driver for Xcalibur 62 Tray Configuration page 56 tray type selecting with the PAL Control Terminal 21 Trays screen 21 Tune window making single injections from 53 V variables defining 48 108 Thermo PAL User Guide W Waiting for contact closure status for LC pump 22 Thermo Scientific
16. standards replacement parts and additional components options and peripherals must be ordered from Thermo Fisher Scientific or one of its authorized representatives 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 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 ph
17. to their default values 30 Thermo PAL User Guide Thermo Scientific 2 Getting Started Viewing the Method Summary Viewing the Method Summary To view a summary of your autosampler portion of an instrument method 1 Open the Instrument Setup view for the autosampler see Specifying the Instrument Method Parameters for the Autosampler on page 24 2 Choose File gt Open and select the instrument method that you want to review 3 Click the Method Summary tab The Method Summary page appears with a summary of the autosampler parameters for the active instrument method see Figure 21 Thermo Scientific Thermo PAL User Guide 31 2 Getting Started Viewing the Method Summary Figure 21 Method Summary page Method Setup L Description Duplication of PAL local LC Inj cycle This is only a sample method for short runs For analytical work the method paramet ers must be set according to the specific needs Syringe 100ul Macro Sequence LC Inj Step 1 of 1 Air Volume pl 0 Pre Clean with Solvent 1 0 Pre Clean with Solvent 2 0 Pre Clean with Sample 0 Filling Speed pls 50 Filling Strokes 1 Inject to LC Vlv1 Injection Speed pls 100 Pre Inject Delay ms 500 Post Inject Delay ms 500 Post Clean with Solvent 1 1 Post Clean with Solvent 2 0 Valve Clean with Solvent 1 1 Valve Clean with Solvent 2 1 Recommended Injection Yolume Volume 10 00 Injection Look Ahead Delay Time 0 00 Macros
18. window appears see Figure 22 Thermo Scientific Thermo PAL User Guide 33 3 Creating Custom Templates and Macros Using the Template Editor to Create Custom Templates Figure 22 Template Editor page of the Pal Template Macro Editor window a Pal Template Macro Editor File PAL View Help Dad amp 2 Template Editor Macro Editor Template Summary m Template Description Macro Default New Methar Default Al Variables Syringe x LC Inj Device Status lt unknown gt 34 Thermo PAL User Guide Thermo Scientific 3 Creating Custom Templates and Macros Using the Template Editor to Create Custom Templates 2 Optional In the Template Description box type a description of your custom template 3 In the Syringe list select the appropriate syringe size for the parameters to be specified in the template 4 To add macros to the template a Under Macro select a macro from the list The Insert Above and Insert Below buttons become available b Click Insert Above or Insert Below The selected macro appears in the Macro Sequence list 5 To delete macros from the Macro Sequence list a Select the macro that you want to delete from the Macro Sequence list b Click Delete 6 To replace a macro in the Macro Sequence list a Under Macro select a macro from the list b Select the macro that you want to replace in the Macro Sequence list c Click Replace 7 To save the
19. 04 14 Chapter2 Getting Started 0 0c cece eee eee eee eee eens 15 Adding the Autosampler to the Xcalibur Instrument Configuration 15 Firmware Versions Supported a b ne ona cidade town ade towdadesed anced 20 Using the Autosampler Control Tetiainal 4 20 0cierck enn bee vee eben es 20 Selecting the Tray Type tet ations pein ese narrer 21 Changing the Pulse Time Setting o n cee ke dns vee vase pees eae es 22 Specifying the Instrument Method Parameters for the Autosampler 24 Viewing the Method Summary 2 cecv by ceded ee tenvnbe ti dade th eedes 31 Chapter3 Creating Custom Templates and Macros 0e0eee cece eens 33 Using the Template Editor to Create Custom Templates 33 Testing a Custom Templat 4 vein ca eee ey ine ta EE EE a 37 Viewing the Template Sumimatycc sc cteieecteks oe kde keen eee ake 40 Standard Master vive inedi tya techn rehs che teeter acre rpesdaryees 42 Using the Macro Editor to Create Custom Macros 0 00000000 43 Defining Variables in cid enw sd ona ce daniami iana a a ted ban Ges 48 Thermo Scientific Thermo PAL User Guide vii Contents viii Chapter 4 Chapter 5 Thermo PAL User Guide Using the Direct Controls to Operate the Autosampler 51 Opening the Direct Control Dialog Box 0 2 eee eee ee 51 Making Single Injections from the Tune Window 000004 53 Changing the Tray Configuration coi teien are oa ab
20. 1 Getting Connected Connecting the Contact Closure Cables Figure 8 External contact trigger cable supplied by Thermo Fisher Scientific g 7 Connect to the MS detector Connect to the Agilent pump SIDOVLNOD AV144Y Thermo Scientific Thermo PAL User Guide 11 1 Getting Connected Connecting the Contact Closure Cables Figure 9 Contact closure with an Agilent pump the autosampler and a Thermo Scientific MS detector firmware 2 5 2 Surveyor MSO Plus TSO Series LTO Series D 1 1 1 1 1 1 1 1 1 1 i 1 1 1 1 a Zz aS SSS SSS SS S Start In 30V Max Start In Start In External contact trigger cable supplied by Thermo Fisher Scientific Autosampler RELAY CONTACTS AUX1 AUX2 Agilent pump INTERFACE 1 REMOTE 000 Cbl 7890 CE 3 DB15 to DB9 cable supplied by CTC Analytics 12 Thermo PAL User Guide Thermo Scientific 1 Getting Connected Connecting the Contact Closure Cables Figure 10 Contact closure with an Agilent pump the autosampler and a Thermo Scientific MS d
21. AM E O My Documents E LC Inj DLW Fast_Rev03 PME 2KB PMEFile 3 31 2010 9 28 AM E 3 My Computer E LC Inj DLW Standard_Rev03 PME 3KB PMEFile 3 31 2010 9 28 AM JB 3 Floppy a E Multi Step LC Injection PME 4KB PMEFile 3 31 2010 9 28 AM E S Local Disk C E Single Step LC Injection PME 2KB PMEFile 3 31 2010 9 28 AM B DB Program Files E Startup Shutdown PME 1KB PMEFile 3 31 2010 9 28 AM O Projects DB Quarantine Tech Pubs S O test amp Thermo S Instruments amp LC Devices AccelaOpenas S ThermoPAL a PaL B Macros 5 In the Template list select a Template that represents the task that you want to do The autosampler comes with three templates Single Step LC Injection pme Multi Step LC Injection pme and Startup Shutdown pme For high throughput applications use Single Step LC Injection pme If your applications require more pre and post injection cleaning steps use Multi Step LC Injection pme The Startup Shutdown pme template is reserved for future use In addition to these templates you can create your own custom templates see Using the Template Editor to Create Custom Templates on page 33 When you store a custom template in the same folder as the standard templates the template appears in the Template list Figure 20 shows the macro sequence and the macro variables for the Single Step LC Injection template 26 Thermo PAL User Guide Thermo Scientific Figure 20 Method Set
22. Index 1 In this box type the vial index to be used with the method SL index 2 In this box type the vial index to be used with the method SL index2 Trays 1 From this list select the tray to be used with the method SL tray 2 From this list select the tray to be used with the method SL tray2 Volume 1 In this box type the injection volume to be used with the method SL volume 2 In this box type the second injection volume to be used with the method SL volume 2 Injectors 1 From this list select the injector to be used with the method SL injector 2 From this list select the second injector to be used with the method SL injector2 Injections Per Vial Type the number of replicate injections to be made from each vial Run Runs the selected method Thermo PAL User Guide 55 4 Using the Direct Controls to Operate the Autosampler Changing the Tray Configuration Changing the Tray Configuration Use the Tray Configuration dialog box to specify the tray types to be used for direct control injections while you have the Direct Control dialog box open The autosampler uses this tray information instead of the tray information specified in the autosampler Control Terminal IMPORTANT The autosampler does not store the tray configuration that you specify on the Tray Configuration page of the Direct Control dialog box When you close the dialog box the tray configuration resets to the autosampler Control
23. L User Guide 17 2 Getting Started Adding the Autosampler to the Xcalibur Instrument Configuration 8 In the Cycle Composer Macro Importer area import the macros that you plan to use to create injection methods a In the Import Path box type the location where the macros reside Or click Browse to locate the directory that contains the appropriate macros b In the Overwrite existing macros list make one of the following selections e Never The autosampler does not import the specified macro if it has the same filename as an existing macro e Ask The autosampler asks you if you want to overwrite existing macros e Always Imported macros overwrite existing macros c Click Import to import the macros 9 In the Active Trays area select the trays that you want to use You can use trays that have a Yes in the Allow Use column Clicking the tray name clears the Allow Use cell and removes the tray from the list of available trays in the Xcalibur data system IMPORTANT Use the autosampler control terminal to specify the tray information You can change the tray information when you are controlling the autosampler from the Xcalibur data system but these changes are temporary When you close and reopen the Xcalibur data system the tray information resets to the autosampler control terminal settings 10 To accept the configuration settings and close the Pal Configuration dialog box click OK 11 Configure the other instr
24. Method Template Macro Editor Enable Enable m r Cycle Composer Macro Importer Import Path C Overwrite exisiting macros Never Import Browse Active Trays Tray01 Stack1 Tray02 Stack Tray03 Stack1 Tray04 Stack1 TrayO5 Stack1 Te NC Cte nl lt 5 Select the data system computer Com port that the autosampler is connected to a Inthe Com Port list select the Com port that the autosampler is connected to Or click Auto Select Tip The autoselect feature works only if the autosampler is connected to the data system computer and turned on b Ifyou have already connected the autosampler to the data system computer click Check to verify the connection 6 To shorten the time between injections select the Enable check box under Look Ahead Injections When you enable look ahead injections the autosampler sets up for the next injection during the current run The set up for the next injection involves carrying out the steps up to but not including the injection Note Do not modify or delete a sequence while the data system is running with the Look Ahead Injections enabled Use the stop function to finish the current injection before you modify or delete a sequence 7 To make the Method Template and Macro Editor dialog boxes available in the Instrument Setup window select the Enable check box under Method Template Macro Editor Thermo Scientific Thermo PA
25. Select the command by rolling the cursor over the command no click is needed highlighting each command in blue Clicking the command displays it in this list highlighted in blue Simultaneously the command parameters are displayed in the Parameters area below the Command list At the bottom of this area below the Parameters area is a pane that describes the function of the selected command Parameters The Parameters area displays the command parameters used by the autosampler command that you select in the Command list Parameters with specific allowed values discrete parameters are displayed in lists Continuous parameters are displayed in panes The allowed values of discrete parameters may be chosen from those presented in the list for the parameter The allowed values for continuous parameters are displayed when you place the cursor over the respective pane for the parameter The desired value for the continuous parameter may be typed in its pane You can view other allowed continuous parameter values in a shortcut menu This menu is activated by right clicking the continuous parameter box of interest The parameter you select from the shortcut menu appears in the box Command Description A description of the command displayed in the Command list Save Macro Saves the macro command sequence under the current filename overwrites the current file Save As Saves the macro command sequence under a new filena
26. Start on the sample pump Table 4 on page 5 lists the pin assignments of the Accela Pump Surveyor MS Pump Plus and the Surveyor LC Pump Plus Figure 6 shows two Accela Pumps connected together for contact closure 8 Thermo PAL User Guide Thermo Scientific 1 Getting Connected Connecting the Contact Closure Cables Figure 6 Dual pump setup with two Accela Pumps INTERFACE 1 soooeoee To the MS detector n To the autosampler 6yuo9 auis ouuay L 199 Start pump ano N BaNSSsad CO Aqvaa dWNd Ul 70H LIINI O Cbl Thermo Dual Config Sample pump eS ea an9 as an9 N dOLS dWNd W lavis avag gt ATYIY dWNd UI 10H LIINI O Thermo Scientific Thermo PAL User Guide 9 1 Getting Connected Connecting the Contact Closure Cables Making Contact Closure with the Autosampler an Agilent Pump and an MS Detector To make contact closure between the autosampler and an Agilent pump and between an Agilent pump and a Thermo Scientific MS detector you must have the following cables e PAL interface cable supplied by CTC or Agilent for an Agilent pump see Figure 7 e External contact trigger cable supplied by Thermo Fisher Scientific see Figur
27. a a LC Inj pma a Method Entry pma E Method Exit pma E Pulse Output Signal pma E Reset pma s Set Output Signal pma a SL Entry pma 23 SL Exit pma laa Switch valve to Inject pma E Switch Valve to Load pma a Transfer Liquid and Mix pma E Transport Yial pma E Wait for Data System pma a Wait Signal pma y a Wait pma Thermo Scientific 3 Creating Custom Templates and Macros Using the Macro Editor to Create Custom Macros Using the Macro Editor to Create Custom Macros Macros are the building blocks that you use to create templates Creating a Custom Macro This section provides information about how to create a custom macro To create a custom macro 1 Open the Macro Editor dialog box a Open the Instrument Setup view for the autosampler b From the menu bar choose PAL Auto Sampler gt Template Macro Editor c Click the Macro Editor tab The Macro Editor page of the Pal Template Macro Editor window appears see Figure 28 Thermo Scientific Thermo PAL User Guide 43 3 Using the Macro Editor to Create Custom Macros Figure 28 Macro Editor page of the Template Macro Editor window 44 Creating Custom Templates and Macros im Pal Template Macro Editor Aspirate File PAL Yiew Help EETGEREI oi saru Template Editor Macro Editor Template Summary Macro Aspirate v Macro Description Fill syringe from a vial or a wash station Sample volume air
28. ace RAN SA ead a eee 56 Specifying the Location of the Direct Control Methods 57 Wrapping Direct Control Injections with Additional Macros 60 Using Dynamic Load and Wash DLW 0000cceeeeeeeeees 61 OVENI EW oe Sla gut olan ase wala ee erates E EA A tase eae aS 61 Installing Cycle Composer Macros or ICC Cycles n 00 0 cece eee 62 General Considerations sc airs casue pew kee ee bi caste 64 Priming the Solvent Lines Washl and Wash2 000000040 64 Standard DLW Injection Cycl se tec kee Aeh hoe Ma ee BN ark 66 Fast DLW Injection Cycles co tvs date enii a apatites E wale 68 Operating Dynamic Load and Wash DLW 0 0 0 c ccc eee eee 70 Priming che Solent bates s f edere hate es Palen eeii i Wk ee aay Was 70 Location of Solvent and Waste Bottles n n 00 cee eee eee eee ene 70 DEW PUM ps ons erp ern ennn ge are h ooo Era Glee Whe pie ae SS 71 DLW Actuator Solenoid is bss thes Sek ahaa wi ewe Ses 71 DEW Cycle Step by Step ocna Sat e AEE E E weet oe oa dae 73 Cycle for Standard Injection tatiesilo mene pele ep le ees Ais 73 Additional Valve Toggle Step to DLW Standard Cycle 04 86 Cycle for Fast Injection vai oera es tae eee aude Re ae kate 95 WOK E E EE E E E E neve mae 107 Thermo Scientific ee i Preface The CTC PAL autosampler manufactured by CTC Analytics is supplied by Thermo Fisher Scientific as part of a solution for high throughput LC MS
29. alve toggle steps Counter 1 enable valve toggle steps If the counter is set to 1 follow the described steps below If the counter is set to 0 the macro finishes at this point The injection moves to the injection valve The valve is switched to the Active position The valve is rinsed with Wash Solvent 2 followed by Wash Solvent 1 Stator Wash Time Solvent 2 Stator Wash Time Solvent 1 Remark The loop is filled with the last rinse with Wash Solvent 1 Verify the composition of Wash Solvent1 The solvent should have a lower elution power than the solvent gradient starting conditions or sample solvent composition This is important for partial loop filling The injection valve is switched back to the Standby position End of macro DLW Priming Thermo PAL User Guide 65 5 Using Dynamic Load and Wash DLW Installing Cycle Composer Macros or ICC Cycles Standard DLW Injection Cycle 66 Thermo PAL User Guide Macro Name Standard Injection Accela Open_Rev03 Table 16 Macro Standard Injection Accela Open Sheet 1 of 3 Macro description The PAL system waits first for the Sync Signal Ready before the injection cycle is started Macro variable Remark Sync Signal setting Start The injection valve is brought in a defined Inject to Standby position Standby The Rear air segment is pulled into the Holding Airgap Volume Loop Filling Speed The sum of Rear Sample List and Front Vo
30. appears e Optional In the Comment box type additional information about the method f Click OK Xcalibur or other Thermo Scientific data acquisition application such as LCquan stores the method as a meth file in the specified file location Instrument Setup Parameters Thermo Scientific Use the Method Setup page to specify instrument method parameters for the autosampler Table 6 Method Setup page parameters Sheet 1 of 2 Parameter Template Selection Description Template This box shows the names of the default method templates After you select a template the Template box changes to a pane This pane shows the path to the chosen method template file Method Folder This pane shows the path to the default template folder location before a default method template is chosen After a default method template is chosen via the Template box the Method Folder label disappears leaving the Template label next to a pane that shows the path to the chosen template Browse New Template The Browse button can be seen next to the Method Folder pane before the method template is chosen in the Template box Click the browse soft button to browse through the computer file system for the method template of your choice When you select a method template the window changes to show the path to the chosen template and the Browse button changes to the New Template button This soft button appears after a meth
31. cientific LC pumps and a Thermo Scientific MS detector Figure 2 shows the Thermo Single Configuration cable assembly that you use to connect one LC pump and a Thermo Scientific MS detector to the autosampler The cable assembly consists of a DB15 connector with two 2 pin legs One leg connects to the LC pump and the other leg connects to the MS detector During the installation of the LC MS system a Thermo Fisher Scientific field service engineer uses the appropriate mini comb icon connectors to complete the contact closure cable assembly and then connects the assembly to the appropriate pins on the LC pump or LC pumps and the MS detector Figure 2 Contact closure cable for LC MS with one Thermo Scientific LC Pump 300 cm lt 10 ft gt Clear E Cbl Thermo Single Config mD o2 0 0 Oo O O 0 O 0 oO 0 o2 o To connect the contact closure cable to the LC pump and the MS detector 1 Plug the DB15 connector of the contact closure cable into the 15 pin receptacle on the back of the autosampler The receptacle label depends on the autosampler model see Table 3 Table 3 PAL contact closure receptacle PAL model Receptacle label HTC LC Interface HTS Interface 1 2 Using an 8 pin combicon connector connect one leg of the contact closure cable to the appropriate pins
32. ctions if the Delay Time mins box is available type the amount of time that you want the autosampler to wait after it completes the current injection before it starts the next injection During a look ahead injection the autosampler aspirates the sample for the next injection and waits until the end of the current run to inject the sample into the valve When you add a delay time the autosampler does not begin the next injection cycle immediately after completing the current injection cycle If you enter a delay time longer than the method run time the autosampler begins the next injection at the end of the current run This means that adding a long delay time does not add additional run time to the method run time but it does cancel the effect of using the Look Ahead Injection feature Note The Look Ahead Injections feature is available if you selected the Enable check box in the Look Ahead Injections area of the PAL Configuration dialog box Specify the acquisition parameters for the other devices of your LC or LC MS instrument Save the method a From the Instrument Setup window menu bar choose File gt Save As The Save As dialog box appears b Select an appropriate file location for the method c In the File name box type an appropriate name for the method Thermo Scientific 2 Getting Started Specifying the Instrument Method Parameters for the Autosampler d Click Save The File Summary Information dialog box
33. de Thermo Scientific 4 Using the Direct Controls to Operate the Autosampler Making Single Injections from the Tune Window Making Single Injections from the Tune Window Thermo Scientific You can make single injections from the Tune window K2 bd I 2 To make single injections from the Tune window Open the Tune window for your mass spectrometer Open the Inlet Direct Control dialog box see Opening the Direct Control Dialog Box on page 51 Specify the location of the methods that you want to use see Direct Control Tray Configuration Page on page 57 Specify the tray types that are loaded in the autosampler L tray holders see Changing the Tray Configuration on page 56 Click the Methods tab The Methods page appears The Syringe area lists the size of the configured syringe The Device Status area lists the status of the autosampler In the Method list select a method A description of the method appears in the Description box see Figure 32 The method list depends on the file locations specified on the Direct Control Configuration page Thermo PAL User Guide 53 4 Using the Direct Controls to Operate the Autosampler Making Single Injections from the Tune Window Figure 32 Methods page of the Inlet Direct Control dialog box Inlet Direct Control Thermo Pal Accela Pump Methods Tray Configuration Direct Control Configuration Duplication of PAL local LC Inj A
34. detector and an autosampler You can order the DB15 x 15 wire cable from Agilent or Thermo Fisher Scientific Table 2 Contact closure cables used to connect an Agilent pump Part number Supplier Description CBL 7890 CTC Analytics PAL Interface Cable for APG Remote DB15 connector x DB9 connector cable 00012 27716 Thermo Fisher Scientific DB15 connector x 15 wire cable G1103 61611 Agilent DB15 connector x 15 wire cable Setting Up an LC MS System with the Autosampler 2 Thermo PAL User Guide Typical pentop setups include placing the autosampler on top of the MS detector on top of the two pumps in a dual pump setup and to the left of the MS detector Ensure that the pentop area for the autosampler is level and provide adequate space behind the autosampler for system cables CAUTION To prevent damage to the injection unit during operation place the autosampler on a level surface For information on assembling the PAL and connecting the solvent lines refer to the CTC Analytics PAL System User Manual supplied in hard copy format with the autosampler During the installation of a Thermo Scientific MS detector a Thermo Fisher Scientific field service engineer connects the LC system to the MS detector Thermo Scientific 1 Getting Connected Connecting the Contact Closure Cables Figure 1 shows a front view of the Thermo PAL During installation a Thermo Fisher Scientific field service engineer connects the solvent lines between t
35. e 8 To make contact closure between the autosampler an Agilent Pump and a Thermo Scientific MS detector 1 Using the PAL interface cable see Figure 7 connect the Agilent pump to the CTC PAL e Connect the DB15 connector to the INTERFACE HTC or INTERFACE 1 HTS receptacle on the back panel of the PAL see Figure 9 and Figure 10 e Connect the DB9 connector to the REMOTE receptacle on the back panel of the Agilent pump see Figure 9 and Figure 10 Figure 7 PAL interface cable for an Agilent pump supplied by CTC Analytics lt 170 cm gt uw 2 E hilg E Cbl 7890 PE oJ O Lu eo J J m Connect to the Connect to the Agilent pump autosampler 2 Using the external contact trigger cable see Figure 8 connect the Agilent pump to the MS detector e Connect the DB15 connector to the RELAY CONTACTS receptacle on the back panel of the Agilent pump see Figure 9 and Figure 10 For information on installing the external contact board refer to the Agilent Getting Connected Guide 1100 Series or 1200 Series that is provided as a PDF with LC Devices e Connect the white wire to the Start In pin and the brown wire to ground on the MS detector see Figure 9 and Figure 10 Secure the remaining 13 wires to the cable with duct tape 10 Thermo PAL User Guide Thermo Scientific
36. e Toggle times Figure 52 Timing for Stator Wash Step w a Valve Toggle S 5 1 2 7 o 3 Start rT T I rT T I IE Time From the chromatographic point of view the optional cleaning step is important to understand Assuming that the valve stator between ports 1 and 6 example standard Cheminert valve is contaminated and cannot be cleaned during the injection process the valve toggle brings the engraving back between the two ports Flushing the valve with both wash solvents eliminates remaining sample material located between stator ports 1 and 6 What points must you consider when you use the Stator Wash or Valve Toggle option Observe the rules if biofluid samples are injected First sample contact should always be with an aqueous solution to avoid protein precipitation After washing with organic solvent higher elution power the system must be flushed again with wash solvent 1 The first toggle near the end of the chromatographic cycle provides the advantage that the sample loop is already flushed out first with the mobile phase with a solvent of high elution power assuming gradient application Thermo PAL User Guide 87 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step The second valve toggle time follows immediately after finishing the second solvent flush A second switching time cannot be programmed The waiting time for the second valve toggle should be
37. e second injection volume to be used with the method SL volume2 Injections Per Vial Type the number of replicate injections to be made from each vial Run Run the selected method Cancel Cancel any changes and close the page Viewing the Template Summary 40 To view a summary of a template 1 Open the PAL Template Macro Editor window see Using the Template Editor to Create Custom Templates on page 33 2 Open the template that you want to review by choosing File gt Open Method Template The default path to open a template is as follows C Thermo Instruments LC Devices ThermoPAL PAL methods 3 Click the Template Summary tab Thermo PAL User Guide Thermo Scientific 3 Creating Custom Templates and Macros Viewing the Template Summary The Template Summary page appears with a summary of the active template see Figure 26 Figure 26 Template Summary page a Pal Template Macro Editor File PAL view Help Dw e3 Template Editor Macro Editor Template Summary Description Default New Method Syringe 100ul Macro Sequence LC Inj Step 1 of 1 Air Volume pl 0 Pre Clean with Solvent 1 0 Pre Clean with Solvent 2 0 Pre Clean with Sample 0 Filling Speed pl s 50 Filling Strokes 1 Inject to LC Vlv1 Injection Speed l s 100 Pre Inject Delay ms 500 Post Inject Delay ms 500 Post Clean with Solvent 1 1 Post Clean with Solvent 2 1 Valve Clean with Solvent 1 1 Valve Cl
38. ean with Solvent 2 1 Macros used within method Macro name LC Inj COMPLETE CYCLE XXXXXXXXXXXXXXXXXXXXXXXK Duplication of PAL s local LC injection cycle Tray Name Sample Number and Sample Volume are taken from the sample list Variables 14 Air Volume pl 0 0 SYR Max Yolume Pre Clean with Solvent 1 0 0 99 Pre Clean with Solvent 2 0 0 99 Pre Clean with Sample 0 0 99 Filling Speed pl s S A Fill Speed SYR Min Speed SYR Max Speed Filling Strokes 1 0 99 Inject to NJECTOR Injection Speed pl s SR Inject Speed S A Min Speed SYR Max Speed Thermo Scientific Device Status Ready To Download Thermo PAL User Guide 41 3 Creating Custom Templates and Macros Standard Macros Standard Macros Figure 27 shows the macros that are provided with a standard installation Figure 27 Standard macros C Xcalibur system PAL Wacros File Edit View Favorites Q Back 7 A i ye Search le Folders Tools max Help Address la C Xcalibur system PAL Macros LE Folders B xcalibur data examples Install Logs E methods E Project system a par O Macros methods programs temp E templates 42 Thermo PAL User Guide gt x E Add to Sample and Mix pma a Aspirate Sample pma Aspirate pma laa Clean Syringe pma a Clean Yalve pma as Clear Output Signal pma E Dispense pma E Error Entry pma E Error Exit pma Home pma a Inject pm
39. er to the compatibility tables provided by the manufacturer of PEEK material or components Thermo PAL User Guide 71 5 Using Dynamic Load and Wash DLW Operating Dynamic Load and Wash DLW Note Current applied from the actuator control PCB to the actuator solenoid activates a green LED This activation does not indicate that the solenoid opens or closes Figure 36 DLW Manifold and Actuator Solenoid Closed Solvent NC DLW Flow Diverter Solvent 1 Solvent 2 Figure 37 Inserting DLW Flow Diverter Syringe Ot Holding Loop 72 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step DLW Cycle Step by Step This section provides illustrations to demonstrate a step by step DLW cycle e Cycle for Standard Injection e Additional Valve Toggle Step to DLW Standard Cycle e Cycle for Fast Injection Cycle for Standard Injection Figure 38 to Figure 51 illustrates a step by step cycle for the standard injection Figure 38 Standard Cycle start Solenoid Actuator Valve Pump gt Pump gt Holding Loop C Thermo Scientific Thermo PAL User Guide 73 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 39 Standard Step 1 A spirate rear air segment Solenoid Actuato
40. er Method dialog box Run Auto Sampler Method Vial Index Injectors 1 fi 1 Lev 2 f 2 Lev z Trays r Volume 1 CStk1 01 1 fio 2 CStk1 01 v 2 jio Injections Per Vial j 7 E 1 Cancel Help 4 Make the appropriate entries and selections 5 Click Run The autosampler executes the macros listed in the template Run Auto Sampler Method Dialog Box Use the Run Auto Sampler Method dialog box to enter the Methods information required for the PAL to carry out autosampling Table 8 Run Auto Sampler Method dialog box parameters Sheet 1 of 2 Parameter Description Vial Index 1 In this box type the vial index to be used with the method SL index 2 In this box type the vial index to be used with the method SL index2 Thermo Scientific Thermo PAL User Guide 39 3 Creating Custom Templates and Macros Viewing the Template Summary Table 8 Run Auto Sampler Method dialog box parameters Sheet 2 of 2 Parameter Description Trays 1 From this list select the tray to be used with the method SL tray 2 From this list select the tray to be used with the method SL tray2 Injectors 1 From this list select the injector to be used with the method SL injector 2 From this list select the second injector to be used with the method SL injector2 Volume 1 In this box type the injection volume to be used with the method SL volume 2 In this box type th
41. etector firmware 4 1 2 Surveyor MSQ Plus TSO Series LTO Series OR OR J Startin Start I Statin 1 _ 30V Max i p i Start In i n T i JA i z pa i T ARRES ENAA TRAFANTA RNA PA EPERE EPEAL EEEIEE External contact trigger cable supplied by Autosampler Thermo Fisher Scientific _ RELAY CONTACTS T T o ala o Oe 1 p 7 j J i mj o i s CR L o f Agilent pump NTERFACE 1 REMOTE DB15 to DBS cable supplied by x CTC Analytics Cbi 7890 Thermo Scientific Thermo PAL User Guide 13 1 Getting Connected Connecting the PAL to the Data System Computer Connecting the PAL to the Data System Computer To connect the PAL to the data system computer Using the serial cable that is supplied with the autosampler connect the SER 1 port on the back panel of the auto
42. finition dialog box Parameter Description Variable Type A Numeric Value Select this if the parameter is a numeric value If you are editing an existing numerical parameter this box is marked with a black dot An Object Select this if the parameter is an object If you are editing an existing object parameter this box is marked with a black dot Variable Name If you are editing an existing variable this box shows the name of the variable Type your choice for the name of the variable if you are adding a new one OK Accepts the new Variable Definition or accept the edits to an existing Variable Definition Cancel Deletes changes made in the Variable Definition dialog box Numeric Value Variable Type Variable Units If you are editing an existing variable this list shows the units for the selected variable If you are adding a new variable you may enter units appropriate for that variable When you click the list arrow you can select the appropriate units from the options in the list Default Value The nominal or center value of the variable Lower Limit The lowest acceptable value of the variable Upper Limit The highest acceptable value of the variable Object Variable Type Please check what objects this variable may be 50 Thermo PAL User Guide Select one or more objects that are described by the variable Thermo Scientific ee i Using the Direct Controls t
43. g Loop 96 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 61 Fast Step 2 Get sample aspirate rear inject and front volume Solenoid Actuator Valve Pump gt Pump2 gt Holding Loop Thermo Scientific Thermo PAL User Guide 97 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 62 Fast Step 3 4 Aspirate front air segment Solenoid Actuator Valve 98 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 63 Fast Steps 5 6 Dispense front air segment and front sample volume to waste Solenoid Actuator Valve auu Thermo Scientific Thermo PAL User Guide 99 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 64 Fast Steps 7 8 Valve is switched to LOAD position loop is filled with Inject Volume Solenoid Actuator Valve an Column Pump 100 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 65 Fast Step 9 Valve is switched to INJECT position start chromatographic process Solenoid Actuator Valve aun Pump Thermo Scientific Thermo PAL User Guide 101 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 66 Fast Step 10 Rear sample volume and air segment are dispensed to waste Solenoid ft ji Act
44. gs Acca Pine a Q1 Peak Width PWH Thermo Scientific 2 Getting Started Specifying the Instrument Method Parameters for the Autosampler 3 In the view bar click Thermo Pal The Method Setup page for the autosampler appears see Figure 18 Figure 18 Method Setup page for the autosampler Method Setup Method Summary Template Selection Template Method Folder C Xcalibur System PAL Methads Browse Template Description Macro Variables Browse button Syringe Macro Sequence Recommended Injection Volume Volume fpl Look Ahead Injections Delay Time mins Help yam 4 Under Template Selection click Browse and browse to the folder that contains the autosampler methods pme For a standard installation the folder that contains the autosampler method is located in the following directory see Figure 19 C Thermo Instruments LC Devices ThermoPAL PAL methods Thermo Scientific Thermo PAL User Guide 25 2 Getting Started Specifying the Instrument Method Parameters for the Autosampler Figure 19 Location of Thermo PAL autosampler templates C Thermo nstruments LC Devices ThermoPAL PAL methods ds File Edit View Favorites Tools Help Q sak Q E JO seach By Foer E Address C ThermolInstruments LC Devices ThermoPAL PAL methods Folders x Name Size Type Date Modified Desktop A E DLW Priming_Rev01 PME 2KB PMEFile 3 31 2010 9 28
45. he injection valve and the LC pump and between the injection valve and the Thermo Scientific mass spectrometer Figure 1 PAL autosampler Injection unit Control terminal Syringe Courtesy of CTC Analytics Connecting the Contact Closure Cables Thermo Scientific During an injection cycle the PAL sends and receives electrical signals To start an injection cycle the autosampler must receive an electrical signal from the LC pump When the autosampler completes an injection cycle it sends an electrical signal to the LC pump For more information on interfacing the PAL with other devices refer to the CTC Analytics PAL System User Manual Interfacing the PAL to Other Devices section This section describes how to hardwire one or two LC pumps and a Thermo Scientific MS detector to the PAL for contact closure To make the contact closure connections follow the procedure for your LC MS system e Making Contact Closure with Thermo Scientific Devices Thermo PAL User Guide 3 1 Getting Connected Connecting the Contact Closure Cables e Connecting the Start Pump to the Sample Pump in a Dual Pump System e Dual pump setup with two Accela Pumps Making Contact Closure with Thermo Scientific Devices The accessory kit supplied by Thermo Fisher Scientific contains the contact closure cables that you need to connect the PAL to an LC MS system with one or two Thermo S
46. hod Template and Macro Editor to be accessed via Instrument Set Up Ensuring the check box is clear prevents access to the Method Template and the Macro Editor Cycle Composer Macro Importer Import Path Enter the path to the Cycle Macro to be imported Overwrite existing macros Choices are Never Ask Always Uses chosen action to determine if existing macros are to be overwritten when a new macro is imported Import Import the chosen macro Browse Search through files and folders to find a macro Active Trays Tray Name Hardware configured tray name Stack Stack location of a given Tray Name Allow Use Click to switch between YES and blank YES means that a given tray IS accessible to the PAL system for obtaining samples use is allowed A blank in this row means that the tray is NOT accessible to the PAL system for obtaining samples use is NOT allowed Communications Com Port Select the computer port where you plug the autosampler communication cable Auto Select Instructs the system to automatically determine the computer y y P port where you plug the autosampler communication cable Thermo PAL User Guide 19 2 Getting Started Using the Autosampler Control Terminal Firmware Versions Supported For Thermo PAL autosampler the only supported firmware versions are 2 5 2 and 4 1 2 Using the Autosampler Control Terminal For general information on using the autosampler control
47. i AUX1 Surveyor MS Pump Plus Surveyor LC Pump Plus Connecting the Start Pump to the Sample Pump in a Dual Pump System Thermo Scientific Thermo PAL User Guide 7 1 Getting Connected Connecting the Contact Closure Cables In a dual pump system the start pump triggers the sample pump To connect the start pump to the sample pump you can use the contact closure cable that CTC Analytics supplies or you can use one insulated electrical wire to connect the ground pins and one insulated electrical wire to connect the GRAD START or PROG START pins Figure 5 shows the contact closure cable that you can order from CTC Analytics Figure 5 Contact closure cable supplied by CTC Analytics used to connect two LC pumps 100 cm lt 39 inches m Cbl Thermo Dual Config a Ks T 2a To make contact closure for a dual pump system 1 Connect the DB15 connector of the Thermo Single Config cable to the INTERFACE 1 or INTERFACE receptacle on the back panel of the Thermo PAL 2 Connect on of the two pin legs of Thermo Single Config cable to the start pump 3 Connect the other two pin leg of the Thermo Single Config cable to the Thermo Scientific MS detector 4 Connect the start pump to the sample pump e Connect the start pump ground pin to the sample pump ground pin e Connect the Grad Start or Prog Start pin on the start pump to the Grad Start or Prog
48. id is activated to Inject to deliver Wash Solvent 2 into the Holding Loop to Wash2 clean the injection valve from Port 1 to Port 2 Needle Gap Valve Clean Valve Clean Time Solvent 2 For this step the needle tip is lifted releasing the sealing pressure to enable rinsing around the tip Remark For complete details on the sealing point Needle Gap Valve Clean see DLW Priming Wash Solvent 1 follows to prepare the valve for Wash1 the next injection Inject to Needle Gap Valve Clean Valve Clean Time Solvent 1 Thermo Scientific Thermo PAL User Guide 69 5 Using Dynamic Load and Wash DLW Operating Dynamic Load and Wash DLW Table 17 Macro Fast Injection Accela Open Sheet 3 of 3 Macro description Macro variable The injection unit is moved back to the DLW Wash1 Wash station Wash1 position to flush the syringe Post Clean Time Solvent 1 needle inside and out with Wash Solvent 1 This is a preparation step for the next injection and is especially important for biofluid samples Cycle end for LC Inj DLW Fast macro Operating Dynamic Load and Wash DLW This section describes how to operate the Dynamic Load and Wash DLW option e Priming the Solvent Lines e Location of Solvent and Waste Bottles e DLW Pumps Priming the Solvent Lines Note For trouble free DLW operation make sure the two solvent lines are free of air bubbles at all times If the solvent lines are being connected for the first time or during
49. lication Thermo Scientific Thermo PAL User Guide 27 2 Getting Started Specifying the Instrument Method Parameters for the Autosampler 28 Thermo PAL User Guide 7 In the Syringe list select the size of syringe that is installed in the autosampler 10 11 The default variable settings for the Single Step LC Injection template and the default setting of 10 uL in the Recommended Injection Volume box are suitable for a 100 uL syringe Changing the syringe size can change the allowable ranges for the recommended injection volume and the variables specified in the LC Inj macro IMPORTANT Make sure that your syringe selection matches the size of the syringe that is installed in the autosampler e Ifthe autosampler is set up to recognize the installed syringe size an error message appears when you download methods that specify a different syringe size e Ifthe autosampler is not set up to recognize the installed syringe and the specified syringe size does not match the actual syringe size the autosampler does not inject the specified injection volume Under Recommended Injection Volume in the Volume uL box type the volume of sample that you want the autosampler to inject The allowable injection volume range is based on the syringe size IMPORTANT For partial loop injections variable volume make sure that the recommended injection volume is less than half the sample loop size Under Look Ahead Inje
50. lume is aspirated into the Front Volume Rear Volume Holding Loop SL volume The Front air segment is aspirated Airgap Volume Filling Speed Pullup Delay The injection unit moves to the DLW Wash Station Wash1 position The needle is inserted dipped for 1 second to wash the outer needle surface No plunger movement at this step The injection unit moves to the specified Inject to injection valve Front Volume The Front and Airgap Volume is ejected Airgap Volume Injection Speed The PAL system waits for the data system Wait for DS The injection valve is switched to Active Inject to position Pre Inject Delay The time Pre Inject Delay is awaited The loop is filled with the sample volume as SL volume specified in the sample List Injection Speed The injection valve is switched to Standby position the loop content is injected Timer 1 Delay Stator Wash is started and a Start signal to the HPLC system is sent Post Inject Delay Timer 1 Thermo Scientific 5 Using Dynamic Load and Wash DLW Installing Cycle Composer Macros or ICC Cycles Table 16 Macro Standard Injection Accela Open Sheet 2 of 3 Macro description The plunger of the DLW Syringe is pushed down to dispense the Rear Sample and Air Segment to Waste The Holding Loop is still filled with Wash Solvent 1 Macro variable Syr Eject Speed The DLW Actuator Solenoid is activated to deliver Wash Solvent 2 into the H
51. me in a new location or with both a new filename and location that you type in the Save As dialog box Thermo Scientific Thermo PAL User Guide 47 3 Creating Custom Templates and Macros Defining Variables Defining Variables Variables are the building blocks that you use to create macros Creating Custom Variables This section provides information about how to create custom variables To create custom variables 1 Open the Macro Editor dialog box a Open the Instrument Setup view for the PAL autosampler see Specifying the Instrument Method Parameters for the Autosampler on page 24 b From the menu bar choose PAL Auto Sampler gt Template Macro Editor c Click the Macro Editor tab The Macro Editor page of the Pal Template Macro Editor window appears see Figure 28 2 Click Add The Variable Definition dialog box appears see Figure 29 Figure 29 Variable Definition dialog box Variable Definition Variable Type C An Object OK Cancel Variable Name __ Cancel Variable Units Help Default Value Lower Limit Upper Limit 3 Select a variable type e To create a variable that is a numeric value select the A Number Value option Then go to step 4 e To create an object variable select the An Object option A list of objects appears Go to step 5 48 Thermo PAL User Guide Thermo Scientific Thermo Scientific 3 Creating Custom Templates and Macros Defining Variables
52. mo Scientific Setup Objects O p Out Signals I Injected Injected Destination SW Out1 Pulse Time 40s Oms 9 9s Set Home Defit To change the pulse time setting a Open the Injected screen In the Job Queue screen select the Menu screen by pressing the F1 key see Figure 15 Rotate the outer knob to move the cursor bar highlight to Setup and then press the inner knob button The Setup screen appears Rotate the outer knob to move the cursor bar highlight to Objects and then press the inner knob button The Objects screen appears Rotate the outer knob to move the cursor bar highlight to Out Signals and then press the inner knob button The Out Signals screen appears Rotate the outer knob to move the cursor bar highlight to Injected and then press the inner knob button The Injected screen appears see Figure 16 Rotate the outer knob to move the cursor bar highlight to Pulse time and then press the inner knob button The time cell is highlighted Rotate the out knob to change the pulse time to 4 0 seconds and then press the inner knob button to set this selection as the default Return to the Job Queue screen by pushing the F4 key Home Thermo PAL User Guide 23 2 Getting Started Specifying the Instrument Method Parameters for the Autosampler Specifying the Instrument Method Parameters for the Autosampler To inject a sample
53. n Macro This list displays existing autosampler macros Select the macro that you want to edit Macro Description A description of the macro selected in the Macro list Macro Variables Variables used by the macro selected in the Macro list Add Adds a new variable to the macro variables The new variable is defined in an Edit Parameter dialog box that opens when you click Add The Edit Parameter dialog box has a check box for the Parameter Type numeric or object If you select a numeric Parameter Type you see a pane in which you enter the new parameter name a list for the parameter units and panes in which you enter the default value for the parameter along with the lower and upper limits for the parameter If you select an object Parameter Type you see a check list of objects that might be represented by the parameter Thermo Scientific Thermo PAL User Guide 45 3 Creating Custom Templates and Macros Using the Macro Editor to Create Custom Macros Table 9 Macro Editor page parameters Sheet 2 of 3 Parameter Edit Description Edits an existing macro variable The editing is carried out in an Edit Parameter dialog box that opens when you click Edit The Edit Parameter dialog box has a check box for the Parameter Type numeric or object If you select a numeric Parameter Type you see a pane in which you enter the new parameter name a list for the parameter units and panes in which you enter the default val
54. ns 4 To delete file locations a Select the file location in the box below the row of buttons b Click Delete 5 To reset the location of the methods files to the default folder click Reset 58 Thermo PAL User Guide Thermo Scientific 4 Using the Direct Controls to Operate the Autosampler Specifying the Location of the Direct Control Methods Direct Control Direct Control Configuration Page Thermo Scientific Use the Direct Control Configuration page in the Direct Control dialog box to enter the Direct Control Configuration information required for the autosampler to carry out autosampling Table 13 Direct Control Configuration page parameters Parameter Description Wrap each direct control method run with the following macros Sequence Entry Exit Use this check box to wrap methods with the sequence list entry and exit macros SLentry and SLexit Method Entry Exit Use this check box to wrap methods with the method entry and exit macros Method Entry and Method Exit Method Search Paths Path Use this box to specify the extra path you want added to the method search routine Browse Use this button to search for a path Add Use this button to add the current path to those searched Delete Use this button to delete the currently selected path Reset Use this button to remove all of the user added paths text box This text box displays the directories that the autosampler searches for method
55. o Operate the Autosampler This chapter describes how to operate the autosampler from the Direct Control dialog box Contents e Opening the Direct Control Dialog Box e Making Single Injections from the Tune Window e Changing the Tray Configuration e Specifying the Location of the Direct Control Methods e Wrapping Direct Control Injections with Additional Macros Opening the Direct Control Dialog Box The direct control pages for the autosampler are available from the Instrument Setup window and the Tune window To open the Direct Control dialog box from the Instrument Setup window 1 In the view bar click Thermo Pal 2 The Instrument Setup view for the autosampler appears 3 From the menu bar choose PAL Auto Sampler gt Direct Control The Direct Control dialog box appears with the Methods page displayed see Figure 31 Thermo Scientific Thermo PAL User Guide 51 4 Using the Direct Controls to Operate the Autosampler Opening the Direct Control Dialog Box Figure 31 Direct Control dialog box Direct Control O e To open the Inlet Direct Control dialog box from the Tune window 1 From the menu bar choose Setup gt Inlet Direct Control 2 Click the Thermo Pal tab The Inlet Direct Control dialog box for the autosampler appears with the Methods page displayed The Inlet Direct Control dialog box has the same functionality as the Direct Control dialog box shown in Figure 31 52 Thermo PAL User Gui
56. od template is chosen in the Template box Selecting this button brings back the Template box Method Folder pane and Browse button These are used to find a new method template Template Description A description of the template chosen in the Template Selection portion of the Method Setup page Syringe This list contains the allowed syringe volumes Select the appropriate syringe volume Macro Sequence Displays the sequence of macros that make up the method chosen in the Template window Select a macro name to be displayed in the Macro area its variables also appear in the Variables area See table continuation Thermo PAL User Guide 29 2 Getting Started Specifying the Instrument Method Parameters for the Autosampler Table 6 Method Setup page parameters Sheet 2 of 2 Parameter Description Recommended Injection Volume Volume pl 1 When you select an instrument method for use to generate a new sequence on the Xcalibur Home Page the injection volume is set to what is entered in this box 2 When From AS From Auto Sampler is specified in the LCquan injection volume sequence cell the CTC PAL autosampler uses the volume in this box when you submit the LCquan sequence for acquisition Look Ahead Injections Delay Time mins Enter the Delay Time in minutes between injections when using the Look Ahead feature You enable the Look Ahead Injections option from the PAL Configuration dialog bo
57. olding Loop to clean the injection valve from Port 1 to Port 2 For this step the needle tip is lifted releasing the sealing pressure to enable rinsing around the tip sealing point Wash2 Inject to Needle Gap Valve Clean Valve Clean Time Solvent 2 Remark For a detailed explanation of the Needle Gap Valve Clean see DLW Priming The injection unit is moved to the DLW Wash Station Wash2 position The needle is rinsed inside and out with Wash Solvent 2 Wash2 Syr Eject Speed Post Clean Time Solvent2 The injection unit is moved back to the injection valve The Inlet Port and engraving to waste Port are flushed with Wash Solvent 1 to prepare the valve for the next injection The injection unit is moved back to the DLW Wash Station Wash1 position to flush the syringe needle inside and out with Wash Solvent 1 This is a preparation step for next injection and especially important for biofluid samples Wash 1 Inject to Needle Gap Valve Clean Valve Clean Time Solvent 1 Washl Post Clean Time Solvent 1 Cycle end for LC Inj DLW Standard macro An optional cleaning step is attached to the DLW Standard injection cycle Stator Wash or valve toggle A Repeat End loop can be activated with the Count Stator Wash Stator Wash count 1 Cleaning step active Stator Wash count 0 Cleaning step disabled If Stator Wash is activated the following steps will be executed Thermo PAL Use
58. ones 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 EC 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 es
59. p by Step Figure 51 Standard Cycle end Solenoid Actuator Valve Pump 1 gt Pump2 gt Holding Loop Ka m om Additional Valve Toggle Step to DLW Standard Cycle This section contains information about additional steps that are necessary for a DLW Standard Cycle 86 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Considerations for Additional Stator Wash Cleaning Step Thermo Scientific The DLW Standard Cycle has the built in option for the user to toggle the injection valve at the end of the chromatographic run before equilibration of the column to the start conditions If the method variable Stator Wash is set to 1 the extra cleaning process for the valve with Valve Toggle is part of the standard cycle If the method variable is deactivated setting O the DLW Standard cycle ends as shown in Figure 51 The macro cycle is written so that the optional valve toggle steps can be executed before re equilibration of the column You must synchronize the time to switch the valve with the chromatographic method using the method variable Delay Stator Wash The two wash solvents are timed by the method variables Stator Wash Time Solvent 1 and Stator Wash Time Solvent 2 After these wash times have elapsed the valve is switched back to the start position Figure 52 illustrates the recommended retention time for Stator Wash or Valv
60. posed to light Filtering the wash solvents before filling the bottle especially if salt buffers are used is mandatory to avoid any clogging of the solvent paths From the control point of view the DLW pumps respond in the same manner as the fast wash station Power out signals activate the pumps Because the electric current setting for the DLW is different the corresponding PAL Firmware Objects must be loaded for the DLW wash station type The wetted parts in the pump are made from the following materials e Membrane Kalrez FFPM e Body valves Ryton PPS The pumps are self priming with a suction lift of up to 3 m water column DLW Actuator Solenoid Thermo Scientific The DLW Actuator Solenoid has the function of separating and completely shutting off the lines in the direction of the syringe sample loading or the wash solvent lines After opening the DLW Actuator Solenoid for the wash solvent lines you can pump the desired wash solvent into the system by activating the corresponding DLW pump Figure 67 illustrates this functionality The wetted parts in the DLW Actuator Solenoid are made from the following materials e Solenoid body PEEK e Seal material FFKM Simriz Note PEEK exhibits excellent chemical resistance to most of the chemicals used However the following solvents are not recommended for use with PEEK DMSO THE methylene chloride dichloromethane nitric acid or sulfuric acid For more details ref
61. q r Yolume 1 CStk1 01 1 p10 2 CStk1 01 2 jio Injections Per Vial 7 Cancel 4 Make the appropriate entries and selections e Under Trays select the appropriate trays e Under Vial Index type an appropriate vial location for this template you are testing e Under Volume type the volume that you want to inject e In the Injection Per Vial box type the number of injections that you want to make from each vial 5 Click Run The autosampler performs the actions specified in the template step by step At the completion of each step The autosampler pauses the injection sequence and prompts you with the Pal Method Editor dialog box see Figure 24 Figure 24 Pal Method Editor dialog box Pal Method Editor Current Macro is SL Entry Current Command is SET OUT_SIG CCRuning 1 0 Stop Run 6 Do one of the following e To continue stepping through the template click Step 38 Thermo PAL User Guide Thermo Scientific 3 Creating Custom Templates and Macros Testing a Custom Template e To run the remaining portion of the template click Run e To stop the run click Stop Run Torun the complete sequence of macros in the template without pausing 1 If the Template Editor dialog box is closed open it 2 If you closed the custom template choose File gt Template gt Open 3 Click Run The Run Auto Sampler Method dialog box appears see Figure 25 Figure 25 Run Auto Sampl
62. r 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 and 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 Release history Revision A released December 2005 Revision B released February 2009 Revision C released in April 2010 Software version Xcalibur 2 0 or higher Thermo PAL 1 0 Firmware Version 2 4 0 for the PAL autosampler 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 CTC Analytics PAL System User Manual 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 not specifically authorized and qualified by Thermo Fisher Scientific To ensure continued compliance with EMC and safety
63. r Guide 67 Table 16 Macro Standard Injection Accela Open Sheet 3 of 3 Macro description The injection unit is moved to the injection valve From the last step above the Holding Loop is filled with Wash Solvent 1 Timer 1 is awaited to switch the valve Toggle into Active position fill loop Macro variable Inject to Delay Stator Wash Active The DLW Actuator Solenoid is activated to deliver Wash Solvent 2 to the Holding Loop and into the valve system The first solvent flush arriving at the valve is Wash Solvent 1 parked in the Holding Loop at the beginning followed by Wash Solvent 2 Inject to Wash2 Stator Wash Time Solvent 2 Wash Solvent is changed to Wash Solvent 1 The injection valve is switched back to the Standby position Fast DLW Injection Cycle Inject to Washl Stator Wash Time Solvent 1 Inject to Standby The Fast injection cycle differs from the Standard cycle as follows The needle is not dipped in the Wash station Wash1 after sample pickup and before it moves to the injection valve e The wash steps after injection are reduced to Valve Clean with Wash Solvent 1 and Wash Solvent 2 The DLW needle is flushed in the DLW Wash Station with Wash Solvent 1 only e Stator Wash valve toggle is not available Macro Name Fast Injection Accela Open_Rev03 Table 17 Macro Fast Injection Accela Open Sheet 1 of 3 Macro description The PAL system waits first for
64. r Valve Pump 1 gt Pump2 gt Holding Loop 74 Thermo PAL User Guide Column Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 40 Standard Step 2 Get sample aspirate rear inject and front volume Solenoid Actuator Valve Pump 1 gt Pump2 gt Holding Loop Column Thermo Scientific Thermo PAL User Guide 75 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 41 Standard Steps 3 4 A spirate front air segment Solenoid Actuator Valve Pump gt Pump2 Holding Loop 76 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 42 Standard Steps 5 6 Passive needle clean outside dip in wash position 1 Solenoid Actuator Valve Column Thermo Scientific Thermo PAL User Guide 71 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 43 Standard Steps 7 8 Dispense front air segment and front sample volume to waste Solenoid Actuator Valve waa 78 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 44 Standard Steps 9 10 Valve is switched to LOAD position loop is filled with Inject Volume Solenoid Actuator Valve Pump 1 lt gt Column Thermo Scientific Thermo PAL User Guide 79 5 Using Dynamic Load and Wash DLW
65. rmation of general interest Tip Highlights helpful information that can make a task easier 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 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 copy manuals from the Internet Go to mssupport thermo com and click Customer Manuals in the left margin of the window x Thermo PAL User Guide Thermo Scientific Thermo Scientific Preface To suggest changes to documentation or to Help Fill out a reader survey online at http www surveymonkey com s aspx sm R7gKOvhLXn3NTkpK2BefHQ_3d_3d e Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com Thermo PAL User Guide xi S B Getting Connected The Thermo PAL is a high throughput autosampler manufactured by CTC Analytics and supplied by Thermo Fisher Scientific For high throughput LC MS applications use the PAL a Thermo Scientific or an Agilent liquid chromatography LC pump and a Thermo Scientific MS detector This chapter describes the contact closure connections be
66. rmo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 55 Stator Wash Step 3 Valve clean with Wash Solvent 2 Solenoid Actuator Valve Column Pump Thermo Scientific Thermo PAL User Guide 91 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 56 Stator Wash Step 4 Wash Solvent 2 dispensed by Wash Solvent 1 Solenoid Actuator Valve Column Pump 92 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 57 Stator Wash Step 5 Second valve clean with Wash Solvent 1 Solenoid Actuator Valve Column Pump Thermo Scientific Thermo PAL User Guide 93 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 58 Stator Wash Step 6 Valve switched back to Inject Position toggle Solenoid Actuator Valve Column Pump 94 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Cycle for Fast Injection Figure 59 to Figure 70 illustrate a step by step cycle for the Fast Injection Figure 59 Fast Cycle start Solenoid Actuator Valve Pumpi Pump2 lt gt Holding Loop Thermo Scientific Thermo PAL User Guide 95 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 60 Fast Step 1 Aspirate rear air segment Solenoid Actuator Valve Pump 1 gt Pump 2 gt Holdin
67. rovides information about how to specify configuration options for the autosampler To specify the configuration options for the autosampler 1 Open the Instrument Configuration window from the computer desktop For Xcalibur 2 1 0 or higher choose Start gt All Programs gt Thermo Foundation 1 0 gt Instrument Configuration The Unloading Device Drivers dialog box appears followed by the Thermo Foundation Instrument Configuration window see Figure 13 Thermo Scientific Thermo PAL User Guide 15 2 Getting Started Adding the Autosampler to the Xcalibur Instrument Configuration Figure 13 Thermo Foundation Instrument Configuration window 23 Thermo Foundation Instrument Configuration Device Types All Available Devices Configured Devices i TSQ Vantage Accela Pump E aF Thermo Pal Core Ce _ 2 In the Device Types list select Alll 3 In the Available Devices list double click autosampler A copy of the Thermo Pal icon appears in the Configured Devices list h 4 In the Configured Devices list double click wae Thermo Pal The PAL Configuration dialog box appears see Figure 14 16 Thermo PAL User Guide Thermo Scientific 2 Getting Started Adding the Autosampler to the Xcalibur Instrument Configuration Figure 14 Pal Configuration dialog box Pal Configuration Communications Com Port pa Auto Select m Look Ahead Injections r
68. s Firmware Version Specifies the firmware version downloaded from the autosampler Thermo PAL User Guide 59 4 Using the Direct Controls to Operate the Autosampler Wrapping Direct Control Injections with Additional Macros Wrapping Direct Control Injections with Additional Macros 60 Thermo PAL User Guide Use the Direct Control Configuration dialog box to specify whether the autosampler is to run the SL Entry and SL Exit the Method Entry and Method Exit or all of these macros before and after an injection To specify the use of the SL Entry and SL Exit macros Select the Sequence Entry Exit check box To specify the use of the Method Entry and Method Exit macros Select the Method Entry Exit check box Thermo Scientific ee Using Dynamic Load and Wash DLW This chapter describes how to use the Dynamic Load and Wash DLW option which includes how to install the Cycle Composer Macros or ICC Cycles how to operate the DLW and a step by step illustration of the DLW cycles Contents e Overview e Installing Cycle Composer Macros or ICC Cycles e Operating Dynamic Load and Wash DLW e DLW Cycle Step by Step Overview This section contains an overview of the Dynamic Load and Wash DLW option Figure 35 Dynamic Load and Wash DLW Thermo Scientific Thermo PAL User Guide 61 5 Using Dynamic Load and Wash DLW Installing Cycle Composer Macros or ICC Cycles The DLW option represen
69. s from Open the Standard DLW macro in that some steps are left out to shorten the cycle time Installing the Cycle Composer Macros or ICC Cycles Thermo Scientific The autosampler is shipped with a CD ROM containing various cycles for the DLW option Macros for Xcalibur are installed by the LC Devices 2 4 installer Copy these macros to your Thermo PAL driver method folder or corresponding folder for application within the integrated system 1 bd P To copy cycles to your Cycle Composer Navigate in Windows Explorer to the Thermo PAL driver folder The usual folder location is as follows C Thermo Instruments LC Devices ThermoPAL PAL Ifyou wish to add the DLW option macros to an existing method folder copy the macros pma and the methods pme files from the DLW Option folder on the CD ROM to the method folder If the PAL system is integrated in a data system software that controls the PAL using the Cycle Editor for PAL ICC interpretation for example Analyst ChemStation Empower EZChrom MassLynx Xcalibur an ICC Cycle is used and not the Cycle Composer Macro the cycle extension is cyx Note You can convert a Cycle Composer macro to a cycle extension cyx by using the Cycle Editor software Conversion is available starting with Cycle Editor version 1 4 0 4 Note The provided macros are written for standard injection valve drives which are controlled and activated through the AUX interface
70. s or ICC Cycles You can only operate the autosampler DLW option in combination with PAL control software such as Thermo PAL driver for Xcalibur or Cycle Editor for ICC interpretation in another data handling system software For software control three macros or three cycles are provided The first of three macros covers the initial and daily priming of the solvent lines and covers a complete injection cycle a second macro is used for Standard speed with optimized washing possibilities and the last for a Fast cycle for optimized throughput and less focus on carryover See Table 14 For detailed descriptions of all macros or cycles see Table 14 Table 15 and Table 16 62 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW Installing Cycle Composer Macros or ICC Cycles Table 14 The DLW macro definitions Macro name Macro description Priming AccelaOpen For initial and daily routine priming of the solvent lines and DLW manifold The Clean Time for both wash solvents is a variable for the user to define the intensity of washing Standard Injection Standard injection cycle using all possibilities of the DLW option Accela Open The injection valve inlet port and the needle are washed with both wash solvents inside and out You can add an extra Stator Wash for intensive washing of the injection valve valve toggle Fast Injection Accela Tuned for speed and high throughput application It differ
71. sampler to the serial port on the back panel of the data system computer see Figure 11 and Figure 12 Figure 11 Data system connection firmware 2 5 2 Data system computer Autosampler j z ai r E a DB9 to DB9 serial cable Figure 12 Data system connection firmware 4 1 2 Data system computer Autosampler TERMINAL SERI LAN MODBUS suzen wasi INTERFACE1 INTERFACE 2 AUX2 POWER FUSE C ac lt e DB9 to DB9 serial cable 14 Thermo PAL User Guide Thermo Scientific ee i Getting Started This chapter describes how to add the autosampler to the Xcalibur instrument configuration how to specify the available tray types from the PAL control terminal and how to specify the injection parameters for the autosampler from the Xcalibur data system Contents e Adding the Autosampler to the Xcalibur Instrument Configuration e Using the Autosampler Control Terminal e Specifying the Instrument Method Parameters for the Autosampler Adding the Autosampler to the Xcalibur Instrument Configuration The Thermo Pal device driver provides control of the autosampler from the Xcalibur data system To control the autosampler from Xcalibur add the autosampler to the Xcalibur instrument configuration and specify the data system COM port that the autosampler is connected to Specifying the Configuration Options This section p
72. set automatically you must create an instrument method that contains the chromatographic conditions and mass spectrometer data acquisition settings and then create an acquisition sequence that specifies the instrument method and vial location for each run This section describes how to specify the basic instrument method parameters for the autosampler For information about creating acquisition sequences refer to the Sequence Setup view Help Creating an Instrument Method 24 Thermo PAL User Guide This section provides information about how to create an instrument method To specify the instrument method parameters for the autosampler 1 Open Xcalibur from the computer desktop For Xcalibur version 2 1 0 or higher choose Start gt All Programs gt Thermo Xcalibur gt Xcalibur The Roadmap Home Page appears PERE 2 Click Instrument Setup The Instrument Setup window appears with the configured devices displayed in the view bar see Figure 17 By default the view for first device is open A bright green triangle in the lower right corner of the device icon indicates that the view for the device is open Figure 17 Instrument Setup window 9 Untitled Instrument Setup aA File TSQ Help Dsm S x Fa A A A oA oA A cA oA A A A AA OO A A Scan Editor Divert Yal Run Settings MS Acquire Time mii _ j Bright green triangle TSQ Vantage A Chrom Filter Peak Wi fe Tune Method C 5x SRM Settin
73. t 1 Station position Wash1 Eject Speed DLW Syringe The injection unit moves to the DLW Wash Clean Time solvent 1 Station position Wash2 Eject Speed DLW Syringe The DLW system is rinsed with Wash Solvent 1 in position Waste 64 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW Installing Cycle Composer Macros or ICC Cycles Table 15 Macro Priming Accela Open AS Sheet 2 of 2 Macro description The injection valve is cleaned first with the content of DLW syringe Wash Solvent 1 followed by Wash Solvent 2 and finally the last wash to prepare the system for injection cycle rinsed with Wash Solvent 1 again Remark The Atom Rinse Inj is new available starting with FW 4 1 x The DLW actuator solenoid is activated the Wash Solvent pump the Needle Gap and the Rinse Time are selectable Macro variable Needle Gap is a parameter from Rinse Inj Atom The variable in this macro is Needle Gap Valve Clean The function of this parameter is to raise the needle in the injection port very little to allow rinsing around the needle tip The pressure of the spring loaded balls in the DLW Syringe Holder assembly is released by moving approx 3 mm up default This leaves a gap between the needle tip and the valve bottom of approximately 1 mm to enable a flush at this contact point A Repeat End loop enables adding an extra rinsing step valve toggle Stator Wash Counter 0 disable v
74. t marqu par le symbole suivant Thermo Fisher Scientific s est associ avec une ou plusieurs compagnies de recyclage dans chaque tat membre de lunion europ enne et ce produit devrait tre collect ou recycl par celles ci Davantage d informations sur la conformit de Thermo Fisher Scientific 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 la directive RoHS sont disponibles sur www thermo com WEEEROHS ee Contents Prelate ee ee ee ere er cr ee eer rer ix Related Documents j4 i49 0es Meee eee oe cde ee te oh RRS Ras ix Safety and Special Notices sesi iceeces due enric saree enwbtetngawe ix Contacting US er issa cate eae eed tiaa bad EENI EAEE aed ERA E x Chapter1 Getting Connected 0 cece cece eee eee eee eae 1 Ordering Informati n ee rcrs ee Rd ay dernire Ree Koda een ee RRE S 1 Setting Up an LC MS System with the Autosampler 000 2 Connecting the Contact Closure Cables aioe Uplink ee eee eee eee es 3 Making Contact Closure with Thermo Scientific Devices o n annaa 4 Connecting the Start Pump to the Sample Pump in a Dual Pump SYSE eene aa aR ER aia ahs aint a AE eee 7 Making Contact Closure with the Autosampler an Agilent Pump and an MS DECRG s eae k cies dee ee eka ci AEE robber Rees RUE WEES 10 Connecting the PAL to the Data System Computer 0 0 000
75. template a Click Save As The Save As dialog box appears b Select a file location c In the File name box type an appropriate name d Click Save The autosampler saves the template with the file extension pme Template Editor Page Use the Template Editor page of the Pal Template Macro Editor window to make a new template a sequence of macros Each macro in the sequence is made up of variables You may also edit these variables on this page Table 7 Template Editor page parameters Sheet 1 of 3 Parameter Description Template Description Enter the method description in this box Syringe Select the syringe volume from this list Thermo Scientific Thermo PAL User Guide 35 3 Creating Custom Templates and Macros Using the Template Editor to Create Custom Templates Table 7 Template Editor page parameters Sheet 2 of 3 Parameter Macro Sequence Description This box displays the macros chosen for the method being made in the Method Template Editor The macros in this sequence are selected from the Macro list see below Double clicking a macro in the Macro Sequence box displays it in the Macro list as described later in this table along with the variables that make up the macro in the Variables area below the Macro list Insert Above A Macro in the Macro list see below is placed above the macro selected in the Macro Sequence box highlighted in blue Insert Below A Macro in the Macro
76. terminal refer to the CTC PAL System User Manual To select the sample trays and to change the default pulse time setting to 4 0 seconds follow these procedures e Selecting the Tray Type e Changing the Pulse Time Setting 20 Thermo PAL User Guide Thermo Scientific Selecting the Tray Type Thermo Scientific To select the tray type 2 Getting Started Using the Autosampler Control Terminal 1 In the Job Queue screen select the Menu screen by pressing the F1 key see Figure 15 Figure 15 Autosampler control terminal with the Job Queue screen displayed JOB QUEUE Menu Ins Del Pause Job Job F1 F2 F3 F4 Ese re STOP 2 Open the Tray screen as follows a Inner knob button Outer knob In the Menu screen rotate the outer knob to move the cursor bar highlight to Setup Press the inner knob button to select Setup Rotate the outer knob to move the cursor bar to Objects Press the inner knob button to select Objects Rotate the outer knob to move the cursor bar to Trays Press the inner knob button to select the Trays screen Thermo PAL User Guide 21 2 Getting Started Using the Autosampler Control Terminal The Trays screen lists the available trays 3 Select a tray as follows e Rotate the outer knob to move the cursor bar to the Tray to be selected Select the Tray by
77. the Sync Signal Ready before the injection cycle is started Macro variable Remark Sync Signal setting Start The injection valve is brought to a defined Inject to position Standby Standby The Rear air segment is pulled into the Holding Airgap Volume Loop Filling Speed 5 Using Dynamic Load and Wash DLW Installing Cycle Composer Macros or ICC Cycles Table 17 Macro Fast Injection Accela Open Sheet 2 of 3 Macro description The sum of Rear Sample List and Front Volume is aspirated into the Macro variable Front Volume Rear Volume Holding Loop SL volume Airgap Volume The Front air segment is aspirated Filling Speed Pullup Delay The injection unit moves to the specified Inject to injection valve The Front and Airgap Volume is ejected to Waste Front Volume Airgap Volume Injection Speed The PAL system waits for the data system Wait for DS The injection valve is switched to Active position The Pre Inject Delay time is awaited The loop is filled with the sample volume as specified in the sample list The injection valve is switched to Standby position the loop content is injected Inject to Pre Injection Delay SL volume Injection Speed Post Inject Delay The plunger of the DLW Syringe is pushed down to dispense the Rear Sample and Air Segment to Waste The Holding Loop is still filled with Wash Solvent 1 Injection Speed The DLW Actuator Soleno
78. ts a new wash station concept that combines an injection cycle with wash steps The linked combination of the two steps which are usually separate minimizes cycle time and carryover There are two characterizing features for the DLW option e The sample solution never contacts the syringe itself it is held between the holding loop e Wash solvents are pumped from back to front into the DLW system to intensely flush all critical parts that are in contact with the sample The DLW option consists of two self priming micro pumps mounted on a dedicated bracket and the wetted parts are Ryton PPS and Kalrez FFPM The pump IN ports are connected to the wash solvent bottles and the OUT ports are connected to the DLW manifold which is part of the assembly of the dedicated DLW syringe holder A holding loop separates the syringe and the DLW actuator to avoid sample from contacting these parts The syringe and holding loop are preloaded with wash solvent 1 at the start The sample is picked up and remains separated from wash solvent 1 by an air gap After loading the loop and injection wash solvent 1 is pushed into the system followed directly by wash solvent 2 to flush the critical valve paths The DLW syringe assembly is moved to the wash station for further cleaning steps and for preparing the Syringe and holding loop for the next cycle For further details refer to DLW Cycle Step by Step on page 73 Installing Cycle Composer Macro
79. tween the PAL one or two Thermo Scientific LC pumps or an Agilent pump a Thermo Scientific MS detector and the Xcalibur data system computer For information on setting up the PAL refer to the CTC Analytics PAL System User Manual CAUTION Follow all of the recommendations given in the Safety Information section of the CTC Analytics PAL System User Manual The Safety Information section includes information on the PAL electrical hazards lithium battery and safety labels Contents e Ordering Information e Setting Up an LC MS System with the Autosampler e Connecting the Contact Closure Cables e Connecting the PAL to the Data System Computer Ordering Information The Thermo PAL options that Thermo Fisher Scientific supplies include the serial communication cable that you use to connect the Thermo PAL to the data system computer and the contact closure cable that you use to connect the Thermo PAL to a Thermo Scientific LC pump and a Thermo Scientific MS detector Thermo Scientific Thermo PAL User Guide 1 1 Getting Connected Setting Up an LC MS System with the Autosampler Table 1 lists the Thermo PAL options that you can order from Thermo Fisher Scientific Table 1 Thermo PAL ordering information Part number Description OPTON 13008 HTS PAL OPTON 13009 HTC PAL OPTON 13010 HTC PAL with the 98 x 2 mL tray holder Table 2 lists the contact closure cables that you use to connect an Agilent pump to a Thermo Scientific MS
80. two Thermo Scientific pumps 8 control terminal attached to the autosampler 20 cycle composer macros 62 cycle composer macros or ICC cycles installing 62 Cycle Editor 62 delay time 28 Direct Control Configuration page 57 Direct Control dialog box opening 51 DLW characterizing features 62 cycle 73 cycle for fast injection 95 cycle for standard injection 73 fast injection cycle 68 macro definitions 63 operating 70 overview 61 priming solvent lines 64 standard injection cycle 66 Thermo Scientific DLW Actuator Solenoid 71 DLW Pumps 71 E electromagnetic compatibility iii external contact board for Agilent pump 10 external contact closure cable connections 5 F FCC compliance iii file types instrument methods meth 29 macro pma 45 templates pme 35 ICC cycles 62 Injected screen on hand held controller 23 Inlet Direct Control opening 52 Instrument Configuration window 15 Instrument Setup window opening 24 J Job Queue screen 21 L level surface importance of 2 lithium battery 1 look ahead injections 17 Macro Editor enabling 17 opening 43 macros creating 43 Thermo PAL User Guide 107 Index N importing 18 list of standard 42 Menu screen 21 method parameters specifying 24 numeric variables 49 0 object variables 49 ordering information 2 output signal to LC pump 3 P part numbers 2 priming solvent lines 64 pulse time of the out signals setting 23 pumps
81. uator Valve L Pump c gt waa 102 Thermo PAL User Guide Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 67 Fast Steps 11 12 Valve clean with Wash Solvent 2 Solenoid Actuator Valve uuu Pump Thermo Scientific Thermo PAL User Guide 103 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 68 Fast Steps 13 14 Valve clean with Wash Solvent 1 Solenoid Actuator Valve Pump gt Column Sample 104 Thermo PAL User Guide Thermo Scientific Thermo Scientific 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 69 Fast Step 15 Active syringe needle wash with Wash Solvent 1 Solenoid Actuator Valve Pumpi gt Pump2 gt Thermo PAL User Guide 105 5 Using Dynamic Load and Wash DLW DLW Cycle Step by Step Figure 70 Fast Cycle end Solenoid Actuator Valve Pump lt gt Pump2 lt gt Holding Loop lt D aan 106 Thermo PAL User Guide Thermo Scientific ee Index A autosampler control terminal using 20 C cables DB9 to DB9 serial cable 14 external contact trigger cable 10 PAL interface cable 10 Thermo Dual Configuration cable 8 Thermo Single Configuration cable 4 compliance FCC iii regulatory iii computer Com port 17 contact closure connections for a Thermo Scientific LC pump 5 for a Thermo Scientific MS detector 5 for an Agilent pump 10 for
82. ue for the parameter along with the lower and upper limits for the parameter If you choose an object Parameter Type you see a check list of objects that may be represented by the parameter Delete Command Sequence Deletes the selected Macro Variable The sequence of commands that make up the macro selected in the Macro list Double clicking one of the commands highlights it in blue and causes it to be displayed in the Command area In the Command area the command parameters are shown in both panes continuous variables and lists discrete variables Insert Above The command shown in the Command area is inserted above the command selected highlighted in blue in the Command Sequence pane Insert Below Replace The command shown in the Command area is inserted below the command selected highlighted in blue in the Command Sequence pane The command selected highlighted in blue in the Command Sequence pane is replaced by the command shown in the Command area Delete 46 Thermo PAL User Guide Deletes the command selected highlighted in blue in the Command Sequence pane Thermo Scientific 3 Creating Custom Templates and Macros Using the Macro Editor to Create Custom Macros Table 9 Macro Editor page parameters Sheet 3 of 3 Parameter Description Command Individual autosampler commands are displayed in a list These individual commands make up the command sequence of a autosampler macro
83. uments of your LC MS system such as the LC pump and the mass spectrometer 12 In the Thermo Foundation Instrument Configuration window click Done PAL Configuration Parameters Use the PAL Configuration dialog box to select the PC Com port where the autosampler is connected specify Macros to import and select sample trays or stacks Table 5 PAL Configuration dialog box parameters Sheet 1 of 2 Parameter Description Communications Com Port Select the computer port where you plug the autosampler communication cable Auto Select Instructs the system to automatically determine the computer port connected to the autosampler through the autosampler communication cable 18 Thermo PAL User Guide Thermo Scientific Thermo Scientific 2 Getting Started Adding the Autosampler to the Xcalibur Instrument Configuration Table 5 PAL Configuration dialog box parameters Sheet 2 of 2 Parameter Description Check Instructs the system to verify the computer port connected to the autosampler through the autosampler communication cable Look Ahead Injections Enable Selecting this check box enables Look Ahead Injections When Look Ahead Injections is enabled the autosampler sets up for the next injection during the current run The set up for the next injection involves carrying out the steps up to but not including the injection Method Template Macro Editor Enable Select this check box when you want the Met
84. up page with LC Inj template Method Setup Method Summary 2 Getting Started Specifying the Instrument Method Parameters for the Autosampler Template Selection Template C Xcalibur System PAL Methods Single Step LC Injection pme Template Description Duplication of PAL local LC Inj cycle This is only a sample method for short runs For analytical work the method parameters must be set according to the specific needs r Syringe 100ul v Macro Sequence Recommended Injection Voluine Volume ul j 0 000 Look Ahead Injections Delay Time mins 0 00 Macro LC Inj 1 of 1 r Variables Air Volume fpl Pre Clean with Solvent 1 Pre Clean with Solvent 2 Pre Clean with Sample Filling Speed pls Filling Strokes Inject to Injection Speed pls Pre Inject Delay ms Post Inject Delay ms Post Clean with Solvent 1 Post Clean with Solvent 2 Valve Clean with Solvent 1 Valve Clean with Solvent 2 Help Default All Macro sequence for the Single Step LC Injection template Variables list When you select a template the macros used by the template appear in the Macro Sequence area When you click on a macro listed in the Macro Sequence area the variables used by the Macro appear in the Variables area 6 In Variables area keep the parameters set to the defaults or type the appropriate values for your app
85. used within method Macro name LC Inj COMPLETE CYCLE XXXXXXXXXXXXXXXXXXXXXXXX Duplication of PAL s local LC injection cycle Tray Name Sample Number and Sample Volume are taken from the sample list Variables 14 Help Method Summary 32 Use the Method Summary page to view the details of the Macro Sequence that makes up a autosampler Method or Template The contents of the Method Summary Template Summary page is read only Thermo PAL User Guide Thermo Scientific ee Creating Custom Templates and Macros This chapter describes how to create custom templates and macros Contents e Using the Template Editor to Create Custom Templates e Testing a Custom Template e Viewing the Template Summary e Standard Macros e Using the Macro Editor to Create Custom Macros e Defining Variables Using the Template Editor to Create Custom Templates Three standard templates are provided with the autosampler To create a custom template use the Template Editor dialog box Creating a Custom Template This section provides information about how to create a custom template To create a custom template 1 Open the Template Editor page a Open the Instrument Setup view for the autosampler see Specifying the Instrument Method Parameters for the Autosampler on page 24 b From the menu bar choose PAL Auto Sampler gt Template Macro Editor The Template Editor page of the Pal Template Macro Editor
86. variables are displayed in boxes You may choose the allowed values of discrete variables from those presented in the list for the variable The allowed values for continuous variables are displayed when you hover the cursor over the respective box for the variable The desired value for the continuous variable is then typed in its box Save Template Saves the Method Template under the current file name overwrites the current file Save As Saves the Method Template under a new file name or in a new location that you type in the Save As dialog box Testing a Custom Template This section provides information about testing a custom template Using the Template Editor dialog to Test a Custom Template You can test a custom template from the Template Editor dialog box To test your new template step by step 1 If the Template Editor dialog box is closed open it 2 Open the template that you want to review by choosing File gt Open Method Template The default path to open a template is as follows C Thermo Instruments LC Devices ThermoPAL PAL methods Thermo Scientific Thermo PAL User Guide 37 3 Creating Custom Templates and Macros Testing a Custom Template 3 Click Step The Run Auto Sampler Method In Step Mode appears see Figure 23 Figure 23 Run Auto Sampler Method In Step Mode dialog box Run Auto Sampler Method In Step Mode Vial Indes _ r Injectors 1 j 1 LC viv 2 f 2 Leyi v Trays
87. volume filling speed and filing strokes are specified as parameters Macro Variables Air Volume pl 0 0 SYR Max Volun A Filling Speed pl s SYR Fill Speed C aranda Vinh fllOVD hdi Vinh Ms lt i gt lete TA Edit Command Sequence GET_SAMPLE Insert Above Insert Below Replace Delete 2 Under Macro select a macro from the list Command DISPENSE_DIL Default All m Parameters Dilutor Volume ul Eject Speed pl s Dispense Delay ms Dilutor Eject Speed 0 Device Status Ready To Download The description of the selected macro appears under Macro Description and a list of macro variables appears under Macro Variables Thermo PAL User Guide Thermo Scientific 3 Creating Custom Templates and Macros Using the Macro Editor to Create Custom Macros 3 To add a variable to the macro click Add The Variable Definition dialog box appears 4 Define the variable see Defining Variables on page 48 5 To save the macro a Click Save As The Save As dialog box appears b Select a file location c In the File name box type an appropriate name d Click Save The autosampler saves the macro with the file extension pma PAL Template Macro Editor Page Use the Macro Editor page of the Pal Template Macro Editor window to create custom macros Table 9 Macro Editor page parameters Sheet 1 of 3 Parameter Descriptio
88. x When you enable this option the next Look Ahead Injection is delayed the amount of time entered in this box The delay time countdown begins at the completion of any post injection steps This prevents a sample from being held in the injection syringe for the duration of the current run If the entered Delay Time is too long or the current run ends prematurely the entered Delay Time is canceled and the next injection commences in the normal manner Macro The Macro area shows the name of the macro selected in the Macro Sequence pane The sequence number x of the selected macro out of the total number of macros y in the Macro Sequence is also displayed next to the name of the selected macro Macro name x of y This area also lists the Variables associated with the macro chosen in the Macro Sequence pane Variables The variable parameters used by the selected macro are displayed in this portion of the Macro area Variables with specific allowed values discrete variables are displayed in lists Continuous variables are displayed in panes The allowed values of the discrete variables may be chosen from those presented in the list for the variable The allowed values for continuous variables are displayed when you hover the cursor over the respective pane for the variable The desired value for the continuous variable may be typed in its pane Default All This button changes the variables used in the selected Macro Sequence

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