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Cycle Composer User Manual Ed 8 4.2 MB

1. 50 PASSO PAL Cycle Composer User Manual The Cycle Composer Sample List is quickly filled out with the help of the graphical tool To select the samples for the Sample List click and drag the mouse over the range of wells or vials to be run The selected samples will be shown in red This graphical interface helps to avoid typing errors To run a standard non FIA sequence with these samples select the PAL method e g Single Step LC Injection You will also need to specify a file name 5 character prefix counter injection volume Volume ChemStation method CS Method and sample name SampleNam To add the selected samples to the Sample List select Add Vials To insert additional vials to the sample list you may return to the Trays view to select additional sample positions You may then use the nsert Vials selection to add these to the Sample List The user has the choice to fill out the filename directly in the column Filename Another approach is to specify the constant root of the filename and let the Cycle Composer complete the name with incrementing a 3 digit number e g W_Nov001 W_Nov002 W_Nov003 etc Note If the Sample List exceeds 1000 lines the ChemStation software will run the Sample List as two or more sequences Data file naming will continue with a 4 character prefix counter format i e samp1234 d To run the Sample List be sure the Use Manual Injection is select
2. 75 PASO PAL Cycle Composer User Manual 3 4 Starting a Sequence Create with File New Sequence a new Sequence or use the corresponding Icon to start an existing sequence A pop up window Run Sequence will allow the user to specify the sequence according to his demands w E gt mju 2 C XXcalibur methods PAL Test__ Stk1 01 1 C XXcalibur D ata C Xcaliburkmethods PAL Test Stk1 01 2 C Xcalibur D ata a C calibur Data Run Sequence i C Xcalibur D ata EE C scalibur Data C Xcalibur D ata C Xcalibur D ata Los o A C calibur Data C Xcalibur Data i C Xcalibur D ata C Xcalibur D ata C Xcalibur D ata C calibur Data C Xcalibur D ata C calibur Data C Xcalibur D ata C Xcalibur D ata C calibur Data reste Wier Summa C Xcalibur D ata C Xcalibur D ata C Xcalibur D ata C Xcalibur D ata C calibur Data C Xcalibur D ata C Xcalibur D ata C Xcalibur D ata 27 10 00 C Xcalibur D ata INUM 30 11 99 17 07 NOT SAVED 7 Specify in the field Acquisition Options the PAL Autosampler as starting device Use the button Change Instrument to enter changes if necessary 76 PASO All other parameters for the GC or the HPLC System and the MS System have to be set and used according to the instruction manuals from the corresponding
3. Sample List Name Fl Demo hs Start Start signals the start of an FIA series 10 TrayO1 Single Step FIA Injection 10 TrayO1 Single Step FIA Injection 10 TrayO1 Sample Fl4De003 C7 Single Step FIA Injection 10 TrayO1 Sample Fl De004 C7 Single Step FIA Injection 10 Tray01 5 Sample Fl De005 C7 Single Step FIA Injection 10 Tray01 Sample Fl De006 C7 Single Step FIA Injection 10 TrayO1 Single Step FIA Injection 10 TrayO1 Single Step FIA Injection 10 TrayO1 FIA Done 10 Tray01 Sample FIADe001 C7 Sample FIADe002 C7 Buon Sample Fl De007 C7 Sample FIADe008 C7 Sample Fl4De009 C7 Sample FIADe010 C7 2 voo Done Done signals the end ofan FIA series Injecting into LC VIVI Although each injection is shown as a separate line in the Sample List and the field FileName is also incremented the data is ACTUALLY collected to a single data file with the filename taken from the first line of the FIA sample list In addition to using the First FIA Injection method the first line of the FIA Sample List must also contain a Start indicator in the FIA column This signals the PAL software to begin an FIA series Likewise the FIA Done method and Done indicator in the FIA column signal the end 56 PASO PAL Cycle Composer User Manual Notes a The ChemStation method MUST be a FIA method The ChemStation FIA table is ignored except for the time between injections This is gener
4. ae Sequence templates Methods A Data Analysis Report Layout Il Ready A ao The Configure menu will display following window BE configuration 10 x Configuration screen r System Parameters r Debu m Sample Info Field Formatting in GC MSD Chemstation Softyare 4 447 Format Sample Info Field 15 Include Fieldname in Sample Info Field 46 List Separator Character Available Fields 4 4 r CycleComposer Settings i File Based CC Ver 152 or older 2 Store Activity into STATUS ACT Selected Fields 01 Method 10 Sample ID Message Based CC Ver 153 or up Pp 02 Volume 5 Message Time out 1000 mSec 6 Message Retry Count 10 7 IV Use long file names I Use multiple sequence files oF Injector 2 9 35 Duration max 3600 seconds 1 Infinite Check RunState 12 10 36 Duration max O seconds 1 Infinite 7 Check CTC_EndOfRun 43 10 seconds after each run 14 37 Wait for 08 Vial lt lt 09 Inj Vial gt r End of Run determination GC MSD Chemstation Software Chemstation Datapath IV Override Standard Chemstation path 20 Datapath C Chem32 1 DATANERIC2 21 Browse 24 2 im A 58 PASO PAL Cycle Composer User Manual The meaning of the individual items is explained by the number 1 Set the debug mode when the ChemStation software is started Whe
5. PASO PAL Cycle Composer User Manual Now start to compose the sequence of operations in the box labeled Method Macro Sequence using the available Macros from the list on the right side labeled Selected Macro Moving the cursor to the Macro name displays a hint with a short description of the Macros function PAL Cycle Composer C Programme PAL Cycle Composer HTS PAL File Help Sample List Method Editor Method Name Selected Macro Muti Step LC Injection n wait Signal bd Default All Add to Sample and Mix Aspirate Aspirate Sample Clean Syringe Clean Valve Clear Output Signal Dispense Home Method Description Injection cycle with 2 pre and post cleaning steps for the syringe and 2 post cleaning steps for the valve Number of cleaning cycles air volume filling gt Method Syringe 100ul Method Macro Sequence ooo After a Macro has been selected modify any required parameters presented in the table beneath it on the screen When these are complete select the Insert button under the sequence table and the Macro will be placed in the sequence below the current position Repeat this process for each step in the sequence If a parameter for any Macro has to be modified select the Macro in the sequence for which the modification is to be made then change the desired value If the Macro itself is not changed then the new v
6. All rights reserved Neither this publication nor any part of this publication may be copied photocopied reproduced translated or reduced to any electronic medium or machine readable form without the prior written permission of CTC Analytics AG except as allowed under the copyright laws CTC Analytics AG acknowledges all trade names and trademarks used as the property of their respective owners PARSO PAL Cycle Composer User Manual PASO PAL Cycle Composer User Manual Table of Contents PAL Cycle Composer 7 User Manual PAL Driver for 33 Agilent ChemStation Data System Installation Guide PAL Driver for 63 ThermoFinnigan Xcalibur Data System Installation Guide PARSO PAL Cycle Composer User Manual PALE PAL Cycle Composer User Manual PAL Cycle Composer Installation Guide User Manual Software Revision 1 5 4 PARSO Release History Software Revision CC1 0 Software Revision CC1 3 Software Revision CC1 3 2 Software Revision CC1 4 Software Revision CC1 5 PAL Cycle Composer User Manual Original Release of Cycle Composer Software Cycle Composer Software compatible with ChemStation and Xcalibur Driver Cycle Composer Software compatible with Windows NT 4 0 Administrator User rights Cycle Composer Software compatible with PAL Firmware 2 2 0 or higher serial communication supported by framing protocol Software Changes for Cycle Composer PAL Configuration file offline pal po eliminated Syste
7. HEMA Tray Sample Type Tray01 DW96 gt Show Vial Numbers C Show Sample Types Add vials Insert vials Close SelectAll Deselect All To run a standard non FIA sequence with these samples select the PAL method Single Step LC Injection You will also need to specify a FileName 5 char prefix counter injection volume Volume ChemStation method CS Method and sample name SampleNam To add the selected samples to the Sample List select Add Vials Note If the Sample List exceeds 999 lines the ChemStation software will run the Sample List as two or more sequences Data file naming will continue with a 4 char prefix counter format i e samp 1234 d To insert additional vials to the sample list you may return to the Trays view to select additional sample positions You may then use the nsert Vials selection to add these to the Sample List To run the Sample List be sure the Use Manual Injection is selected in ChemStation then select Start from the Sample List Screen You must save the Sample List before a sequence can be started The name is limited to 8 characters This name will be used to build a ChemStation sequence table as the Sample List is run As the Sample List is being run the Status column will indicate Preparing Running or Done 55 PASO PAL Cycle Composer User Manual 3 6 Running a FIA Sequence Sample List Setting up a sample li
8. If an Autosampler of the Agilent Series1100 is configured it has not to be removed from the configuration to install the PAL System GC6890 and GC MSD The Autoprep Run is activated through the Driver software at the start Therefore it is not necessary to configure the GC in this mode The Gas saver option is fully available Variable for ChemStation Report function InjVol added to PALSEQ MAC GC MSD Version Parameter ExtraWaitForStart added Support for newer Chemstation version has been added 34 PASO PAL Cycle Composer User Manual PAL Driver for Agilent ChemStation Data System Table of Contents 1 Requirements 37 1 1 Software Requirements 37 1 2 Workstation Requirements 37 1 3 Synchronization Requirements for the PAL System and the Agilent Instrument 38 2 Installation Procedure 38 2 1 Order of Installation 38 2 2 Installation for GC HPLC LC MSD 39 2 3 Installation for a GC MSD 40 2 4 Files used for Agilent ChemStation and Cycle Composer 47 2 5 Injector Naming Nomenclature 47 2 6 Uninstalling the PAL Cycle Composer Driver for the ChemStation 48 3 Starting PAL Cycle Composer Software in Synchronization with HP ChemStation 48 3 1 Principle of Synchronization 48 3 2 Starting the PAL Cycle Composer Software 49 3 3 Creating a Sequence 49 3 4 Customize a ChemStation Report Template 52 3 5 Running a Standard Non FIA Sequence Sample List 54 3 6 Running a FIA Sequence Sample List 56 3 7 Configuring
9. If this is not appropriate for the application the user can compose his own sequence Small building blocks so called Macros are combined to construct a new sampling cycle A Multi Step Method consists of a sequence of Macros each having its own set of parameter values A set of standard Macros is installed together with the Cycle Composer program A list and description of these is provided in chapter Standard Macros 6 3 Composing a new Method To create a new Multi Step Method select New Method under the File menu and give it a name Then select a syringe to be used for this Method It is essential that the syringe is selected before Macros are added to the Method The selected syringe sets different default values and ranges for volumes and flow rates It is possible to change the syringe for an existing Method but it may happen that Macro values are no more within the valid range and have to be adjusted PAL Cycle Composer C Programme PAL Cycle Composer HTS PAL File Sample List Method Editor Method Name 17 Selected Macro Multi Step LC Injection wait Signal x Default All Method Description Sync Signal Start Injection cycle with 2 pre and post cleaning steps for the syringe and 2 post cleaning steps for the valve Number of cleaning cycles air volume filling M Help Method Syringe Insert Replace Delete Run Step Connected to Pal 25
10. With every injection a temporary file is created called Temp s Using this concept it is not possible to make multiple injections from the same vial The run file will be overwritten for each sample and only the latest file is stored Sequence Temp s 3 For GC Instruments it is not possible to use the Dual Injection Mode 4 Calculation with the so called Bracket Mode is not active 5 In the GC MSD version it is not possible to select a sample of a user defined type or a Keyword Sample These values are not loaded with the PAL Driver Macro 6 Only one Cycle Composer Software can be installed on a workstation Therefore the control of several Agilent Instruments with one workstation is not possible 7 The HPLC System Model 1090 is supported with this version of the driver Limitations have to be made that the highest upgrade level to hardware as well as software has to be implemented 8 The ChemStation Version Cerity is not supported 61 PARSO PAL Cycle Composer User Manual 62 PARSO PAL Cycle Composer User Manual PAL Driver for ThermoFinnigan Xcalibur Data System Installation Guide Software Revision 1 5 6 PASO PAL Cycle Composer User Manual Printing History Preliminary Installation Guide October 1999 Software Revision 1 1 Edition 1 December 1999 Software Revision 1 2 Edition 2 May 2001 Software Revision 1 3 Edition 3 July 2001 Software Revision 1 3 1 Release History Software R
11. Cony pu ca Help J Use the arrow keys to select entry Select OK to close the sequence editor 43 PASSO PAL Cycle Composer User Manual Save the new sequence by selecting the menu Sequence Save Save the sequence with the name Empty ctc Save Sequence 44 PASO PAL Cycle Composer User Manual Change the Sequence Default Run Mode The new sequence will run in reprocess mode by default This mode must be changed to be able to run in data acquisition mode To do this you must select the menu Sequence Run trata AE CLAS MER Method Instrument Abort Window Qualify Help Na Data File nf101 4 d Chromatography ni o e Top Enhanced CLASS M 7 temp s View Secured Control PAL Help Lodo Save Edit Sample Log Table 1 CAMSDeher t ni cle 2CAMSDchem 1 sequence EMPTY CTCS When the run dialogue opens click the Full method setting then click OK K instiumert BY CLASS M Et Method Instrument View Abort Window Qualify Help a men eu Forgot j Sample Name gt Datos i 2 Data File as nf1014 d SE Run Time 6 00 Sample Hee i CEE CEE Detectors Ss IRINA Met i Sections To n TEMES On Barcode Mismatch Full Method E Injectanyway o Reprocessing Only o o Don t Inject Di M Overwrite Existing Data Files Sequence Comment Operator Name ee Data File Director
12. Device Types Configured Devices PAL Autosampler PAL Autosampler Add gt gt lt lt Remove Configure o 69 PASO PAL Cycle Composer User Manual Activate the Icon PAL Autosampler in the field Configured Devices and click on the button Configure and follow the steps Specify the corresponding Serial Port e g COM1 Select the Method Folder e g C Program Files PAL Cycle Composer HTS PAL Get Configuration from PAL click the Start button The serial connection will be established and the software will receive the configuration from the PAL System After the successful upload one will get the message XX objects received from the PAL E Pal Configuration OF x Serial Port comi Method Folder C ProgrammeSPAL Cycle Composer HTS PAL Browse Get Configuration from P et Lonfiguration from ra OK Hel 79 objects received from Pal Z Close the section Instrument Configuration 70 PASO PAL Cycle Composer User Manual 3 2 Instrument Setup Start the program from the desktop Icon Xcalibur Num 20 71 99 Choose the section Instrument Setup As a difference to the standalone Cycle Composer software the user will get a Method Template 9 Unbenannt Instrument Setup Deb S x 2 Duplication of PAL local LC Inj cycle 01 LC Inj 71 PASO PAL Cycle Composer
13. User Manual To change or to add a new method Template call the Cycle Composer from the drop down menu PAL This is the actual Method Editor ste Unbenannt Instrument Setup 01 LC Inj Create a new method and use save as to give a unique name Ry save Method Fast Screening Pel Fast Screening Pel Pel Fast Screening Peptided Fast Screening Per Plates 01 LC Inj 72 PASSO PAL Cycle Composer User Manual Close the Method Editor and go back to Instrument Setup The new created template is now available File PAL Help II AACA A AS IL AAAA E AS ALMAS AS E AA AS AS IS i i A AA A A A A A AL A AS ISI II A A A n IA IS A MA i i se A i Choose Method Template 01 LCAnj 3 Fast Screening Peptides x Default All 5 Method Description Air Volume pl Fast Screening Peptides using MicroTiter Pre Clean with Solvent 1 Plates Autosampler 4 Pre Clean with Solvent 2 Pre Clean with Sample i Method Syringe Filing Speed pls 5 100ul E r Fillinn Strokes 3 3 Sequence Setup Choose the section Sequence Setup Select New Sequence from the menu File Fill out the page as described in the Xcalibur manual Unbenannt Open Sequence Setup ol xi File Edit Change Actions View GoTo Help afa OPP osla eel SNE SF Eee 2 Inst Meth Position Inj
14. Vol Status Acquisition Queue New Sequence Template Eg El Run Manager M General Ready To Download Sequence Base File Name Starting Number fi Sample Name Working On Path C Xcalibur Data Browse Position Raw File Instrument Method C gt lt calibur methods F astScreeningPeptides Inst Method PAL Autosampler Processing Method Browse Ready to Download Calibration File Browse m Samples Number of Samples 4 Tray Type Trayt Injections per Sample fi Initial Vial Position Trao IV Re Use Vial Positions Base Sample ID Select Vials Cancel Selection Visually select vials from tray r Bracket Type C None Open Non Overlapped Overlapped r Calibration QC TT Add Standards TF Add OCs Numenor brackets fi fe After First Calibration O mg For Help press F1 Injections per Level Atte Even Calibration 73 PASSO PAL Cycle Composer User Manual In the section Samples of the Sequence Template one is confronted with specific buttons for the combination of Xcalibur with the Cycle Composer Select Tray Type e g Stk1 01 Select Vials The button Select Vial will bring the user the full comfort with graphical selection of the vials CTC highly recommends to use this graphical tool not only for ease of use but also to avoid typing errors The Xcalibur Sequence demands the Tray Name and the Vial Position in one field separated by a colon
15. be released The Fiber is moved to the selected GC Injector and the analytes will be thermally desorbed The Fiber remains in this position until the timer of Desorption Time reaches Zero The Fiber is retracted and the vial is taken back into position The Macro contains the complete sampling cycle all parameters are on a single page 30 PASO PAL Cycle Composer User Manual SPME Agitated amp Heated Special Penetration Complete Cycle This macro is a duplication of the macro SPME Agitated amp Heated with the differences that the user has more flexibility with the parameters Vial Needle Penetration Vial Fiber Exposure Injection Needle Penetration and njection Needle Exposure The Macro contains the complete sampling cycle all parameters are on a single page SPME Heated Complete Cycle This Macro has the exact same structure as the Macro SPME Agitated amp Heated The only difference is that the analytical sample is heated only and not agitated The Agitator is turned off during the Pre Incubation Time as well as during the Extraction Time The Macro contains the complete sampling cycle all parameters are on a single page SPME Out of Tray Complete Cycle The SPME Fiber is moved to the selected vial in the corresponding Tray is inserted and exposed for the desired Extraction Time to reach the equilibrium The Fiber is retracted and the synchronization sign
16. do The sample list editor is the main interface of the CC program It allows the operator to generate a sequence of samples to be run and initiate the run on the PAL The Sample List is either created directly line by line or is generated using a graphical representation of the trays All file and setup operations are accessed via the File menu These include creating a new Sample List saving with a different name printing etc Available saved Sample Lists are accessed from the pull down list next to the title box Sample List Name 5 2 The Sample List Table Each line in the Sample List represents a sample in the sequence and contains fields for the controlling parameters The table can be edited directly Values for numeric fields must be typed in The Method Tray and Injector fields are filled by selecting the desired item from the pull down lists Use the TAB key to go to the next field All fields must have a valid entry PAL Cycle Composer C Programme PAL Cycle Composer HTS PAL BB x File Help Sample List Method Editor Sample List Name Diagonal Scanning of Plate in Stk1 01 x Start Pause Reset PAL View Log file Append line Insert Line Delete line i Stk1 01 Unknow Stk1 01 Unknow Stk1 01 Unknow Stk1 01 Unknow Stk1 01 Unknow Stk1 01 Unknow Stk1 01 Unknow Stk1 01 Unknow Stk1 01 Unknow Stk1 01 Unknow Stk1 01 Unknow Stk1 01 Unknow LC Injection Single Step LC Injection Single Step
17. l o za ne E Headspace Injector 2 IC Visible 9 Headspace Vial 1 IV Visible 10 Headspace JE ancl Headspace Inj Vial 1 IV Visible 12 Headspace Sample ID I Visible 13 Headspace same sd DE 14 Headspace PE Sample pal BY DES fe Uaadanann l FileName W Nov IV Visible CS Method HS 1 M y IM Visible SampleName Water IV Visible Cal Level IV Visible F1 Help F3 Recall F5 StartRun F6 StartSeqRun F8 Stop F11 NextWindow Shows current sequence name and sequence modification status The Cycle Composer software maintains the full functionality For example the button Select Vial opens a window for the graphical selection of the vials U Instrument 1 online Method amp Run Control TES File RunControl Instrument Method Sequence PAL View Abort Help Method and Run Control E SPME_01 M 2 temp s 2 Run Method Method Sequence Trays ai Tray Holder THldr1 X i Tray1 VT32 20B mg a LE Travl E Add Sample type unknown 800 700 Add Vials from To Increment 600 500 400 300 200 100 32 e Online Plot E 80 70 a 60 Method Volume Ini via Type FileName CS Method SampleName CalLevel Update RF soc Test SPME 0 1 Sample CTC SPME O1 M TestSample 3 4 I gt 40 7 Show Vial Numbi SelectAll Deselect All DE Show lumbers ITEFA Select Deseleci 20 No sample list in progress
18. not be mixed up with the Keyword Functions The execution of the Keywords is not possible See Limitations Chapter 4 2 5 Injector Naming Nomenclature The injector names should correspond with the nomenclature used in the ChemStation for detecting the front and the rear injector In order to be able to select the front or the rear injector one can use only specific injector descriptions in the local control of a Combi PAL System For the rear or back injector use Rear Back B or GCInj2 All other names will automatically refer to the front inlet of the GC To insert another injector in the PAL System use the local control terminal and perform the following steps Menu F3 Setup Objects Injector press F2 Insrt Inj Give a name to the new injector according to the nomenclature described above Teach the injector position as described in the Combi PAL manual After establishing the serial connection the Cycle Composer will receive all objects from the PAL System The software will learn at this moment which injectors are configured in the PAL System With the driver linked to the ChemStation it is ensured that the desired injector will be used This nomenclature of naming is important for GC instruments No special convention or configuration is necessary for HPLC instruments 47 PASO PAL Cycle Composer User Manual 2 6 Uninstalling the Cycle Composer Driver for the ChemStation To unins
19. tray and the syringe is flushed To be able to overlap the incubation time with the GC Runtime the GC Ready signal is not checked before the vial is inserted into the agitator but it is checked before injection The Macro is terminated after a delay time of GC Runtime Incubation Time which started at the injection moment For a GC Runtime which is shorter than Incubation Time the next vial is inserted immediately If the GC Runtime is longer than Incubation Time the vial is inserted with sucha delay that it will be incubated for the correct time when the GC gets ready This Macro contains the complete sampling cycle all parameters are on a single page SPME Agitated amp Heated Complete Cycle Set temperature of Agitator to the desired value After temperature has stabilized the vial is transported into the Agitator If Pre Incubation time is selected the sample is shaken and heated The movement of the Agitator is stopped the needle guide is blocked Exp Fiber and the SPME Fiber is inserted into the vial The vial penetration for the fiber is fixed not selectable by the user The Fiber is exposed into headspace or the liquid phase The Agitator is started and moves on a fixed speed slowest possible speed to yield in a round movement The sample is heated and the equilibrium will be reached during the selected time Extraction Time The SPME Fiber is retracted the synchronization signal is awaited and the needle guide will
20. 3 2 Running Off line If there is no PAL detected when the program starts it will load a set of objects from the file called latest_pal pol The file offline_pal pol has been eliminated with this Revision 1 5 to simplify the CC handling in an off line situation 15 PASO PAL Cycle Composer User Manual 4 Initial Setup There are 5 setup options available from Main screen under File menu C Programme PALXCycle Composer HTS PAL PAL Cycle Composer Help New Sample List Save Sample List Save Sample List As Delete Sample List Print Sample List Reset PAL View Log file Append line Insert Line Delete line Trays Import Options Port Exit Reload Pal Configuration Choose method folder Status Box Format Sample List tray va invia sample S Connected to Pal 4 1 Port This setup option allows the user to define which COM port on the PC is to be used to connect to the PAL By default COM1 is used Connect this port to the serial port SER1 of the PAL using the null modem cable provided Switching the port reconnects to the PAL and loads the configuration Choose serial port PAL 1 Serial Line Statistics Please choose the proper serial port Sends 0 COM3 COM3 Length errors 0 Receives 0 COME Checksum errors 0 Disconnects 0 Reconnects O Retries D Bad characters 0 If some other program is using the select
21. A Done 10 Tray01 MultF005 CTCFIA M pons for each FIA series in First FIA Injection 10 Tray01 MultFO06 CTCFIA M tart th am 1 Li t Single Step FIA Injection 10 Tray01 MultFO0 CTCFIA M e S p Si Single Step FIA Injection 10 Tray01 MultF008 CTCFIA M Single Step FIA Injection 10 Tray01 MultFO09 CTCFIA M FIA Done 10 Tray01 MultFO10 CTCFIA M Done Resetting PAL To run the FIA Series Sample List select the Start button of the Sample List Screen You will be prompted to set the Pump Off time to Off if it currently has some time value Select Ok This prevents a stop signal from being generated during the FIA series Note When the sample list is running the Start button changes to Stop 57 PAL Cycle Composer User Manual PARSO 3 7 Configuring the Chemstation interface From the ChemStation menu it is now possible to run the configuration dialog for the interface between Cycle Composer and ChemStation Two menu items inside the Chemstation PAL menu are available the Configure and the Debug menu io File RunControl Instrument Method Sequence PAL View Abort Help N A a IS ISS 1 25 S o Methods La kh METANOMNW M SS Composer sequences amp ed eric2 s onfigure Method and DT O EEEF ES Method and Run Control Debug on A BG C CHEM32 1 SEQUENCE a def_gc s Jes ER eRIC2 S ER TEMP S Reprocess Data Mode Last Data File 1
22. Cycle Composer Sample List ChemStation specific fields are CS Method File Name Sample Name Update RF Multiplier Sample Amount Update QI Dilution Cal Level Update RT Interval ISTD Type FIA 49 PASSO PAL Cycle Composer User Manual The fields columns appearing in the Cycle Composer Sample List can be hidden by unmarking the column name in the File Option Format Sample List window Instrument 1 online Method amp Run Control lej xj File BunControl Instrument Method Sequence PAL View Abort Help Method and Run Control E HS_1 M E temp s 5 Run Method FE me T Sent 8 E PAL Sequence Manager C Programme PAL Cycle Composer Combi PAL File Help Sample List Method Editor FEDE Sequence tell temp s ChemStation Status Back x Name Sample List Name Define columns of sample list Comment Front eme W Nov 99 Default values for columns in the sample list E Comer Sit Pas Status M Visible UpdateRF average M Visible Method Headspace Injection IV Visible Update RT Average 7 I Visible E Volume 500 M Visible Interval I Visible tT Headspace e RO 2 ERES Tray Tray IV Visible Sample Amount 1 Visible 3 Headspace Injector GC Inj I Visible ISTD Amount TT Visible 4 Headspace Volume 2 0 o I Visible Multiplier 1 I Visible 5 Headspace I 6 Headspace Tray 2 Tray2 IV Visible Dilution 1 IV Visible Headspace
23. Data System Consult the Xcalibur Manual or a representive of ThermoFinnigan 1 3 Requirements for the PAL System The PAL Driver for Xcalibur can communicate with the following Firmware levels of the PAL System e Combi PAL 2 2 0 or higher e GC PAL 2 2 0 or higher e HTS PAL 2 2 0 or higher e HTC PAL 2 2 0 or higher e LC PAL 2 2 0 or higher 1 4 Synchronization Requirements for the PAL System and the ThermoFinnigan Instrument The synchronization of start stop ready signal between the PAL System and the ThermoFinnigan Xcalibur Workstation is done via serial connection Use the PAL connector SER1 and any serial connector at the workstation The PAL System is the Starting Device for the combined system The setup for the PAL synchronization signal has been pre configured by the factory with the setting of the synchronization signal Start immediat Do NOT change this value if working in combination with Xcalibur 67 PASO PAL Cycle Composer User Manual Note In the CTC manual it is mentioned that the Start signal shall be changed from immediat to TTL In1 This is valid for a stand alone situation but not working in combination with Xcalibur If the PAL System has been used already as a standalone unit it is necessary to change back the Sync Signal settings using the local terminal as follows Path Menu Setup Objects Sync Signals Start 2 Installation Procedure Order of Installation 1 Xcalibur Softwa
24. Help Report Layout E EMPA4 M Fe 1 CTCHPOIFRP e Percent Percent x h h MENES Se Fal S Area gt 78x60 Method aj Header General Operator jection Date Vial vial gina Injection Volume ISTA Set up computed Text user defined Macro Instrument 2 Macro Setup Macro Name USR L S Macro File c Ahpchemicoretpalseq mac Select File Edit Macro Edit Macro Append new Macro Frame to File Format Options O left aligned right aligned Empty String Substitution Injection Volume 19 3 24 4 5x1 53 PASO PAL Cycle Composer User Manual 3 5 Running a Standard Non FIA Sequence Sample List Launch Cycle Composer from ChemStation This will bring up the PAL Sample List From this utility you can build and customize Sample Lists i e sequences or studies and edit the HTS PAL method parameters The Cycle Composer Sample List determines the ChemStation method sample volume tray and vial positions etc that will be run The Sample List is used to build a ChemStation Sequence Table which is used to control the LC GC or MS instruments for data collection and for reprocessing data PAL Sequence Manager C Program Files PAL Cycle Composer HTS PAL Help New Sample List Save Sample List Save Sample List As Delete Sample List Print Sample List Reset PAL View Log File Append Line Insert Line De
25. L Cycle Composer C Programme PAL Cycle Composer HTS PAL File Help Sample List Method Editor Method Name Selected Macro Single Step LC Injection z 7 Detauta Method Description 1 Air Volume pl Duplication of PAL local LC Inj cycle Pre Clean with Solvent 1 Pre Clean with Solvent 2 fr Pre Clean with Sample Method Syringe 100ul Method Macro Sequence 01 LC Inj Insert Beplace Delete Run Step Filing Speed pl s 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 0 ll LC Vivi fio 500 500 Connected to Pal Because a Single Step Method consists of a single Macro with associated parameter values the sequence of processing steps can not be changed at this level But often it is possible to change some aspects of the cycle by setting some parameters accordingly In the example above cleaning before injection is skipped by setting the three Pre Clean parameters to zero In the description of standard Macros later in this guide all Macros which can be used for a Single Step Method are marked with Complete Cycle 24 PASSO PAL Cycle Composer User Manual 6 2 Multi Step Methods A Single Step Method has a fixed sequence of PAL operations which can not be altered by the user
26. L System and the Agilent Instrument The start stop ready signals between the PAL System and the Agilent Instrument GC HPLC or GC MS is synchronized via hardware signal connection Use the PAL connector Interface 1 and the corresponding Agilent Remote connector An appropriate interface cable is available from CTC P N Cbl HP6890 The setup for the PAL Synchronization Signals requires the following steps 1 Change the remote start signal from mmediat to TTL In1 Path Menu Setup Objects Sync Signals Start Action Change the Source from mmediat to TTL In1 2 Change the state of the TTL 1 signal Agilent specific Path Menu Setup Objects Events TTL In1 Action Change value of Active state from Low to High 3 Verify the state of the Injected signal default settings Path Menu Setup Objects Out Signals Action Change the value Destination from from Off to SW Out1 Note Verify that the AutoPrepRun of the GC 6890 is not active Keyboard GC 6890 Path Configuration Instrument AutoPrepRun Off In this configuration the Gas saver mode is fully active 2 Installation Procedure 2 1 Order of Installation 1 Agilent ChemStation Software 2 Cycle Composer Software 3 Driver for Agilent ChemStation Note It is necessary to exit all programs before installing the PAL Driver software To setup the communication between the Ag
27. LC Injection Single Step LC Injection Single Step LC Injection Single Step LC Injection Single Step LC Injection Single Step LC Injection Single Step LC Injection Single Step LC Injection Single Step LC Injection Single Step LC Injection DNnNI1NNNNNNNNMNUMN Connected to Pal Pressing TAB at the last field of the last line creates a new line with the same content as the previous one but with the sample number incremented Also pressing the down arrow key when a field in the last line is selected appends a new line 19 AUISYSTENS PAL Cycle Composer User Manual Single or multiple lines can be cut out CTRL X or copied CTRL C and inserted at another position CTRL V Select the lines by clicking on a line number and dragging up or down A single field may be copied and applied to the whole column First copy the field then click on the column header to select the column and press CTRL V 5 3 Creating a Sample List in the Trays Screen By clicking on the Trays button an interactive screen allows the user to easily implement a complex sample list using a graphic interface represented by a map for each of the available trays First select the tray holder from the pull down list Then click on the representation of the required tray A map of this tray then appears showing all the available sample positions Tray Holder tak Trays kr rl Add Sample type Unknown x Stk1 01 DWS6 Add V
28. PAL Test C Xcaliburmethods PAL Test C Xcaliburmethods PAL Test Ci Xcalibur methods PAL Test C Xcaliburmethods PAL Test C Xcalibur methods PAL Test C calibur methods PAL Test C Xcaliburmethods PAL Test C calibur methods PAL Test C calibur methods PAL Test C Xcaliburmethods PAL Test C calibur methods PAL Test C Xcaliburmethods PAL Test C Xcaliburmethods PAL Test Ci Xcalibur methods PAL Test C Xcaliburmethods PAL Test Ci Xcalibur methods PAL Test C scalibur methods PAL Test Stk1 01 2 Stk1 01 3 Stk1 01 4 Stk1 01 5 Stk1 01 6 Stk1 01 7 Stk1 01 8 Stk1 01 9 Stk1 01 10 Stk1 01 11 Stk1 01 12 Stk1 01 13 Stk1 01 14 Stk1 01 15 Stk1 01 16 Stk1 01 17 Stk1 01 18 Stk1 01 19 Stk1 01 20 Stk1 01 21 Stk1 01 22 Stk1 01 23 Stk1 01 24 Stk1 01 25 Stk1 01 26 Stk1 01 27 Stk1 01 1 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 E cem ata C Xcalibur D ata C Xcalibur D ata C Xcalibur Data C XcalibursData C Xcalibur D ata C Xcalibur D ata C XcalibursData C calibur D ata C Xcalibur D ata C Xcalibur D ata C calibursData C Xcalibur D ata C calibursData C Xcalibur D ata C Xcalibur D ata C calibur D ata C Xcalibur Data C Xcalibur D ata C Xcalibur D ata C Xcalibur D ata C XcalibursData C calibur D ata C Xcalibur D ata C XcalibursData C calibursDat
29. PARSO PAL Cycle Composer User Manual PAL Cycle Composer and Drivers Installation Guide User Manual Software Revision 1 5 4 PARSO Printing History Edition 1 September 1998 Edition 2 July 1999 Edition 3 November 1999 Edition 4 October 2000 Edition 5 May 2001 Edition 6 June 2001 Edition 7 July 2001 Edition 8 May 2007 PAL Cycle Composer User Manual Software Revision CC1 0 Software Revision CC1 3 Software Revision CC1 4 Manual including Drivers combined Manual no change in Software Revision Software Revision CC1 5 Agilent ChemStation Driver Revision 2 0 3 ThermoFinnigan Xcalibur Driver Revision 1 3 Software Revision CC 1 5 Agilent ChemStation Driver Revision 2 0 4 ThermoFinnigan Xcalibur Driver Revision 1 3 Software Revision CC 1 5 Agilent ChemStation Driver 2 0 4 ThermoFinnigan Driver 1 3 1 Software Revision CC 1 5 4 Agilent Chemstation Driver 2 1 3 PARSO PAL Cycle Composer User Manual Warranty March 2007 CTC Analytics AG reserves the right to make improvements and or changes to the products and programs described in this User Manual at any time without notice CTC Analytics AG makes no warranty of any kind with regards to this product including but not limited to the implied warranties or merchantability and suitability for a particular purpose The software described in this User Manual is furnished under a license and may be used only in accordance with such license 2007 CTC Analytics AG
30. User Manual 13 This will enable the use of a macro parameter to signal readiness of the post run macro s If set the post run macro should contain a statement like this CTC_EndRun 1 Should this line be missing in the post run macro the interface will wait for the maximum time set in item 9 before continuing the next run 14 With this setting the interface can perform formatting of the sample info field based on the settings in items 15 19 15 When selected the fieldnames are also put into the sample info field The format is like method default mth 16 This parameters controls the separator character to be used inside the sample info field for separating the individual entries 17 This listbox contains all available items from the sequence which can be put inside the sample info field 18 Command buttons which enable the user to move fields from the available listbox to the selected listbox gt Add the selected fields s inside the available fields box to the selected fields box lt Remove the selected fields s inside the selected fields box to the available fields box gt gt Add all available fields to the selected fields box lt lt Remove all fields from the selected fields box to the available fields box 19 This box contains all the selected fields which will be put inside the sample info field when a run is started The sample info field however is very limited and care should be taken which fields are put ins
31. a C Xcalibur Data Stk1 01 1 Stk1 01 2 Stk1 01 3 Stk1 01 4 Stk1 01 5 Stk1 01 6 Stk1 01 7 Stk1 01 8 Stk1 01 9 Stk1 01 10 Stk1 01 11 NUM 30 11 99 17 21 NOT SAVED 7 77 PAL Cycle Composer User Manual PARSO 78
32. al is awaited The Fiber is moved to the selected GC Injector The analytes are thermally desorbed and the Fiber remains in this position until the timer for the Desorption Time reaches Zero The Fiber is retracted and the head moves back to home position This Macro does not use the Agitator at all The sample preparation is done at ambient temperature or at selected temperature with a cooled heated sample Tray The Macro contains the complete sampling cycle all parameters are on a single page Bakeout Fiber Complete Cycle This Macro is used in combination with the SPME Fiber Bake out Station After the thermal desorption of the analytes the SPME Fiber is moved to the Bake out Station The Fiber is exposed and conditioned during the selected Bakeout Time After this time the Fiber is retracted The temperature is set by using the local terminal under Menu Utilities Injectors Select Nd Heatr and set the desired temperature at Standby Temp A constant gas flow protects the Fiber 31 PASO PAL Cycle Composer User Manual 8 PAL Folder Structure The following folder structure is created as default by the install program and is recommended for installing PAL related software on your PC C Program Files PAL Cycle Composer GC PAL Combi PAL HTS PAL Loader Backup Update Following this format will make trouble shooting easier and allows to automate some of the update procedures 9 File Exte
33. ally set to the shortest allowable time 0 2 min b If the Sample List exceeds 1000 lines the ChemStation software will run the Sample List as two or more sequences Data file naming will continue with a 4 char prefix counter format i e samp1234 d Method Time Setting X Enable FIA Series in Method Time between Injections min FIA Table w Insert ow _ AppendRow Select MSD Parameters Set Increments Reset Table Line Location FIA Sample Name Inj Loc eee A multiple FIA Series sequence can also be created in the Sample List by adding additional First FIA Injection and Start lines This is functionally equivalent to the Run Multiple FIA methods feature in ChemStation Each FIA series also requires the FIA Done method and Done selection in the FIA column to end the FIA series PAL Sequence Manager C Program Files PAL Cycle Composer HTS PAL x Eile Help Sample List Method Editor Sample List Name MuliFia E Stop Pause Reset PAL View Log File Append Line Insert Line Delete Line Trays Status Method Volume Tra Vial Sample ID Type FileName CS Method S First FIA Injection 10 Tray01 Sample MuktF001 CTCFIA M an Single Step FIA Injection 10 Tray01 MultFOOZ CTCFIA M y Start and Done k Single Step FIA Injection 10 Tray01 MultFOO3 CTCFIA M indicators are required Single Step FIA Injection 10 Tray01 MultFOOS CTCFIA M A 3 FI
34. alue is automatically applied Moving the cursor to the parameter field displays a hint with the minimum maximum and default value PAL Cycle Composer C Programme PAL Cycle Composer HTS PAL File Help Sample List Method Editor Method Name Selected Macro Muti Step LC Injection 7 Clean Syringe Default All Method Description Clean Wash Station Washi x Injection cycle with 2 pre and post cleaning steps for the syringe and 2 post cleaning steps for the valve Number of cleaning cycles air volume filling gt Number of Clean Cycles Range 0 to 99 Default 1 Method Syringe fi OOul Method Macro Sequence 01 Wait Signal 03 Clean Syringe 04 Aspirate Sample 05 Inject 06 Clean Syringe 07 Clean Syringe 08 Clean Valve 09 Clean Valve Insert Beplace Delete Run Step Connected to Pal 26 PASO PAL Cycle Composer User Manual Clicking the right mouse button when the cursor is on a numeric field displays a list of possible special values The default value and special Syringe and Sample List related values Which values are shown depends on the unit of the actual field Values starting with SYR reference the methods syringe min and max volumes and default plunger speeds and values starting with SL reference the Sample List columns Volume Tray Vial Injector etc If a different Macro needs to be put in an existing sequence p
35. an empty sequence is only necessary for the ChemStation G1701B This 16 bit version is used with the MS 5973 with the HPIB communication The 32 bit software G1701C is used for the MS 5973 N For this version and higher the procedure to create the empty sequence file is not needed Create an Empty Chemstation Sequence File The installation program is not able to create an Empty Sequence file which is necessary for the PAL integration to run properly The first time the Chemstation is started after the installation of the driver from the top level menu select Sequence Load and open the default sequence template Default s Ln a DESIO Method Ins Method Sequence View Secured Control PAL Help Load Sequence 1 Re pu Look in sequence i e ei sal i aa Defaults Ga Nfi s Age 2 MES File name fra s Fies of ype Custom E 5 yo Cancel E Open as readony Delete any existing samples in the sequence table using the Cut button until it is empty as shown below Sample Log Table for Rikilt s on line 1 of O Line Type Vial DataFile Method Sample Name Type Vial Data File Method Sample Name Sample f 3 Miscellaneous Information Expected Barcode Sample Amt Multiplier 0 fi Area Repot Lib Search Rep Quant Repot PostQuant Macro Default Default x Default 7 Default 7 CR Database CR Spreadsheet Defaut si Defaut x att i Repeat Cut
36. and the naming of the Tray is case dependent Inst Meth Position Inj Vol P Stat isiti mere atus Acquisition Queue New Sequence Template x ai E Run Manager ESC Ready To Download Sequence Base File Name Starting Number fi Sample Name Working On Path C Xcalibu Data Browse Position ee Raw File Instrument Method C Xcalibur methods PAL Test Browse Inst Method E PAL Autosampler Processing Method Browse Trays x Tray Holder REWA Trays stk O1 E Add Vial type Unknown Add Vials from To Increment Stk1 01 DW96 Positions election Tal For Help Show Vial Numbers ShowWialTypes Select Viale Cancel Select All Deselect Al 74 PASO PAL Cycle Composer User Manual Using the graphical tool from the Cycle Composer will fill out the Sequence List automatically The Trayholder Tray and Vial Numbers are entered in the field of Positions in the Xcalicur specific nomenclature x4 Unbenannt Open Sequence Setup i Sree gt mju 2 C Xcalibur methods PAL Test E Run Manager EtxcaliburimethodsAPAL Test Stk1 01 2 10 00 C Xcalibur D ata Ready To Download C Xcalibur methods PAL Test Stk1 01 3 10 00 CXXcaliburYData Sequence C Xcaliburmethods PAL Test Stk1 01 4 10 00 C Xcalibur D ata Sample Name C Xcalibur methods PAL Test Stk1 01 5 10 00 C Xcalibur Data Working On C Xcaliburmet
37. arted at injection time If the injector has a valve referenced it is switched before injection and switched back after injection Pulse Output Signal Activate the selected Output Signal for specified Pulse Time The output pin on the interface connector and the active state of the signal are defined in the selected Output Signal object Set Output Signal Activate the selected Output Signal The output pin on the interface connector and the active state of the signal are defined in the selected Output Signal object Use the Macro Clear Output Signal to deactivate the signal Transfer Liquid and Mix Transfer liquid from source to target Mix with full plunger strokes 28 PASO PAL Cycle Composer User Manual Transport Vial Transport vial magnetically from Source Tray to Target Tray Wait Signal Wait for Sync Signal The input pin on the interface connector and the active state of the signal are defined in the selected Sync Signal object Wait Wait for selected time delay 7 2 Macros for HTS HTC LC PAL Clean Valve Rinse valve with solvent from selected wash station Default values for all other parameters are taken from the syringe or wash station object Switch Valve to Inject Switch selected valve to inject position after selected time since last injection Switch Valve to Load Switch selected valve to load position after selected time since last injection LC Inj Complete Cycle Duplication of PAL s loca
38. attached to the existing sequence and a new sequence file is created called TEMP s This temporarily file is a sequence file for one sample and will be erased and refreshed for every new injection The complete sequence will be stored in the sequence table which contains all information of all samples and has the same name as the Cycle Composer Sample List 48 PASO PAL Cycle Composer User Manual 3 2 Starting the Cycle Composer Software The PAL Driver installs in the Agilent ChemStation a new menu item called PAL 1 Instrument 1 offline 1 Method amp Run Control File RunControl Instrument Method Sequence PAL View Abort Help rele Gas G Methods Lg laf METANOMNW M Sequences LB lief erica s Fly JH E S S A Configure Peod and Run contri ee 4 E O 104 METANOMNW M 27 Sequence gt HGS C CHEM3211 SEQUENCE ER def_gc s a ERIC S ChemStation Status _ ER ERIC2 5 Si ERIC3 S ER LOADTEST S ET TEMP S eprocess Data Mode Sequence templates Methods Last Data File 1 2 Ex Data Analysis Report Layout Ready This command will start the CTC PAL Cycle Composer PA Activating the menu PAL Cycle Composer opens the Cycle Composer Sample List with all necessary columns for the ChemStation 3 3 Creating a Sequence The Agilent ChemStation specific fields are imported to the existing fields in the
39. ction 500 Tray1 GC Injl Running sample list line 1 13 Headspace Injection 500 Trayl GC Init Method Headspace Injection 2 Hentspace incon me Te ES z Trav Trav vial 1 Resetting PAL Resetting PAL F1 Help F3 Recall F5 StartRun F6 StartSeqRun F8 Stop F11 NextWindow 51 PASO PAL Cycle Composer User Manual 3 4 Customizing a ChemStation Report Template The Report generator of ChemStation allows the user to customize the report template accordingly to his needs All ChemStation fields from the sequence are available as usual The new fields from the Cycle Composer Sample List can be added to the report template by using the Sample Info GC LC LC MS or the Miscellaneous Info GC MSD Instrument 2 online Report Layout IES File Edit View Abort Help I Report Layout 8 BENZ 001 D i EMPASTMO CTCFRP O Er ES E Su ESA Su ESA we AO E CTC ANALYTICS AG Switzerland Data File name Raw Data File Name Method name Method Report CTC New Element Instrument 2 select text h Header constant Text Acq Operator Calculation Based On Area Height mo o acto Dot eN Calculation Sample Purpose Sample Name Raw Data File Name Instrument Name Barcode Injection Date Injection Time Injection Text Method Method Info In this field Sample Info or Miscellaneous Info all Cycle Composer s
40. d would be ready for the next processing step indicating Preparing as status 21 PASO PAL Cycle Composer User Manual 5 5 Restarting a Sample List An existing Sample List can be executed again this will start the list from line 1 If the user wishes to start the Sample List from a selected line highlight the line and press Start All the lines below including the selected line will be processed If a single sample line only shall be executed process as described above and in conjunction with the random access line press the Pause button This operation allows the user to start at a selected sample line without editing the existing Sample List PAL Cycle Composer C Programme PAL Cycle Composer HTS PAL File Help Sample List Method Editor Sample List Name Coffein_01 Start Pause Reset PAL View Loq File Append Line Insert Line Delete Line Trays Status Method Yolum Tray Vial Inj Via Sample Sample Single Step LC Injection 10 Tray01 16 2 Unknown Sei Single Step LC Injection 10 Tray01 1 3 Standard EH Single Step LC Injection 10 Tray01 2 3 Standard EE Single Step LC Injection 10 Tray01 3 2 Blank 4 Single Step LC Injection 10 Tray01 4 2 Blank EF Single Step LC Injection 10 Tray01 5 3 Standard ERA Single Step LC Injection 10 Tray01 6 3 Standard Single Step LC Injection 10 Tray01 7 2 Unknown EA Single Step LC Injection 10 Tray01 8 2 Unkno
41. ed COM port an error message is shown Close that program or select a different port 16 PASO PAL Cycle Composer User Manual 4 2 Reload PAL Configuration If any changes are made to the PAL configuration while Cycle Composer is running these changes are not transferred to the PC and the program is unaware of them It is necessary either to close and restart Cycle Composer or select this option from the menu 4 3 Choose Method Folder After installation the program will store Macros and Methods to the default path beneath the Cycle Composer folder Depending on which PAL configuration has been selected this will be the folder HTS PAL or Combi PAL It is possible to select a different path to save and load Methods and Macros using menu File Options Choose method folder Method Folder Ed Please choose folder for macros methods and sample lists C Programme PAL Cycle Composer HTS PAL Browse Cancel The most recent locations are saved and can be selected in the selection list Click the Browse button to search for a different folder not available in the selection list Changing to a different folder also reloads the PAL configuration This is especially useful when working offline with different configurations 4 4 Status Box Activating this option displays a status window which informs about the sample number of which tray is processed the Method being used and which processing step is
42. ed in ChemStation then select Start from the Sample List screen You must save the Sample List before a sequence can be started The name is limited to 8 characters for some ChemStation versions This name will be used to build a ChemStation Sequence Table as the Sample List is run a BEE File RunControl Instrument Method Sequence PAL View Abort Help Method and Run Control EH HS_1 M E temp s E Run Method eee see HEHE DO OE on En sm5 Back iz T PAL Sequence Manager C Programme PAL Cycle Composer Combi PAL File Help Ready Sample List Method Editor Name Sample List Name re 4 Nov 83 Last Data File Last Run Name std 1 6 6 alment Pause Reset PAL View Log file Append line Insert Line Delete line Trays 2 minutes Status Method Volume Tra Injector Tray 2 a 1 Headspace Injection 500 Tray1 GC Injl 2 Headspace Injection 500 Tray1 GC Injl Front Inlet Temperature 250 En Headspace Injection 500 Tray1 GC Inj Oven Temperature 120 4 Headspace Injection 500 Trap GC Inj Front Det Temperature 270 5 Headspace Injection 500 Tray GC Inj Front Inlet Total Flow 44 6 Headspace Injection 500 Tray1 GC Inj al Headspace Injection 500 Tray1 GC Injl v gs Headspace Injection 500 Tray1 GC Inj 9 Headspace Injection 500 Trayl GC Inj 10 Headspace Injection 500 Tray GC Injl 11 Headspace Injection 500 Tray1 GC Injl ra Headspace Inje
43. evision 1 1 Original Driver for Xcalibur Software Software Revision 1 2 Adaptation to Xcalibur Revision 1 1 Software Revision 1 3 Adaptation to Xcalibur Revision 1 2 Barcode Reader is supported Syringes with volume larger than 1000 ul are supported Open Access is supported Software Revision 1 3 1 Problems with the installation routine registry are solved 64 PASO PAL Cycle Composer User Manual Table of Contents 1 Requirements 67 1 1 Software Requirements 67 1 2 Workstation Requirements 67 1 3 Requirements for the PAL System 67 1 4 Synchronization Requirements for the PAL System 67 and the ThermoQuest Instrument 2 Installation Procedure 68 3 Using the Xcalibur Software 69 in Combination with Cycle Composer Software 3 1 Instrument Configuration 69 3 2 Instrument Setup 71 3 3 Sequence Setup 73 3 4 Starting a Sequence 76 65 PARSO PAL Cycle Composer User Manual 66 PASO PAL Cycle Composer User Manual PAL Driver for Xcalibur Data System 1 Requirements 1 1 Software Requirements Xcalibur Software Revision Level 1 2 Xcalibur Patch 9537 Cycle Composer 1 5 The Xcalibur Patch 9537 is a correction to the ThermoFinnigan Xcalibur Software and has to be requested at ThermoFinnigan The Patch is needed to support the Barcode Reader and the scaling in the window Real Plot is corrected also 1 2 Workstation Requirements The Hardware requirements are given by the ThermoFinnigan Xcalibur
44. executed PAL Status Ed Running sample list line 1 Method Simple LC Injection Tray Stk1 01 Vial 1 Cleaning Syringe at Wash2 cycle 0 of 1 17 PASO PAL Cycle Composer User Manual 4 5 Format Sample List This option allows the operator to select which Sample List columns are visible for editing in the Sample List table as well as which defaults are used for all fields After installation the fields for Method Volume Tray Vial Sample Type and Sample ID are marked as visible Define columns of sample list PAL 1 Default values for columns in the sample list Status Method Multi Step GC Injection M Visible efault Volume 1 O IV Visible efault Tray iv Visible efault Injector Visible efault Volume 2 Visible efault w Tray 2 Visible efault Injector 2 Visible efault Vial Iv Visible efault Inj Vial Visible v Sample Type Unknown vr iv Visible efault w Sample ID iv Visible Default Excel Columns D E D x D 7 D 7 D 7 D E D EZ D EZ Q o a x Excel Start Import with Line Apply OK Cancel In the Excel Columns fields the correspondence between Cycle Composer sample list column and the column of an imported Excel file can be selected If the Excel sheet contains some header lines above the sample list the first sample line can be selected in Start Import with Line 18 PASO PAL Cycle Composer User Manual 5 Sample List Editor 5 1 What does it
45. hods PAL Test Stk1 01 6 10 00 C Xcalibur Data Position C Xcalibur methods PAL Test Stk1 01 7 10 00 C Xcalibur Data Raw File C Xcalibur methods PAL Test Stk1 01 3 10 00 C XcaliburkData Inst Method C Xcalibur methods PAL Test Stk1 01 9 10 00 C Xcalibur Data E PAL Autosampler C Xcaliburmethods PAL Test Stk1 01 10 10 00 CAXcalburData Ready to Download C Xcaliburkmethods PAL Test Stk1 01 11 10 00 C Xcalibur Data C Xcaliburmethods PAL Test Stk1 01 12 10 00 C Xcalibur D ata C calibur methods PAL Test Stk1 01 13 10 00 C Xcalibur D ata C Xcaliburmethods PAL Test Stk1 01 14 10 00 C Xcalibur D ata C Xcaliburkmethods PAL Test Stk1 01 15 10 00 C Xcalibur methods PAL Test Stk1 01 16 10 00 C xcalibur Data C Xcalibur methods PAL Test Stk1 01 17 10 00 C Xcalibur D ata C Xcaliburmethods PAL Test Stk1 01 18 10 00 C Xcalibur D ata C Xcalibur methods PAL Test Stk1 01 19 10 00 C Xcalibur D ata C Xcaliburkmethods PAL Test Stk1 01 20 10 00 C Xcalibur Data C Xcaliburmethods PAL Test Stk1 01 21 10 00 CAXcalburD ata C calibur methods PAL Test Stk1 01 22 10 00 C Xcaliburk D ata C Xcaliburkmethads PAL Test __ Stk1 01 23 C xcaliburiData StK1 C Xcaliburmethods PAL Test Stk1 01 24 00 C calibur Data C Xcalibur methods PAL Test Stk1 01 25 10 00 C Xcalibur D ata C lt calibur methods PAL Test Stk1 01 26 10 00 C Xcalibur D ata CM AOA 7A It
46. ials from To Increment 50 1 sessi 50 4 e Show Vial Numbers ShowWialTypes Add Insert Close Select All Deselect Al Select individual or groups of samples on the tray by clicking on their positions or clicking and dragging across multiple positions Make selections in the other fields for the Method to be run Injector and the volume etc Finally click on the Add button to add the samples to the end of the Sample List or the Insert button to add lines above the selected line 20 PASO PAL Cycle Composer User Manual If the tray type of the desired tray is not the correct one right click on the tray symbol on the left side and select the correct one out of the list of all available tray types which fit to this tray Trays Tray Holder Stack X Trays Stk1 02 v Add Sample type Unk nown e Add Vials from To Increment MT96 MT384 DW 96 1 gt e Show Vial Numbers ShowWialTypes Add Insert Close Select All Deselect All 5 4 Running a Sample List A Sample List is ready to run after one or more lines are entered To start the run click the Start button The PAL will process each line in the list until all are completed Pause will temporally halt the PAL without aborting the run The Status field will display Running after completion of the sample handling or injection step the Cycle Composer will continue to the next line an
47. ich contains an activity log for all Cycle Composer sessions This file may be printed out for documentation purposes The content of the file is the full history To print out a specific section only one can highlight the lines of interest and print those selectively Log File x Contents of Log File 1 Record 703449 Bad data Barcode 4 Method Test Read Barcode completed elapsed time 0 21 Record 703524 Bad data Barcode Method Test Read Barcode completed elapsed time 0 21 3 Closed program Started program main activate Tray type of Tray2 set to VT 78 13 36 Tray type of Tray2 set to T32 20 21 35 Method Test Read Barcode completed elapsed time 0 27 11 48 19 Closed program 1999 11 15 12 04 14 Started program 1999 11 15 12 06 10 main activate 1999 11 15 12 06 26 Closed program 1999 11 15 12 16 25 Started program 1999 11 15 12 18 12 main activate 23 PAL Cycle Composer User Manual PASSO 6 Method Editor 6 1 Single Step Methods Single Step Methods use a single Macro which has the complete cycle built into it All values which control the cycle are shown on a single page A typical Single Step Method is provided with the Cycle Composer program It mimics the on board PAL Method for the selected instrument type A number of sampling parameters can be changed to optimize the Method to suit the conditions of the run When modified in this way it can be stored with a unique name PA
48. ide the sample info field For the GC MSD version the size of this field is only 40 characters 20 This setting will enable the user to override the data path as set by the ChemStation for storing the data files In the latest releases of the chemstation a nasty bug is present When a run is aborted the datapath last selected becomes the base datapath for the next to follow runs resulting in data being stored in the wrong location In order to prevent this from happening a feature has been created for which the interface will set the default datapath each time a run is started from the Cycle Composer to the datapath as set in the configuration dialog in item 21 21 This parameter contains the datapath to be used when parameter 20 is enabled If the path is non existent the interface will try to create the full path as set here This will only function if the user has enough privileges for the selected path 22 Use this button to store the modified configuration 23 Use this button to return to the original configuration before making any modifications 24 Use this button to show an explorer style dialog to select a datapath for item 21 60 PASO PAL Cycle Composer User Manual 4 Limitations The following limitations are known at the level as described in this Installation Guide 1 Some versions of the ChemStation do not allow a file name longer than 8 Characters This is valid for the run files as well as for the Sample List 2
49. ilent ChemStation and the Cycle Composer it is necessary that the Agilent ChemStation and the Cycle Composer are installed on the workstation It is advisable to test each software individually If both programs are working satisfactory the PAL Driver for Agilent ChemStation can be installed The types of ChemStation environments are ChemStation for GC HPLC ChemStation for LC MSD ChemStation for GC MSD Note CTC Analytics advises to check always the read me file on the Cycle Composer CD for any latest changes or information 38 PASO PAL Cycle Composer User Manual 2 2 Installation for GC HPLC and LC MSD Select the folder Driver ChemStation 2 1 3 and double click the file setup exe program This program will install PAL Chemstation E Welcome to PAL Chemstation Driver Setup Driver on your computer It is strongly recommended that you exit all Windows programs before running this Setup Program Click Cancel to quit Setup and close any programs you have running Click Next to continue with the Setup program Te a WARNING This program is protected by copyright law and international treaties Unauthorized reproduction or distribution of this program or any portion of it may result in severe civil and criminal penalties and will be prosecuted to the maximum extent possible under law BILIA Continue to Choose Destination Location select the ChemStation Folder Choose Des
50. itial installation E Cycle Composer Version 1 54 Select Components Select the components you want to install clear the components you do not want to install Components Program Files I HTS HTC amp LC PAL Methods and Macros Combi PAL Methods and Macros GC PAL Methods and Macros Description Cycle Composer Application Files Space Required 13344 K Space Available 1778648 K lt Back Next gt Cancel After entering the location for the Program Icon folder the installation will progress automatically Setup will place a program icon on your desktop EJ Click the Finish button to complete the installation process Cycle Composer If manual installation has been selected at the first program start a dialog box will prompt the user to select the path where the Cycle Composer files are stored Method Folder PAL 1 13 PASSO PAL Cycle Composer User Manual Windows Vista To use Cycle Composer with Windows Vista proceed as follows e Log in as administrator e Navigate to the Cycle Composer folder usually C Program Files PAL Cycle Composer e Right click the file cyc comp exe e From the drop down menu select Properties e Select the tab Compatibility e Check the option Run this program as an administrator e Close the properties window PA cyc comp Properties Ex General Compatibility Security Details Previous Versions If you have problems
51. itor 6 1 Single Step Methods 6 2 Multi Step Methods 6 3 Composing a new Method 6 4 Method Description 6 5 Testing with Run and Step 6 6 Saving Changes 7 Macros for Cycle Composer Software 7 1 Standard Macros 7 2 Macros for HTS HTC LC PAL 7 3 Macros for GC PAL 7 3 Macros for Combi PAL 8 PAL Folder Structure 9 File Extensions PAL Cycle Composer User Manual 11 11 11 11 PARSO PAL Cycle Composer User Manual PASO PAL Cycle Composer User Manual 1 Introduction to PAL Cycle Composer 1 1 What does it do Cycle Composer is a 32 Bit Windows based software Cycle Composer allows customization of sampling cycles for the CTC PAL System It enables the user to go beyond the capabilities of the local stored LC GC Headspace and SPME cycles Virtually any conceivable sequence of operations can be generated and saved as Cycle Composer CC Methods The program consists of a Method Editor in which the processing of a sample is defined and a Sample List Editor in which a sample sequence is created in a tabular format where assignments to the Methods to be run and location of the samples are made The program accesses the PAL directly via the serial port obtaining information from the PAL about which objects are available and presenting these objects as choices in the Editors When a Sample List is run the program takes direct control of the PAL executing the sequence of steps defined in each Method assigned to the current samp
52. l LC injection cycle Tray Name Sample Number and Sample Volume are taken from the sample list This Macro contains the complete sampling cycle all parameters are on a single page 7 3 Macros for GC PAL GC Inj Complete Cycle Duplication of PAL s local GC liquid injection cycle Tray Name Sample Number and Sample Volume are taken from the sample list This Macro contains the complete sampling cycle all parameters are on a single page 29 PASO PAL Cycle Composer User Manual 7 4 Macros for Combi PAL Start Agitator Starts the Agitator with selectable speed run and pause times Wait Agitator Stops the Agitator after a selectable run time Set Temperature Sets the temperature of a heated object to a selectable value The macro returns before the temperature is reached Wait Temperature Wait until a specified temperature of a heated object is reached GC Inj Complete Cycle Duplication of PAL s local GC liquid injection cycle Tray Name Sample Number and Sample Volume are taken from the sample list This Macro contains the complete sampling cycle all parameters are on a single page Headspace Complete Cycle Set temperatures of Agitator and syringe to the desired values After temperatures have stabilized the vial is transported into the Agitator activates the Agitator and waits for a selectable incubation time Then the sample is taken out of the headspace and injected The vial is moved back into the sample
53. lace the cursor at the location in the sequence where the replacement is to be made then select the new Macro set the parameters as desired and click the Replace button 6 4 Method Description It is important to stress the benefit of a good description for each Method The description entered in the Method Description box will provide information to the user in the Sample List screen These are displayed whenever the user rests the cursor over each Method in the Sample List Likewise each Macro contains a description which will be displayed when the user rests the cursor on the selected Macro in the Method Editor screen 6 5 Testing with RUN and STEP When a Method has been created it can be tested before implementing it into a Sample List by selecting the Run or Step button The operator is prompted to enter values which are normally passed by the Sample List These are used to run this test If Step mode is selected each Atom sent to the PAL is displayed before it is executed A Macro may be built of several PAL Atoms The Macros SL Entry Method Entry Method Exit and SL Exit are macros which are automatically appended in front and at the end of the method macro sequence They are used for initialization before the sequence and method and cleanup after the method and sequence 6 6 Saving Changes Whenever a Method has been changed this change is not saved immediately to the disk This is d
54. le 1 2 System Requirements Cycle Composer Software Revision 1 5 4 requires PAL Firmware 2 2 0 or higher 2 Installation and Setup Note Administrator access privileges are required to install PAL Cycle Controller It is necessary to exit all programs before installing the CC software The program is compatible with Windows 98SE Windows 2000 Windows XP and Windows Vista To install the software place the CD ROM in the CD drive browse to the folder Cycle Composer 1 5 4 Double click the file CycleComposer1 5 4Inst exe to run the installation program Note CTC Analytics advises to check always the Readme txt file on the CD ROM for any latest information After consenting to the Licensing agreement the user name the organization name and the serial number have to be entered The serial number is printed on the backside of the CD ROM packaging The software serial number is case dependent Be sure to use ALL CAPS Installing an Upgrade Version requires that one of the previous version is installed on the hard disk During the installation process the software will check for an existing CC version If the software can not detect a CC version the installation process will be stopped automatically 11 PASSO PAL Cycle Composer User Manual The operator is asked which options shall be installed Cycle Composer Version 1 54 Setup Type Click the type of Setup you prefer then click Next Cycle Compo
55. lete Line Trays Import Options e TT sms 1 figle Step LC Injection 2 Single Step LC Injection 10 TrayO1 3 Single Step LC Injection O TrayO 4 Single Step LC Injection 10 TrayO1 5 Single Step LC Injection 10 TrayO1 6 Single Step LC Injection O TrayO 7 Single Step LC Injection 10 TrayO1 8 Single Step LC Injection 10 TrayO1 g Single Step LC Injection O TrayO 10 Single Step LC Injection 10 TrayO1 11 Single Step LC Injection 10 TrayO1 12 Single Step LC Injection O TrayO 13 Single Step LC Injection 10 TrayO1 14 Single Step LC Injection 10 TrayO1 15 Single Step LC Injection 0 Pal Reset To begin building the Cycle Composer Sample List select New Sample List from the File menu You will be prompted to name the new Sample List The Sample List name is limited to 8 characters for some ChemStation versions To specify the samples that will be run select the Trays button This will bring up a list of the Tray Holders which are configured for the HTS PAL system The tray s for the selected Tray Holder will be displayed on the screen indicating the tray orientation and well or vial numbers The sample tray can consist of test tubes vials or a variety of well plates 54 PASO PAL Cycle Composer User Manual To select the samples for the Sample List click and drag the mouse over the range of wells or vials to be run The selected samples will be shown in red Trays x Tray Holder
56. m will use latest_pal pol to recognize the PAL Configuration Sample List Status differentiates in between Running and Preparing Limitation of maximum 1000 sample line entries eliminated Practically unlimited number of sample lines are accepted Agitator Off Non numerical value is accepted Random access to start existing Sample List Highlight any line in Sample List to start the sequence again at a selected point PAL Terminal will be locked at the execution of a Cycle Composer method Unlock with Reset PAL Improved handshake with Agilent Chemstation Driver Start Stop Abort situations are reliably executed New SPME cycle added SPME Agitated amp Heated Special Penetration Complete Cycle with more flexibility for vial and injector penetrations Configuration dialog added and enhanced PASO Table of Contents 1 Introduction to PAL Cycle Composer 1 1 What does it do 1 2 System requirements 2 Installation and Setup 3 Connection to PAL 3 1 Running On line 3 2 Running Off Line 4 Initial Setup 4 1 Port 4 2 Reload PAL Configuration 4 3 Choose Method Folder 4 4 Status Box 4 5 Format Sample List 5 Sample List Editor 5 1 What does it do 5 2 The Sample List Table 5 3 Creating a Sample List in the Trays Screen 5 4 Running a Sample List 5 5 Restarting a Sample List 5 6 Importing a Sample List from an Excel File 5 7 Other Function Buttons 6 Method Ed
57. manufacturer PAL Cycle Composer User Manual The principle of Data Acquisition does not change using the PAL Driver for the Xcalibur Data System The full comfort of the Xcalibur Software is maintained As an example the Acquisition Queue is displayed ba Unbenannt Open Sequence Setup File Edit Change Actions View GoTo Help REI ES Es E AO Ha Status Acquisition Queue v All Sequences E Temporary sequence Sequence Row 1 Sequence Row 2 Sequence Row 3 Sequence Row 4 Sequence Row 5 Sequence Row 6 Sequence Row 7 Sequence Row 8 Sequence Row 9 Sequence Row 10 Sequence Row 11 Sequence Row 12 Sequence Row 13 Sequence Row 14 Sequence Row 15 Sequence Row 16 Sequence Row 17 Sequence Row 18 Sequence Row 19 Sequence Row 20 Sequence Row 21 Sequence Row 22 Sequence Row 23 Sequence Row 24 Sequence Row H25 Inst Meth Inj Vol D O S ee MENE Bl S z juju 2 Position Sampl For Help press F1 C Xcalibur methods PAL Test C calibur methods PAL Test C caliburmethods PAL Test C calibur methods PAL Test C Xcaliburmethods PAL Test C Xcaliburmethods PAL Test C calibur methods PAL Test C Xcaliburmethods PAL Test C Xcalibur methods PAL Test C calibur methods
58. mposer User Manual 2 4 Files used for Driver Agilent ChemStation Cycle Composer File ChemStation Type Description SETUP exe For all types Installation Program to setup the communication between ChemStation and Cycle Composer STATUS exe GC HPLC LC MS Program to monitor the status of the ChemStation by DDE PALSEQ mac GC HPLC LC MS Communication Macro CTC mcx GC HPLC LC MS Communication functions for the driver CTC ini GC HPLC LC MS INI File created during installation EMPTY ctc GC MSD Empty Sequence File TOPMENU mac GC MSD Modified version of standard file Topmenu mac which is replaced and renamed in Topmenu ctc during installation TOPMENU ctc GC MSD Renamed standard file Topmenu mac CTC_MENU mac GC MSD Macro to change the top menu CTC_INFO mac GC MSD Communication Macro CTC_PRE mac GC HPLC LC MS In this macro any other pre run macro can be included Listed as the first line in Sequence the Note 1 macro will be executed CTC_POST mac Note 1 GC HPLC LC MS In this macro any other post run macro can be included Listed as last line in Sequence the macro will be executed Note 1 Do not use the original ChemStation macro possibilities if one macro shall be executed as a pre post run macro Including the pre post run macro in the ChemStation directly would result in executing the specified macro after every injection The pre post run macro shall
59. n enabled a file called CTC_INFO LOG is created in the msexe or core directory right beneath the chemstation directory Enabled or disables the creation of a file called STATUS ACT This file contains the steps in time taken by the interface The numbers in this file refer directly to the secondary tab steps when in debug mode When an older version of the Cycle Composer is installed older then 1 5 2 the messaging mechanism of windows is not supported yet So commands between the two modules Status exe and Cycle Composer are exchanged by means of files In some rare occasions this might lead to file sharing violations and should only be used when the Cycle Composer 1 5 2 or newer is not at hand Message based command exchange is enabled with this setting see explanation for item 3 When Item 4 is enabled this setting is used to control the time out between the two modules in case of problems When Item 4 is enabled this parameter sets the number of retries used between the two modules to exchange messages This setting will enable the use of long filenames The maximum length is then depending on the maximum length allowed inside the chemstation version Warning Older versions of ChemStation might not support this setting This setting is used to split up sequence files when they become too long more then 1000 entries for most chemstation versions The interface will then split up the sequence files created in the Cycle Composer in se
60. nn E E Install De Install If an LC MSD is configured only nstrument 1 should be active Note that 1100 series LC modules are detected as InstType 1050 Enter the correct path for the Cycle Composer software and select the corresponding instrument Reboot the computer after the installation of the Agilent ChemStation Driver If an 1100 Series autosampler is configured on the LC system the Use Manual Injection option in the Method amp Run View section of the ChemStation has to be selected when Cycle Composer is launched from the PAL menu 40 PASO PAL Cycle Composer User Manual 2 3 Installation for a GC MSD This ChemStation version requires a somewhat different installation since this software does not recognize the AddOn interfacing strategy The installation program will automatically recognize the installed GC MSD version 1701B or C The corresponding dll files will be executed accordingly The installation program will modify the standard TOPMENU MAC This macro is located in the MSEXE directory right below the main ChemStation sub directory During installation the original TOPMENU MAC macro is copied by the installation program The location of this file is also in the MSEXE directory The name of the copy is TOPMENU CTC Furthermore the installation will copy two macro files into the MSEXE directory of the main ChemStation sub directory The names of these file
61. nsions Following file extensions are used by the Cycle Composer software Methods pme PAL Method Macros pma PAL Macro Sample List psl PAL Sample List PAL Configuration pol PAL Object List latest_pal pol Latest Pal Configuration uploaded Objects from PAL 32 PARSO PAL Cycle Composer User Manual PAL Driver for Agilent ChemStation Data System Installation Guide Software Revision 2 1 3 PASO Printing History Edition 1 November 1999 Edition 2 May 2001 Edition 3 June 2001 Edition 4 July 2001 Edition 5 February 2007 PAL Cycle Composer User Manual Software Revision 1 0 1 Software Revision 2 0 3 Software Revision 2 0 4 Software Revision 2 0 4 Software Revision 2 1 3 Release History Software Revision 1 0 1 Software Revision 2 0 3 Software Revision 2 0 4 Software Revision 2 1 3 Original Driver for ChemStation Software Various improvements and adaptations for new ChemStation Versions Installation Routine checks automatically for 16 32 Bit ChemStation Versions Improved handshake to pause stop a PAL Cycle Composer sample list in combination with ChemStation Injection Volume and Vial readable by ChemStation Sequence Print out via Miscellaneous Info or Sample Info fields Filenaming improved and equal for all 3 ChemStation versions New created ChemStation method available in drop down menu selection of sample list field CE Method LC MS ChemStation
62. one explicitly with the menu File Save or File Save as If the user switches to the Sample List but did not yet save the Method a dialog box asks if the changed Method should be saved 27 PASO PAL Cycle Composer User Manual 7 Macros for Cycle Composer Software 7 1 Standard Macros Add to Sample and Mix Aspirate liquid from Liquid Reservoir Dispense into sample vial specified in Sample List Mix by selected number of full plunger strokes Aspirate Fill syringe from a vial with Tray Name Sample Volume Air Volume Fill Speed and Fill Strokes specified as parameters Aspirate Sample Fill syringe from a vial with Tray Name Vial Number and Sample Volume specified in the Sample List and Air Volume Fill Speed and Fill Strokes specified as parameters Clean Syringe Clean syringe using selected wash station and number of clean cycles Default values for all other parameters are taken from the syringe or wash Clear Output Signal Deactivate the selected Output Signal The output pin on the interface connector and the active state of the signal are defined in the selected Output Signal object Dispense Dispense syringe content to a selected position using speed Parameters Home The PAL moves the injection head back to home position Inject Inject syringe content to a selected injector with speed pre and post inject delays and output signal as parameters Sync signal Inject is waited before injection and timer 1 is st
63. pecific parameters are listed e g Method Volume Tray Sample ID If the Injection volume is the only parameter to be reported the function of Computed Text can be used as described below 52 PASSO PAL Cycle Composer User Manual The Injection Volume is one field of the Sample List and is written directly into the ChemStation Sequence Since this field is not generated by an Agilent autosampler it is necessary to retrieve the value by a Computed Text This allows to print the Injection Volume on the report l Instrument 1 online Report Layout oy x File Edit View Abort Help Report Layout TECEM esa CTC HPOIFRP 8 Percent IS SE area None EH a o pj 78x60 a Header CTC ANALYTICS AG Switzerland Data Data File name name Raw Data File Name x nome Method name Method New Element Instrument 1 Report Report CTC select text Report Creation Date p Header Report Creation Time Penca __ Reporting of uncalibrated Compounds Ref Comp used for Quantification of Unkn r vial rial inject Sample Info Column Dead Volume Unit Software Revision Integrator Version X _ EW bus Define the Macro Name as InjVol Macro File path as c lhpchemicorelpalseg mac The Empty String Substitution field has no direct effect on the reporting Instrument 2 online Report Layout Je XI File Edit View Abort
64. re 1 2 2 Xcalibur Patch 9537 3 Cycle Composer 1 5 4 4 PAL Driver for Xcalibur 1 5 6 To setup the communication between Xcalibur and the Cycle Composer it is necessary that both programs are installed on the workstation It is advisable to test both software individually If both programs are working satisfactory the installation of the PAL Driver for Xcalibur can be made Insert the Cycle Composer CD and navigate to the folder Driver Xcalibur 1 5 6 Double click the program PALVI 1 5 6 Installation exe to start installation Follow the dialog and enter the correct path for Xcalibur and for Cycle Composer Restart the computer after the successful installation Note CTC Analytics advises to check always the read me file on the Cycle Composer CD for any latest changes or information 68 PASO PAL Cycle Composer User Manual 3 Using the Xcalibur Software in Combination with Cycle Composer Software In this guideline only the two sections Instrument Setup and Sequence Setup are covered These sections are directly related to the PAL System How to use the other Xcalibur sections is outlined in the corresponding manual from ThermoFinnigan 3 1 Instrument Configuration Start the program from the desktop Icon nstrument Configuration Select the Icon PAL Autosampler from the Available Devices and drag and drop it into the page Configured Devices Instrument Configuration x
65. s are CTC INFO MAC and CTC MENU MAC During the installation process an Empty ChemStation Sequence File has to be created This is only required for the ChemStation G1701B Details are given below see chapter 2 3 2 On the Cycle Composer CD select the folder Driver ChemStation 2 1 3 and run setup exe This will launch the installation utility which loads the software Follow the instructions of the setup utility and check the correct path as shown for ChemStation and Cycle Composer in the figure below Select the Instrument to be integrated only one supported Select the Install button Ei PAL chemstation interface configuration program 2 1 3 iol x Sl This configuration program enables the cycle composer software to interface with the Agilent Chemstation environment Select below the chemstation instrument the PAL system is attached to then click the install button to complete the installation Instruments with the label INSTALLED already have the PAL system installed Installation information Install From C Program Files PAL Cycle Composer Chemstation Chemstation path C msdchem Cycle Composer Path C PROGRA 1 PAL CYCLEC 1 cyc_comp exe Find Browse Instrument Name InstType J Instrument 1 Instrument 1 Mustang Po installed TT Instrument 2 Instrument H2 Mustang 2 stated Instrumenta Instrumento E Install Demsa 41 PASSO PAL Cycle Composer User Man
66. ser for Combi PAL Cycle Composer for GC PAL Cycle Composer for HTS HTC and LC PAL Cycle Composer Program Only Select Installation Components Manually Description Installs Cycle Composer with standard Methods and Macros for a Combi PAL lt Back Cancel Cycle Composer for GC PAL Installs Cycle Composer with Standard Methods and Macros for a GC PAL and creates a shortcut of the program in the Start menu Cycle Composer for Combi PAL Installs Cycle Composer with Standard Methods and Macros for a Combi PAL and creates a shortcut of the program in the Start menu Cycle Composer for HTS HTC and LC PAL Installs Cycle Composer with Standard Methods and Macros for a HTS HTC or LC PAL and creates a shortcut of the program in the Start menu Cycle Composer Program Only Cycle Composer Program Files only After installation use File Import to load custom Methods and Macros This option can be used in an upgrade situation If the user has made specific changes to existing Standard Macros and saved those with the same name these would be overwritten by the standard installation process selecting the options GC PAL or Combi PAL or HTS HTC LC PAL Using this installation option will install the Cycle Composer program files only 12 PASO PAL Cycle Composer User Manual Select Installation Components Manually Customized installation Can be used if you want to add Methods and Macros for a second type of PAL after in
67. st for FIA is very similar to setting up a non FIA sample list Select menu PAL Cycle Composer to bring up the Cycle Composer Sample List Select New Sample List from the File menu Select the Trays button to specify the samples that will be run Specify the tray holder and tray to be used then click and drag the mouse over the range of wells or vials to be run The selected samples will be shown in red To create an FIA sequence with these samples select the PAL method Single Step FIA Injection from the Trays method pulldown Also specify the injection volume Volume FileName 5 char prefix counter ChemStation method CS Method and sample name SampleNam Select the Add Vials button to add the selected samples to the Sample List Close the sample selection window to return to the Sample List Change the Method of the first line of the FIA series to First FIA Injection and select Start in the FIA column This is generally the last column in the Sample List Note If the FIA column is not visible in the Sample List use the menu File Options Format Sample List Activate the FIA field Change the Method of the last line of the FIA series to FIA Done and select Done in the FIA column At this point the Sample List should look something like the figure bellow PAL Sequence Manager C Program Files PAL Cycle Composer HTS PAL File Help Sample List Method Editor Macro Editor
68. tall the Cycle Composer Driver from the ChemStation use the following procedure e Insert the Cycle Composer CD and run the program setup exe in the folder Driver ChemsStation 2 1 3 e For GC LC configurations remove PALSEQ MAC e For GC MSD configuration remove EMPTY CTC rename TOPMENU CTC back to TOPMENU MAC 3 Starting Cycle Composer Software in Synchronization with Agilent ChemStation 3 1 Principle of Synchronization Opening the ChemStation software a new menu item PAL is added at the top menu of the ChemStation This menu item will run a macro which will start the Cycle Composer software Instrument 1 offline 1 Method amp Run Control File BunControl Instrument Method Sequence CC Mode View Abort Help Method and Run Control ii MEILS Run Method The Cycle Composer will take control of processing samples The sequence to run is created by the Cycle Composer including all specific parameters After creating a complete sequence in the Cycle Composer software and starting the sequence using the Start button the software will check the status of the ChemStation and all information of the current running sample is saved in the INI file If the ChemStation gets into Ready State the Cycle Composer will start the processing of the sample list which contains the ChemStation Method The macro running the ChemStation will collect the information of the current sample The information is
69. the Chemstation Interface 58 4 Limitations 61 35 PARSO PAL Cycle Composer User Manual 36 PASO PAL Driver for Agilent ChemStation Data System 1 Requirements 1 1 Software Requirements PAL Cycle Composer User Manual Agent Version s Instruments Shemetaton Tested Number Type G2070AA A 06 03 and higher GC 5890 6890 Leochem Yes G2170AA A 06 03 and higher 1100 etc Leochem Yes G2710AA A 08 04 LC MS Leochem Yes G2070AA B 02 01 and higher GC 5890 6890 Leochem Yes G2170AA B 02 01 and higher 1100 etc Leochem Yes G2710AA B 02 01 and higher LC MS Leochem Yes G1701BA B 01 00 GC MSD Mustang No G1701BA B 02 00 GC MSD Mustang No G1701CA B 01 00 GC MSD Mustang Yes G1701CA C 01 00 GC MSD Mustang Yes G1701CA D 00 01 GC MSD Mustang Yes G1701CA D 01 02 GC MSD Mustang Yes G1070CA D 03 00 GC MSD Mustang Yes Cerity No 1 5 4 or higher 2 2 7 or higher Cycle Composer Software PAL Firmware Optional G2731AA ABI MDS Sciex Analyst Software for LC MSD data analysis Revison 1 1 1 or higher The PAL Driver is running under Windows 2000 XP ChemStation Cerity is not supported 1 2 Workstation Requirements The hardware requirements are given by the HP ChemStation Data System Consult the Agilent Manual or a representative of Agilent Technologies PARSO PAL Cycle Composer User Manual 1 3 Synchronization Requirements for the PA
70. tination Location Select the folder used for installation of PAL Chemstation Driver To install into a different folder click Browse and select another folder You can choose not to install PAL Chemstation Driver by clicking Cancel to exit Setup Destination Folder CA PAL Cycle Composer Chemstation Browse 39 PASSO PAL Cycle Composer User Manual The installation program analyzes the ChemStation configuration to detect configured instruments Select the instrument to be used with the PAL Autosampler The installation program will automatically create backup copies of all files replaced during the installation process Path Program Files PAL Cycle Composer Chemstation Backup 10 x Ei PAL chemstation interface configuration program 2 1 3 This configuration program enables the cycle composer software to interface with the Agilent A Chemstation environment Select below the chemstation instrument the PAL system is attached to then click the install button to complete the installation Instruments with the label INSTALLED already have the PAL system installed Installation information Install From C Program Files PAL Cycle Composer Chemstation Chemstation path C Chem32 Cycle Composer Path C PROGRA 1 PAL CYCLEC 1 cyc_comp exe Find Browse Instrument Name InstType TT Instrument 1 Instrument 1 Leochem fl stated InstrumentZ J instrumentos Instrumenta E
71. ts of 1000 entries The name will be adjusted for the last digit to become a counter This parameter sets the maximum time used to determine the end of a run when item 12 is enabled So should the runstate parameter of the chemstation not change to the proper status the interface will automatically stop once this maximum time out value is reached timer starts together with the run start So take in account the normal time of a run 10 This parameter sets the maximum time used to determine the end of macro time for setting the CTC_EndRun parameter If this parameter is used it is up to the post run macro to set the CTC_EndRun to 1 in order to signal all actions in the post run macro are finished This mechanism is used to create an extra wait time for the next injection when the post run activities are very time consuming and it is not desired that the next run is started already when post run activities are still going on 11 This will set extra wait time after each run 12 This will enable that the interface keeps checking the runstate parameter of the ChemStation in order to wait for the next run to be started In some cases the ChemStation runstate parameter in not always accurate and can cause trouble in the interface If the parameter is not used the interface will always prepare the next run while the actual run is started The interface will wait in the pre run phase until the actual run is completed 59 PASO PAL Cycle Composer
72. ual The installation process is automatically completed The following message is displayed minheer ze durar aire DESTAS RIFATTA t This configuration program enables the cycle composer software to interface with the Hewlett Packard AL Chemstation environment Select below the chemstation instrument the PAL system is attached to then click the install button to complete the installation Instruments with the label INSTALLED already have the PAL system installed Installation information Install From E DRIVER 64 Chemstation path C MSDchem Cycle Composer Path C Pra Find o Software has been installed Instrument Name Instrument 1 Instrument 1 e a e 2 Installer Exit De Install installation in progress Note It is essential to close all programs and re boot the computer before proceeding 2 3 1 Extra Timer for GC MSD ChemStation There are some indications that the ChemStation sends already a start signal while the report processing is still in progress To avoid any possible communication conflict a special parameter has been built into the driver starting with revision 2 0 4 Path HPChem Core CTC CS x ini Parameter ExtraWaitForStart 0 default 0 seconds In case communication problems are observed the value of this parameter can be increased 42 PASO PAL Cycle Composer User Manual 2 3 2 Empty Chemstation Sequence File The procedure described below to create
73. with this program and it worked correctly on an earlier version of Windows select the compatibility mode that matches that earlier version Compatibility mode Settings Run in 256 colors Run in 640 x 480 screen resolution Disable visual themes Disable desktop composition Disable display scaling on high DPI settings Privilege Level Run this program as an administrator 1 Show settings for all users o cce Ao Cycle Composer is now able to write to the Cycle Composer folder and can also be run as a regular user without administrative rights 14 PASO PAL Cycle Composer User Manual 3 Connection to the PAL 3 1 Running On line When the CC program is started it checks the available serial ports for the presence of a PAL If one is found then all the objects on the PAL are uploaded and a message on the Status line displays nn objects loaded from PAL If there is a mismatch with the serial port setup or no PAL connected an information message is displayed stating that the program will run off line See chapter 4 1 how to select the correct COM port Each time the program successfully connects to a PAL the set of loaded objects is saved to a disk file called latest pal pol The program will check for consistency between the set of objects loaded and those required by each Method Any objects used in a Method which are missing in the PAL are reported in a warning message
74. wn g Single Step LC Injection 10 Tray01 9 2 Unknown 10 Single Step LC Injection 10 Tray01 10 2 Unknown Single Step LC Injection 10 Tray01 11 2 Unknown P Single Step LC Injection 10 Tray01 12 2 Unknown 13 Single Step LC Injection 10 Tray01 13 2 Unknown 14 Single Step LC Injection 10 Tray01 14 2 Unknown 15 Single Step LC Injection 10 Tray01 15 2 Unknown 16 EI al Reset 5 6 Importing a Sample List from an Excel File Using menu File Import Excel Sheet it is possible to import a sample sequence from an Excel sheet into the Cycle Composer sample list The correspondence between Excel column and sample list column has to be set correctly in Format Sample List window see chapter 4 5 22 PASO PAL Cycle Composer User Manual 5 7 Other Function Buttons Reset PAL is available if a list is not in progress It allows the user to easily re initialize all the devices on the PAL This is useful if a run has been aborted and the injection head or syringe are not in the home position Another function of the Reset PAL is to unlock the local terminal For Utilities Functions like change syringe activate valve and others it is necessary to utilize the local terminal Starting the Cycle Composer method again the local terminal will be locked automatically Insert Row and Delete Row button allows quick rearrangement of the Sample List Table View Logfile opens a text file wh
75. y CABACKUP DATA2 CLASS02 s Posten Macro Cm pea Run sequence Lex Cancel Help Jl Enter a command to gt perform before the sequence m Re save the method with the same name Empty CTC 45 PASSO PAL Cycle Composer User Manual In Windows Explorer find the Empty CTC s Sequence File Right click on the file and select rename sequence dl 11 6 2000 10 49 AM ka CLASS02 s i 11 6 2000 11 12 AM im Default s i 12 20 1999 1 08 PM EET Empty cte s i 1145 2000 11 03 AM Ga Nfis i 9 15 2000 10 36 AM fa old s i 11 6 2000 11 12 AM Ba Rikilt s i 6 2 2000 11 46 AM ia temp s i 11 6 2000 11 12 AM rrrrrr r r a N D2 d i i 11 6 2000 10 49 AM ER rikit 5 i 11 6 2000 11 12 AM EA rikit std al i i 12 20 1999 1 08 PM Ea rito ES Empty tc pd i 11 6 2000 11 03 AM A Rivm e f 3 9 15 2000 10 36 AM S Rookgas1 d 1146 2000 11 12 AM ia Rookgas2 d 6 2 2000 11 46 AM a SS 11 6 2000 11 12 AM 9 unigema a Methods 8 sequence a Custrpt 9 Diag GA Drivers rrrrrr r r E Nfi01 d n ARRE KI EH Nfi02 d T i 11 6 2000 10 49 AM A rikit i 11 6 2000 11 12 AM ca nikiltl std i 12 20 1999 1 08 PM Sej rikik3 amen CTC File 11 6 2000 11 03 AM sa Rivm 1 a Nfis 5 File 9 15 2000 10 36 AM x i S File 11 8 2000 11 12 AM i S File 6 2 2000 11 46 AM t as at S File 11 6 2000 11 12 AM unigema 3 Methods 8 sequence Custmt rrrrrr r r 46 PASO PAL Cycle Co

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