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ChromQuest User Guide for the SpectraSYSTEM

1. 18 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters When the table is complete the view can be switched to see a line graph of the gradient profile Changes in flow are not shown on the graph Figure 18 Instrument Setup P4000 Line Graph E Instrument Setup q methanol water pmp Max pressure 2o00 psi Gradient delay fi mL Equilibration time 20 min Gradient curve inea T Shutdown method Min pressure Minutes Shutdown method Select the Shutdown Method checkbox to create a pump method for a shutdown method A pump shutdown method can have a flow rate of zero A pump shutdown method can have one timeline Detector Parameters The five SpectraSYSTEM detectors are UV1000 UV2000 UV3000 UV6000 FL2000 3000 This topic contains information on the Instrument Setup dialogs for each of these detectors Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 19 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters UV1000 Detector Setup The UV1000 is a single wavelength time programmable detector The Instrument Setup dialog box for the UV1000 detector is shown below Figure 19 Instrument Setup UV1000 dialog box E Instrument Setup lol x pooo uv1000 As1000 2 lt Aux Traces A Baseline Check 3e Trioger UV
2. Starting wavelength 200 nm Ending wavelength 200 nm Data interval nm 5 nm r Lamp Options J Deuterium lamp on IV Tungsten lamp on Rise time 11 0 x sec Run time fio min Data rate s207 Hz I Shutdown method T Indirect detection J Prep only method ChromQuest User Guide for the SpectraSystem LC 23 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters In the scanning mode the UV3000 can operate in either the UV range 190 380 nm or in the Visible range 366 800 nm The starting and ending wavelengths must be separated from the end of the range by at least half of the data interval chosen When in the scan mode the high speed monochromator in the detector moves rapidly from the starting wavelength to the ending wavelength and then returns to the starting position to begin the cycle again The data interval determines how often the detector stops during its traversal from the beginning wavelength to the ending wavelength As the data interval is reduced from 10 nm to 1 nm the resolution of the UV scan data increases Because the detector is operating at a fixed data rate 96 Hz increasing the number of wavelengths scanned decreases the number of data points acquired for each wavelength The data rate can not be changed directly by the user However by decreasing the wavelength range or increasing the data interval or both the effective data rate increases
3. 2008 Thermo Fisher Scientific Inc All rights reserved ChromQuest is a trademark of Thermo Fisher Scientific in the United States Microsoft and Windows are registered trademarks of Microsoft Corporation All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries Thermo Fisher Scientific Inc provides this document to its customers with a product purchase to use in the product operation This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc The contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Scientific Inc makes no representations that this document is complete accurate or error free and assumes no responsibility and will not be liable for any errors omissions damage or loss that might result from any use of this document even if the information in the document is followed properly This document is not part of any sales contract between Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between
4. UV6000 Detector Setup The UV6000 detector is a full functioned PDA photo diode array with the capability to collect data over the entire UV and Visible spectrum from 190 nm to 800 nm Scan data and discrete channel data can be collected simultaneously Figure 23 Instrument Setup UV6000 dialog box E Instrument Setup miax EI P4000 s UV6000 UV6000 Events As3000 2 lt Aux Traces UL Baseline Check Sy Trigger sec Run time fi 0 min Rise time M Scans 2 0 7 Min wavelength 220 nm Scan rate fi x Hz 5 7 nm Max wavelength 360 nm Bandwidth Step 2 nm Typical file size 170 KB IV Discrete Scan rate Channels a 10 vy Hz Wavelength A 254 nm Bandwidth 44 v nm wavelength B j0 nm Bandwidth po nm wavelength C pa nm Bandwidth ee nm py Lamp Options J Shutdown method IV Deuterium Lamp On T Prep only method IV Tungsten Lamp On The Instrument Setup dialog box for the UV600 detector contains the following parameters e Run time In the Run Time box type a numeric value for the length of time that you want to collect absorbance data The allowable values are 0 to 655 35 min 24 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters e Rise time Select an appropriate rise time filter from the Rise Time list The de
5. all wavelengths chosen must be in either the UV region 190 380 nm or the Visible region 366 800 nm CAUTION In either the dual or the triple wavelength modes if you want to collect a wavelength in the range from 367 nm to 380 nm do not request it as the first wavelength 22 ChromOuest User Guide for the SpectraSystem LC Thermo Scientific Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Figure 21 Instrument Setup UV3000 Program type Single wavelength dialog box E Instrument Setup oj x 2 poooo uv3000 As3000 lt Aux Traces UL Baseline Check R Trigger Time min Wavelength rm r Program type 3 C Dual wavelength C Triple wavelength C Scanning r Lamp Options V Deuterium lamp on IV Tungsten lamp on Rise time 11 0 v sec Run time fi 0 min Data rate 12 Hz J Shutdown method J Indirect detection J Prep only method IV Zero on wavelength change The UV3000 can also function as a high speed scanning detector to provide UV scan data similar to a PDA detector This is done by selecting the scanning mode as shown in Figure 22 Figure 22 Instrument Setup UV3000 Program Type Scanning dialog box E Instrument Setup iol xi e2 p2000 UVv3000 453000 IX Aux Traces UL Baseline Check Trigger r Program type Single wavelenath C Dual wavelength Triple wavelength
6. specify the sampling rate When you select a sampling rate a prompt appears indicating the narrowest peak width for which this sampling rate is adequate Note It is recommended that you use the Graphical Events Programming to determine the optimum sampling rate for your chromatography Frequency This selection is in Hz samples per second This is the selection for most chromatography applications Click the down arrow to get a list of the frequencies available for the configuration of your system Period When you select this type of sampling you must select the number of seconds or milliseconds between data points e Run time Run Time determines the length of time data is sampled Acquisition delay Acquisition Delay is the interval between the start of run Trigger and the time when sampling starts for this channel When you have completed the acquisition parameters click the X box in the upper right corner of the dialog box to exit the dialog 40 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters External Events After you configure external events for your instrument you can program the events in your method To open the External Events dialog box choose Method gt Instrument Setup and then click the External Events tab Note that this dialog box will not appear in your Instrument Setup window unless you ha
7. 0 C to 60 C This field is available only if your configuration indicates that this option is installed in your autosampler e Column oven The Column Oven option button allows you to turn the column oven on if this option is installed The allowable settings are 15 to 80 C The temperature can be controlled in increments of 1 C beginning at temperature of 5 C above ambient Therefore if your ambient room temperature is 20 C you can control the temperature of the column oven compartment in the range of 25 to 80 C Remember to take the boiling point of your mobile phase into consideration e Prep only method Selecting this checkbox allows you to run a sample preparation program without making an injection The AS3000 and AS1000 both have the ability to control four switchable time functions TF1 to TF4 which can be programmed as a function of analysis time Normally these would be used to control external devices such as fraction collectors or column switching valves The functions correspond to pins 9 to 12 on the back panel of the autosampler These pins are open collector outputs capable of sinking handling currents up to 600 mA at voltages up to 24 VDC In the State column the red arrow indicates that a function is turned On while the absence of the red arrow indicates that the function is turned off 32 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Contr
8. 190 380 nm Vis 366 800 nm Rise time 20 x sec Data rate fio 7 Hz JV Autozeto gt Time fo min m Lamp options I Deuterium lamp on T Shutdown method I Tungsten lamp on Program type T Prep only method IV Zero on wavelength change e Program type Select either the UV range of 190 380 nm or the Visible range of 366 800 nm You cannot crossover between the UV range and the Visible range during a run e Rise time The rise time filter is selectable from 0 0 to 5 0 seconds The longer the rise time the slower the response of the detector to changes in light intensity but also the lower the noise of the detector Generally the default value of 2 0 s is adequate for LC To avoid peak broadening select a rise time that is no greater than one tenth the width of the narrowest peak at half height in your chromatogram For example if the narrowest peak in your chromatogram has a width of 20 s select a rise time of 2 s or less to avoid broadening the peak e Data rate The data rate is selectable from 20 Hz down to 4 Hz For optimum integration use a data rate that produces collects at least twenty data points across the narrowest peak of interest For example if the narrowest peak in your chromatogram has a baseline width of 5 s a data rate of 4 Hz would be adequate Higher settings provide more data points but result in data files that take up more hard disk space e Autozero he autozer
9. Configuration to open the SN4000 configuration dialog box 6 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 2 Configuring Thermo SpectraSystem LC Modules Configuring the Instrument Modules Figure 6 SN4000 Configuration dialog box SN4000 Configuration x K Port com 1 Cancel ID Number Help Detect Devices b From the Port list select the serial port COM1 COM2 and so on where the SN4000 is attached c Click Detect Devices All devices connected to the SN4000 are added automatically Detectors that are connected directly to the chromatography interface computer such as the UV3000 and the UV6000 must be added to the configuration manually d Click OK Before you exit the Thermo SpectraSystem LC dialog box continue on to the next procedure Configuring the Instrument Modules to complete the configuration of each module Configuring the Instrument Modules After you add the modules of your instrument to its configuration complete the configuration of each module Typically a Thermo SpectraSystem LC instrument contains an autosampler a pump and a detector Refer to the following topics contained in this section to complete the configuration of your instrument e Autosampler Configuration e Pump Configuration e Detector Configuration Autosampler Configuration Thermo Scientific If you used the Auto Configuration utility some of the information about your
10. Min pressure and Max pressure Enter values for the minimum and maximum pump operating pressures under which you want to continue pumping mobile phase Integer values from 0 to 6000 psi 0 to 414 bar or 0 to 41 MPa are allowed The maximum pressure must be greater than the minimum pressure The maximum pressure setting allows you to automatically turn off the pump flow if the backpressure of your system rises excessively above a specified level This is important because the pump can be damaged and the column ruined if the backpressure of your system rises excessively above its typical operating level The minimum pressure setting allows you to automatically turn off the pump flow if the backpressure of your system falls below a specified level This is important because you do not want to run the pump dry e Gradient delay volume Pre column volume The gradient delay volume is the volume of mobile phase in milliliters that the pump delivers before the autosampler starts the injection The default value is 0 mL This parameter is used to adjust for systems with differing precolumn volumes e Equilibration time This is the time the pump maintains the solvent composition and flow selected before sending a Ready signal to the system The default value is 0 min For gradient methods adding an equilibration time equal to twenty column volumes can help in obtaining reproducible retention times Thermo Scientific ChromQuest User Guide for the S
11. Mixture met a multilevel calibration met Cancel Help dai File name jl Save as type Method files met 7 r Description Method for running LC test mix Creating Shutdown Methods Thermo Scientific Shutdown methods can be created to automatically turn off the pump and the detector lamp s at the end of a sequence run 1 Choose File gt Method gt New to open the Instrument Setup window 2 To turn off the pump flow a Open the Pump Instrument Setup dialog box b Select the Shutdown Method check box c Type 0 in the Flow Rate box 3 To turn off the lamps of the detector a Open the Detector Instrument Setup dialog box b Select the Shutdown Method check box c Deselect the Deuterium Lamp On check box and the Tungsten Lamp On check box 4 Save the method with the Save As command In practice it is useful to give the method a name that identifies it as a shutdown method ChromQuest User Guide for the SpectraSystem LC 43 3 Creating a Method for Instrument Control Adding a Shutdown Run to the End of a Sequence Adding a Shutdown Run to the End of a Sequence A Shutdown run can be appended to the end of a sequence The method contained in a shutdown run is downloaded to the instruments but the autosampler is not activated and no injection occurs To add a Shutdown run to the end of a sequence 1 Choose Sequence gt Edit Place the mouse cursor in the first blank Run T
12. No The UV6000 Events table can be used to program a fraction collector For example you can program a fraction collector to collect the column eluent when the On event occurs and to output to waste whenever the Off event occurs Or you can program a fraction collector to collect the column eluent when the absorbance for one of the three discrete channels of the detector reaches a particular level a peak is eluting In this case you must select Level from the Event list and then type an absorbance value in the Level box and a delay time in the Delay box The delay time accounts for how long it takes the mobile phase to move from the detector to the fraction collector This delay time is dependent on the flow rate and the tubing connections and must be determined empirically The Off event turns off the Event but will not keep it off The On event is triggered again whenever the signal rises above the selected value Therefore to keep the Event turned off set up another level condition for Channel A at a value in mAU far above the highest peak in your chromatogram Since this Level value is never reached the On event will not occur again during the run If the baseline drifts in your run you can select the Zero event to reset the baseline at a particular time during the run Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 29 3 Creating a Method for Instrument Control Entering the Instrument
13. SpectraSystem LC 27 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters e PMT voltage This list allows you to select the voltage that is applied to the photo multiplier tube PMT embedded in the detector Higher values increase the sensitivity of the detector at the expense of lamp lifetime similar to the situation with the lamp flash rate A good starting point is 600 volts the default value Higher values are required for trace level analyses e Autozero time This box allows you to enter a time in the run when you want to zero the baseline e Zero on wavelength change This check box allows you to zero the baseline between wavelength changes in the wavelength timetable e Lamp state This area allows you to select from three modes Run Off and On If you select either the Off option button or the On option button the lamp is turned off or on respectively when the method is downloaded to the detector Selecting the Run option button turns the lamp on at the beginning of each run and off at the end of each run The Run state preserves lamp lifetime but decreases the baseline stability e Shutdown method This check box allows you to select this method as a shutdown method e Prep only method Deselecting this check box allows you to run a sample preparation program without making an injection when this checkbox is selected e Wavelength Timetable The FL2000 FL3000 detector can be programmed
14. View intensity and absorbance spectra Test the digital inputs and outputs Calibrate the dark current Perform wavelength calibration View and print the status log Most of the above are specified as routine maintenance Contents e Opening the Diagnostics Program e Calibrating the Detector Opening the Diagnostics Program To use the UV6000 diagnostics software the instrument must be configured and the hard cable RS232 connected to the specified serial port on the computer kod l Thermo Scientific To open the Diagnostics program From the Instrument window in ChromQuest choose Control gt Instrument Status The screen displays a set of tabs with all of the configured instrument modules Choose the UV6000 tab and click it on with the left hand mouse button Position the cursor in the middle of the screen and click the right mouse button A menu appears Choose Diagnostics from the menu ChromQuest User Guide for the SpectraSystem LC 53 5 UV6000 Diagnostics Opening the Diagnostics Program A set of five tabs appears corresponding to the functions you want to perform They are e Lamps Tab e Control Tab e Display Tab e Error Log Tab e Calibration Tab Lamps Tab There are two separate controls in this page which allow you to access information and control of each of the lamps D2 for UV and W for Visible The On and Off buttons toggle the lamps on and off The Status display depicts the current mo
15. across the whole spectra There are a maximum of three and a minimum of zero that can be chosen The parameters here are essentially the same as described in the Scan dialog box e Default Get From Detector And Load to Detector Buttons Default This button puts the pre programmed default parameters into the dialog boxes described above Get From Detector This button uploads the operational parameters from the UV6000 to the Control tab Load to Detector This button downloads the method that is in the previously described dialog boxes to the detector for the purposes of diagnostics and adjustments in the Display Tab Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 55 5 UV6000 Diagnostics Opening the Diagnostics Program Display Tab The Display tab has two trace screens that show data from the Scan and Discrete Channels methods loaded from the Control Tab The top screen corresponds to the former and the bottom screen to the latter Also included in the Display Tab is a Status box for ROM RAM and PIC Lamps Discrete Channels and Inputs The Status and Data On Off buttons to the right of the status boxes control the display of the trace screens and the status boxes Once a method has been downloaded from the Control tab screen Click On in the Status control box on the right of the Display tab screen The status boxes then become activated with data from the instrument according to the parameters
16. autosampler was detected automatically The Auto Configuration option determines the Tray Option and whether or not the Column Oven or Sample Prep options are installed Information about the syringe size and the loop size must be added manually ChromQuest User Guide for the SpectraSystem LC 7 2 Configuring Thermo SpectraSystem LC Modules Configuring the Instrument Modules To complete autosampler configuration 1 In the Configured Modules box double click the icon for your autosampler to open its configuration dialog box Figure 7 AS1000 Configuration dialog box 451000 Configuration Syringe size 250 x uL 0 Loop size i00 x me Cancel Tray Option Help None 120 vials Vial cooler 105 vials Tray temperature 105 vials Ix dili 7 Column oven installed ID number Default injection volume fi D pl 2 From the Syringe Size list select the size of the syringe that is attached to your autosampler 3 From the Loop Size list select the size of the sample loop that is attached to the injection valve of your autosampler 4 If you did not use the Auto Configuration utility do the following a In the Tray Option area select the option that applies to your autosampler b If your autosampler has a built in column oven select the Column oven installed check box c If your autosampler has the sample preparation feature installed select the Sample Prep installed check bo
17. box d Continue at step 6 5 For a UV3000 or a UV6000 detector do the following a From the Detector Model list select the model of your detector 10 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 2 Configuring Thermo SpectraSystem LC Modules Configuring the Instrument Modules Figure 12 Detector Configuration dialog box x Detector Name juveooo o Detector Model Acquisition Source fuveoooaco Y Axis Units mou Y Axis Multiple oomoo OK Cancel Help b Click the button next to the Acquisition Source list to open the configuration dialog box as shown in Figure 13 Figure 13 UV6000 Configuration dialog box U 6000 Configuration Xi a Pott comz a Cancel ID number Help c From the Port list select the Com port of your computer to which your detector is connected d Inthe ID number box type an appropriate label such as the serial number of your detector e Click OK to exit the dialog box for your specific detector 6 In the Y Axis Units box type the units to be displayed on the Y Axis of your chromatogram For example type microvolts or AU depending on the detector units of measurement ChromQuest acquires your analog signal and stores it in microvolts If you want to display the signal in different units you must use the correct multiplier Consult the table below for commonly used Y axis labels and corresponding multipliers Thermo Scien
18. bubble The solvent selection valve rotates to the sample needle line The prep syringe moves forward and expels solvent thus flushing the dead volume with the select solvent and expelling the second air bubble leaving only the selected solvent behind Pickup Each Pickup step programs the sample syringe to withdraw the specified volume 0 100 uL from the source vial Sample Sample 1 Sample 2 Sample 3 Reagent A Reagent B or Reagent C The Pickup step is a 6 step process R 2 The hook moves to the selected vial position and picks up the vial The autosampler arm brings the vial to the sample tower and pushes the funnel out of the way Note Ifyou have the Tablet Dissolution Option the sample tower may be referred to as the injection tower to distinguish it from the Sampling Tower used to withdraw samples from the dissolution vessels The sample syringe draws an air bubble to isolate the sample or reagent from the selected solvent already present in the solvent holding loop from the Load step ChromQuest User Guide for the SpectraSystem LC 35 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters 4 The vial is raised in the sample tower Sample is then drawn into the sample needle line 5 The vial is lowered and the sample syringe draws an air bubble to isolate the sample slug and prevent sample loss 6 The hook returns the vial to the sample tray This process is
19. for the SpectraSystem LC 47 4 Direct Instrument Commands UV3000 Direct Command Menu Table 1 Diagnostic commands for the UV3000 FOCUS detector Command Wavelength nm Description You can manually adjust the wavelength setting from this field The lamp shutter is automatically positioned to allow the proper source to illuminate the optical system Type a wavelength into the box Press Enter J or Close to activate the wavelength change When you press enter or Close you will be exited out of the diagnostics menu Re enter the diagnostics menu to continue a diagnostics procedure Zero Click this button to zero the detector absorbance level Auto Cal Click this button to run the automatic calibration procedure This procedure automatically calibrates the wavelength to the lamp 656 nm deuterium lamp emission peak Lamp control Click the On or Off buttons to turn the lamps on or off Sample Reference This group contains five vertical columns of numbers arranged in two rows The values in this group provide general light level information as follows e V F voltage to frequency The voltage to frequency values are responsive to light level changes You should expect a sizable increase jump in the reference values when a detector lamp is first turned on If not suspect a failed lamp or a shutter problem e Osc Oscillator These columns contain base values used in the V F calculations The specific va
20. repeated if a second Pickup step is used Pickup large The Pick large Pickup Large step is the same as the Pickup step s except that it uses the solvent syringe to transport larger volumes 0 1000 mL Add The Add step delivers a specified volume 0 1000 mL to the specified target vial Sample Sample 1 Sample 2 Sample 3 Reagent A Reagent B or Reagent C During the Add step two specific events occur 1 The hook moves to the designated target vial position and transports the vial into the sample tower 2 The prep syringe expels the desired volume from the solvent holding loop and sample needle lines into the target vial Note Because the Add step uses the prep syringe the maximum volume that can be delivered is the sum of the Load and Pick large volumes That is you can t add more than you ve withdrawn into the prep syringe during the Load and Pick large steps Mix vial for Specify the mixing time 0 0 9 9 minutes in this field Heat vial for Specify the heating time 0 0 99 9 minutes Wait in tray for Pauses the autosampler for the specified amount of time with the target vial in the tray You can use this step to program a reaction time or to allow the liquid layer in an extraction to separate and so on Remove uL to waste at 2 0 mm needle height Positions the bottom of the vial at the specified distance 0 0 20 0 mm from the needle tip withdraws a desired volume of sol
21. set in the method Now click on the Start button in the Data box to the right The trace screens become activated at this time and real time data is displayed in the screens The utility of this data in adjusting the attenuators and monitoring the light intensity is described in the UV6000LP manual Descriptions of the data displayed in the various status boxes are given below e Status These are the versions of the software firmware that are currently in the instrument e Lamps This box displays the current status of the two lamps as well as their total hours since last being changed e Discrete Channels Displayed here is the number of counts or absorbance units for each of the discrete wavelengths e Inputs The input parameters are from external sources and are except for the wheel holmium oxide wheel located in the front of the detector accepted from the rear panel of the detector Error Log Tab The Error Log Tab is an ongoing record of critical and non critical errors in the UV6000 The log is kept by and inside the detector itself and is a very helpful trouble shooting feature to assess firmware and software discrepancies in the detector To use the error log simply click the tab and then the Get button to the right of the screen The log is uploaded to the blank portion of the screen It contains the times and dates as well as descriptions of any nuances that have occurred To print or clear the log you need only click the r
22. the two documents Software Version ChromQuest 5 0 For Research Use Only Not regulated for medical or veterinary diagnostic use by U S Federal Drug Administration or other competent authorities Contents Thermo Scientific Chapter 1 Chapter 2 Chapter 3 ct ee ee ee eee reer eer rr Te rere v About This Guides brew Le hes en inner niet nad bad i RE v Related Documentation fw on i 0 1a qu daw enced erener sacs aoe aue ead v Safety and Special Notices uuueeuuunnn nerea v Contacting Us ice cetti ome eee Mies ea alae A a e a aa vi QVEIVIEW is ctuccsnatesentin tenn ame kE naaa na a a E 1 Configuring Thermo SpectraSystem LC Modules 00 0000 3 Adding the Modules to the Instrument Configuration 000 3 Configuring the Instrument Modules 23 0 0 0 205428 cies Ohetdws Oat e dees 7 Autosampler Configuration sssssseessuu urrune erer 7 Pump Configuration auesse sunaa narrer 9 Detector Configuration s s s sussuri eee the eS eS ee 9 Creating a Method for Instrument Control a aunan 13 Opening the Instrument Setup Window 0 00 0 e eee ee eee 13 Entering the Instrument Setup Parameters 4054 lt sereed awe nse eran eas 16 Pump Parameters es 4 f004 See ee ieee end Mebane boa ee aes 17 Detector Paraimeters smi sr dees osc le pitts oE hegre Rie heh E blo nls ad oo 19 UV 6000 Events cig css aidoaiy Quek ceed e Rew gesemieese E Kas eae 29 Autosampler Parameters AS3000 and A
23. C analyses Higher scan rates increases the data file size proportionately but will not add significantly to the quality of the data unless you are doing very high speed LC ChromQuest automatically calculates a typical file size based on the parameters number of wavelengths and scan rate selected Bandwidth Select an appropriate bandwidth from the Bandwidth list The bandwidth setting is an electronic filter that allows you to reduce the short term detector noise Decreasing the short term noise results in higher sensitivity at the expense of spectral resolution The bandwidth calculation uses a Savitsky Golay filter to bunch the data from adjacent diodes The calculated intensity for a particular wavelength is a weighted average of all the wavelengths within the bandwidth range with the wavelength of interest being weighted more heavily For example with a bandwidth setting of 11 nm the calculated intensity for 250 nm would be a weighted average of the measured intensities for the diodes in the range from 245 nm to 255 nm ChromQuest User Guide for the SpectraSystem LC 25 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters e Discrete To collect discrete channel chromatograms select the Discrete check box Select the number of discrete channels that you want to collect from the Channels list You can collect 1 3 discrete channels These channels are independent of the scan data and can therefore be co
24. Instrument window is activated as indicated by its title bar 5 Close the Navigation bar 6 Open the Instrument Setup window e To create a completely new method choose File gt Method gt New e To modify an existing method that is open in the instrument window choose Method gt Instrument Setup or click the Instrument Setup button The Instrument Setup window contains a tab for each configured module as well as a tab for the Baseline Check feature if you did not deselect it when you configured your instrument a tab for Aux traces if the instrument contains a pump or an autosampler and a tab for setting up the trigger mode If you chose to create a new method the method contains default parameters for each module of your instrument Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 15 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Figure 16 Instrument Setup window Mf Instrument Setup Entering the Instrument Setup Parameters Typically a Thermo SpectraSystem LC instrument contains an autosampler a pump and one or more detectors If your system contains an autosampler with built in temperature control zones you can set up auxiliary traces to monitor these zones during a run If your system contains a pump you can set up an auxiliary trace to monitor the backpressure of your system during a run The information contained in the auxiliary traces is
25. S1000 0000 30 Autosampler Sample Preparation Parameters AS3000 only 33 Method Development Language Tabs cduhcvenduimde niesanen dies 38 Analog Detector Parameters SS420 Board 0 cee eee eee eee 39 External Events cii 2 4 04 580 4899 cee REG ES Ee ES KO LOSE 41 Auxiliary Traces oca sen ke kaha E a we EN oad ae ee 4 TCE pices chp ees See S heels beta a kiwis ko 42 Saving the Method svewkwrte bree sieht hoe caw del uae as 42 Creating Shutdown Methods 25 54 iat jeadee election ted waab hed OR skes 43 Adding a Shutdown Run to the End of a Sequence 000000000 44 ChromQuest User Guide for the SpectraSystem LC Contents Chapter4 Direct Instrument Commands 200cc cece eee eee eee eee eee 45 P1000 1500 2000 4000 Direct Command Menu 0 2 eee 46 UV1000 2000 Direct Command Menu sg 05 04 Seen eee a ee tae 46 WV 3000 Direct Command Mente 24 25 3 4apcm 2 eee ok 3 rrean 47 AS1000 AS3000 Direct Commands ca s42 c8 epee a ae eee ak ee hae 50 Chapter5 UV6000 Diagnostics 0 cece eee eens 53 Opening the Diagnostics Program ss reise beta tee uke eee Ee ee 53 GCalibiatine the Detector cei katana E eeu ned N 57 MUOKKAA ara EA AEEA DANAE wee EAA NAA 59 iv ChromQuest User Guide for the SpectraSystem LC Thermo Scientific Preface About This Guide This guide describes how to control the Thermo SpectraSystem LC from the ChromQuest 5 0 data system Rel
26. Scans box sets the parameters for a spectral scan The units here are different depending on the mode that has been chosen The Start value is the beginning of the scan and the End value is the end Together they comprise the range of the scan either in wavelength nm for the absorbance mode or pixels for the intensity mode The range is between 190 and 800 nm absorbance and 2 and 511 pixels intensity The step size refers to the how often the data is sent to the program A step increment of 1 means that each wavelength or pixel is displayed in the trace while a value of 4 means that every fourth data bit is used and so on The bandwidth box sets the Savitsky Golay filtering for the absorbance mode Wider bandwidths decrease both spectral noise and the resolution of the spectra For sensitive measurements the detector bandwidth setting should not exceed the bandwidth at half height of the narrowest spectral feature of interest The scan rate measured in Hz has the same units for both modes Simply stated a rate of 1Hz is once per second and 10Hz 10 times per second so for each Hz a scan across all the chosen wavelengths or pixels takes place each second The higher the value here the more data is collected but rates that are too high tax a computer s ability both in memory and in processing speed e Discrete Channels This function works much the same as the scan except that only discrete wavelengths or channels are used instead of a scan
27. Select the Control Instrument Status command 2 Left click and a set of tabbed pages appears 3 Mouse over to the AS1000 tab or the AS3000 tab and left click 4 Place the cursor anywhere on the tabbed page and right click A dialog box appears Home Arm Change Injector Position Flush Prep Syringe Refer to Table 2 for a description of the direct commands that can be used with the AS1000 and AS3000 autosamplers Table 2 Direct commands for the AS1000 AS3000 Command Description Home Arm Clicking on Home Arm moves the arm from its present position to its home location to the left of the rear left corner of the tub Change Injector Position This command allows you to manually switch the injector valve between the inject and fill positions 1 Click Change Injector Position to open the Change Injector Valve Position dialog box Change Injector Position Valve position Inject V OK Load Cancel 2 Select Load from the pull down option menu 3 Press OK 4 Select Inject from the pull down option menu 5 Press OK 50 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 4 Direct Instrument Commands AS1000 AS3000 Direct Commands Table 2 Direct commands for the AS1000 AS3000 continued Command Description Flush Prep Syringe If you purchased the sample preparation option you can flush the large 2 5 mL sample preparation syringe and external solvent line manually 1 Fill each solvent bottle with
28. Setup Parameters The Event remote output can be programmed by the detector to respond as a function of time as follows 1 Click the UV6000 Events tab to open the UV6000 Events dialog box Figure 26 Instrument Setup UV6000 Events dialog box lox P4000 pau UVE000 s UVE000 Events 453000 28 Sample Prep 2 MDL Program 2 lt Aux Traces gt mA a 2 To create enter an event in the table do the following a Type a numeric time value into the Time column b Select an Event from the list in the Event column c For the Level event in addition to entering a time select a channel from the drop down list in the Channel column Type an absorbance value in the Level column and a delay time in the Delay column Autosampler Parameters AS3000 and AS1000 The AS3000 and AS1000 autosamplers are very similar except that the AS3000 can do variable volume injections whereas the AS1000 can perform only fixed loop fixed volume injections The screens for the autosamplers are the same except the AS3000 can perform three different types of injections Full Loop PushLoop and Pull Loop In Full Loop very high reproducibility is possible at the expense of flexibility For most users the TSP patented PushLoop injection mode provides the injection volume flexibility required while also providing reproducibility that is nearly as good as fixed loop Pull Loop is available for compatibility with other older Sp
29. ample position the stock standards in the Reagent A B and C positions We have also used the vial positions in a sequential order However the autosampler doesn t limit you to this approach kod l To develop custom procedures In each cycle you have seven vial positions to work with three source vial positions Reagents A B and C and four vial positions that may be either source or target vials Sample Sample 1 Sample 2 and Sample 3 You can arrange your Pickup and Add vials in any order you wish within a cycle as long as you remember that the autosampler locates the extra vials Sample 1 3 in relationship to the vial you ve assigned to the Sample position For example you could Pickup form the Sample 3 vial and Add to the Sample vial But you couldn t Add to the Reagent A vial since according to rule 1 it cannot be a target vial You can use the vial positions in any order you wish within a dilution cycle For example even though the autosampler cannot skip Sample vial positions you can program it to prepare interspersed calibration vials by Adding to the Sample 2 position without using the Sample 1 position in any of the steps in a given dilution cycle ChromQuest User Guide for the SpectraSystem LC 37 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Note In loading your sample tray if you want your first calibration vial to be A01 then you can use rule 3 and t
30. an appropriate solvent 2 Click the Flush Prep Syringe command to open the Flush Prep Syringe dialog box Flush Prep Syringe Flush volume uL OK Solvent Position Flush Bottle V Cancel Solvent 1 Solvent 2 Solvent 3 Solvent 4 3 Enter the desired flush volume into the Flush volume dialog box 4 Choose the appropriate solvent from the solvent position pull down option menu 5 Press OK after the appropriate choices have been made This command is unavailable on the AS1000 The command line is grayed out The AS3000 must be configured for sample prep to activate this command If the autosampler is not configured for sample prep this command line is grayed out Flush Prep Syringe This command lets you manually flush the 250 mL sample syringe 1 Fill your flush solvent bottle 2 Click the Flush Sample Syringe Command to access the Flush Sample Syringe dialog box Flush Sample Syringe Flush Volume uL OK Cancel 3 Enter the desired flush volume into the dialog box and press OK The autosampler automatically flushes the sample syringe and flush lines with the specified volume of flush solvent and returns the syringe to its starting position Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 51 UV6000 Diagnostics The UV6000 is equipped with diagnostics software that lets you verify its operation calibrate it and view its status log You can Check lamp status and usage
31. anual dilution you draw a specific amount of sample into a pipette and expel a measured volume into a volumetric flask Next you dilute to final volume with a desired amount of solvent and mix your sample solvent mixture for a specific amount of time In the manual dilution just described solvent and sample are added to the target container one at a time In contrast the AS3000 autosampler first draws all of the liquids for a given dilution into the solvent holding loop and sample needle lines An air bubble is drawn before and after each liquid to isolate the liquid in the loop Once all of the liquids have been drawn into the lines the autosampler delivers them to the target vial simultaneously The vortex mixture then mixes the target vial for the specified amount of time Delivery lines transport liquid and air through the sample preparation system as programmed in the steps of the cycle template Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 33 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Each step influences the operation of one or more of the six major components in the sample preparation system l A a A o N Prep syringe Sample syringe with 6 port flush valve Solvent holding loop 6 port solvent selection valve with four solvent bottles Heater vortex mixer Needle The Instrument Setup dialog box for the Sample Prep contains the following parameter
32. ated Documentation In addition to this guide Thermo Fisher Scientific provides the following documents for the ChromQuest 5 0 data system ChromQuest 5 0 Installation Guide ChromQuest 5 0 Administrator Guide ChromQuest 5 0 User Guide ChromQuest 5 0 Reference Guide The data system also provides Help Safety and Special Notices Make sure you follow the precautionary statements presented in this guide The safety and other special notices appear in boxes Safety and special notices include the following CAUTION Highlights hazards to humans property or the environment Each CAUTION notice is accompanied by an appropriate CAUTION symbol IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or might contain information that is critical for optimal performance of the system Thermo Scientific ChromQuest User Guide for the SpectraSystem LC v Preface Contacting Us Note Highlights information of general interest Tip Highlights helpful information that can make a task easier Contacting Us There are several ways to contact Thermo Fisher Scientific for the information you need To contact Technical Support Phone 800 685 9535 Fax 561 688 8736 E mail TechSupport C MS thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at www mssupport thermo com To contact Customer Service for ordering informatio
33. bbed page Click the Right hand mouse button After clicking the Right hand mouse button a dialog box appears Autozero Lamp Diagnostics Only the Autozero command is available during a run Zero the detector response by highlighting the Autozero command and clicking the mouse Autozero To turn the detector lamps on or off highlight the Lamp command A second menu box appears to the right of the Lamp command Autozero Lamp Deuterium Lamp On Diagnostics Tungsten Lamp On During a run this second menu box is grayed out The deuterium lamp is on if a check appears to the left of the Deuterium Lamp On command The tungsten lamp is on if a check appears to the left of the Tungsten Lamp On command To change the status of a lamp highlight the command line for the lamp of interest and make a left mouse click The lamp is turned off if no check appears to the left of the command Diagnostics To access diagnostics highlight the Diagnostics command line and click the mouse The UV3000 Diagnostics menu appears on the screen From the diagnostics menu the chromatographer can zero the detector absorbance level run the automatic calibration procedure turn on off the deuterium and tungsten lamps and perform light intensity diagnostics Because diagnostics may not be accessed during a run the Diagnostics command is grayed out during a run Refer to Table 1 for a list of diagnostic commands available ChromQuest User Guide
34. de both signals must be either in the UV range 190 365 nm or in the Visible range 366 700 nm The detector timetable allows you to change wavelengths as a function of time during the run In the single wavelength mode wavelengths can be changed from the UV range to the Visible range In the dual wavelength mode all wavelengths in the table must be in the same wavelength range All other functions are the same as the UV1000 above Figure 20 Instrument Setup UV2000 dialog box E Instrument Setup 2 pooo 2 uv2000 As1000 lt Aux Traces UL Baseline Check R Trigger Program type Single wavelength UV Vis 190 800 nm oi Te C Dual wavelength Vis 366 700 Rise time 2 0 Me sec 10 Hz dv Autozero fo min Lamp options IV Deuterium lamp on IV Tungsten lamp on nm Data rate ne Time I Shutdown method J Prep only method IV Zero on wavelength change UV3000 Detector Setup The UV3000 detector can function as either a single wavelength detector like the UV1000 or a dual wavelength detector like UV2000 or it can function as a triple wavelength detector Lamp options rise time and data rate are similar to the UV1000 and UV2000 detectors Unlike the UV2000 wavelength programming is available only in the single wavelength mode and the zero on wavelength change is activated only between actual wavelength changes In multiple wavelength modes
35. de of the lamp on off starting or failed and the Hours display tells you the number of total hours of use on the lamp The Reset button is used when a lamp has been changed and resets the Hours display back to zero The Last Reset display tells the date and hour of the last time that the lamp was changed Control Tab The Control tab is used to set the parameters for the diagnostics and the traces in the Display tab It is used like the dialog box under Instrument Setup to program the various parameters described below e Mode Two selections are possible for the mode box Intensity and Absorbance The absorbance data is displayed in wavelengths by increments of 1 nm The intensity is displayed in pixels Each pixel corresponds to one of the 511 diodes used in the diode array There are 512 diodes in the array of which 0 and 1 are not used Diode 2 corresponds to 190nm wavelength and diode 511 corresponds to 800nm This gives a diode spacing of 611nm 509 diodes 1 2nm diode The data is interpolated to give integer values e Filter This sets the rise time of the program It is an electronic filter set in seconds to eliminate baseline noise in the absorbance mode A value of 2 sec is used for detector noise measurements Outputs These buttons set the active Hi Lo for the various outputs 54 ChromOuest User Guide for the SpectraSystem LC Thermo Scientific 5 UV6000 Diagnostics Opening the Diagnostics Program e Scans The
36. e Click the Calibration Tab The two boxes on the left of the screen are labeled Wavelength and Array Go down to the Array box and click the Execute button The status box becomes activated with the various tasks that the instrument is performing to complete the procedure When it is finished you can either apply or cancel the calibration If you wish to continue click Apply Wavelength Calibration Thermo Scientific To perform the wavelength calibration you must meet the conditions described above in the array calibration Go to the wavelength file box and click Open A set of five wavelength calibration files wcl files are displayed Descriptions of the utility of these programs are in the UV6000LP manual Choose the appropriate file and open Data is displayed in the screen above Next go down to the wavelength box and click Execute The system prompts you for conditions and tell you the proper position of the holmium oxide wheel Click OK You are then prompted to re position the wheel Do so and click OK You are prompted to apply the calibration Click Apply to continue ChromQuest User Guide for the SpectraSystem LC 57 Index A Acquisition Delay 40 Acquisition Setup 39 Acquisition Delay 40 Channel Status 40 Run Time 40 Sampling Rate 40 Autosampler pause for reaction time 36 autosampler configuring 7 direct commands 50 autozero 21 Autozero button 46 C Calibration vials apply prep method to 34 changing the inj
37. e number of the cycle you 34 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters want to program in the Cycles field You can select up to four cycles To activate a cycle select the Cycle Used box The cycles are performed in numerical order To use individual lines in the cycle check the box next to the line required Load The Load step flushes the lines with the solvent volume 0 1500 uL specified in the Load field and the desired solvent Solvent 1 4 specified in the From field You specify the solvent tray location in the Sample Queue Menu The flush cycle is a 6 step process 1 The 6 port solvent selection valve rotates to the air position to draw an air bubble into the solvent holding loop The solvent selection valve then rotates to the solvent position specified in the Load step from field The preparation prep syringe draws the specified amount of solvent 0 1500 uL plus a constant excess amount into the solvent holding loop The excess solvent is used in step 6 to flush the dead volume from the solvent selection valve to the needle tip The air bubble drawn into the solvent holding loop isolates the selected solvent this step from the flush solvent already present in the lines The solvent selection valve moves back to the air position and the prep syringe draws another air
38. e vial The sample loop is overfilled and the excess sample is expelled to waste Select the Pushloop option button if you want to vary the injection volume In the Pushloop injection mode the autosampler withdraws an excess of 15 uL from the sample vial For reproducible Push Loop injections limit the maximum injection volume to one half the sample loop size Select the Pull Loop option button if you want to vary the injection volume and you have a limited quantity of sample In the Pull Loop injection mode the autosampler withdraws an excess of 1 1 uL from the sample vial The Pull Loop injection mode is the least precise of the three injection modes Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 31 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Flush volume This box allows you to set the amount of solvent that is used to flush the syringe and needle line after an injection is performed The allowable range is 100 to 6000 uL The default value is 400 uL e Needle height from bottom This box allows you to set the height that the needle descends to when it withdraws sample from a vial The height is the distance from the bottom of a sample vial The allowable range is 0 to 20 mm The default value is 2 mm e Tray temperature control The Tray Temperature Control option button allows you to turn on the tray temperature control feature The allowable settings are from
39. ector position 50 COM port 7 data rate 20 Detect Devices button 7 detectors FL2000 FL3000 27 UV1000 20 UV2000 22 detectors configuring 9 deuterium lamp 21 diagnostics for the UV3000 48 direct commands for the autosampler 50 direct commands for the UV3000 47 E equilibration time 17 events 29 External Events 41 Extra vials 39 Thermo Scientific Sample Prep 34 F Fields Prep Calibs also 34 flash rate 27 flushing the syringe 51 G gradient curves 18 delay volume 17 H Heat for See Heat vial for Heat vial for described 36 Heater mixer Sample prep 34 injection modes 30 L lamp state 28 Method Development Language 38 Method Development Language Tab 38 Mix See Mix vial for Mix vial for described 36 Mixer heater controlling 38 Mixing vial contents 36 needle height 32 ChromQuest User Guide for the SpectraSystem LC 59 Index P 60 P Pause autosampler with vial in tray 36 Period 40 PickLg Pickup large See Pickup large Pickup described 35 PMT voltage 28 Prep Calibs Also 38 Sample Prep 34 Prep Calibs also 34 pump operating pressures 17 Remove uL to waste described 36 rise time 20 Run Time 40 S Sample prep customizing the template 37 extra vials 34 Heater mixer 34 programing rules 37 Sample prep steps Add 36 Load 35 Mix vial for 36 Pickup 35 Pickup large 36 Sampling Frequency 40 Save Method As 42 scan rate 25 shutdown 44 Shutdown button for the pumps 46 shutdow
40. ectra Physics autosamplers Refer to the AS3000 manual for more details 30 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Figure 27 Instrument Setup P4000 dialog box iix ET P4000 p UVE000 UVE000 Events EF As3000 Sample Prep 38 MDL Program 2 lt Aux Traces Lal gt Sample viscosity Normal Medium High Injection type Full loop Push loop tm Pull loop Flush volume 400 uL Needle height from bottom j2 mm r Tray temp control On Off Temp 25 T Column oven On C Off Temp faa E J Prep only method The Instrument Setup dialog box for the AS3000 autosampler allows you to set the following parameters e Sample viscosity This area allows you to select the draw rate of the syringe The default sample viscosity value of Normal is adequate for most samples e Injection type This area allows you to select from three injection modes Select the Full Loop option button if you want to make fixed loop injections equal in volume to the size of the sample loop that is attached to the injection valve of the autosampler In the Full Loop injection mode the amount of sample needed for your injection volume is equal to 70 uL plus 1 33 times your injection volume Therefore to inject 100 uL the autosampler withdraws 203 uL from the sampl
41. espective buttons below the Get button 56 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific Calibration Tab 5 UV6000 Diagnostics Calibrating the Detector The Calibration Tab allows for the complete calibration of the UV6000LP This is accomplished in two basic steps the array calibration or dark current calibration and the wavelength calibration The diode array produces a current even when both lamps are off This dark current must be subtracted from the total current that is present when the diodes are receiving light energy from the lamps This is the function of the array calibration The wavelength calibration is used to set and correct for the alignment and positioning of the optical bench and or the lamps These factors can become out of true due to such things as a shock or blow to the instrument or by changing the lamps Calibrating the Detector Array Calibration The procedures for performing these calibrations are as follows e Array Calibration e Wavelength Calibration Before attempting to perform either or both of the calibration procedures it is necessary to run HPLC grade methanol through the flow cell for at least 1hour The lamps should be turned on for 1 1 2 hours prior to beginning A reminder of these conditions is displayed after the user selects the button that starts the calibration procedure Make sure that there is no method running from the Control and Display pages described abov
42. fault rise time value of 2 0 seconds is adequate for most standard LC applications The available values are 0 0 1 0 2 0 5 1 2 5 and 10 s Increasing the rise time filter decreases the baseline noise but it can also result in peak broadening A good rule of thumb is to select a rise time that is no higher than one tenth of the base peak width for the narrowest peak of interest e Scans To collect scans select the scan checkbox Min wavelength Type the beginning scan wavelength in the Min Wavelength box The allowable values are 190 to 800 with a default value of 220 nm Max wavelength Type the ending scan wavelength in the Max Wavelength box The allowable values are 190 to 800 nm with a default value of 360 nm The maximum scan wavelength must be larger than the minimum scan wavelength Step Select an appropriate step size for the scan from the Step list The step size nm is the wavelength increment for the scan data A step size of 1 nm allows you to collect chromatograms for all the integer wavelengths within the scan range Increasing the step size decreases the spectral resolution of the scan data and the size of the data file If you are collecting scan data to create library spectrum files use a step size of 1 nm Scan rate Select an appropriate data rate from the scan rate list The scan rate is variable from 0 5 Hz once every two seconds up to 20 Hz The default value is 1 Hz which is adequate for most L
43. gt All Programs gt Chromatography gt ChromQuest b In the Main Menu window right click the instrument that you want to configure Figure 2 ChromQuest Main Menu window ChromQuest 5 0 2 The Enterprise Configure Instrument E mail c From the shortcut menu choose Configure gt Instrument 4 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 2 Configuring Thermo SpectraSystem LC Modules Adding the Modules to the Instrument Configuration The Instrument Configuration dialog box appears Figure 3 Instrument Configuration dialog box Instrument Configuration xi Instrument name SpectraSystem Instrument type Thermo SpectraSystem LC fname es OK Cancel Help 4 In the Instrument Configuration dialog box do the following w w Ty wo a In the Instrument Name box type an identifying name b In the Instrument Type list do one of the following e To modify the configuration of an existing Thermo SpectraSystem LC instrument do not select an instrument type as doing so erases the current configuration settings Go to step 5 e To configure a new Thermo SpectraSystem LC instrument select Thermo LC from the Instrument Type list Go to step 4c c In the warning message dialog box see Figure 4 click OK to return to the Instrument Configuration dialog box Figure 4 ChromQuest warning message window ChromQuest Xx A Changing the in
44. he autosampler s wrap feature by assigning the First Sample Vial as C39 Sample 2 will then be A01 However you still need to create to sample sets one to prepare and the other to run your calibration and sample vials You will discover other shortcuts as you integrate your autosampler into your laboratory practices Method Development Language Tab With sample preparation templates you can customize the individual parameter values to your application needs but you cannot alter the order of steps in the templates Figure 29 Instrument Setup MDL Program dialog box RE J Prep calibs also Estra vials fo e Window In this Prep style the window has several parameter fields and the scratchpad Mixer Heater Enable this checkbox to turn on the heater mixer and to set the heater temperature from 30 100 C Prep calibs also Enable this checkbox if you want to apply your sample preparation procedure to the calibration vials in your sample set 38 ChromOuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Extra vials This field sets the number of extra target vials required after each sample You must enter this value when using an MDL script ChromQuest cannot determine this number directly e Edit menu The lower portion of this pull down menu lets you obtain and export and print sample P P y p P P p
45. ith the reference photodiode beamsplitter or one of the printed circuit boards A sudden decrease in the Sample light level with a normal Reference light level can indicate a problem with the flowcell sample photodiode beamsplitter or one of the printed circuit boards A sudden decrease in the Reference light level and Sample light level can indicate a problem with the lamp grating or one of the printed circuit boards To investigate this problem turn off the lamp and check to see if the light levels change If they do not then the instrument is not generating or is not detecting light If this is the case follow standard troubleshooting procedures to isolate the fault In general a dirty flowcell yields acceptable reference levels and poor sample to reference ratios However use care since excess solvent absorbance can generate the same results as a dirty flowcell A weak lamp yields poor reference and sample light levels with an acceptable or near acceptable sample reference ratio Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 49 4 Direct Instrument Commands AS1000 AS3000 Direct Commands AS1000 AS3000 Direct Commands The AS1000 AS3000 has several direct commands designed to enable you to manipulate some of the autosampler s components the arm injector valve etc These commands are useful for maintenance and troubleshooting procedures To access the direct commands for AS1000 AS3000 1
46. llected using a different scan rate and bandwidth Wavelengths Type integer values for the wavelengths that you want to collect in the Wavelength boxes Scan Rate Select an appropriate scan rate for the discrete wavelength channels Increasing the scan rate of the discrete wavelength channels does not add substantially to the data file size Bandwidth Select an appropriate bandwidth for each discrete channel from the Bandwidth list e Lamp Options Deuterium Lamp On Select the Deuterium Lamp On check box if you are collecting data in the UV range from 190 nm to 365 nm Tungsten Lamp On Select the Tungsten Lamp On check box if you are collecting data in the Visible range from 366 nm to 800 nm e Shutdown method Select the Shutdown Method checkbox if you want to deselect both lamps e Prep only method Select the Prep Only Method check box if your method includes a sample preparation program and you do not want to make an injection 26 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Detector Setup FL2000 FL3000 The FL2000 and FL3000 detectors measure the fluorescence or phosphorescence signals emitted from some types of compounds Fluorescence occurs when the molecule is excited into a higher energy state by the absorption of electromagnetic radiation and then decays to a lower state releasing energy
47. lues in these columns are not useful for diagnostic purposes However during normal operation the Osc values are continually updated If these values remain constant suspect an instrument problem and contact your Thermo Fisher Scientific service representative e Bias These values indicate a general background noise level the specific values in this column are not useful for diagnostic purposes However during normal operation the Bias values should not be 0000 Contact your Thermo Fisher Scientific service representative if you obtain a 0000 value in this column 48 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 4 Direct Instrument Commands UV3000 Direct Command Menu Table 1 Diagnostic commands for the UV3000 FOCUS detector continued Command Description Light Level Diagnostics To diagnose the condition of the flowcell and lamps access the UV3000 diagnostics to check the light levels at all wavelengths appropriate for the application The best way to use light levels in troubleshooting is to know the typical light levels for a particular setup Then if you suspect a problem you can compare the typical levels with the current levels Note that light levels significantly changes with such factors as lamp age and flowcell type The following general guidelines can help in troubleshooting detector problems A sudden decrease in the Reference light level with a normal Sample light level can indicate a problem w
48. ment Wizard is displayed if it is set up to open at instrument startup Otherwise the Instrument window is activated as indicated by its title bar To use the Instrument Wizard you can invoke it by clicking the Instrument Wizard button in the command toolbar Instructions for using the Instrument Wizard and the Method Wizard are contained in Chapter 2 Tutorial of the ChromQuest 5 0 Chromatography Data System User Guide 14 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Control Opening the Instrument Setup Window Figure 15 ChromQuest Offline Instrument window with the Navigation bar and Instrument Wizard f SpectraSystem Offline Method untitled met Data None Project Default 10 x HO A S t uveoozsom X Dp ep Ast BBEFR AH S gt SsRO x Navigation Method EP Instrument Setup Integration Events Peaks Groups 4 Review Calibration E Advanced P Custom Report i PDA Options Instrument Wizard SpectraSystem Offline Z System Suitability B Data St Manual Integration Fixes E B Tiled Display i Create or modify a method F EB Integration Event Bd Peaks Groups Table Z s ES System Suitability Create a sequence Manual Integration cal Process a sequence IV Show at instrument startup SERA aANYANM ARAN Os A RAMANA oe I ThA Ase ey For Help press F1 4 If the Instrument Wizard appears click OK to close it The
49. meters e Saving the Method e Creating Shutdown Methods e Adding a Shutdown Run to the End of a Sequence Opening the Instrument Setup Window Each instrument in the Enterprise has an Online Instrument window and an Offline Instrument window From the Online Instrument window you can perform both instrument control and data processing operations From the Offline Instrument window you can perform only data processing operations such as creating methods and reprocessing data files To open the Offline Instrument window 1 Depending on the data system do the following e For ChromQuest choose Start gt All Programs gt Chromatography gt ChromQuest Then go to step 2 For ChromQuest SI choose Start gt All Programs gt Chromatography gt ChromQuest SI Offline Then go to step 4 2 In the Main Menu window right click the icon that represents your instrument to display a shortcut menu and choose Open Offline Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 13 3 Creating a Method for Instrument Control Opening the Instrument Setup Window 3 If the Login dialog box appears login a Type your user name for ChromQuest in the User Name box b Type your ChromQuest password in the Password box c Select a project from the Project list d Click Login Figure 14 Login window User name E A Cook i Password Project Cancel Help The Offline Instrument window appears The Instru
50. n Phone 800 532 4752 Fax 561 688 8731 Web site www thermo com ms To copy manuals from the Internet Go to mssupport thermo com and click Customer Manuals in the left margin of the window To suggest changes to documentation or to Help e Fill out a reader survey online at www thermo com Icms techpubs e Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com vi ChromQuest User Guide for the SpectraSystem LC Thermo Scientific Overview This manual contains configuration and instructions specific to Thermo Scientific LC instruments controlled from the ChromQuest 5 0 data system It does not duplicate those sections of the main manual that are common to all implementations of ChromQuest Please refer to the ChromQuest Chromatography Data System User Guide for general information This manual includes e Instructions for configuring ChromQuest for use with SpectraSYSTEM instruments UV1000 UV2000 UV3000 UV6000 P1000 P1500 P2000 P4000 AS1000 and AS3000 e A description of available LC method development options e Instructions for setting up SpectraSYSTEM instruments for data acquisition Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 1 Configuring Thermo SpectraSystem LC Modules In ChromQuest configuration of the modules of your instrument pumps autosamplers detectors and so on is done from the Main Menu window in ChromQuest A user can configure as man
51. n methods 19 Solvent extraction 36 Status Log 41 step size 25 T Target vials number of 34 time functions 32 Trigger 42 tungsten lamp 21 U UV3000 direct commands 47 ChromQuest User Guide for the SpectraSystem LC V Vial heating 36 Vial heating time acquisition method 36 vial tray temperature 32 Vials number of after each sample 34 W Wait in tray for described 36 Y Y axis labels for chromatograms 12 Thermo Scientific
52. o setting determines when and if the detector is set to output zero volts at a 8 p particular time 20 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Zero on wavelength change Normally the detector is zeroed at the beginning of the run and during wavelength changes Clearing the Zero on wavelength change check box allows you to enter wavelength changes in the wavelength time table without automatically zeroing the baseline Wavelength Timetable The UV1000 can also be programmed to do wavelength changes during the run using the timetable provided Lamp options check boxes Selecting the Deuterium Lamp On check box or the Tungsten Lamp On check box or both check boxes turns on the selected lamp s when the method is downloaded to the instrument One lamp must be selected for acquisition methods Both lamps can be deselected if the Shutdown method check box is selected Prep only method This checkbox allows you to avoid making an injection if you are performing a sample preparation method ChromQuest User Guide for the SpectraSystem LC 21 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters UV2000 Detector Setup The UV2000 is a time programmable dual wavelength UV Visible absorbance detector It operates in both single and dual wavelength modes In the dual wavelength mo
53. of a slightly different wavelength Figure 24 Instrument Setup FL2000 FL3000 dialog box ioi xi 52 P4000 FL2000 FL3000 As3000 33S Aux Traces VL Baseline Check R Trigger m Detection type Fluorescence Phosphorescence Rise time 2 0 v sec Data rate 10 Hz Lamp flash rate 100 wi Hz PMT voltage 600 f V Autozero time 0 min IV Zero on wavelength change I Shutdown method Lamp state I Prep only method e Run C Off C On e Detection type This area allows you to select between Fluorescence or Phosphorescence The difference between the two types is the longer half life of the phosphorescent signal See your FL3000 detector manual for more details e Rise time This list allows you to select an appropriate level of filtering for the detector signal A longer rise time reduces the short term noise However if the rise time is excessively high the signal might be skewed or even completely eliminated To minimize peak broadening select a rise time that is no higher than one tenth of the base peak width for the narrowest peak of interest For most LC analyses a rise time of 1 0 to 2 0 seconds is adequate e Lamp flash rate This list allows you to select the number of times per second that the Xenon lamp strobes The allowable values are 20 and 100 Hz with the higher value offering higher sensitivity at the expense of lamp lifetime Thermo Scientific ChromQuest User Guide for the
54. ol Entering the Instrument Setup Parameters Autosampler Sample Preparation Parameters AS3000 only The AS3000 autosampler has an optional sample preparation capability If you selected the Sample Prep Installed check box when you configured your autosampler the Instrument Setup window contains a Sample Prep tab Click the Sample Preparation tab to display the Sample Preparation dialog box Figure 28 Instrument Setup Sample Prep AS3000 only dialog box ox EF P4000 p LV6000 UVE000 Events 3 as3000 3S Sample Prep MDL Program 2 lt Aux Traces Lal gt Description m Prep viscosity Normal Fa or Copy From Cycle Medium gi i High MV Load foo uL from Sovent1 z 7 Mixer Heater AE ul from Sample gt Temp 30 c B Picket i uL from same z J Pickup large a ul from Sample J Prep calibs also V Add foo uL to Sample gt Extra vials 0 IV Mix vial fort ps minutes m Reagent vials J Heat vial for oO minutes amp T Mix vial for 2 a minutes B a P Wait in tray for oO minutes E pooo J Remove oC UL to waste at aril fim needle height IV Flush prep syringe with a000 uL from Solvent 1 i The steps in sample preparation programming for the AS3000 autosampler are grouped into dilution cycles that contain specific steps corresponding to specific instrument operations A dilution cycle is easily understood by comparing it to a manual dilution procedure In a m
55. or 1 Detector Model anaog st Acquisition Source 55420 E Ed Y Axis Units rots Y Axis Multiplier oomoo OK Cancel Help 2 In the Detector Name box type a descriptive name for the detector for example UV1000 UV3000 and so on as in the Detector Model Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 9 2 Configuring Thermo SpectraSystem LC Modules Configuring the Instrument Modules 3 Depending on the model of your detector do one of the following e Ifyou have a UV1000 UV2000 or FL2000 3000 detector continue at step 4 e Ifyou have a UV3000 or a UV6000 detector continue at step 5 4 Fora UV1000 UV2000 or FL2000 3000 detector do the following a From the Detector Model list select the model of your detector For the UV1000 UV2000 and FL2000 3000 detectors the SN4000 is automatically selected as the acquisition source after you select the detector model Figure 10 Detector Configuration dialog box xi Detector Name jovi Detector Model uvin Ed Acquisition Source sngo00aco F Y Axis Units a YzAxis Multiplier oomoo Cancel Help Click the button next to the Detector Model list to open the configuration dialog box as shown in Figure 11 Figure 11 UV1000 Configuration dialog box xi ID number ooo Cancel Help Type an identifying value such as the serial number of the detector in the ID number box Then click OK to close the dialog
56. pectraSystem LC 17 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters e Gradient curve The P4000 pump is capable of pumping either a linear gradient normal operation or convex and concave gradients for special applications The concave gradients change much more slowly in the beginning of the analysis and then change rapidly at the end The convex gradients operate in the opposite way for example they change rapidly at the beginning of the run and then change more slowly at the end Experimentation determines if one of these curves improves the chromatographic separations e Pump Table After selecting the solvent and various pump options fill in the pump table by entering a time value in minutes and the desired solvent proportions The solvent concentrations automatically adds up to 100 As each additional value is added for a particular solvent that amount is subtracted from Solvent A maintaining the total at 100 If necessary Solvent A can be edited and any amount that is added or deleted from it is deleted or added from Solvent B Figure 17 Instrument Setup window P4000 page io x E2 p4coo uvz000 38 4s3000 3 lt Aux Traces U Baseline Check R Trigger p Solvents Min pressure fi 0 psi Use Name VA methanol Max pressure f2o00 psi eB water SS Gradient delay fi mL Equilibration time 20 min Gradient curve J Shutdown method
57. reparation programs and starter scripts oe Import Copies an MDL file into the scratchpad Select Import to display the Open MDL Prep Program Dialog where you specify the filename drive and directory of the program you wish to import Click OK Select Cancel to exit this dialog without making a choice Analog Detector Parameters SS420 Board For any analog detector in your LC system that is connected to an 420 data acquisition board you must set up the data acquisition parameters This information is entered in the Analog Detector dialog or whatever name you have given to your analog detector A dialog box appears which displays the data acquisition parameters required for the type of data acquisition configured for this instrument Figure 30 Instrument Setup SS420 dialog box il Instrument Setup q 5 xi MB 5420 A Baseline Check I Trigaer Sampling Frequency 10 me lake Period z mSec Suitable for minimum peak width at base of 0 033 Min Run time fi Min Acquisition delay fo Min Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 39 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Acquisition Channel On Select this box to turn the acquisition for this channel ON If this box is not selected no data is acquired for this channel e Sampling This is the rate at which data is sampled by the system You can choose how you want to
58. s Description Enter your sample preparation method name in this box Prep viscosity Specify the sample preparation viscosity Normal Medium or High The viscosity setting affects the draw rate of the 2 5 mL prep syringe Selecting the High setting decreases the syringe draw rate to give a viscous sample more time to be drawn into and through the sample lines Decreasing the draw rate also reduces cavitation caused by low boiling point solvents The Normal setting option is appropriate for most applications Note The High setting option is the most appropriate setting for normal phase chromatography Mixer Heater Select this check box to turn on the heater mixer and to set the heater temperature from 30 100 C Specify the heating and mixing times in the Cycle group Heat vial and Mix vial steps respectively Prep calibs also Select this checkbox if you want to apply your sample preparation procedure to the calibration vials in your sample set Extra vials This readback field automatically displays the number of extra target vials required after each sample The displayed value is the highest number of vials specified in the Load Pickup Pick large or Add step from fields Cycles The autosampler automatically prepares your sample s according to the values specified in the Cycle group fields You can program the autosampler to repeat dilution cycles up to four times to carry out more complex procedures Select th
59. start the system manually that is from the keyboard In this case a message appears that allows you to start the data collection Figure 33 Instrument Setup Trigger dialog box 210 BD Extemal Events MBB 5420 UL Baseline Check T Trigger Type External z None ediately after clicking on Start Sequence acquisitions do not pause between runs Manual Operator has to press Enter to start the run Sequence acquisitions pause for confirmation between runs External If the data sampling is started from an external trigger select this option The type of trigger is designated in instrument configuration Select when using a contact closure from an autosampler or manual injector nn E Saving the Method After you enter the instrument set up parameters for your modules you must save the method before you can use it to acquire a data file To save the method 1 Choose File gt Method gt Save As command from the menu bar The Save Method File As dialog box appears 2 Select the directory where you want to save the method 3 Type the name of the method in the File Name box 4 Click Save You are now ready to use your method for data acquisition 42 ChromOuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Control Creating Shutdown Methods Figure 34 Save method file as dialog box Save method file as 2 xi Save in gS Methods gt c z a For LC Test
60. stored in the acquired data file In addition to entering the instrument control parameters for all your instrument modules you also need to define the trigger that starts the instrument into a run This section contains the following topics that describe the dialog boxes in the Instrument Setup section of the method e Pump Parameters e Detector Parameters e UV6000 Events Autosampler Parameters AS3000 and AS1000 Autosampler Sample Preparation Parameters AS3000 only e Method Development Language Tab e Analog Detector Parameters SS420 Board External Events Auxiliary Traces e Trigger 16 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Pump Parameters The four types of SpectraSYSTEM pumps are P1000 P1500 P2000 and the P4000 The P1000 and P1500 are isocratic pumps The P1500 has two solvent channels The P2000 and P4000 are gradient pumps The P2000 can be programmed to produce binary mobile phases The P4000 can be programmed to produce quaternary mobile phases In addition the P4000 contains stored programs for twenty one gradient profiles Solvents Use check boxes Select the number of solvents A B C and D depending on the pump model that you want to use with the check boxes Name Type the names of the solvents in the Name boxes The names automatically appear in the pump table below e
61. strument type will erase ALL device settings cne 5 In the Instrument Configuration dialog box see Figure 3 click Configure to open the Thermo LC dialog box Figure 5 Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 5 2 Configuring Thermo SpectraSystem LC Modules Adding the Modules to the Instrument Configuration Figure 5 Thermo SpectraSystem LC dialog box Thermo SpectraSystem LC Fa Available modules Configured modules Event Configuration 451000 6S 3000 P1000 S2 P1500 8 P2000 8 P4000 _ 5N4000 tle Options Auto Configuration Cancel Help 6 Add the modules of your instrument to its configuration e To manually add a module go to step 7 To auto configure your instrument go to step 8 7 To manually add a module to the instrument configuration a In the Available Modules box double click the icons that represent the module of your LC system The icons appear in the Configured Modules box on the right b Continue on to Configuring the Instrument Modules on page 7 All detectors UV1000 UV2000 UV3000 UV6000 FL2000 and FL3000 are available under the generic Detector icon When you double click the detector icon in the Available Modules box it crosses over to the Configured Modules box as the Analog icon 8 Alternatively if you have an SN4000 System Controller you can use the Auto Configuration button to set up your LC system a Click Auto
62. the Control Instrument Status command 2 Click the Left hand mouse button A set of tabbed pages appears 3 Move the mouse cursor over to the pump tab Click the Left hand mouse button 4 Place the cursor anywhere on the tabbed page Click the right hand mouse button After clicking the right hand mouse button a shutdown button appears Click the Shutdown button to stop the pump UV1000 2000 Direct Command Menu To access the direct command menu for the UV 1000 2000 1 Select the Control Instrument Status command 2 Click the Left hand mouse button A set of tabbed pages appears 3 Move the mouse cursor over to the UV1000 tab or the UV2000 tab 4 Click the Left hand mouse button Place the cursor anywhere on the tabbed page 5 Click the right hand mouse button After clicking the right hand mouse button an Autozero button appears Clicking the Autozero button zeros the detector s response The detector signal can be zeroed at any time during a run 46 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 4 Direct Instrument Commands UV3000 Direct Command Menu UV3000 Direct Command Menu R kod 1 Thermo Scientific To access the direct command menu for the UV 3000 detector Select the Control Instrument Status command Click the Left hand mouse button A set of tabbed pages appears Move the mouse cursor over to the UV3000 tab Click the Left hand mouse button Place the cursor anywhere on the ta
63. tific ChromQuest User Guide for the SpectraSystem LC 11 2 Configuring Thermo SpectraSystem LC Modules Configuring the Instrument Modules The following shows commonly used Y axis labels and their corresponding multipliers Y Axis Label Y Axis Multiplier Volts or AU 0 000001 Millivolts or mAU 0 001 Microvolts or pAU 1 Other Enter a number such that when multiplied by microvolts gives you the desired units 7 In the Y Axis Multiplier box type the conversion factor to be applied 8 Click OK to exit the Detector Configuration dialog box 9 Click OK to exit the Thermo SpectraSystem LC dialog box 10 For ChromQuest SI click Close to exit the ChromQuest SI Configuration dialog box see Figure 1 11 Restart the instrument application for the configuration to take effect 12 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific Creating a Method for Instrument Control A ChromQuest method contains the information required to control your instrument modules and process your chromatographic data A Thermo SpectraSystem LC instrument can contain one analytical pump one autosampler and one or more detectors This chapter contains information on how to enter the chromatographic conditions for these modules into your method You must enter these conditions into your method before you can use the method to acquire a data file Contents e Opening the Instrument Setup Window e Entering the Instrument Setup Para
64. to change the excitation wavelength and the emission wavelength as a function of time The emission wavelength must always be greater than the excitation wavelength And for the highest sensitivity it is best to ensure that both wavelengths correspond to the excitation and emission maxima for the compound s of interest The detector signal is normally zeroed at the beginning of a run Autozero time of 0 minutes and also should be zeroed at each wavelength change 28 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters UV6000 Events The UV6000 detector has a remote output on its rear panel called EVENT The EVENT output is an open collector and is capable of sinking lt 30 mA at 30 Vdc suitable for connecting to TTL and other families of ICs The sense setting of this output must match those of the connecting equipment inputs Figure 25 UV6000 events sense settings a a 5V EVENT READY RUN roe 1 Foe spare CoM CoM CoM e J amp w Hbddidiiiisik Ch1 Ch2 START ZERO SPARE time 4 2 100 mv 5 COM COM COM T a RS232 OO00000000000 OUTPUT s a E e Oo0o0oo0000000000 ATAA J790 e Model UV6000LP Serial
65. ve configured external events for your instrument Figure 31 External Events dialog box E External Events Pel x l Evert O O State Pifvaves o 2 500 Close FZ Valve 1 1 200 Open To program an event select it from the list of configured events by clicking the Event field Enter the time at which the event is to actuate the length of time you wish the event to remain in the desired state Duration and the State of the event during the event Close or Open You can configure as many events as you want for the run Auxiliary Traces During a run the pump pressure pump flow stability and column temperature can be monitored and stored in the data file as auxiliary traces Figure 32 Instrument Setup Aux Traces dialog box E Instrument Setup E lol x Li f m P4000 Pressure pi 2 amp P4000 Flow Stability 3 4 OvenTemperatue sss CCCCSCid Thermo Scientific ChromQuest User Guide for the SpectraSystem LC m 3 Creating a Method for Instrument Control Saving the Method Trigger The Trigger dialog box of Instrument Setup allows you to configure how the modules are started You typically select the External trigger for a Thermo SpectraSystem LC instrument which means that the SpectraSYSTEM autosampler performs an injection and then trigger the pump and detector at the end of injection If you have only an analog detector connected to an 420 board you might want to make a manual injection and then
66. vent 0 1500 uL and delivers it to waste 36 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 3 Creating a Method for Instrument Control Entering the Instrument Setup Parameters Sample Preparation Programming Rules To develop sample preparation Place the extra vials in the three vial positions subsequent to the Sample vial position Sample 1 Sample 2 and Sample 3 It is impossible to add delete or change the order of the steps within the Cycle group however you can skip any step except an Add step by setting its volume to 0 uL Specify one cycle for each delivery of chemicals to or for each operation performed on the target vial Specify the desired final target vial volume in the Add step To perform an operation on but not deliver to the target vial set the Add step volume to 0 uL The volume specified in the Add step in a given dilution cycle must be less than or equal to the sum of the Pick large and Load step volumes The Add step makes deliveries to the target vial on a last in first out basis The autosampler injects only from the last vial referenced in the last Add step Customizing Sample Preparation Thermo Scientific In our discussion so far we have assumed that the contents of the vials in the Cycle group steps have matched the autosampler s names for those positions in the Sample Queue Menu For example we have assumed the sample to be in the S
67. x 5 Optional Type an ID number for example serial number or asset tag in the ID number box to help identify the instrument for GLP Good Laboratory Practices documentation 6 Type a default injection volume in the Default Injection Volume box This value can be overridden in the Single Run Acquisition dialog box and the sequence table 7 Click OK to exit the autosampler configuration dialog box 8 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific 2 Configuring Thermo SpectraSystem LC Modules Configuring the Instrument Modules Pump Configuration To complete pump configuration 1 In the Configured Modules box double click the icon for your pump to open its configuration dialog box 2 From the Pressure Units list select the pressure units that you want to use to display the backpressure of your system psi bar or megaPascal 3 From the Head Size list select the head size of the pump pistons either Analytical or Prep 4 Optional Type a label in the ID number box Figure 8 P4000 Configuration dialog box P4000 Configuration Ed Pressure units MPs Cancel Head size Analytical 10 mL min 7 cance H ID number elp Detector Configuration To complete detector configuration 1 In the Configured Modules box double click the icon for your detector to open the Detector Configuration dialog box Figure 9 Detector Configuration dialog box x Detector Name Detect
68. y systems as they want however only as many systems as there are licenses can be run simultaneously In ChromQuest SI configuring the data system to recognize your instrument modules is done from the Instrument Configuration application Note For ChromQuest you must have instrument administration privileges to configure instruments To configure an instrument you need to add the modules of the instrument to its configuration and then you need to configure each module Contents e Adding the Modules to the Instrument Configuration e Configuring the Instrument Modules Adding the Modules to the Instrument Configuration To add modules to the instrument configuration 1 Depending on the data system do one of the following e For ChromQuest go to step 3 e For ChromQuest SI go to step 2 2 For ChromQuest SI do the following a Choose Start gt All Programs gt Chromatography gt ChromQuest SI Config The ChromQuest SI Configuration dialog box appears See Figure 1 Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 3 2 Configuring Thermo SpectraSystem LC Modules Adding the Modules to the Instrument Configuration Figure 1 ChromQuest SI Configuration dialog box ChromQuest SI Configuration b Click Instrument Configuration The Instrument Configuration dialog box appears see Figure 3 c Goto step 4 3 For ChromQuest do the following a From the Windows desktop choose Start
69. ype cell at the end of the sequence Double click in the cell to open the Sample Run Type dialog box Select the Shutdown run type Open a Shutdown method in the Method field Nn NO A o N Save the sequence The sample injection amount and the calibration level are automatically set to 0 The number of repetitions is automatically set to 1 The data file is automatically assigned a time stamp name unless otherwise specified Note Do not enter other run types into the same row as a shutdown run Shutdown runs are highlighted in red on the view screen 44 ChromQuest User Guide for the SpectraSystem LC Thermo Scientific Direct Instrument Commands This chapter describes the types of direct instrument commands that can be invoked from ChromQuest Refer to the following for a list of instruments that have direct command menus Instrument Direct Command Menu Detectors UV1000 Yes UV2000 Yes UV3000 Focus Yes FL2000 3000 No Autosamplers AS1000 Yes AS3000 Yes Pumps P1000 Yes P1500 Yes P2000 Yes P4000 Yes Contents e P1000 1500 2000 4000 Direct Command Menu e UV1000 2000 Direct Command Menu e UV3000 Direct Command Menu e AS1000 AS3000 Direct Commands Thermo Scientific ChromQuest User Guide for the SpectraSystem LC 45 4 Direct Instrument Commands P1000 1500 2000 4000 Direct Command Menu P1000 1500 2000 4000 Direct Command Menu To access the direct command menu for the P1000 1500 2000 4000 1 Select

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