NOTICE: Varian, Inc. was acquired by Agilent Technologies in May 2010. This document is provided as a courtesy but is no longer kept current and thus will contain historical references to Varian. For more information, go to www.agilent.com/chem. Varian, Inc. 2700 Mitchell Drive Walnut Creek, CA 94598-1675/USA Saturn® 2000 GC/MS MS Workstation Version 6 Operation Manual ©Varian, Inc. 2003-2009 Printed in U.S.A.
Contents Getting Started........................................................................................................................11 About this Manual/Help ............................................................................................................................................11 Additional Manuals/Help...........................................................................................................................................11 MS Workstation Toolbar ..........
Specifying Per-Sample Data Handling Parameters ...............................................................................................109 Specifying a RecalcList ..........................................................................................................................................110 Monitoring the Status of the Run ............................................................................................................................110 Using QuickStart.......................
System Control Toolbar .......................................................................................................151 Main Toolbar...........................................................................................................................................................151 2000 MS Method Basic Scan Functions .............................................................................153 Introduction ................................................................................
Tandem Mass Spectrometry (MS/MS) ...................................................................................................................219 Automated Methods Development .........................................................................................................................221 MS/MS ....................................................................................................................................................................
3800 GC System Control Command Reference .................................................................303 Status and Control Window ....................................................................................................................................303 Setup Ethernet Ports Dialog Box............................................................................................................................327 8400/8410 SampleList Window Extensions ..........................................
Sequence Window..................................................................................................................................................414 Automation File Editor .........................................................................................................415 Overview.................................................................................................................................................................415 Accessing the Automation File Editor.....
Save Method As Dialog Box...................................................................................................................................464 Saturn Printer Setup Dialog Box.............................................................................................................................465 Preferences Dialog Box..........................................................................................................................................
Batch Report Printing without Recalculating ..........................................................................................................530 Viewing a Report for a Single Run .........................................................................................................................531 Method Builder Dialog Boxes..............................................................................................535 Create/Open Method File Dialog Box.......................................
File Revision Settings .............................................................................................................................................572 Standard GC Reports Command Reference ......................................................................575 File Menu ................................................................................................................................................................575 Search Menu .............................................
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Getting Started About this Manual/Help This manual/help system contains information about how to acquire data, build methods, and operate the Saturn GC/MS through the Varian MS Workstation. This manual also describes the configuration of the 3800 and 3900 GCs for standard Ethernet communication with the Saturn 2000 and MS Workstation’s System Control application. Use this manual in conjunction with the other manuals supplied with your MS Workstation and your 3800 GC or 3900 GC.
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MS Workstation Toolbar Overview Saturn GC/MS Workstation is a suite of applications for controlling chromatographs, collecting data from chromatograph detectors, and analyzing those data. The MS Workstation Toolbar provides quick and easy access to the Saturn GC/MS Workstation applications. When activated, the MS Workstation Toolbar behaves very much like the Windows Taskbar.
Elements of the MS Workstation Toolbar Application Buttons for immediate access to the selected application. Tooltip shows the application name when the cursor rests on the Application Button. Quick Link Buttons provide menu selections of operations to be performed on the listed file. Application Descriptions give a brief description of the application that will be opened when the cursor rests on the Application Button.
Application Buttons Used to monitor instrument status, perform automated injections, and perform batch recalculations. Used to view and edit instrument operation, data acquisition, and data handling methods. Used for off-line editing of SampleLists, RecalcLists and Sequences. Used to review chromatograms and spectra, perform library searches, and review and process quantitation results. Used to create, edit, and view standard MS reports. Used to create, edit, and view customized MS reports.
Quick Link Buttons Most Recently Used Data File. A menu of operations that can be performed on the Most Recently Used Data File are displayed when the button is pressed. A different data file can be selected from a list of most recently used files. Most Recently Used Method. Menu of operations that can be performed on the Most Recently Used Method will be displayed when the button is pressed. A different method can be selected from a list of most recently used methods.
MS Workstation Toolbar Options Right-click the bar to display the Toolbar Options. A menu of MS Workstation Toolbar configuration options and operations that may be performed will be shown.
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Launching Applications from the MS Workstation Toolbar Using the Application Icon Buttons Saturn GC/MS Workstation applications appear as icon buttons on the MS Workstation Toolbar. As you move the mouse over these buttons, the name of the application is shown in a tooltip window below the cursor. Click any icon in the MS Workstation Toolbar to launch the corresponding application.
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MS Workstation Toolbar Options Moving the MS Workstation Toolbar The MS Workstation Toolbar can be moved to any edge of the Windows screen. Click a portion of the MS Workstation Toolbar that does not contain application or Quick Link buttons and drag the toolbar to the edge of the screen that you desire. When you release the mouse, the toolbar will remain on that edge. The MS Workstation Toolbar remembers its location the next time it is started.
Move to Windows Taskbar You can display the MS Workstation Toolbar as a Windows Taskbar icon. Taskbar icons appear in the lower right (or bottom) of the Windows Taskbar (the bar on which the “Start” button appears). When displayed as a Taskbar icon, the toolbar no longer takes up space on the screen. When you click the MS Workstation Toolbar icon, the options menu is displayed. Show/Hide Applications on Toolbar Selecting this option displays the Show and Hide Applications on Toolbar dialog box.
This dialog box allows you to select which Saturn GC/MS Workstation instrument modules are available from this Workstation. When an instrument module is available, it will appear in System Control if the corresponding instrument is connected and powered-on, you will be able to create a Method section for it, and you will be able to format reports for it. The top list box shows all instrument modules that are currently installed and enabled in the Saturn GC/MS Workstation.
Run Application This hierarchical menu item lists all applications showing on the MS Workstation Toolbar. When you select an item from this list, the corresponding application is launched. Help on This hierarchical menu item lists all applications showing on the MS Workstation Toolbar. When you select an item from this list, the online help corresponding to the application is displayed.
2000 MS Module Control Starting System Control the First Time Before you enter System Control for the first time, confirm that the proper instrument modules have been enabled and that any instrument modules that are not part of the system have been disabled. To enable or disable instrument modules refer to the section of the MS Workstation Toolbar, Enable/Disable Instrument Modules.
Refer to the installation instructions packaged with your Ethernet card for information on installing the Ethernet card in your computer. Before proceeding, your Ethernet card should be recognized by your Windows version. When done, the Network Neighborhood icon should appear on your Windows desktop. NOTE: For the following procedure, the use of disks other than the ones that were used for the original Windows installation may result in a Ethernet driver version mismatch that keeps Windows from starting.
The Network dialog box is displayed. 3. If TCP/IP is already listed in the list of network components, skip to the Note after step 5, otherwise, click Add. The Select Network Component Type dialog box is displayed. 4. Select Protocol and click Add.
The Select Network Protocol dialog box is displayed. 5. Select Microsoft as the manufacturer. Select TCP/IP as the protocol. Click OK. The protocol is added to your installed network Component list. NOTE: If you are not connecting your Workstation to a company network (that is, you are not assigned an IP address by a Network Administrator), follow the next three steps. If you are connecting your Workstation to a company network, skip to Configuring the GC for a Company Network.
Enter an IP address in the range 10.2.128.1 through 10.255.255.254. Note that if you are adding more than one Workstation to this network, each Workstation PC must have a unique IP address within this range. The Subnet Mask will be automatically set to 255.0.0.0. Do not change this value.
Ensure that no entries have been made in your Gateway, and that Domain Name Server (DNS) and WINS Configuration have been disabled. These entries are not used in an isolated network and may cause problems if they are present. Delete any settings that may have been entered from a previous configuration. 2. Click OK. Reboot Windows for the changes to take affect.
Contact your Network Administrator (or whoever assigns IP addresses for your network) to see what the appropriate settings are for your Gateway, and whether Domain Name Server (DNS) and WINS Configuration are needed. 5. Your Network Administrator may also instruct you to specify parameters in the Bindings and Advanced tabs. 6. Click OK. Reboot Windows for the changes to take affect.
Configuring the 3800 or 3900 GC Communication (No Company Network) Use the following instructions if either a 3800 or 3900 GC and Varian MS Workstation PC are being connected to an isolated network, that is, a network dedicated to Varian MS Workstations and the instruments they control. In this case, a Network Administrator will not be involved in assigning IP addresses.
From the Setup Ethernet Ports, click Setup for IP Address Management [BOOTP Server]. Click Setup. When the Setup BOOTP Server dialog box is displayed, turn on the 3800 or 3900 GC that has been connected to the network. NOTE: If more than one Workstation is being connected on the same network, only one Workstation should manage the IP addresses for all GCs connected (all others should have the Manage IP addresses from this Workstation checkbox unchecked).
Click the Manage IP addresses from this Workstation checkbox to manage your GC’s IP address from this Workstation. As the GC is turned on, its Ethernet address is added to the list.. The IP address is automatically generated. Enter a host name for each GC. This name is used to identify the GC in the Workstation. You cannot connect to a GC until you provide it a name. Click OK after entering host names for each GC. NOTE: Proceed to Using a Password to Protect BOOTP Settings.
Click System Control/Automation. When System Control has started for the first time, the Star Assistant Communication Configuration Wizard will appear to guide you through the setup and network connections of your GC. NOTE: Before proceeding with this section, consult your Network Administrator about whether a central BOOTP Server is available on the network. 1. If IP addresses are managed by a central BOOTP Server, then proceed to Specifying IP Addresses from a Central BOOTP Server. 2.
From the Setup Ethernet Ports dialog box select Setup to display the BOOTP Server dialog box. Select Setup to display the BOOTP Server dialog box. The BOOTP Server dialog contains a table listing all 3800 and 3900 GCs to which IP addresses may be assigned.
NOTE: If more than one Workstation is being connected on the same network, only one Workstation should manage the IP addresses for all GCs connected (all others should have the Manage IP addresses from this Workstation checkbox unchecked). The Workstation acting as BOOTP Server must remain running all the time to allow other Workstations to connect to GCs. If more than one Workstation is managing IP addresses, naming conflicts may arise. Check this box to enable the BOOTP Server.
When the Assign # IP addresses starting from: #.#.#.# radio button is selected, the bottom portion of the dialog changes. You may select to consecutively assign IP addresses beginning from a particular address. Enter the number of IP addresses you want to assign automatically. Enter the starting address here. As 3800s are powered on, IP addresses are automatically assigned starting with this address. NOTE: Proceed to Using a Password to Protect BOOTP Settings.
The Instrument menu is displayed. Press 1 to select the Remote/ Local Control screen. The Ethernet address, IP address and Alias (which may not yet be assigned) are displayed. ACTIVE METHOD EDIT METHOD Method 1 Method 1 CTRL RUN TIME END TIME 0.00 20.00 REMOTE / LOCAL CONTROL Enable Ethernet Address: XX:XX:XX:XX:XX:XX IP Address: XXX.XXX.XX.XXX Alias: 3800A Use the Ethernet address shown here when setting up the BOOTP Server.
Ethernet Ports dialog box is not displayed, select the Setup Ethernet Communications menu item from the Instrument menu to display the Star Assistant Communication Wizard. Click Next. Select Setup to display the BOOTP Server dialog box. The BOOTP Server dialog is displayed. Check this box to enable password protection. The next time you enter the BOOTP Server dialog box from the Setup Ethernet window, you will be prompted for a password. Enter a password here.
Adding a GC and Varian MS to the Instrument in System Control Once you have configured your Workstation computer and 3800 or 3900 GC for network communication, you may select one GC to be controlled from each Varian MS Workstation. If it is not already running, start System Control. The Star Assistant Communication Configuration Wizard will be displayed if you have not yet configured your GC Ethernet connections. Click Next. Click Address to attach to a 3800 GC on the Ethernet network.
This 3800 GC is connected to Port 44. The status indicates the availability of the GC. The IP address of the GC is shown here. Click OK, and wait for the 3800 to connect. When the GC connects to System Control, it will be represented by an icon at the bottom of the Configuration Window. The icon will have a label reading 3800.44, and will include the Host Name of the GC appended to the label.
Elements of the Configuration Screen After the 3800 or 3900 connects to System Control, configure it in an Instrument by moving its icon from the bottom of the Configuration Window into the Instrument Area. System Control will remember where to put the icon the next time that the 3800 connects. If the 3800 is to be operated with an 8200, make the 8200 the AutoControl Module. Place the GC icon in the AutoControl Module if either a CP-8400 or CP8410 AutoSampler will be used with the GC.
Instrument Parameters, Instrument Name, Operator Name, and Instrument status are listed here. AutoStart Module area. Place the 8200 AutoSampler Module icon in this box. Module icon showing that 3800 GC Module 44 has been configured to Instrument #1. Click button to enter or change the Instrument Name, Operator Name, and Maximum allowable error count. Modules that have logged in and are available for configuration into an instrument are displayed here. Once the modules are in place you are ready to proceed.
software versions (i.e. the forth software system). When the maximum number of non-fatal errors is exceeded during automation, the automation sequence halts. Setting this value to zero disables this feature. You are optionally prompted for this information when you start an automated sequence of injections or recalculations. Running an MS Method Without a GC Method To run an MS method without the GC module or GC method, open System Control. Under the menu Instrument, select Configuration.
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2000 MS Instrument Control Command Reference Saturn Module Dialogs Saturn Module Keypad Dialog This dialog can be hidden by clicking on Hide Keypad.
Spectrum Toolbar Click the green arrow t hide the toolbar. Click the upper left of the full screen display to restore the toolbar. Click full scale to normalized to chromatogram. Double-clicking the chromatogram does the same. Click to return the xy axes to the previous scale. Click spectrum plot to open a preview of the spectrum. Click scale to choose between Auto Scale and Fixed Scale Intensity. Click mass range to choose between Acquired Mass Range, Fixed Mass Range, or Maximum.
Item Description Manual Control Click the Manual Control to turn on or off the trap controls (rf, Filament, and Multiplier) and to open the CI and Cal gas valves. Also adjust the rf response, the CI gas pressure, and the Cal gas pressure. This mode is also used to select the current trap filament and to adjust the axial modulation voltage. Although scans may be taken and displayed under method conditions of any one of the MS Method segments, data may not be acquired while in this mode.
Instrument Settings Item Description Method button Opens the Method Editor program. Segment # box Select the current segment of the active method. Scan Mode Ionization mode of the current segment, such as EI-Auto. Ion Prep. Ion preparation method of the current segment, such as MS/MS. Setpoints tab Item Description Filament Selection Click to select the current filament. Saturn has 2 filaments so the system can be used if one burns out.
Item Description Adjust Cal Gas Click to adjust the cal gas pressure. Adjust rf Ramp Change the rf setting for the instrument by turning the screw at the bottom front panel. Adjust Set the proper CI reagent pressure for CI analysis. The pressure is very dependent on the reagent gas used. Reagent Gas Selection Box Choose which CI gas you are using. Done Used when you complete your adjustment.
Item Description Start Auto Tune Begins the event sequence that will tune the instrument. Only checked boxes will be executed. Reset Stops the auto tune process. Continue Starts the next selected function if the single step option has been checked. Hide Keypad Causes upper portion of the screen to be removed so that the lower portion can be expanded in the display. Display Selection Select the display.
Item Description Electron Multiplier Voltage Manual adjustment of the Final Gain Setting determine from the Auto Tune check. SIS Amplitude Adjust Factor Adjust each trap system for optimum ion sensitivity and ejection. The voltage adjustment range is between 50 to 200%. The default is 100%. Temperatures Item Description Start Bakeout Execute the bakeout conditions, which removes volatile material from the ion trap surface. Reset End a bakeout before the specified time.
Item Description Start Click Start to execute the desired test Reset Cancel a test executed with Start. System Test Item Description Run To Completion Click to run all tests without stopping. Halt On Error Halts the system checks when an error is detected. Detailed test of the heater zones Item Description Trap Tests the Ion Trap heater element May take up to 13.5 hours to complete. Manifold Tests the Manifold Heater element. Transfer Line Tests the Transfer Line heater element.
Monitor Window Item Description Multiplier check box Display the voltage (center left) on the multiplier when on. rf check box For Service Engineers. Filament check box Display the status of the system filaments (upper right). Ion gauge check box View the vacuum status using the filament selected by the Filament Radio Button. Filament Select a filaments and view the ion gauge vacuum system test.
Shutdown Mode Item Description Shutdown button Shuts down the system in an orderly manner. The pump speed is slowly reduced and the heaters are turned off so that the system slowly cools. Reset button Brings the system back to a ready state if the Shutdown procedure was started. This restarts the pumps and turns on the heaters. Diffusion Pump Shutdown Sequence NOTE: The Diffusion Pump System shutdown sequence takes at least 30 minutes: The Saturn GC/MS heaters are turned OFF.
Turn OFF main power by placing switch at rear of system into OFF (down) position. Manually vent the system for at least 5 minutes using the lever on front panel. NOTE: DO NOT ATTEMPT to VENT SYSTEM by any other method (via transfer line, foreline vacuum clamps, etc.). Rapid, improper venting of the system will cause diffusion pump fluid to backstream into the manifold and ion trap.
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2000 MS Instrument Window The 2000 MS Instrument Window System Control has four major sections: the System Control Menu bar, System Control Toolbar, Saturn Keypad Dialog, Chromatogram and Spectrum Toolbar, and Spectrum Display.
Activate Method allows you to choose a method from those already prepared. This will set the conditions for the GC, MS, AutoSampler and data handling. Other sections will also be activated if they are part of the method. Upload Active Method from Modules will allow you to get the conditions from the existing modules to be saved in a new method. Whichever method is active will now be converted to the conditions of the active modules. New Sample List allows you to open the dialog box to create a sample list.
Edit Menu Click the Edit menu and highlight Edit Module Info. Each module in your system (3800GC, 2000MS, 8200 AutoSampler) contains its own message log and documentation screen. The Module Documentation screen shown below allows you to keep a record of performance, maintenance, hours used, or any other comments you wish to make. Use the Add, Edit, and Delete buttons to record any information you wish about the MS module.
Inject Single Sample Menu The command will allow you to give the sample information prior to an injection. The dialog box below will appear when this command is invoked. The 2000 module window must be in acquisition mode for the system Not Ready to convert to Ready and then a manual injection can be made. If an AutoSampler is used, click Inject in the bottom left corner. The sample type can be changed by double clicking in the field below Sample Type. The following displays your choices.
Automation Menu Below is a picture of the Automation pull down menu and a description of the functions. Begin Sample List will cause an automation to start at line 1 and end at the last line. Begin Sequence will allow you to change methods and sample list during an automation. An example of this might be to run a set of samples using EI and then the same set of samples using a different MS method for CI. Begin At starts an automation at a particular line and runs until the last line is completed.
Begin RecalcList will allow you to start an automated recalculation. A recalculation list must already be prepared and selected to do this. A New Recalc list may need to be made. Begin at Selected RecalcList Line allows you to process a recalculation list starting with a chosen line and proceeding with the rest of the list. View Calibration Curves will allow you to view any of the curves for the calibrated compounds in the active method. An example of the calibration curve screen is given below.
Instrument 1 Faults allows you to see if there are any faults in any of the modules contained in Instrument 1. An example of this screen is shown below. The update key will allow you to periodically check for new faults without opening and closing the dialog box. 2000 faults are not reported in this window. Setup Ethernet Communication will allow you to set up the communication between the 3800 GC and System Control.
Instrument 1 Status allow you to view the status of the modules connected to the system. Message Log allows you to view the event log for the MS module. The log display is shown below. All error messages for the Saturn Module will show up here. 2000 module allows you to display the Saturn module control screen. Help Menu Click an item in the Contents box to open online help.
In the Help dialog box, from the Index tab, you can select a particular topic. Click the selection, go to the bottom of the screen and click Display.
System Control Toolbar The system control toolbar is located near the top of your screen. A picture of this toolbar is displayed below. Clicking on this button will allow you to create a new automation file. Clicking on this button will allow you to select a new automation file. Clicking on this button will allow you to view/edit or print a method. Clicking this button will allow you to activate a method. Clicking on this button will allow you to edit notes for an automation file.
Clicking on this button allows you to start a sample list that you have created. The list must already be selected. Clicking on this button allows you to start a sequence list that has been created. Clicking on this button allows you to suspend a list that is running. Clicking on this button allows you to begin a list. Clicking on this button is used to stop a list that is already running. Saturn Module Keypad Dialog This dialog can be hidden by clicking on Hide Keypad.
Spectrum Toolbar Click the arrow to hide the toolbar. Click the upper left of the screen to restore the toolbar. Click full scale to normalize the chromatogram in the vertical and horizontal directions. Double-click the chromatogram to do the same. Click this to return the xy axes to the previous scale. Clicking on the spectrum plot button will cause a window previewing the spectrum to be displayed. Clicking on the scale button allows you to choose between Auto Scale Intensity and Fixed Scale Intensity.
Choosing the Chromatogram only option will allow you to see a live chromatogram as in the example below. Click Hide Keypad to expand the chromatogram. Notice in the following picture the text information at the top is hidden. To bring the keypad display back, click Show Keypad. Configuring the Real-Time Spectrum Display During an analysis it is possible to observe the spectrum in the system control screen.
Choosing the Spectrum only will allow you to see a live spectrum as in the example below. Click hide keypad to expanded the display.
Click Show Keypad to display the keypad. Status and Control Window You are now ready to program the GC/MS to perform fully automated data acquisition. Initially the MS Module Window will look similar to the figure below. If you do not see this screen, go to the pull down menu labeled Instrument, and select the item “Saturn GC/MS”. The upper left side of the window shows the ion trap schematic, which allows the ion trap to be turned on. If the trap is displayed in red, it is currently disabled.
You must select a method segment that is not a Filament/multiplier delay segment for the ion trap to be enabled. This method and segment selection is located in the center of the screen. This center section deals with the active method and the instrument set points.
The informational fields displayed in the above dialog are taken from the currently executing method. The Scan Mode describes the ionization mode of the current segment, for example, EI-Auto. The Ion Prep. is the ion preparation method of the current segment, such as MS/MS. The Range will show the mass range being scanned by the current segment. Operating Conditions The Operating Conditions located to the far left of the Saturn Module window allows you to observe the current instrument information.
Two filaments are provided to reduce down time for maintenance. The selection of the filament is made by choosing the radio button. The Axial Modulation voltage can be changed by using the up/down arrows and then clicking the apply button. The Axial Modulation Voltage is applied to the endcap electrodes as described in the section Saturn Method Editor. Proper setting of this voltage is critical to resolution and sensitivity in the ion trap.
When the rf Modulator Response screen is displayed, it shows a real time view of the rf modulator response from 20 to 650 m/z. The vertical axis of the display is in percentage of counts, and the horizontal axis is mass units. One scan, over the entire mass range, requires about 1s. The Counts are displayed as Average rf modulator response and Highest rf modulator response in counts. To monitor the rf voltage, observe the displayed ramp.
When it is properly adjusted, the dialog will say the rf response is within limits. When you are finished, select the Done button. To adjust the Cal gas pressure click “Adjust Cal Gas”. You obtain a screen from which you can check and adjust the setting of the calibration compound needle valve. When adjusting the cal gas, the following happens automatically.
In CI, as in EI, the Saturn GC/MS is tuned to achieve the best combination of maximum peak height (sensitivity), optimum resolution of peaks, and smooth peak shape. And in CI, as in EI, the key to proper tuning is to optimize the number of ions in the ion trap: Too few ions, sensitivity suffers; too many ions, resolution and peak shape suffer. In CI, the two main factors that affect the number of ions in the ion trap are the ionization time and the reaction time.
Increase the CI gas pressure by adjusting the CI needle valve on the front of the 2000. Turn the knob clockwise to increase the pressure. When the pressure is correct you will see the picture below. If you increase the pressure too much, you will see a picture like the one below and you will have to decrease the pressure until you get the picture above. Once the pressure is adjusted properly you are finished and ready to perform chemical ionization experiments.
Control and Status The Auto Tune methods are started from this display by clicking on the Start Auto Tune button. The method maybe stopped by clicking on the Reset button. The State displays whether the Saturn MS is currently executing an auto tune function or is idle. The Function shows which tuning function is currently being performed. Method and Set Points There are four auto tune checks to automatically set up, tune and calibrate the mass spectrometer.
An example: The dialog for the air/water check is shown below. The mass 28 peak width is used to determine if air is present in the trap. The progress bar labeled “Air Level” is a graphical representation of the peak width. The mass 19/18 ratio value is used to determine if water is present in the trap. The progress bar labeled “Water Level” is a graphical representation of the ratio. Spectrum and Event Message Window On the left side of the auto tune screen you will see the picture below.
Auto Tune Checks In the top center of the screen you will see 4 check boxes. These are the auto tune steps that are to be performed. If your system does not contain SIS, or MS/MS the Trap Function Calibration does not need to be performed. To perform the auto tune click the check boxes and click Start Auto Tune. Each one of the items that you selected in the check boxes will now be executed.
On the left side of the dialog box is an progress bar that indicates the relative amount of AIR in the system. A message is displayed below the bar. If the display reads OK, there is essentially no air leak in the system. If the message MAYBE is displayed, there is a small air leak. The system can be operated, but performance might not be optimum. If the display reads HIGH, there is a significant air leak. The leak must be found and corrected before the system can be operated.
The Electron Multiplier Tune will determine three proper settings: the Integrator Zero, the 105 gain for the Electron Multiplier and the Electron Multiplier voltage boost for optimum peak intensity and resolution. The Integrator Zero Set obtains the average value of the signal level coming from the Integrator Circuitry when the filament is off. When the filament is off, the major source of signal coming from this circuitry is electronic noise.
sensitivity and resolution. This setting is also the value displayed in the Set Points dialog, in the Electron Multiplier voltage field. Mass Calibration The mass calibration function adjusts the rf Scale for a coarse full mass range calibration and, then locates several FC-43 masses for a multi-point calibration curve. To initiate mass calibration based on FC-43, click the button to the left of FC-43 Calibration.
is outside of these limits, check if the rf voltage amplitude is adjusted properly over the entire mass range). Straight Line Mass Calibration To initiate a straight line mass calibration, click Straight Line Calibration and Start Auto Tune. A straight line calibration assumes a linear relationship between DAC steps and mass. It is used for certain hardware adjustments.
SIS Amplitude Adjust Factor. Each trap system must be adjusted for optimum ion sensitivity and ejection. See Tutorial on SIS Calibration for your system. The voltage adjustment factor may be set between 50 to 200%. The default is 100%. Temperatures Mode The temperature settings to control the Saturn and the transfer line are accessible by clicking on the Temperature button located in the top center of the instrument control screen. When you select this a screen like the following opens.
Whenever you execute changes, the event log at the bottom of the screen will be updated with the time and the event that has occurred. The screen below is an example. At the conclusion of the bakeout, the trap, and manifold temperatures will return to the set point values. New setpoint values can be applied during a bakeout. A bakeout must be halted, by clicking the reset button, before a new bakeout duration or new bakeout temperatures can be set.
The Monitor and Event Message window will detail results of the basic system. If a fault had occurred, the message would indicate what test failed and the source of the problem. A more detailed test of the heater zones can be done by clicking in the box of the zone to be tested under Heater Test. To complete these tests can take up to 13.5 hours for the trap, 2 hours for the manifold, and three hours for the transfer line. The manifold and transfer line tests can be run simultaneously.
Also, present temperature values for each of the heating zones is displayed. Monitoring diagnostics on startup will identify any problems. Please refer to the Trouble Shooting section of the Hardware manual for additional information. Shutdown Mode The shutdown procedure is used to shut the system down in an orderly fashion. The screen is shown below and it is accessed by clicking on the top button labeled Shutdown.
action will cause the heaters to be turned off and the system will begin to cool. Additionally, the turbo pump will be slowly turned off. In the screen below the shutdown command has been activated. Notice that the turbo pump speed is being reduced as the temperature is being cooled. Should you wish to restart the system after you have activated the shutdown, simply hit the reset button on the left side of the screen above. This will restart the pumps and turn on the heaters.
the cooler has warmed to the point that it won’t condense water vapor, and the pump is considered to be off. The DIFFUSION PUMP STATUS then changes from COOLING to OFF. NOTE: If the word “FAULT!” is displayed in the Vacuum Status box, click on the Diagnostics mode button for detailed information on the cause of the fault. The vacuum status represents the state of the diffusion pump. To precisely identify the problem, the USER should go to the Diagnostics mode and run "System Test to Completion”.
NOTE: The Vacuum System status should be periodically checked during Startup for foreline pressure. The pressure should read below 500 mTorr in 5 minutes and < 100 mTorr after 45 minutes. Higher values may indicate a leak. Refer to the Troubleshooting chapter in the Hardware manual. Acquisition Selecting the Acquisition button activates the 2000 module for analysis.
In the above screen there are additional buttons which allow you to browse or check data files that already exist to make sure that you are not overwriting an existing file. Prior to making the injection any of these buttons can be selected and checks can be made. The sample type can be changed by double clicking in the field below Sample Type. Note the picture below for the selections that can be made. The same procedure can be used for injection notes.
Select one of the 3 radio buttons and name the recalculation list you are using if appropriate. In order to perform automated injections of a group of samples you must first build a sample list and then a sequence list. An example of a sample list is displayed below. This screen can be activated from the pull down menu under File, New Sample List. You must create the list from the empty table you see on your screen.
scanned out of the ion trap. Thus, when the multiplier gain is changed, there is no change in the actual quantity of ions formed and measured in the prescan measurement, but the peak area of the AGC peak will be changed. The AGC software will misinterpret this change in peak area as a real change in the number of ions created in the ion trap and will adjust the ionization time accordingly. An incorrect ionization time may cause a change in mass resolution.
temperatures and this is okay. In general use the lowest temperature which provides acceptable chromatography. The manifold bakeout functions can be used to do this overnight and reset the temperatures to operating conditions automatically. The trap temperature value selected should be high enough so that chromatographic performance is not affected.
3800 GC System Control Window The Instrument Window Once you have configured your 3800 GC in an instrument, you may view the Instrument Window. The instrument window allows you to monitor the status of all modules assigned to the instrument, perform injections of one or more samples, and perform batch recalculations. Double-click in this area or select the instrument from the Instrument menu to view the 3800 GC Status and Control window.
Elements of System Control Toolbar System Control Toolbar provides you with buttons to do the most common tasks performed in System Control. Most Toolbar buttons correspond to a menu command. You can find what each button does by resting the pointer on the button. Note that the buttons controlling the SampleList, Sequence and RecalcList become available after you activate a corresponding automation file.
Multiple detectors can be viewed horizontally or vertically. The component status display can be changed to view detailed status of each component in the GC. Click on a temperature zone entry to select the corresponding component status or select the component status from the list. Detailed component status is displayed. The 3800 Setup dialog is accessed from the View Setup button.
Installed hardware is listed here. The setup is changed from the 3800 GC front panel. The 3800 Setup dialog for the Saturn 2000R/3800 is also accessed from the View Setup button and shows a different display. The setup is changed from the Varian MS Workstation. The Real-Time Chromatogram Display All detectors installed on the 3800 GC display their chromatographic signals in real time. Configuration of the chromatogram display for all detectors is the same.
Show only the chromatogram display. Continue to view the signal after the run Select the detector(s) to view. Hide/unhide the Toolbar. Set both the amplitude and time axes to full scale. Set the amplitude axis to full scale. Set the time axis to full scale. Use these buttons to move between stored scalings. Enable/disable the Auto Scale feature. Enable/disable the cursor display. Select the background color for the display.
Adjust zero offset. Adjust amplitude scale. Adjust time scale. Hide/unhide vertical amplitude scale slider. Documenting Module Information You may wish to document the configuration of your modules, their installation and most recent service dates, and other information pertinent to your instrument. To do so, use the Module Information Editor accessed from the Edit menu in the instrument window. Click on the module window to give it the focus. Select Edit Module Info.
You may add and edit sections and items in sections. The injections value is updated each time an injection is performed. Select Help for details on creating and editing module information. Click on Done to close the window. Module information is copied into Data Files generated after injections and can be included in the Run Log portion of the results report.
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3800 GC Injecting a Single Sample Overview By now you should have your 3800 GC configured and a basic Method built for data acquisition. If this hasn’t been done, please refer to the previous sections for instructions on doing this. Using the Inject Single Sample Dialog Box You can inject a single sample from System Control by using the Inject Single Sample dialog box.
the Inject Single Sample, double-click on the vial position you wish to inject from in the carrousel display. This will bring up the Inject Single Sample dialog box with the vial number already entered. Specifying the Data File Name and Path Data File names can be up to 255 characters long. Sample ID, injection date, module name, and injection number can be embedded in the file name making the Data File name correlate with each sample injection.
Specifying Per-Sample Data Handling Parameters Most Data Handling parameters are specified in the Method used during the injection. Some parameters may vary on a per-sample basis, and are therefore specified when you perform the injection.
Specifying a RecalcList You can choose to create a new RecalcList, append to an existing RecalcList, or not create nor update a RecalcList. To select the RecalcList option that you want, click on the RecalcList button. The RecalcList Generation dialog box is displayed. If you choose to create a new RecalcList, this automatically generated RecalcList will not overwrite an existing RecalcList.
List of Data Files generated in System Control, and a Quick Link button above provides access to the selected file. Automation actions and errors are logged in the Message Log. The chromatogram is displayed as it is acquired. When you double-click on the status bar at the bottom of the instrument window, the entire Message Log window is displayed. All Message Log entries are stamped with the time they occurred.
Choose the instrument for the injection. Enter information about the sample. Enter the name of the Method you wish to use. Enter the name of the stand-by Method. This Method is downloaded to the modules after the run is complete, and is used to specify the stand-by state of the instrument. Enter sampling information. This information is specific to the type of sampling device installed. Refer to the on-line help for more details on the QuickStart screen. Press Start to begin.
3800 GC Injecting Multiple Samples Introduction By now you should have your 3800 GC configured and a basic Method built for data acquisition. If this hasn’t been done, please refer to the previous sections for instructions on doing this. Using a SampleList in System Control You can inject multiple samples from System Control by using the SampleList. Choose to open either a New SampleList or an existing SampleList from the File menu..
Spreadsheet columns can be sized by dragging their border using the left mouse button. Right click on the column headers for formatting options. Enter notes about the sample. Enter post-run operations to be performed. Enter information about the samples and the injections you wish to perform. Select the location and name for the Data Files generated by the SampleList. Specify RecalcList generation options. Press the Begin button to start injecting samples.
For sequentially numbered Sample names, enter the starting number and the number of entries to add to the SampleList. The Sample Names will have these numbers appended to them. When you press the Begin button, you are prompted for the Method to use. Enter the Method to use for the run……or browse for the Method file. After you click on OK, the Method is downloaded to the 3800 GC and the run will begin.
makes it easy to see how a Data File created with this filename specifications would appear. Specifying Per-Sample Data Handling Parameters Most Data Handling parameters are specified in the Method used during the injection. Some parameters may vary on a per-sample basis, and are therefore specified when you perform the injection.
If you choose to create a new RecalcList, this automatically generated RecalcList will not overwrite an existing RecalcList. If a RecalcList with the same filename exists, the newly created RecalcList will have number appended to its filename to make it unique and to prevent the older RecalcList from being overwritten. Changing Default SampleList Entries When you add a new row into a SampleList, default values are used for each cell.
Click on the Carrousel button. The Carrousel dialog box is displayed. Click on the button to perform the desired operation. The SampleList is then updated with the vial information from the AutoSampler. Default values are used for each entry added to the SampleList. Refer to the 8200/SPME AutoSampler for 3800 GC Manual for details about use of the 8200 AutoSampler with the 3800GC.
List of Data Files generated in System Control, and a Quick Link button above to access the selected file. Automation actions and errors are logged in the Message Log. The chromatogram is displayed as it is acquired. When you double-click on the status bar at the bottom of the instrument window, the entire Message Log window is displayed. All Message Log entries are stamped with the time they occurred.
Select Activate Method from the Sample Type cell. Click on the AutoLink button. The Activate Method dialog box is displayed. Enter the name of the Method to use……or pick the Method from a list of files. When this line is encountered during automated injections, the specified Method is activated. You may specify any number of Methods to be used in the SampleList. Using the Sequence Window The Sequence window allows you to specify multiple Methods and SampleLists to be processed during automation.
The Sequence window for the open Sequence is displayed. Enter the Method and SampleList to use. You may enter any number of Sequence lines. Choose the action to be done in that step of the Sequence from the drop down box. Browse for a Method or SampleList file in the active cell. Press Begin to start the automation.
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3900 GC System Control Window The Instrument Window Once you have configured your 3900 GC in an instrument, you may view the Instrument Window. The instrument window allows you to monitor the status of all modules assigned to the instrument, perform injections of one or more samples, and perform batch recalculations. Double-click in this area or select the instrument from the Instrument menu to view the 3900 GC Status and Control window.
Elements of System Control Toolbar System Control Toolbar provides you with buttons to do the most common tasks performed in System Control. Most Toolbar buttons correspond to a menu command. You can find what each button does by resting the pointer on the button. Note that the buttons controlling the SampleList, Sequence and RecalcList become available after you activate a corresponding automation file.
Multiple detectors can be viewed horizontally or vertically. The component status display can be changed to view detailed status of each component in the GC. Click on a temperature zone entry to select the corresponding component status or select the component status from the list. Detailed component status is displayed. The 3900 Setup dialog is accessed from the View Setup button.
Installed hardware is listed here. The setup is changed from the 3900 GC front panel. The 3900 Setup dialog for the Saturn 2000R/3900 is also accessed from the View Setup button and shows a different display. The setup is changed from the Varian MS Workstation. The Real-Time Chromatogram Display All detectors installed on the 3900 GC display their chromatographic signals in real time. Configuration of the chromatogram display for all detectors is the same.
Show only the chromatogram display. Continue to view the signal after the run Select the detector(s) to view. Hide/unhide the Toolbar. Set both the amplitude and time axes to full scale. Set the amplitude axis to full scale. Set the time axis to full scale. Use these buttons to move between stored scalings. Enable/disable the Auto Scale feature. Enable/disable the cursor display. Select the background color for the display.
Adjust zero offset. Adjust amplitude scale. Adjust time scale. Hide/unhide vertical amplitude scale slider. Documenting Module Information You may wish to document the configuration of your modules, their installation and most recent service dates, and other information pertinent to your instrument. To do so, use the Module Information Editor accessed from the Edit menu in the instrument window. Click on the module window to give it the focus.
Select Edit Module Info. The Module Information Editor window is displayed. You may add and edit sections and items in sections. The injections value is updated each time an injection is performed. Select Help for details on creating and editing module information. Click on Done to close the window. Module information is copied into Data Files generated after injections and can be included in the Run Log portion of the results report.
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3900 GC Injecting a Single Sample Overview By now you should have your 3900 GC configured and a basic Method built for data acquisition. If this hasn’t been done, please refer to the previous sections for instructions on doing this. Using the Inject Single Sample Dialog Box You can inject a single sample from System Control by using the Inject Single Sample dialog box.
Specifying the Data File Name and Path Data File names can be up to 255 characters long. Sample ID, injection date, module name, and injection number can be embedded in the file name making the Data File name correlate with each sample injection. When you click on the Data Files… button, the Data Files Generation dialog box is displayed. This dialog box allows you to select the path and the filename “specification” for the data file.
Specifying a RecalcList You can choose to create a new RecalcList, append to an existing RecalcList, or not create nor update a RecalcList. To select the RecalcList option that you want, click on the RecalcList button. The RecalcList Generation dialog box is displayed. If you choose to create a new RecalcList, this automatically generated RecalcList will not overwrite an existing RecalcList.
The total number of injections completed is shown in the Instrument Status window. Automation actions and errors are logged in the Message Log. The chromatogram is displayed as it is acquired. When you double-click on the status bar at the bottom of the instrument window, the entire Message Log window is displayed. All Message Log entries are stamped with the time they occurred. Using QuickStart QuickStart is a fast way to inject a single sample without having to use System Control directly.
Choose the instrument for the injection. Enter information about the sample. Enter the name of the Method you wish to use. Enter the name of the stand-by Method. This Method is downloaded to the modules after the run is complete, and is used to specify the stand-by state of the instrument. Enter sampling information. This information is specific to the type of sampling device installed. Refer to the on-line help for more details on the QuickStart screen. Press Start to begin.
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3900 GC Injecting Multiple Samples Introduction By now you should have your 3900 GC configured and a basic Method built for data acquisition. If this hasn’t been done, please refer to the previous sections for instructions on doing this. Using a SampleList in System Control You can inject multiple samples from System Control by using the SampleList. Choose to open either a New SampleList or an existing SampleList from the File menu..
Spreadsheet columns can be sized by dragging their border using the left mouse button. Right click on the column headers for formatting options. Enter notes about the sample. Enter post-run operations to be performed. Enter information about the samples and the injections you wish to perform. Select the location and name for the Data Files generated by the SampleList. Specify RecalcList generation options. Press the Begin button to start injecting samples.
When you press the Begin button, you are prompted for the Method to use. Enter the Method to use for the run……or browse for the Method file. After you click on OK, the Method is downloaded to the 3900 GC and the run will begin. If you are using a manual injector or a sampling device that is not controlled by the Varian MS Workstation, you will need to start the device manually. Specifying the Data File Name and Path Data File names can be up to 255 characters long.
The right side of this dialog box allows you to create a filename “specification”. You can combine text entry with the “%” variable symbols shown to specify filenames that contain sample injection specific information. An example of the filename is dynamically updated as you type in the filename specification. This makes it easy to see how a Data File created with this filename specifications would appear.
Changing Default SampleList Entries When you add a new row into a SampleList, default values are used for each cell. To change the default values, click on the Defaults… button in the open SampleList window. The following dialog box will be displayed. Enter the desired default values and click on Save. Monitoring the Status of Runs After an injection is performed, the status of the run can be monitored in the instrument window. Module status is shown in the status and control windows and on the Toolbar.
All Message Log entries are stamped with the time they occurred. Saving SampleLists for Later Use When you make changes to the open SampleList, the changes are automatically saved to the SampleList file and will be used for the automated runs that are in progress. If you want to edit a SampleList other than the open SampleList, use the offline Automation File Editor application described in the next section of this manual.
Enter the name of the Method to use……or pick the Method from a list of files. When this line is encountered during automated injections, the specified Method is activated. You may specify any number of Methods to be used in the SampleList. Using the Sequence Window The Sequence window allows you to specify multiple Methods and SampleLists to be processed during automation. Choose to open either a New Sequence or an existing Sequence from the File menu..
Enter the Method and SampleList to use. You may enter any number of Sequence lines. Choose the action to be done in that step of the Sequence from the drop down box. Browse for a Method or SampleList file in the active cell. Press Begin to start the automation.
System Control Menus File Menu Menu Item Description Activate Method… Displays the Activate a System Control Method File dialog box to activate a Method and download the Instrument Control sections to the modules. Upload Active Method from Modules… Displays the Save a System Control Method File dialog box to allow you to name the Method that will receive the instrument control sections uploaded from all modules connected to the instrument.
Menu Item Description Remember Last Open Files When checked, upon startup System Control will restore the active Method and any automation files that were open when System Control was last closed. Exit Closes System Control. If System Control is in the process of performing a critical operation, you may be prompted before the application is closed. Edit Menu These commands are for use with Sequences, SampleLists, and RecalcLists.
Inject Menu Menu Item Description Inject Single Sample... Opens the appropriate Inject Single Sample Dialog Box for your system. Used to inject a single sample without building a Sequence and SampleList manually. Automation Menu Menu Item Description Begin SampleList Begins execution of the currently open SampleList. Begin Sequence Begins execution of the currently open Sequence. Begin at Selected SampleList Line... Begins the open SampleList at the selected SampleList line.
Menu Item Description Reset Modules Stops the current run, resets all modules simultaneously. Automation proceeds to the next injection after all the modules go to the Ready state. Enable Automated Printing Turns on or off the printing of reports automatically generated during any automation action. This is useful when you wish to disable printing (if the printer is out of paper, for example) without having to modify the Print Options portion of the Report Method.
Menu Item Description #:instrument name Displays the Instrument Status window and Status and Control windows for the named Instrument. i.e. Saturn GC/MS #1 Configuration Displays the Configuration window. Instrument # Faults Displays the Instrument Faults dialog box, showing recent and selftest messages and faults. The list of faults may be printed from this dialog box.
Menu Item Description Arrange Icons Arranges the icons, if any, in a row at the bottom of the System Control window. Sequence:, Opens the window for the selected file or moves it to the front. Used to display the open Sequence, SampleList, or RecalcList. SampleList:, RecalcList: Displays the corresponding window for the instrument or moves it to the front. Used to see the instrument status, Message Log, or Configuration Log.
System Control Toolbar Main Toolbar The System Control main toolbar appears at the top of the Configuration and Instrument Windows. Item Description Creates a new automation file (RecalcList, SampleList or Sequence). You are prompted for the name of the new file. Opens an existing automation file. Displays the Open Automation Dialog Box. Active Method QuickLink button.
Resume automation after a pause. Automation will continue at the point that it was suspended. Stop automation. Stops the current run, resets all modules simultaneously and suspends the Sequence. Instrument status indicator. Shows whether the instrument is not ready, running, computing or printing. When the instrument is ready but not running (idle), no status is shown.
2000 MS Method Basic Scan Functions Introduction The Saturn GC/MS analyzes the gas-phase ions formed from a sample in terms of their mass-to-charge (m/z) ratios and their relative abundances in the resulting spectra. The mass spectrum is a graphical representation of the ion intensities versus the mass-to charge ratio. The Saturn GC/MS creates the mass spectrum with an ion-trap analyzer.
frequency and amplitude is also applied to the endcap electrodes during the analysis to improve ion injection and unit mass resolution. The Saturn GC/MS has two techniques for generating sample ions in the ion trap. Consequently there are two basic scan functions, i.e., the electron ionization scan function and the chemical ionization scan function. A scan function is a representation of the timing sequence for ion trap operation.
2000 MS Method Chemical Ionization Introduction Chemical ionization (CI) provides mass spectral data that complement electron ionization (EI) data for the analysis of complex compounds. In the CI mode of operation, a CI reagent gas is introduced into the ion trap analyzer. The reagent gas is ionized by EI. Then, the sample molecules are ionized by ion molecule reactions with the reagent gas ions. CI is a softer ionization technique than EI.
The figure below shows the scan function for chemical ionization. A Reagent gas ionization, time determined by the previous scan B Ejection of unwanted ions (i.e.
4. Reagent gas ions are ejected. (D) 5. The CI mass spectrum is acquired for the sample ions. (E) SECI ejects all ions above a cutoff mass by applying a waveform between the ionization and reaction periods. This is the preferred mode of operation on the Saturn GC/MS, since all EI artifact ions are eliminated. It should be noted that fragmentation can still be observed in CI spectra due to energy imparted when the proton is transferred from the reagent ion to the sample molecule.
NOTE: Reagent ion formation can be a complex process. For example, for proton transfer CI with methane used as the reagent gas, reagent gas ions are formed as follows: First, methane is ionized to form two primary ions: CH4 + e- (CH4 )+ + 2 eCH4 + e- CH3+ + e- + HThese primary ions then react very rapidly to form predominantly the secondary ions, CH5+ and C2H5+: (CH4 )+ + CH4 CH5+ + CH3 CH3+ + CH4 C2H5+ + H2 The CI Parameters Reagent Gas When you select a standard reagent gas (i.e.
period. The CI storage Level is typically set to a value that is lower than the mass of the reagent ion of interest. The CI Storage Level can be set to any value from 5 to 150 m/z. The optimum CI storage level will depend on the molecular ion of the analyte. Generally, one should use higher CI storage levels for higher molecular ions, without raising the storage level to cause ejection of CI reagent ions. For example, the molecular ion of the analyte is 352 m/z.
Prescan Ionization Time Prescan Ionization Time parameter as used in MS/MS applications is set to 200 sec. Default Parameters for Reagent Gases used in Chemical Ionization Mode Reagent Gas Methane Isobutane Ammonia Maximum Ionization Time (sec) 2000 2000 2000 Maximum Reaction Time (msec) 60 60 60 CI Storage Level (m/z) 13 19 13 CI Background Mass (m/z) 45 65 40 Ejection Amplitude (v) 9.
CI Background Mass Set Too Low. CI Background Mass Properly Set. How to Determine the Proper Ejection Amplitude The proper setting for the Reagent Ion Eject Amplitude will remove EI generated fragments but not affect the reagent ions. With the CI reagent connected and properly adjusted, click the CI Gas control on the Manual Control page in System Control to open the CI gas valve solenoids.
Chemical Ionization Using Fixed Parameters The reaction parameters that are normally set by the Auto Control can also be set manually. For Chemical Ionization using fixed parameters, the instrument uses the Ionization Time entered in the method editor. The reaction time that will be used is determined as follows: ReactionTime= MaximumReactionTime x Set IonizationTime MaximumIonizationTime where the maximum reaction and ionization times are entered below the Ionization Time.
Choice of Liquid CI Reagents Many liquids may be used as CI reagents. The general requirements are a moderate vapor pressure and fairly low molecular weight. If the molecular weight is too high, you may have problems seeing low molecular weight analytes because they will be excluded as the reagent ions are ejected. If the vapor pressure is too low, not enough reagent will enter the Saturn GC/MS for effective CI operation. This may be remedied by passing a stream of helium through the reagent vial.
Setting the Reagent Pressure for Liquid CI Reagents Connect a liquid reagent reservoir containing the chosen liquid to the liquid reagent inlet block. Open the CI needle valve 6-7 turns counterclockwise. Open the CI gas valve solenoids by clicking on the CI Gas Control on the System Control page and allow the vapor flow from the reservoir to equilibrate. If, after several minutes, there is not enough CI gas entering the trap, further open the needle valve (clockwise).
Adjusting the CI Reagent Gas Pressure for Gases Other Than Methane When you install a new supply of reagent gas, you must adjust the pressure of the CI reagent gas in the ion trap. After the reagent gas pressure has been adjusted properly, we recommend that you check the pressure at least once every day if you intend to perform CI analyses on a daily basis. The reagent gas pressure is adjusted (or checked) by using the Adjust CI Gas in System Control. See System control section.
Reagent Ion Spectrum for Ammonia Tuning for CI Operation In CI, as in EI, the Saturn GC/MS is tuned to achieve the best combination of maximum peak height (sensitivity), optimum resolution of peaks, and smooth peak shape. In addition, as in EI, the key to proper CI tuning is to optimize the number of ions in the ion trap: too few ions, sensitivity suffers; too many ions, resolution and peak shape suffer.
The practical advantages of low-pressure CI are: No need for an expensive vacuum pumping system to handle the large amounts of reagent gas Low consumption of expensive high-purity reagent gas Minimal contamination of the ion source The potential of alternating EI and CI scans without the compromises in spectral quality typically seen in high-pressure sources Very good CI sensitivity in the full-scan mode Liquid reagents are easily used Recommended Reading For more information abou
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2000 MS Method Command Reference Spreadsheet editing Item Description Add Duplicates MS parameters of the last segment and adds it to the end of the current table. Insert Inserts a row before the one currently selected with the parameter values of the highlighted row. Delete Deletes the currently selected row. Default Will insert system default parameters. Restore Inserts parameters that were present when the method was first opened, or last saved.
Item Description Segment Description Comment Line. 20 characters can be entered. Start Time Start time of segment in minutes. 0.00 to 649.99 min. End Time Time segment will be terminated. 0.10 to 650 min. Low Mass Lower end of mass range to be acquired. 10 to 650 m/z. High Mass Upper end of mass range to be acquired. 10 to 650 m/z. Ionization Mode Method of ion formation in trap. Ion Preparation Options applied after ionization to alter the ions stored in the trap before analysis.
Ionization Mode Item Description EI-Fixed Ions formed by electrons for a time set in method. EI-Auto Ions formed by electrons for time calculated from AGC function CI-Fixed Ions formed by collisions with CI reagent ions for time set in method. CI-Auto Ions formed by collisions with CI reagent ions for time calculated from previous scan. None Selected when hardware should be turned off (i.e.
Segment Setpoints Item Description Scan Time The duration of each scan (in seconds). Values from 0.10 to 5.00 seconds per scan. Below is displayed the number of micro scans per scan for the selected mass range and scan time. Multiplier Offset 5 Multiplier offset (relative to 10 gain). Range 300 Volts. Emission Current Emission current may be set from 5 to 100 µA. Count Threshold The minimum number of intensity counts per sampling interval required before a signal is recorded.
Ionization Mode - EI Auto Item Description Mass Range Segment Breaks The EI scan is made up of between 1 and 6 scan segments, each holding a contiguous mass-range segment. Overall, the set covers the entire mass range of 10 to 650 m/z. Only the intermediate segment boundaries can be changed by the user. Ionization Storage Level The rf voltage used during the ionization period. Values from 5 to 150 m/z.
Ionization Mode - EI Fixed Item Description Mass Range Segment Breaks The EI scan is made up of between 1 and 6 scan segments, each holding a contiguous mass-range segment. Overall, the set covers the entire mass range of 10 to 650 m/z. Only the intermediate segment boundaries can be changed by the user. Ionization Storage Level The rf voltage used during the ionization period. Values from 5 to 150 m/z.
The CI Parameters CI Auto Reagent Gas Item Description Reagent Gas Select CI reagent for application. Select User-Defined for gas not listed. CI Storage level Value of the smallest mass stored in the ion trap during the ionization and reaction period of the reagent gas. Values from 5 to 150 m/z. Ejection Amplitude (v) This voltage actively ejects unwanted ions (i.e., not reagent ions) that are produced during the ionization stage of the CI scan function.
Item Description Maximum reaction time Maximum time that reagent gas ions are allowed to react with sample molecules to form ions. The maximum reaction time can be set to any value from 1 to 128 milliseconds. Prescan Ionization Time Ionization time of the prescan uses in MS/MS. This is normally set to 200 sec for CI. CI Fixed Parameters Item Description Reagent Gas Select CI reagent for application. Select User-Defined for gas not listed.
Ion Storage (SIS) Parameters Item Description Storage Mass Ranges Table to enter ion(s) or range of ions for selective storage. Enter up to five mass ranges. Low Mass Low m/z integer mass. Mass range from 25 m/z to 650 m/z. High Mass High m/z integer mass. Mass range from 25 m/z to 650 m/z. Ejection Masses Table to enter ion(s) for selective ejection. Enter up to five ions. Ion Mass Integer mass(es) of those ion(s) to be ejected. Use ADD button to enter value.
The MS/MS Ion Prep Method Item Description Isolation Mass to be isolated and window of isolation Parent Ion Mass (m/z) Integer or exact mass. Parent ion mass range is 50 to 650 m/z. Isolation Window (m/z) Integral and fractional mass isolation windows are both accepted. Range is 1.0 to 7.0 m/z and is mass dependent. The default value is 3.0 m/z. Dissociation Waveform type and used for dissociation. Waveform Type Nonresonant or resonant excitation.
Item Description MS q Calculator Use the q Calculator for suggested excitation storage levels. Desired Product Mass Enter product mass expected from dissociation. Desired q Value Empirically observed “q” value of 0.4 provides an optimum yield of product ions. Customize Non-resonant Method Item Description Ionization Storage Level The m/z value the rf is maintained during ionization and the coarse isolation. Range 35 to 160 m/z (upper limit of range depends on parent ion m/z), default = 48 m/z.
Item Description Isolation Time The dwell time during which the rf field is held constant in the high mass ejection step. Range 1 - 10 msec. Excitation Time Time for collision-induced dissociation (CID) by ion excitation. Range 0 to 1000 msec. The default is 20 msec. Customize Resonant Method Item Description Ionization Storage Level The m/z value the rf is maintained during ionization and the coarse isolation.
Item Description Isolation Time The dwell time during which the rf field is held constant in the high mass ejection step. Range 1 - 10 msec. Excitation Time Time for collision-induced dissociation (CID) by ion excitation. Range 0 to 1000 msec. The default is 20 msec Modulation Range Mass range over which the rf storage field is modulated during resonant CID. The range is 0 to 12 steps, default is 2 steps. Value of 0 gives a fixed rf storage field, i.e., no modulation.
Item Description Excitation Storage Level Rf storage level in m/z when the dissociation waveform is applied following isolation. The excitation storage level range depends on the parent mass, but the storage level must lie more than 2 mass units below the lowest product ion value. Excitation Amplitude Range for nonresonant excitation is 0 to 100 volts. For resonant excitation, the range is 0 to 60 volts. Default values for nonresonant excitation is 20 volts and 0.2 volts for resonant excitation.
Item Description High Edge Amplitude Amplitude of broadband waveform used to eject masses above the isolated parent ion. Default is 30 volts. Isolation Time The dwell time during which the rf field is held constant in the high mass ejection step. Range 1 - 10 msec. Excitation Time Time for collision-induced dissociation (CID) by ion excitation. Range 0 to 1000 msec. The default is 20 msec. Modulation Range Mass range over which the rf storage field is modulated during resonant CID.
Excitation Storage Level Rf storage level in m/z when the dissociation waveform is applied following isolation. The excitation storage level range depends on the parent mass, but the storage level must lie more than 2 mass units below the lowest product ion value. Excitation Amplitude Range for nonresonant excitation is 0 to 100 volts. For resonant excitation, the range is 0 to 60 volts. Default values for nonresonant excitation is 20 volts and 0.2 volts for resonant excitation.
MSn MSn uses two parent ions for sequential dissociation. The additional dissociation step can be used to increase selectivity of analyte versus background or for additional structure information. First, work out optimized conditions for MS/MS of the first parent ion. AMD will make this process go faster. Then optimize the conditions for dissociation of that product ion (entered under parent ion 2). You may need to make sequential injections using the MSn method.
Item Description Waveform Type Nonresonant or resonant excitation. Excitation Storage Level Rf storage level in m/z when the dissociation waveform is applied following isolation. The excitation storage level range depends on the parent mass, but the storage level must lie more than 2 mass units below the lowest product ion value. Excitation Amplitude Range for nonresonant excitation is 0 to 100 volts. For resonant excitation, the range is 0 to 60 volts.
Item Description Excitation Time Time for collision-induced dissociation (CID) by ion excitation. Range 0 to 1000 msec. The default is 20 msec. Modulation Range Mass range over which the rf storage field is modulated during resonant CID. The range is 0 to 10 steps, default is 2 steps. Value of 0 gives a fixed rf storage field, i.e., no modulation. Modulation Rate The number of microseconds that will be spent at each step. The range 29 usec to 5600 usec, default is 3000 usec/step.
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2000 MS Method Electron Ionization The Electron Ionization Scan Function with Automatic Gain Control (AGC) The ion trap has a maximum storage capacity, beyond which mass resolution and spectral quality deteriorate. The number of ions created is proportional to the ionization time, with more ions being produced the longer the ionization time. Automatic Gain Control (AGC) controls the ionization time in order to maintain the number of ions in the trap at the optimum level.
GC peaks) the maximum ionization time of 65 milliseconds is selected, which offers maximum sensitivity. As the amount of analyte increases, the ionization time is decreased automatically in order to prevent saturating the ion trap with ions. The ion signals in each microscan are scaled automatically to correct for the variation in ionization time. Microscans are averaged to improve the spectral quality.
The ion current measured during the AGC prescan is known as the AGC peak area. The AGC peak area is proportional to the number of ions formed during the prescan ionization. The AGC software uses the measured ion current as a reference to optimize the ionization time for each scan as a function of analyte concentration. Scan Segment Setup Period The prescan is followed by the first segment of the six scan segments. Each segment can be divided into two parts: a setup period and a scanning period.
mass range and scan time, more than one microscan may be obtained during each scan. (The number of microscans per scan for each set of massrange/scan-time conditions selected is displayed on the data system monitor after these conditions are specified.) If two or more microscans are obtained, they are averaged by the SAP Board and then stored as one mass spectrum by the data system. This averaging of microscans provides improved spectral quality.
Software Parameters Segment Setpoints Scan Time The duration of each scan (in seconds). The scan time can be set to any value from 0.100 to 5.000 seconds per scan. Below the scan time input box is displayed the number of microscans per scan for the selected mass range and scan time. The number of microscans per scan is computed automatically; it cannot be set directly. It is displayed for information only. The minimum duration for the scan time is determined by the selected mass range.
Mass Defect Mass defect is defined as the difference between the nominal mass of an atom (or ion) and its exact mass. Its importance arises from the fact that the Saturn GC/MS reports molecular weights to the nearest integer mass unit only. The software must decide which mass to assign the measured intensity to. If the exact mass of an ion happens to fall close to the dividing line between integer masses, it may be assigned to the wrong mass.
Mass Range Segment Breaks Each EI scan is divided by default into four mass segments: 10 to 99 m/z, 100 to 249 m/z, 250 to 399 m/z and 400 to 650 m/z. For certain applications, the mass ranges in these segments can be adjusted. Additional segments (maximum of 6 segments) can be added by clicking on the Insert button. Ionization Storage Level Each segment has its own ionization storage level. This corresponds to an rf voltage that is used to hold ions in the trap during the ionization period.
Maximum Ionization Time This sets the limit for the longest ionization time which AGC can use. For maximum sensitivity, start with the default value of 25,000 µsec. In certain special cases a smaller value may be used, e.g., to reduce unwanted ionmolecule reactions. The highest Maximum Ionization Time can be set is 65,000 µsec. Prescan Ionization Time (µsec) This ionization time determines the number of ions formed for the prescan.
Ionization Mode - EI Fixed When AGC is off, a fixed ionization time scan function is used to coordinate the processes that occur in the ion trap. This scan function consists by default of four segments that compare qualitatively to those of the Auto scan function. It may contain up to six segments. However, the fixed ionization time scan function contains no prescan. Thus, the ionization times for each segment do not vary as a function of sample concentration.
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2000 MS Method Ion Preparation The Ion Preparation Method The two fundamental processes in mass spectrometry are ion creation and ion analysis. For some applications, the ability to manipulate the ion population following ion creation but prior to ion analysis through such techniques as selective storage or dissociation may be advantageous.
either or both segments of the scan function. Chemical ionization uses the previous scan for ion control. As shown below, the analytical scan includes an ionization period, a reaction period, ISSs, and an rf voltage ramp for mass analysis.
Specifying the Ion Preparation Parameters The Ion Preparation Parameters control how the basic EI or CI scan functions are modified to prepare the ions for scanning. You have control over which ions are ejected, which are retained, and which will undergo dissociation (CID). Your input and the Ion Preparation technique you are using determine how the scan function is constructed and what custom waveforms are created to complete the analysis.
Initially, you specify the mass window of ions to be stored. Because each mass has a unique secular frequency at a given storage rf voltage, it is possible to construct a waveform that does not include frequencies near the secular frequencies of the ions to be stored. The resulting waveform consists of a distribution of discrete frequencies with missing frequencies, called notches, corresponding to the frequencies of the stored ions.
Under Storage Mass Ranges, enter the low m/z integer mass and the high m/z integer mass for each of the mass windows to be selectively stored. Delete any mass range not needed. You may enter up to five mass ranges. The default parameters permit any mass range from 53 m/z to 650 m/z to be stored, given a storage rf of 48 m/z.
As shown below, the window of ions ejected also depends on mass. A single mass can only be ejected at low mass values. If a single high mass value is entered in the table, a range of ions will be ejected. Autoscale Waveform Under default operation (Autoscale = ON), the SIS waveform amplitude is automatically scaled as a function of the frequency components and storage rf voltage selected. NOTE: The amplitude of the waveform should be optimized for each Saturn GC/MS system.
Tips for Using SIS Observe these recommendations for best results when using the SIS application. When selectively storing ions that are easily fragmented by collision-induced dissociation (CID), use wide mass isolation ranges and low amplitude waveforms. As the frequency notches become increasingly narrow and the voltage of the frequency components increases, the ions that you wish to store acquire sufficient energy to dissociate or be ejected.
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2000 MS Method MS/MS Option: Theory of Operation Overview This section describes the four basic operations in Saturn Ion Trap Tandem Mass Spectrometry (MS/MS) for electron ionization (EI): Ion formation and matrix ion ejection Parent ion isolation Product ion formation Product ion mass scanning. Chemical ionization (CI) MS/MS uses a subset of these operations.
MS/MS Scan Function Parent Ion Isolation The parent ions can be completely isolated from any remaining matrix ions in another two-step process. The first step ejects the ions with masses below the parent ion mass by ramping the rf field amplitude with axial modulation applied to the end cap electrodes. This step resonantly ejects all ions having masses up to, and including, the mass just below the parent ion mass. Axial modulation is then turned off.
(parent ion) m/z. The m/z distribution that results from the CID process depends on the characteristics of the parent ion and the amount of energy that has been converted into internal vibrational energy. The translational kinetic energy of the parent ion can be increased using either of two methods. Each method requires application of a waveform to the trap. The waveform amplitude is called the CID excitation amplitude, and the length of time that the waveform is applied is called the excitation time.
multiple chemical bonds or that undergo significant rearrangements. Periodic modulation through ion resonance results in an averaging of the energy coupled into the ion motion and provides a reproducible product ion spectrum, even with changes in concentration. A disadvantage of this method is that two parameters in addition to the excitation time and CID excitation amplitude need to be optimized; these are the modulation range and CID bandwidth.
Note that at a storage level of 48 m/z and a CID bandwidth of 4 kHz, the mass range increases from 3 to 40 m/z when the parent ion mass increases from 100 to 400 m/z. Given a parent ion mass of 400 m/z and a CID bandwidth of 4 kHz, the mass range decreases from 40 m/z for a storage level of 48 m/z to a range of 12 m/z for a storage level of 143 m/z.
level of parent or product ions in the analytical scan results in consistent, reproducible product ion spectra. Lower target values may be required with the MS/MS option to prevent space charging effects. Based on the isolated parent ion, the following target values are recommended. Parent Ion Target 60 m/z 150 10000 150 m/z 500 5000 500 m/z 650 2000 Additionally, the EI-Auto PreScan ionization time must be changed from the default value.
Under the Isolation header, enter the Isolation Window (m/z). The full mass isolation window range is 1.0 to 14.0 m/z; the actual range is mass dependent. The default value is 3.0 m/z. Integral and fractional mass isolation windows are both accepted. If mass isolation windows smaller than 1.5 m/z are used, the exact mass of the parent ion should be entered in Parent Ion Mass.
NOTE: If the excitation amplitude used is too large, the parent ion and product ion spectra will be absent because both ions will be ejected from the trap. If the value is too small, the parent ion spectrum will be dominant and the product ion spectrum will be weak or missing. The MS “q” Calculator For convenience, The MS q Calculator is available in all Ion Preparation Options. Storage rf values are often reported in terms of the Mathieu “q” parameter in the scientific literature.
Customize Parameters window is separated into three sections. Ionization, Isolation and Dissociation. Ionization Ionization Storage Level: The m/z value at which the rf is maintained during ionization and the coarse isolation step. The range is 35 to 160 m/z, with a default value of 48 m/z. Ejection Amplitude: the amplitude (in volts) of the ejection waveform during the coarse isolation step. The default value will work for most ions.
High Edge Offset: The integer value step to optimize the ejection of the mass just above the parent ion mass. The High Edge Offset range is -20 to 20 steps. The default value is 2. High Edge Offset affects the isolation window on the high mass side of the parent ion. Increasing the offset (from 4 to 5 steps) increases the window; decreasing the offset (from 4 to 3 steps) decreases the window. The offset should be adjusted to minimize the amplitude of adjacent masses above the parent ion.
Dissociation Excitation Time: The excitation time is the time required for collision-induced dissociation (CID) by ion excitation. The excitation time range is 0 to 1000 msec. The default excitation time is 20 msec for both resonant and nonresonant excitation. Customize Resonant Method NOTE: Be sure that you have specified the parent ion mass before opening the Customize Parameters window. Customize Parameters window is separated into three sections. Ionization, Isolation and Dissociation.
High Edge Offset: This parameter provides a fine adjustment for the isolation window to optimize the ejection of the mass just above the parent ion mass. The High Edge Offset range is -20 to 20 steps. The default value is a function of the parent ion mass. Large positive values widen the isolation window towards high masses. High Edge Amplitude: Amplitude of broadband waveform used in the two-step isolation to eject masses above the isolated parent ion.
NOTE: This value is not used if the nonresonant CID method is selected. A value of 0 gives a fixed rf storage field, i.e., no modulation Modulation Rate: The number of microseconds that will be spent at each step. The range is 29 usec to 5600 usec, with the default value of 3000 usec/step. The default value is adequate for nearly all applications. Number of Frequencies: Enter an odd integer in the range of 1 to 121 for the number of frequencies.
Increase or decrease the CID (excitation) amplitude until a change in the spectra is observed. In the case of nonresonant CID, use 10 volt steps; for resonant CID, use 0.2 volt steps. Continue to increase or decrease the CID (excitation) amplitude, but in smaller increments until suitable ion spectra are obtained. Adjust the excitation time in 10-ms steps to optimize the spectra.
Automated Methods Development Automated Method Development (AMD) is used to optimize CID conditions for product ion formation in a MS/MS method. AMD uses up to 10 different sets of conditions for the same parent ion. When using Automated Method Development (AMD) option, set the Saturn method for 1 microscan per analytical scan by adjusting the Scan Time (Segments Setpoints). The easiest way to do this is to use the down-scroll button in the Scan Time edit control to reduce the time to its lower limit.
It is a good idea to verify that the parent ion is isolated without a large loss in intensity. This can be done by setting the excitation amplitude for scan segment 1=0 volts. Inject the sample and examine the spectra across the peak Set the excitation rf equal to the lowest mass product ion expected divided by 1.4. If the product ions are not yet known, start with the excitation rf=48 m/z and an excitation time of 20 ms.
Determine the optimum rf level by plotting the product ion intensity data as a function of CID (excitation) amplitude for different rf levels as shown below. Product Ion Formation vs. Excitation RF for a Typical Ion Using Nonresonant Excitation RF=48 m/z P 1000 900 800 700 600 500 400 300 200 100 0 0 10 20 30 RF=63 m/z 40 50 60 RF=95 m/z 70 80 90 100 Excitation amplitude (volts) NOTE: The maximum yield of product ions shifts to higher CID (excitation) amplitudes as the rf level is increased.
MS/MS You can do multiple reaction monitoring by adding lines of different parent ions masses and different dissociation parameters. The limit is nine. Unit Resolution Selected Ion Storage Unit Resolution Selected Ion Storage (uSIS) is capable of isolating up to 9 ions with unit mass isolation. This method is useful for those cases where the standard SIS window is too large. Use uSIS when narrow mass ranges are required by your application.
First, work out optimized conditions for MS/MS of the first parent ion. AMD will make this process go faster. Then optimize the conditions for dissociation of that product ion (entered under parent Ion 2). You may need to make sequential injections using the MS3 method. If the second generation product ion is in the original EI or CI spectrum, then you can use AMD to find the optimum conditions.
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2000 MS Method Section Overview In the 2000 MS Configuration section, you configured your hardware for a 2000 and opened the System Control Window for instrument control and acquisition. At this point, you could simply inject a sample and acquire mass spectra. However, it is not likely that the startup Method will have the method settings that are appropriate for your analysis. Therefore, the startup Method will need to be edited to enter the settings appropriate for your analysis.
You will first be asked to select the instrument configuration for which you want to create a method. Select Instrument 1 for the 2000 module and click on Next.
You will be asked to select the channels on which post-run processing will be performed. When you have selected the data channels and type(s) of post-run processing to be run for each detector, the Star Assistant will create a Method containing all of the sections that are needed to control the hardware, collect data and do the post-run processing specified. These Method sections will contain default values for all of the parameters. These parameters will need to be edited to match your analysis.
The Method Builder Window As you step down through the Method tree, the parameters associated with each section of the Method are displayed for editing. Detailed information about the menu items and Toolbar buttons can be found in the online help. Method Notes The first item in the Method is the Method Notes section. Method Notes is a free form text field where information about the Method or the application can be entered.
The 2000 MS Method Windows Under the Method Directory item 2000 Mass Spec Control, click on the item MS Method Editor. The display on the right will now show the MS method. Note that you may click on the splitter bar separating the Method Directory from the Method Display and adjust the position so that the entire Method is visible on the screen. Alternatively you may click on the display button the Method View toolbar to hide the Method Directory.
Generally, Method Segment 1 is a Filament/Multiplier Delay. This segment will be acquired with the filament and multiplier turned off to protect the instrument until after the elution of the solvent peak. The delay time can be set to 650 minutes, although 150 minutes is the recommended maximum. The Ionization Mode is None. If a Filament/Delay segment is not needed, Delete the row. Select the Method Segment 2 Segment Description to enter purpose of segment. Click or tab to Start Time (min.
Click on the Special Application button. From within the Special Application dialog, one may specify that data should be acquired in Profile Mode (as opposed to Centroid). NOTE: Data Handling cannot process a data file collected in profile mode. Also from within the Special Application dialog, one may specify a preacquisition flow-sampling period. The Flow Sampling Segment The flow sampling segment was designed for air monitoring systems, but can be used for other applications as well.
You now see additional tab dialogs for Segment Setpoints and Ionization Mode. Examine the parameters, which may be adjusted in the Segment Setpoints dialog. Click the tab "Ionization Mode - EI Auto" to see those parameters. Details about these parameters is in the Main Editor Window.
2000 MS Method System Control The Startup Method When you enter System Control and display the Saturn System Control Window, the Startup1.mth (first time) or the last active Method for Saturn is activated. The Startup method is a copy of the Default method and can be used to build new Saturn control methods. The Default method is placed in the file directory to ensure the existence of a skeletal valid method for the operator to build on.
Editing Methods from the Saturn Status and Control Window The Saturn System Control or Acquisition Window contains a "Method:" button that allows you to directly edit the active Method. When you click on this button, Method Builder is opened with the active Method loaded. You can then edit that section or any other section of the Method as described previously. Once you have edited the Method and closed the Method Builder window, you are prompted to reactivate the Method.
Click on the Endtime button. Enter the new end time and click on OK. Importing Method Sections You may wish to copy sections from one Saturn Method file to another. This can be done by opening the Method file that you want to edit in Method Builder. Then from the Method Builder File menu, select Import Section… The Import command prompts you to select the file containing the sections you wish to import. Once you have selected the file, a dialog box of sections contained in the Method file is displayed.
When the desired sections have been highlighted, click on the Import button to import them into the Method being edited. If the Method already has sections with the same module address and channel ID, you will be prompted to reassign a new module address and channel number to the imported section or overwrite the existing section in the current method. Deleting Method Sections To remove sections from a 2000 MS Method, open the Method containing the sections you wish to remove in Method Builder.
When the desired sections have been highlighted, click on the Delete button to delete them from the Method being edited. You will prompted to confirm that you want to delete each section before it is deleted. Printing the Method To print a method from Method Builder, click on the Print button on the Toolbar and select the Method section or sections to be printed. The active Method can also be printed from the System Control Toolbar and the MS Workstation Toolbar.
After a Method has been password protected, the password will be required to save changes to the Method. Once a Method is password protected, it can be activated and used for instrument control and data acquisition. It can also be viewed from Method Builder. Only the saving of changes to the Method will be inhibited unless the correct password is entered.
3800 GC Method Command Reference 3800 GC AutoSampler When the 8400 AutoSampler or 8410 AutoInjector is selected, the AutoSampler window may contain up to five sections. The topmost section is common to all modes of operation. The entries in this section are described below. In addition, all modes of operation also include a Default Clean section and a Clean Mode section. When Viscous, Volatile, or User Defined modes are selected, the Internal Standard section is displayed.
Item Description AutoSampler Type 8400, 8410, or None Specifies whether or not an 8400 AutoSampler or 8410 AutoInjector is installed on the 3800 GC. If an 8400 or 8410 is not installed on the GC or is turned off, select None. When 8400 or 8410 is selected, the following items are displayed for editing. Syringe Size (uL) 5 uL or 10 uL Selects the size of the syringe that is installed on the 8400/8410 for use with this method. A 5 microliter or a 10 microliter syringe may be used with the 8400/8410.
Item Vial Description I, II, or III Specifies which of the three solvent vials will be used by the Default Cleaning Volume (uL) 0 to 10.0 microliters with 10 uL syringe 0 to 5.0 microliters with 5 uL syringe Specifies the amount of cleaning solvent that will be drawn up with each syringe cleaning stroke. Strokes 0 to 10 Specifies the number of times the cleaning solvent will be drawn up into the syringe and expelled into the waste cup. Speed (uL/sec) 0.1 to 50.0 µL per second with 10 µL syringe 0.
Internal Standard Section Item Description Use Yes or No If Yes, an internal standard addition will be used. When internal standard addition is used, the internal standard solution will be drawn up into the syringe from the specified solvent vial before the sample is drawn up. Vial I, II, or III Selects which solvent vial contains the internal standard. Volume (uL) 0 to 9.0 µL with 10 uL syringe 0 to 4.
More User Defined Settings Dialog Box This dialog box is accessed from “More User Defined…” button that is displayed when the User Defined mode is selected. Solvent Plug Settings Item Vial Description I, II, or III Selects which solvent vial to use for the solvent plug. Volume (uL) 0 to 10.0 µL with 10 µL syringe 0 to 5.0 µL with 5 µL syringe Specifies the amount of solvent to be drawn into the syringe before the sample or internal standard. Drawup Speed (uL/sec) 0.1 to 50.
User Defined Settings Item Description Fill Volume (uL) 0 to 10.0 µL with 10 µL syringe 0 to 5.0 µL with 5 µL syringe Specifies the sample volume that will be used for each fill stroke. Fill Strokes 0 to 99 Specifies the number of the times the sample will be “pumped” in and out of the syringe before loading the sample volume into the syringe. Sample Air Gap Yes or No If Yes, 1 µL of room air will be drawn into the syringe to create an air gap before the sample plug. Air Plug after Sample 0 to 10.
Item Description Inject Speed (uL/sec) 0.1 to 50.0 µL per second with 10 µL syringe 0.1 to 25.0 µL per second with 5 µL syringe Specifies the speed at which the contents of the syringe will be expelled into the injector. Pre-Inj Delay (sec) 0 to 99.9 seconds Specifies the length of time the syringe needle resides in the injector before expelling the syringe contents. Post-Inj Delay (sec) 0 to 99.
3800 GC Sample Delivery Item Description Front Valve Oven Middle Valve Oven Rear Valve Oven The 3800 GC can have up to three valve ovens installed (front, middle, and rear). The tabs at the top of the window select the valve oven position. Valve Oven Installed Indicate whether or not the Valve Oven at each position is installed by clicking on the “Yes” or “No” radio buttons.
3800 GC Injector Item Description Front Injector Rear Injector The 3800 GC can have up to three injectors installed (front, middle, and rear). The tabs at the top of the window select the injector position. Injector Type 1041, 1061, 1079, SPT. Middle Injector Specifies the type of injector installed in the selected position. Select “None” if no injector is installed at that position. Injector Oven On or off. Turns the injector oven in the selected position on or off.
1061 Injector Item Description Injector Oven On or off Turns the 1041 injector oven in the selected position on or off. Temperature (C) 50-450 ºC Specifies the oven temperature. 1079 Injector Item Description Injector Coolant On or Off Turns the coolant valve on when the injector is cooling down. The Coolant valve will not be used if the Off position is selected. Enable Coolant at (C) 30-450 ºC Specifies the temperature for the coolant valve to turns on. Coolant Timeout (min) 0.01-999.
Item Description Rate (C/min) 1-200 ºC /min The Rate in the first row is always blank and cannot be edited. Hold (min) 0.01-999.99 min Total (min) 0.01-999.99 min Cannot be edited. Add Adds a line to the spreadsheet. Insert Inserts a line above the currently selected row in the spreadsheet. Delete Deletes the currently selected row(s) in the spreadsheet. Spilt Ratio Dialog Box This dialog is displayed from the 3800 GC Injector window when a 1079 injector is configured with type 1 EFC.
SPT Item Description Injector Coolant On or Off Enable Coolant at (C) 30-450 ºC Coolant Timeout (min) 0.01-999.99 min Temp (C) -185-450 ºC Turns the coolant valve on when the SPT injection device is cooling down. The cryogenic will not be used if the Off position is selected. Specifies the temperature for the coolant valve to turns on. Safety measure to save coolant after the specified time if either the SPT fails to reach its set temperature or the GC does not go into run. Hold (min) 0.01-999.
3800 GC Flow/Pressure Item Description Front EFC The 3800 GC can have up to three injector EFC modules installed (front, middle, and rear). The tabs at the top of the window select the EFC position. Middle EFC Rear EFC EFC Type None, Type 1 (for 1079 injectors), Type 3 (for 1041/1061 injectors), Type 4 (for valved systems). Specifies the type of EFC installed in the selected position. Click on the following EFC types for a description of the parameters that appear when the EFC type is selected.
Item Description Pressure (psi) 0.1-100.0 psi Rate (psi/min) 0.01- 400.00 psi/min The Rate in the first row is always blank and cannot be edited. Hold (min) 0.01- 999.99 min. Total (min) 0.01-999.99 min Cannot be edited. Constant Flow On or off Click on Constant flow to disable the spreadsheet and reveals the constant flow rate value. Column Flow (ml/min) Specifies the desired constant Column Flow. Add Adds a line to the spreadsheet.
Type 4 (for valved systems) Item Description Pressure (psi) Pressure spreadsheet 100.0 psi Rate (psi/min) 0.1-100.0 psi/min The Rate in the first row is always blank and cannot be edited. Hold (min) 999.99 min Time Flow spreadsheet Initial - 999.99 min Total Flow (ml/min) 1-1000 ml/min. Add Adds a line to the spreadsheet. This button appears next to both the top and bottom spreadsheet. Insert Inserts a line above the currently selected row in the spreadsheet.
3800 GC Column Oven Item Column Oven Coolant Description On or Off. Specifies whether or not the column coolant will be used. Enable Coolant at (C) 30- 450 ºC Specifies the temperature at which to enable the coolant. Coolant Timeout (min) 0.01-999.99 min Provides a safety measure to save coolant after the specified time, if either the injector fails to reach its set temperature or the GC does not go into run. Stabilization Time (min) 10.0 min Specifies the column Stabilization Time.
3800 GC Detector Item Description Front Detector The 3800 GC can have up to three detectors installed (front, middle, and rear). The tabs at the top of the window select the detector position. Middle Detector Rear Detector Detector Type None, FID, TCD, TSD, ECD, PFPD Specifies the type of detector installed in the selected position. Detector Oven On or off. Turns the detector oven in the selected position on or off. Electronics On or off.
FID Detector Item Description Detector Oven On or off. Turns the detector oven on or off. Electronics On or Off. Indicates whether the installed FID will be used or not. Temperature (C) 50- 450 C. Time Initial - 999.99 min. Range 9, 10, 11, 12. Autozero Yes or No. Set to yes at initial time means that the FID Autozero is on continuous before the run starts. Add Adds a line to the spreadsheet. Insert Inserts a line above the currently selected row in the spreadsheet.
TCD Detector Item Description Detector Oven On or off. Turns the TCD oven on or off. Electronics On or Off. Indicates whether the installed TDC will be used or not. Temperature (C) 50- 450 C. Specifies the TCD Temperature. Filament Temp (C) 0-390 C. Specifies the Filament Temperature. Time Range Initial - 999.99 min. 0.5 and 5.0 mV. Whenever possible, operate the TCD at the lowest practical filament current. Autozero Yes or No.
Item Description Time Constant Slow or Fast. Carrier Gas He or N2/Argon. Filament Temp Limit (C) 390 or 490 C. EFC Type None, Type 13, Type 14 , Type 16. Specifies the installed type. Make up Flow (ml/min) 0-50 ml/min. Ref/Makeup Flow (ml/min) 0-100 l/min. Methanizer Installed Yes or No. Methanizer Oven On or Off. Temperature (C) 450 C. TSD Detector Item Detector Oven Description On or off. Turns the detector oven on or off. Temperature (C) 50- 450 C. Specifies the TSD temperature.
Item Autozero Description Yes or No. Set to yes at initial time means that the TSD Autozero is on continuous before the run starts. Autozero is automatically disabled once the run starts. Bead Power On or Off. Time Constant Slow or Fast. Add Adds a line to the spreadsheet. Insert Inserts a line above the currently selected row in the spreadsheet. Delete Deletes the currently selected row(s) in the spreadsheet. Sort Sorts the spreadsheet rows by time.
ECD Detector Item Description Detector Oven On or off. Turns the TCD oven on or off. Electronics On or Off. Indicates whether the installed ECD will be used or not. Temperature (C) 50- 450 C. Time Initial - 999.99 min. Range 1 or 10. Autozero Yes or No. Set to yes at initial time means that the ECD Autozero is on continuous before the run starts. Autozero is automatically disabled once the run starts. Add Adds a line to the spreadsheet.
Item Description Methanizer Oven On or Off. Temperature (C) 450 C. PFPD Detector Item Description Detector Oven On or off. Turns the PFPD oven on or off. Electronics On or Off. Indicates whether the installed PFPD will be used or not. Temperature (C) 50- 450 C. Specifies the PFPD Temperature. Square Root Mode On or Off. Time Initial - 999.99 min. Range 8, 9, 10. Autozero Yes or No. Set to yes at initial time means that the PFPD Autozero is on continuous before the run starts.
Item Description Sort Sorts the spreadsheet rows by time. Photomultiplier Voltage (V) 300- 900 V. Gate Delay (msec) 20 msec. Gate Width (msec) 20 msec. Trigger Level (mV) 10- 2000 mV. EFC Type None or Type 15 for the PFPD detector. Air 1 Flow (ml/min) 0- 50 ml/min. H2 Flow (ml/min) 0- 30 ml/min. Air 2 Flow (ml/min) 0- 30 ml/min. Methanizer Installed Yes or No. Methanizer Oven On or Off. Temperature (C) 450 C.
3800 GC Output Item Description Port A The 3800 GC can have up to three output ports installed (A, B, and C). The tabs at the top of the window select the output port position. Port B Port C Port Installed? Yes or No. Indicates whether or not the Port at each position is installed. For the installed Port, the Output time program is used to program the detector signal source and attenuation. Time Initial - 999.99 min. Signal Source Front, Middle Rear. Attenuation Powers of 2 from 1- Infinite.
3800 GC Data Acquisition Item Description Detector Bunch Rate Powers of 2 from 1 to 128 points. Sets the detector bunch rate in numbers of points; shows the resulting frequency in Hz. With increased bunch rates, less disk space is required for storing the data. With decreased rates, more data is collected. Bunch rate should be set appropriately for the narrowest peak of interest in your chromatogram. Monitor Length 16 to 128 bunched points.
3800 GC Method Section Overview In the 3800 GC Configuration section, you configured your hardware for an instrument and opened the System Control Window for the instrument. At this point, you could simply inject a sample, as described in the following sections. However, it is not likely that the default Method will have the method settings that are appropriate for your analysis. Therefore, the default Method will need to be edited to enter the settings appropriate for your analysis.
If you choose Create a New Method File, the Star Assistant Wizard will guide you in building this new method. You will first be asked to select the instrument configuration for which you want to create a method. Select Custom to create a Method for an instrument that is not attached to the Varian MS Workstation. Select the Instrument for which this method will be used.
Select the detectors for post-run processing. For each detector in the Method, you will be asked to select the channels on which post-run processing will be performed.
When you have selected the data channels and type(s) of post-run processing to be run for each detector, the Star Assistant will create a Method containing all of the sections that are needed to control the hardware, collect data and do the post-run processing specified. These Method sections will contain default values for all of the parameters. These parameters will need to be edited to match your analysis.
The parameters window shows the parameters for the highlighted item in the navigation window. Method parameters are viewed and edited in this window. Detailed information about the menu items and Toolbar buttons can be found in the online help. Method Notes The first item in the Method is the Method Notes section. Method Notes is a free form text field where information about the Method or the application can be entered.
The 3800 Method section contains seven Method windows: Sample Delivery, Injector, Flow/Pressure, Column Oven, Detector, Output, and Detector Information. These windows contain all parameters that control the operation of the 3800 GC during a chromatographic run. Spreadsheet editing Certain Method windows contain spreadsheet tables for time, temperature or flow programming. All spreadsheets behave similarly. Add a row at the bottom of the spreadsheet. Insert a row before the currently selected row.
Select rows by clicking and dragging on the row numbers on the left side of the spreadsheet. One or more rows can be selected by clicking and dragging on this column. Spreadsheets that specify time programs can display duplicate times, but all duplicates must be eliminated before you can save your work. Checking Method End times All editing windows other than the column oven window and detector info window show the current end time of the column oven program above the Save and Cancel buttons.
When the Method is downloaded to the 3800 GC, component program end times that exceed the column oven end time will be truncated. Sample Delivery Window The Sample Delivery window contains the Valve Table Program and up to three Valve Oven Programs (Front, Middle, Rear). Use these tabs to select which Valve Oven Program you wish to edit. Indicate whether or not the Valve Oven at each position is installed by clicking on the “Yes” or “No” radio buttons.
Indicate whether or not you will use the installed Valve Oven by clicking on the “On” or “Off” radio buttons. Use the spreadsheet to build a time program to turn the programmable valves on and off. Specify the isothermal temperature of each Valve Oven. The first two rows of the spreadsheet are added automatically. Use the first row to indicate how each Valve is used, by clicking on the arrow in the top cell of each Valve column. Select from the choices displayed in the combo box.
Injector Window The Injector window contains up to three Injector Programs (Front, Middle, Rear). Use the Injector Programs to specify the temperature setpoints of the isothermal 1041, 1061 and 1177 Injectors, and to specify the temperature ramp and split ratio of the programmable 1079 Injector. Use the tabs to select which Injector Program you wish to edit. Select the type of injector (1041, 1061, or 1079) at each position, or select “None” if no injector is installed at that position.
If you indicate that Coolant is turned on, specify the desired “Enable Coolant at” temperature and “Coolant Timeout”. Use the spreadsheet to build a temperature ramp program to heat and/or cool the 1079 injector. The first row of the spreadsheet contains the Initial temperature and hold time for the 1079 injector. The 1079 will equilibrate to this setting when the method is activated, and will be restored to this setting when each chromatographic run is completed.
You can use a spit ratio of 100 after injection to vent the injector of any residual solvent. Use a very low split ratio after flushing to conserve carrier gas. The first row of the spreadsheet contains the Initial Split State and Split Ratio for the 1079 injector. The 1079 will equilibrate to this setting when the method is activated, and will be restored to this setting when each chromatographic run is completed.
You can use a split ratio of 100 after injection to vent the injector of any residual solvent. Use a very low split ratio after flushing to conserve carrier gas. The first row of the spreadsheet contains the Initial Split State and Split Ratio for the 1177 injector. The 1177 will equilibrate to this setting when the method is activated, and will be restored to this setting when each chromatographic run is completed.
Indicate whether or not you will use the installed 1061 Injector by clicking on the “On” or “Off” radio buttons. If you indicate that a 1061 Injector is to be turned on, select the desired Temperature setting. SPT Injection Device If you indicate that a Sample Preconcentration Trap (SPT) is installed, an Oven Power switch and a Coolant switch will appear. Indicate whether or not you will use the installed SPT by clicking on the “On” or “Off” radio buttons.
Flow/Pressure Window The Flow/Pressure window contains up to three EFC Programs (Front, Middle, Rear). Use the EFC Programs to specify the pressure ramp of the Type 1 EFC, the pressure ramp and total flow time program of the Type 4 EFC, and the flow ramp of the Type 3 EFC. Use the tabs to select which EFC Program you wish to edit. Select the type of EFC (Type 1, Type 3, or Type 4) at each position, or select “None” if no EFC is installed at that position.
The first row of the spreadsheet contains the Initial pressure and hold time for the Type 1 EFC. The EFC will equilibrate to this setting when the method is activated, and will be restored to this setting when each chromatographic run is completed. Rows after the first row of the spreadsheet contain the programmed settings for each of the ramp segments. Each segment will ramp to the specified pressure at the specified rate (assuming the rate is achievable), and then hold the pressure for the specified time.
Type 3 EFC (for 1041/1061 Injectors) If you indicate that a Type 3 EFC is installed, a flow ramp spreadsheet will appear. The first row of the spreadsheet contains the Initial flow and hold time for the Type 3 EFC. The EFC will equilibrate to this setting when the method is activated, and will be restored to this setting when each chromatographic run is completed. Rows after the first row of the spreadsheet contain the programmed settings for each of the ramp segments.
Type 4 EFC (for Valved Systems) If you indicate that a Type 4 EFC is installed, a pressure ramp spreadsheet and a flow time program spreadsheet will appear. Pressure spreadsheet. Flow spreadsheet. The first row of the pressure spreadsheet contains the Initial pressure and hold time for the Type 4 EFC. The EFC will equilibrate to this setting when the method is activated, and will be restored to this setting when each chromatographic run is completed.
Column Oven Window The Column Oven window contains the Column Oven Program. Use the Column Oven Program to specify the Coolant Parameters and Stabilization Time of the Column Oven, and to specify its programmable temperature ramp. Indicate whether or not you will use the Coolant by clicking on the “On” or “Off” radio buttons. Use the spreadsheet to build a temperature ramp program to heat and/or cool the Column Oven. Specify the desired temperature at which to enable the coolant.
Detector Window The Detector window contains up to three Detector Programs (Front, Middle, Rear). Use the Detector Programs to specify the operating temperatures, gas flow rates and parameters of the detectors. Use the tabs to select which Detector Program you wish to edit. Select the type of Detector (FID, TSD, TCD, ECD, or PFPD) at each position, or select “None” if no Detector is installed at that position.
Indicate whether or not you will use the installed FID Detector by clicking on the “On” or “Off” radio buttons. If you indicate that an FID Detector is to be turned on and heated, select the desired Temperature setting. Time-program the detector range and autozero in the spreadsheet. Select the desired FID Time Constant by clicking on the “Slow” or “Fast” radio buttons. Select the desired gas flow rates for the detector EFC.
Program the Methanizer in the position corresponding to the tab in the Detector window by clicking on the Methanizer button. The Methanizer Program dialog box will appear. Indicate that a Methanizer is installed by selecting the “Yes” radio button. Indicate whether or not you will heat the installed Methanizer by clicking on the “On” or “Off” radio buttons. If you indicate that a Methanizer is to be heated, select the desired Temperature setting.
If you indicate that an TCD Detector is to be turned on and heated, select the desired Temperature and Filament Temperature setting. Indicate whether or not you will use the installed TCD Detector by clicking on the “On” or “Off” radio buttons. You can time-program the detector range, autozero, and polarity in the spreadsheet. Select the desired TCD Time Constant by clicking on the “Slow” or “Fast” radio buttons. Select the desired Carrier Gas and Filament Temperature Limit from the available choices.
Micro-TCD Detector If you indicate that a Micro-TCD Detector is installed, an Oven Power switch and an Electronics switch will appear in the top portion of the window, and additional detector adjustments will appear below the spreadsheet. NOTE: The Micro-TCD cell temperature is set to 110 C and is not adjustable. Indicate that a Micro-TCD Detector is installed Indicate whether or not you will use the installed Micro-TCD Detector by clicking on the “On” or “Off” radio buttons.
TSD Detector If you indicate that a TSD Detector is installed, an Oven Power switch, an Electronics switch, a Temperature setting, a Bead Current setting and a Time Constant setting will appear. If you indicate that an TSD Detector is to be turned on and heated, select the desired Temperature and Bead Current setting. Indicate whether or not you will use the installed TSD Detector by clicking on the “On” or “Off” radio buttons.
ECD Detector If you indicate that an ECD Detector is installed, an Oven Power switch, an Electronics switch, and a Temperature setting will appear in the top portion of the window, and additional detector adjustments will appear below the spreadsheet. If you indicate that an ECD Detector is to be turned on and heated, select the desired Temperature setting. Indicate whether you will use the installed Detector Oven and Electronics by clicking on the “On” or “Off” radio buttons.
PFPD Detector If you indicate that a PFPD Detector is installed, an Oven Power switch, an Electronics switch, Square Root Mode switch, and a Temperature setting will appear in the top portion of the window, and additional detector adjustments will appear below the spreadsheet. If you indicate that an PFPD Detector is to be turned on and heated, select the desired Temperature setting. Indicate whether you will use the installed Detector Oven and Electronics by clicking on the “On” or “Off” radio buttons.
Output Window The Output window contains up to three Output Port Programs (Port A, Port B, Port C). Use the Output Port Programs to time program the detector signal source and attenuation at each port. Use the tabs to select which Output Port Program you wish to edit. Indicate whether or not the Port at each position is installed by clicking on the “Yes” or “No” radio buttons. Time-program detector signal source and attenuation in the spreadsheet.
Data Acquisition Window The Data Acquisition window contains instructions for collecting a baseline noise sample (Noise Monitor) and for selecting the full scale for the FID and TSD detectors. The Varian MS Workstation will sample the baseline noise on the first derivative of the detector signal before each run. This sample is used to estimate the baseline noise. The estimate is more accurate as the sample size is increased, but the sample takes longer to acquire.
Autosampler Window The Autosampler window contains sampling parameters for the 8400/8410 Autosampler when attached to the 3800 GC. The parameters include selection of the sampling syringe size, the penetration depth for sample and solvent wash vials, the default clean and clean modes, and the injection modes. Default clean steps are used in the case that automation is stopped or a serious fault is detected. Select Pre and Post injection syringe clean modes.
Auto-Configuring the Method to Match the 3800 GC Hardware When you edit a 3800 GC Method while the corresponding GC is online in System Control, you are warned if the Method configuration does not match the hardware on the GC. Click on Yes to change the Method to match the GC. Click on No to accept the Method as is. If you choose to auto-configure the Method, the following dialog is displayed.
You are then prompted for the name of the file under which to save the Method. The active Method in System Control is updated to reflect the parameters obtained from the 3800 GC. The Startup Method When you start System Control and display an Instrument Window, the last active Method for that instrument is activated. When System Control is started, it will return to the initial settings in the Method that was last used on the instrument.
Once you have edited the Method and closed the Method Builder window, you are prompted to reactivate the Method. Reactivating the Method downloads the changes to the Module. Importing Method Sections You may wish to copy sections from one 3800 Method file to another. This can be done by opening the Method file that you want to edit in Method Builder. Then from the Method Builder File menu, select Import Section… The Import command prompts you to select the file containing the sections you wish to import.
When the desired sections have been highlighted, click on the Import button to import them into the Method being edited. If the Method already has sections with the same module address and channel ID, you will be prompted to reassign a new module address and channel number to the imported section or overwrite the existing section in the current method. Deleting Method Sections To remove sections from a 3800 Method open the Method containing the sections you wish to remove in Method Builder.
When the desired sections have been highlighted, click on the Delete button to delete them from the Method being edited. You will prompted to confirm that you want to delete each section before it is deleted. Printing the Method To print a method from Method Builder, click on the Print button on the Toolbar and select the Method section or sections to be printed. The active Method can also be printed from the System Control Toolbar and the MS Workstation Toolbar.
After a Method has been password protected, the password will be required to save changes to the Method. Once a Method is password protected, it can be activated and used for instrument control and data acquisition. It can also be viewed from Method Builder. Only the saving of changes to the Method will be inhibited unless the correct password is entered.
3800 GC System Control Command Reference Status and Control Window The 3800 Status and Control window is divided into five display areas. These are the 3800 Operation display, the Temp. Zones Status display, the Component Status display, the 8400/8410 Carrousel display, and the Chromatogram display. The left-most display area is the 3800 Operation display, which contains information about the current run and the overall state of the GC. The next display area to the right is the Temp.
graphical representation of the 8400 or 8410 Carrousel. This display graphically shows which vials are to be sampled, which vials have been sampled, which vial is currently being sampled. Below these display areas is the Chromatogram display. A selection box above the chromatogram allows you to select the channels for which you want to view the realtime chromatogram. 3800 Operation Display The 3800 Operation display is in the left portion of the 3800 Status and Control window.
Temp Zones Status Display The temperature zones status display is in the middle portion of the 3800 Status and Control window. The display includes the setpoints and actual temperatures of the column oven, the three coolable zones, and the three heatable-only zones of the 3800 GC. The display is “Fault” if a fault occurs in the zone component or “Off” if the zone oven is off. If the zone has not been configured by the 3800 GC, then “N/A” is displayed for the setpoints and actual temperature.
Column Oven Status: Item Description Ready Yes or No. The column oven is Ready (Yes) if the setpoints have been achieved and stabilized. The column oven is Not Ready (No) if readiness to start a run has not been achieved or if, during a run, the oven becomes not ready or goes “out of tolerance”. Some reasons the GC may go Not Ready during a run are: the temperature program is too aggressive, the oven door is opened, the coolant runs out, the power line voltage drops, etc. Fault Yes or No.
AutoSampler Status: This option is only shown on 3800 GCs that have an 8400 AutoSampler or 8410 AutoInjector connected to them. Item Description 8400/8410 State Ready or Running Current Vial 0 through 99 for 8400 AutoSampler 1 through 21 for 8410 AutoInjector Plunger Strokes Displays the number of times that the syringe plunger has been stroked up and down. This can be used to help monitor syringe wear and plan for syringe replacements.
Sample Delivery Status: Item Description Valve 1 through Valve 7 If the valves are configured in the 3800 GC, displays the assigned valve name and current state at the 3800 GC. The possible valve names, default state of the valve, and the energized state of the valve are listed below.
1177 Injector Status: Item Ready Description Yes or No. The 1177 injector oven is Ready (Yes) if the setpoints have been achieved and stabilized. The 1177 injector oven is Not Ready (No) if readiness to start a run has not been achieved or if, during a run, the oven becomes not ready or goes “out of tolerance”. Fault Yes or No. Displays if a fault in the 1177 injector component has occurred. 1177 Oven On or Off. Displays if the 1177 injector oven component is turned off or on at the 3800 GC.
Item Description Displays the actual temperature of the 1079 injector oven at the 3800 GC. Split State On or Off. Displays the current split state of the 1079 injector method. Split Ratio 1 to 10000 or Off Displays the current split ratio of the 1079 injector method. The split ratio is defined as the Column Flow + the Split Flow / the Column Flow. Enable 1079 Injector Coolant at 30 °C to 450 °C Timeout 0.01 min to 999.
SPT Injector Status: Item Description Ready Yes or No. The SPT injector oven is Ready (Yes) if the setpoints have been achieved and stabilized. The SPT injector oven is Not Ready (No) if readiness to start a run has not been achieved or if, during a run, the oven becomes not ready or goes “out of tolerance”. Some reasons the GC may go Not Ready during a run are: the temperature program is too aggressive, the oven door is opened, the coolant runs out, the power line voltage drops, etc. Fault Yes or No.
Item Description Displays if a fault in the Type 1 EFC component has occurred. Type 1 Pressure Setpoint 0.1 to 100 psi Displays the programmed column head pressure setting in the active method. Actual Pressure 0.1 to 100 psi Displays the actual column head pressure at the 3800 GC. Column Flow Displays, in ml/min, the column flow rate calculated from the column head pressure, column temperature, and column parameters (carrier gas, column length, and internal diameter).
Type 4 Injector EFC Flow/Pressure Status: Item Ready Description Yes or No. The Type 4 Injector EFC component is Ready (Yes) if the setpoints have been achieved and stabilized. The Type 4 Injector EFC component is Not Ready (No) if readiness to start a run has not been achieved or if, during a run, the EFC becomes not ready or goes “out of tolerance”.
Item Description Displays the TCD Range initial condition setting or the timeprogrammed setting in the active method. Time Const Fast (50 msec) or Slow (200 msec) Displays the electrometer time constant setting from the TCD Adjustments in the active method. Filament Temp 0 to 490 °C Displays the TCD Filament Temperature setting in the active method. Current Displays, in mA, the actual TCD current. Balance Pct Displays, in %, the TCD bridge balance.
Item Description microTCD Adjustments in the active method. Current Displays, in mA, the actual microTCD current. Balance Pct Displays, in %, the microTCD bridge balance. On the 3800 GC, the bridge is balanced automatically and should normally set around 0%. A large offset in bridge balance (+ or -) could indicate a potential problem. Polarity positive or negative Displays the microTCD Polarity initial condition setting or time-programmed setting in the active method.
GC. Bunch Size Displays the data acquisition bunch size. Freq Displays the data acquisition bunch rate, in Hz.
ECD Status: Item Ready Description Yes or No. The ECD detector is Ready (Yes) if the setpoints have been achieved and stabilized. The ECD detector is Not Ready (No) if readiness to start a run has not been achieved or if, during a run, the ECD detector becomes not ready or goes “out of tolerance”. Some reasons the GC may go Not Ready during a run are: the temperature program is too aggressive, the oven door is opened, the coolant runs out, the power line voltage drops, etc. Fault Yes or No.
Item TSD Bead Power Description On or Off Displays the TSD Bead Power initial condition setting or the time-programmed setting in the active method. Range 9, 10, 11, or 12 Displays the TSD Range initial condition setting or the timeprogrammed setting in the active method. Time Const Fast (50 msec) or Slow (200 msec) Displays the electrometer time constant setting from the TSD Adjustments in the active method. Bead Current 2.4 to 3.
Type 11 Detector EFC Status: Item Description Type 11 Displays the Detector EFC type. Detector EFC Type 11 has 3 channels and is used for FID detector gas control. Ready Yes or No. The Detector EFC is Ready (Yes) if the setpoints have been achieved and stabilized. The Detector EFC is Not Ready (No) if readiness to start a run has not been achieved or if, during a run, the Detector EFC becomes not ready or goes “out of tolerance”.
Type 13 Detector EFC Status: Item Description Type 13 Displays the Detector EFC type. Detector EFC Type 13 has 1 channel and is used for either ECD or TCD detector gas control. Ready Yes or No. Fault Yes or No. Ch 1 (Makeup) Set, Actual Displays, in ml/min, the programmed and actual channel 1 flow rate for TCD detector gas control. Ch 1 (Reference) Set, Displays, in ml/min, the programmed and actual channel 1 flow rate for ECD detector gas control.
Type 15 Detector EFC Status: Item Description Type 15 Displays the Detector EFC type. Detector EFC Type 15 has 3 channels and is used for PFPD detector gas control. Ready Yes or No. Fault Yes or No. Ch 1 (Air 1) Set, Actual Displays, in ml/min, the programmed and actual channel 2 flow rate. Ch 2 (H2) Set, Actual Displays, in ml/min, the programmed and actual channel 2 flow rate. Ch 3 (Air 2) Set, Actual Displays, in ml/min, the programmed and actual channel 2 flow rate.
8400/8410 Carrousel Display When an 8400 AutoSampler or 8410 AutoInjector is connected to your 3800, the Carrousel display will be visible in the 3800 GC Status and Control window. 8400 AutoSampler Carrousel 8410 AutoInjector Carrousel Item Description Red fill Indicates vials listed in the active SampleList that have not yet been sampled or are missing. Green fill Indicates the vial (vials in Dual Mode) currently being sampled.
Chromatogram Display Toolbar Shows or hides the toolbar. Full Scale: zooms all traces to their full scale values. This button is the same as double clicking in the chromatogram display window. Vertical Full Scale: the chromatogram is zoomed such that all of the trace is visible within the given time range. This command only affects the displayed amplitude range, the time range is unaffected. This button is the same as double clicking in the Y axis of the chromatogram display window.
Chromatogram Zooming and Scrolling The following mouse actions are possible for the chromatogram display window: Action Effect of Action Left mouse button click Expands selected section of chromatogram to fill the and drag a selection. entire window. Left mouse button double click. Zooms to full scale. Left mouse click and hold Zooms isometrically from the mouse position, or, if you are holding the control key down, zooms out from that point.
8400/8410 Dual Mode Setup Dialog Box When the 8400 AutoSampler or 8410 AutoInjector is used in Dual Mode, this dialog box is used to assign the detector channels to the datafile for the corresponding sample. In Dual Mode operation, two datafiles are created; one for the first sample injected, the other for the second sample injected. The samples that are injected are identified by their 8400/8410 Injection Position as either Position 1 or Position 2.
Field Description 8400/8410 Mounting Position (Informational entry only) Front or Rear 8400/8410 Injection Position (not user modifiable) Pos 1 and Pos 2 Injector (not user modifiable) When the 8400/8410 Mounting Position is set to match the physical mounting location of the 8400/8410, this column will show the 3800 injector that corresponds to each of the 8400/8410 Injection Positions.
Setup Ethernet Ports Dialog Box This dialog box is displayed the first time that the Star Assistant guides you through the setup of your 3800 in System Control. This dialog box is also accessed from the Instrument/Setup Ethernet Communications menu item of System Control. Field Description Address 44, 45, 46, or 47 Click the Address button to attach to a 3800 GC on the Ethernet network.
Setup... Click to setup IP address management (BOOTP Server). The Setup BOOTP Server Dialog Box is displayed. Select the Workststion IP Address... Allows you to select from one of the IP addresses configured for this computer. Setup BOOTP Server Dialog Box If IP addresses are managed by a Network Administrator from a central source, the 3800 GCs must be added to the list of devices requiring IP addresses. IP addresses must be assigned to GCs using a BOOTP Server.
Field Description dialog box to avoid inadvertent or unauthorized changes to IP address assignments. If this item is checked, the next time you enter the BOOTP Server dialog box, you will be prompted for a password. The initial password is blank (no password). To set your password initially, enter the desired password in the Enter new password and Re-enter new password fields. Subsequent entry into the BOOTP Server will require this password.
Advanced BOOTP Settings Dialog Box Item Description Assign Private Class A addresses to Hosts Manually Checked or not checked Use Subnet Mask Enter the subnet mask here. This is only used when the Manage IP addresses from this Workstation checkbox is checked in the Setup BOOTP Server dialog box. Use Gateway Enter the gateway address here. This is only used when the Manage IP addresses from this Workstation checkbox is checked in the Setup BOOTP Server dialog box.
Field Description 2nd Sample Name (Dual Mode operation only) Up to 19 characters Sets the name of the second sample injected. This column is only displayed when the 2nd Injection is “Advance” or “Clean & Adv”. 2nd Inject Notes (Dual Mode operation only) up to 180 characters Vial 0 through 99 for 8400 AutoSampler Opens the Notes window for the selected second sample to edit or create a note about the sample. This column is only displayed when the 2nd Injection is “Advance” or “Clean & Adv”.
Field Description injection positions, entering the wrong position will cause the sample line to be skipped and a “Bad Injector” message entered into the message log. To run samples in Duplicate Mode or Dual Mode, you must select either “1 then 2” or “2 then 1”. 2nd Injection (Duplicate Mode or Dual Mode operation only) Duplicate, Advance, Clean & Dup, or Clean & Adv Specifies the action that the 8400 will take before making the second injection during a run.
3900 GC Method Command Reference 3900 GC AutoSampler When the 8400 AutoSampler or 8410 AutoInjector is selected, the AutoSampler window may contain up to five sections. The topmost section is common to all modes of operation. The entries in this section are described below. In addition, all modes of operation also include a Default Clean section and a Clean Mode section. When Viscous, Volatile, or User Defined modes are selected, the Internal Standard section is displayed.
Item Description AutoSampler Type 8400, 8410, or None Specifies whether or not an 8400 AutoSampler or 8410 AutoInjector is installed on the 3900 GC. If an 8400 or 8410 is not installed on the GC or is turned off, select None. When 8400 or 8410 is selected, the following items are displayed for editing. Syringe Size (uL) 5 uL or 10 uL Selects the size of the syringe that is installed on the 8400/8410 for use with this method. A 5 microliter or a 10 microliter syringe may be used with the 8400/8410.
Item Vial Description I, II, or III Specifies which of the three solvent vials will be used by the Default Cleaning Volume (uL) 0 to 10.0 microliters with 10 uL syringe 0 to 5.0 microliters with 5 uL syringe Specifies the amount of cleaning solvent that will be drawn up with each syringe cleaning stroke. Strokes 0 to 10 Specifies the number of times the cleaning solvent will be drawn up into the syringe and expelled into the waste cup. Speed (uL/sec) 0.1 to 50.
Internal Standard Section Item Description Use Yes or No If Yes, an internal standard addition will be used. When internal standard addition is used, the internal standard solution will be drawn up into the syringe from the specified solvent vial before the sample is drawn up. Vial I, II, or III Selects which solvent vial contains the internal standard. Volume (uL) 0 to 9.0 microliters with 10 uL syringe 0 to 4.
More User Defined Settings Dialog Box This dialog box is accessed from “More User Defined…” button that is displayed when the User Defined mode is selected.
Item Description Vial I, II, or III Selects which solvent vial to use for the solvent plug. Volume (uL) 0 to 10.0 microliters with 10 uL syringe 0 to 5.0 microliters with 5 uL syringe Specifies the amount of solvent to be drawn into the syringe before the sample or internal standard. Drawup Speed (uL/sec) 0.1 to 50.0 microliters per second with 10 uL syringe 0.1 to 25.0 microliters per second with 5 uL syringe Specifies the speed at which the solvent will be drawn up into the syringe.
Item Description Fill Volume (uL) 0 to 10.0 microliters with 10 uL syringe 0 to 5.0 microliters with 5 uL syringe Specifies the sample volume that will be used for each fill stroke. Fill Strokes 0 to 99 Specifies the number of the times the sample will be “pumped” in and out of the syringe before loading the sample volume into the syringe. Sample Air Gap Yes or No If Yes, 1 microliter of room air will be drawn into the syringe to create an air gap before the sample plug.
Default Settings for Predefined AutoSampler Modes The following table lists the parameter settings used for each of the Predefined 8400/8410 modes using a 10 microliter syringe. If the predefined modes do not work acceptably for your samples, use the User Defined mode to enter settings that will work better with your samples. The values listed in this table provide a starting point for setting the various parameters.
3900 GC Injector Section 1177 Injector Item Description Injector Oven On or off. Turns the 1177 injector oven in the selected position on or off. Temperature (C) 50 to 450C. Specifies the oven temperature. Spilt Ratio Dialog Box This dialog is displayed from the 3900 GC Injector section when an 1177 injector is configured with type 1 EFC.
Item Description Time 0.00 to 999.99 min. Split State On/Off. If the split state is ON, then the sample is split according to the split ratio specified. If the split state is OFF, then all the sample enters the column. Split Ratio Off, 1 to 10,000. Use a split ratio of 100 after injection to vent the injector. Use a very low split ratio after flushing to conserve carrier gas. Add Adds a line to the spreadsheet. Insert Inserts a line above the currently selected row in the spreadsheet.
3900 GC Flow/Pressure Section Type 1 (for 1177 injector) Item Description Pressure (psi) 0.1 to 100.0 psi. Rate (psi/min) 0.01 to 400.00 psi/min. The Rate in the first row is always blank and cannot be edited. Hold (min) 0.01 to 999.99 min. Total (min) 0.01 to 999.99 min. Cannot be edited. Constant Flow On or Off Click on Constant flow to disable the spreadsheet and reveals the constant flow rate value. Column Flow (ml/min) Specifies the desired constant Column Flow.
3900 GC Column Oven Section Item Description Stabilization Time (min) 10.0 min. Specifies the column Stabilization Time. Temp (C) 30 - 450 C. Rate (C/min) 0.01- 100.0 C/min. The Rate in the first row is always blank and cannot be edited. Hold (min) 0.01-999.99 min. Total (min) 0.01-999.99 min. Cannot be edited. Column Oven End Time (Total) is displayed in all time-programmed windows of the Method. Add Adds a line to the spreadsheet.
3900 GC Method Section Overview In the 3900 GC Configuration section, you configured your hardware for an instrument and opened the System Control Window for the instrument. At this point, you could simply inject a sample, as described in the following sections. However, it is not likely that the default Method will have the method settings that are appropriate for your analysis. Therefore, the default Method will need to be edited to enter the settings appropriate for your analysis.
If you choose Create a New Method File, the Star Assistant Wizard will guide you in building this new method. You will first be asked to select the instrument configuration for which you want to create a method. Select Custom to create a Method for an instrument that is not attached to the Varian MS Workstation. Select the Instrument for which this method will be used.
For each detector in the Method, you will be asked to select the channels on which post-run processing will be performed.
When you have selected the data channels and type(s) of post-run processing to be run for each detector, the Star Assistant will create a Method containing all of the sections that are needed to control the hardware, collect data and do the post-run processing specified. These Method sections will contain default values for all of the parameters. These parameters will need to be edited to match your analysis.
Detailed information about the menu items and Toolbar buttons can be found in the online help. Method Notes The first item in the Method is the Method Notes section. Method Notes is a free form text field where information about the Method or the application can be entered. Method Notes are displayed in the File Open dialog boxes used whenever you select a Method. Method Notes can help explain to the operator when a Method should be used.
The 3900 Method section contains two Method windows: GC Control, and Autosampler. These windows contain all parameters that control the operation of the 3900 GC during a chromatographic run. Spreadsheet editing Certain Method windows contain spreadsheet tables for time, temperature or flow programming. All spreadsheets behave similarly. Add a row at the bottom of the spreadsheet. Insert a row before the currently selected row. Delete currently selected rows.
One or more rows can be selected by clicking and dragging on this column. Spreadsheets that specify time programs can display duplicate times, but all duplicates must be eliminated before you can save your work. Checking Method End times All editing windows other than the column oven window show the current end time of the column oven program above the Save and Cancel buttons. The column oven endtime is shown.
GC Control Window The GC control window contains sections (Flow/Pressure, Injector, and Column Oven). Flow/Pressure Section Use the EFC Programs to specify the pressure ramp of the Type 1 EFC. Type 1 EFC (for 1177 Injectors) With a Type 1 EFC is installed, a pressure ramp spreadsheet will appear. Use the spreadsheet to build a pressure ramp program to control the Type 1 EFC. The first row of the spreadsheet contains the Initial pressure and hold time for the Type 1 EFC.
Rows after the first row of the spreadsheet contain the programmed settings for each of the ramp segments. Each segment will ramp to the specified pressure at the specified rate (assuming the rate is achievable), and then hold the pressure for the specified time. (Note that the Rate in the first row is always blank and cannot be edited. Also note that the entire Total column cannot be edited.
1177 Injector With a 1177 Injector is installed, an Oven Power switch, a Temperature setting and a Split Ratio table will appear. Indicate whether or not you will use the installed 1177 injector by clicking on the “On” or “Off” radio buttons. Set the desired Temperature. NOTE: You must have already configured the Type 1 EFC in the corresponding position in the Flow/Pressure Section before you can program the split ratio.
You can use a split ratio of 100 after injection to vent the injector of any residual solvent. Use a very low split ratio after flushing to conserve carrier gas. The first row of the spreadsheet contains the Initial Split State and Split Ratio for the 1177 injector. The 1177 will equilibrate to this setting when the method is activated, and will be restored to this setting when each chromatographic run is completed.
Specify the desired Stabilization Time. Use the spreadsheet to build a temperature ramp program to heat and/or cool the Column Oven. The first row of the spreadsheet contains the Initial temperature and hold time for the Column Oven. The Column Oven will equilibrate to this setting, and stabilize for the specified Stabilization Time, when the method is activated, and will be restored to this setting when each chromatographic run is completed.
available. Selecting User Defined mode allows you access to all 8400 autosampler parameters to fine-tune your injection. Consult the Online Help for a detailed description of all Injection Mode parameters. Auto-configuring the Method to Match the 3900 GC Hardware When you edit a 3900 GC Method while the corresponding GC is online in System Control, you are warned if the Method configuration does not match the hardware on the GC. Click on Yes to change the Method to match the GC.
To upload the Method from the 3900 GC to System Control, select “Upload Active Method from Modules…” from the File menu. You are then prompted for the name of the file under which to save the Method. The active Method in System Control is updated to reflect the parameters obtained from the 3900 GC. The Startup Method When you start System Control and display an Instrument Window, the last active Method for that instrument is activated.
Method… button When you click on this button Method Builder is opened with active Method loaded and the corresponding Instrument Module selected. You can then edit that section or any other section of the Method as described previously. Once you have edited the Method and closed the Method Builder window, you are prompted to reactivate the Method. Reactivating the Method downloads the changes to the Module. Importing Method Sections You may wish to copy sections from one 3900 Method file to another.
import by clicking on them. If you click on one section and the hold down the shift key while clicking on another section, all of the sections in between will be selected. Holding down the control key while clicking on a section will add that selection to those files already selected. Clicking on a highlighted section while holding down the control key will remove that section from the list of selected files.
A dialog box of sections contained in the Method file is displayed. Highlight the sections that you wish to delete by clicking on them. If you click on one section and the hold down the shift key while clicking on another section, all of the sections in between will be selected. Holding down the control key while clicking on a section will add that selection to those files already selected.
Printing the Method To print a method from Method Builder, click on the Print button on the Toolbar and select the Method section or sections to be printed. The active Method can also be printed from the System Control Toolbar and the MS Workstation Toolbar. Click on the Active Method Options button on the System Control Toolbar or on the Method Operations button on the MS Workstation Toolbar and select Print Method.
3900 GC System Control Command Reference Status and Control Window The 3900 Status and Control window is divided into four display areas. The leftmost display area is the 3900 Operation Display, which contains information about the current run and the overall state of the GC. The middle displays area is the temperature zone status display, showing the setpoint and current actual temperature of each heated zone in the GC, the Oven Status, and the Injector EFC Status display.
Item Description Runtime Shows the elapsed time in minutes since the beginning of the run. The maximum run time is 999.99 minutes. Endtime Shows the time at which the run will end. State Ready, Running, Stabilizing, Equilibrating, Computing, or Not Ready Shows the state of the GC. The light appears green if the GC is Ready or Running. Otherwise, the light is red. Fault/No Fault indicator No Fault (green light) or Fault (red light).
Item Description Col Oven Setpoint Abient+5 °C to 450 °C Displays the column oven programmed temperature setting in the active method. Col Oven Actual Abient+5 °C to 450 °C Displays the actual temperature of the column oven at the 3900 GC 1177 Setpoint 50 to 450 °C Displays the 1177 injector oven programmed temperature setting in the active method. 1177 Actual 50 to 450 °C Displays the actual temperature of the 1177 injector oven at the 3800 GC.
Item Description Stabilization Time 0.00 - 10.00 min Shows the 3900 GC column oven stabilization time in minutes. The stabilization time counts down from the programmed method value and then displays 0.00 minutes when the stabilization period is over. Injector EFC Status Display Injector EFC Status: Item Flow Ready Description Yes or No. The Type 1 Injector EFC component is Ready (Yes) if the setpoints have been achieved and stabilized.
Item Description Linear Velocity Displays, in cm/sec, the column linear velocity calculated from the column head pressure, column temperature, and column parameters (carrier gas, column length, and internal diameter). Total Flow Displays, in ml/min, the total flow rate through the system. Split State On or Off. Split Ratio 1 - 10000 Displays the current split state of the 1177 injector method. Displays the current split ratio of the 1177 injector method.
when it is activated. It also allows the configuration of the 3900 GC to be changed from the Saturn GC/MS Workstation. Item Description Column, Rapid MS Mode On/Off When a Rapid-MS column is used in the 3900 GC, the Rapid-MS Mode should be set to On. This will configure the GC to set the proper parameters for the Rapid-MS column. The column length and inside diameter entries will be grayed out. Column, Length The length of the column in meters. Values range from 0 to 250 meters.
Item Description splitless runs in which the split vent is opened. Injector EFC, Gas Saver Flow The lowest system flow rate that will be maintained during the gas saver period. This has a range of 1-100 mL/min and defaults to 20 mL/min. Injector EFC, Gas Saver Timeout A non-zero value entered for this parameter will cause the system to initiate a timer once a method is activated.
Item Description poor operation but will not harm either the GC or the AutoSampler. AutoSampler, Syringe Speed 1 to 30 (cm/sec), default=30 The Injector Injection Speed parameters define the rate at which the needle will penetrate the injector septum and descend to the set Injector Needle Depth. AutoSampler, Needle Depth 0 to 100, default=100 The Injector Needle Depth parameters define how far into the designated injector the needle will penetrate.
Item Description Calibrate Vial 0 Position, Start Calibration To start the Vial 0 (or Vial 1) calibration, make certain a vial with the same form factor and cap as the ones you will be using for your analyses is placed in the 0 position of the carrousel (or the Vial 1 position of the CP-8410). Press the Start Calibration button. Calibrating the Vial 0 (or Vial 1) position involves manipulating the positions of three different components.
Item Description always approach the final calibration position with clockwise movements. To help facilitate this rule, the carrousel will backup 10 steps when a counterclockwise action is selected but will move one step when a clockwise tower rotation is selected. Calibrate Vial 0 Position, Tower Clockwise Moves the tower 1 step in the clockwise direction each time the button is pressed.
Item Description needle guide, so this height will give you optimum penetration depth.). Calibrate Injector Position, Start Calibration Press the Start Calibration. The CP-8400/8410 will rotate the tower so that it is over the Injector position and lower the syringe sled so that it is over the injector.
Item Description Calibrate Vial 0 Position, Start Calibration To start the Vial 0 (or Vial 1) calibration, make certain a vial with the same form factor and cap as the ones you will be using for your analyses is placed in the 0 position of the carrousel (or the Vial 1 position of the CP-8410). Press the Start Calibration button. Calibrating the Vial 0 (or Vial 1) position involves manipulating the positions of three different components.
Item Description Calibrate Vial 0 Position, Use Mouse Buttons to Rotate Carrousel Clicking this button will display the following dialog box. Calibrate Vial 0 Position, Use Mouse Buttons to Raise/Lower Syringe Clicking this button will display the following dialog box. Calibrate Injector Position, Start Calibration Press the Start Calibration. The CP-8400/8410 will rotate the tower so that it is over the Injector position and lower the syringe sled so that it is over the injector.
Item Description Calibrate Injector Position, Use Mouse Buttons to Raise/Lower Syringe Using the Syringe Up button adjust the height of the needle guide such that the sled is just resting on or very slightly depressing the Injector Switch and is covering the locator cone. Clicking this button will display the following dialog box.
Setup Ethernet Ports Dialog Box This dialog box is displayed the first time that the Star Assistant guides you through the setup of your 3900 in System Control. This dialog box is also accessed from the Instrument/Setup Ethernet Communications menu item of System Control. Item Address Description 44, 45, 46, or 47 Click the Address button to attach to a 3900 GC on the Ethernet network.
Item Description Actual IP Displays the actual IP address of the connected 3900 GC. Setup... Click to setup IP address management (BOOTP Server). The Setup BOOTP Server Dialog Box is displayed. Setup BOOTP Server Dialog Box If IP addresses are managed by a Network Administrator from a central source, the 3900 GCs must be added to the list of devices requiring IP addresses. IP addresses must be assigned to GCs using a BOOTP Server.
Item Description Manage IP addresses from this Workstation Checked or not checked Require password entry for this dialog box Checked or not checked Ethernet Address Displays the Ethernet address of any 3900 GCs already connected to the network and powered on. You may also manually enter an Ethernet address for a 3900 GC (available from the 3900 GC front panel display). IP Address Displays the IP address of any 3900 GCs already connected to the network and powered on.
Advanced BOOTP Settings Dialog Box This dialog lets you enter advanced settings. Item Description Assign Private Class A addresses to Hosts Checked or not checked Manually Determines whether IP addresses must be entered in the Setup BOOTP Server dialog box (checked) or if they are generated (unchecked). Use Subnet Mask Enter the subnet mask here. This is only used when the Manage IP addresses from this Workstation checkbox is checked in the Setup BOOTP Server dialog box.
8200 AutoSampler Instrument Control Command Reference 8200 AutoSampler Status and Control Window 381
Item Description RunTime The elapsed time since the start of the run. EndTime The time when the AutoSampler Method will end. Mode Standard or SPME. Standard is used with liquid sampling syringes. SPME is used with Solid Phase MicroExtraction fibers and holders. Status light Shows the state of the AutoSampler. When the AutoSampler is ready to prepare and inject a sample, the light is green. Otherwise, it is red.
AutoSampler Carrousel Display Item Description Black dot Indicates the vials found during Vial Check. Red fill Indicates vials listed in the active SampleList that have not yet been sampled. Blue fill Indicates the vial currently being sampled. Green fill Indicates the vials in the active SampleList that have been sampled.
Hardware Dialog Box Item Description Sampling Device Specifies the size and type of syringe installed in the 8200 AutoSampler, either a 10 microliter liquid sampling syringe, a 100 microliter liquid sampling syringe, or a Solid Phase MicroExtraction (SPME) fiber and holder. Wait for Read In When checked, the AutoSampler waits for a hardware Ready input signal before starting. When unchecked, the hardware Ready input is ignored.
8200 SampleList Window Extensions When an 8200 is controlled by the Varian MS Workstation, the SampleList for that instrument contains the following device-dependent fields. Refer to the help on the generic SampleList Window for a description of the fields not listed here. Item Description Vial 1 - 48 with standard sample vial tray. 1-12 with large sample vial tray. Sets the AutoSampler vial number of each sample in the SampleList. Volume 01. to 8.
Item Description Volume 0.1 to 10 ul with 10 ul syringe, or 1 to 100 ul with 100 ul syringe Sets the volume in microliters to be drawn into the syringe and add to the vial to be sampled. Mixes 0 to 100 Sets the number of mixing strokes to be done. Mix Stroke 0.1 to 10 ul with 10 ul syringe, or 1 to 100 ul with 100 ul syringe Sets the volume to be drawn into the syringe in microliters for each mixing stroke. Washes 0 to 9 Sets the number of times the syringe will be washed after this step.
Carrousel Dialog Box Item Description Copy Replaces the entire SampleList with a copy of the Default Sample parameters for each vial in the carrousel. Delete Deletes each line in the SampleList for which no vial can be found in the carrousel. Append Appends a new line to the SampleList for each vial in the Carrousel that is not entered in the SampleList. Cancel Cancels the operation and closes this Dialog Box without changing the SampleList.
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8200 Method Command Reference 8200 Configuration Window Item Description Carrousel Type 12 Vials or 48 Vials Select the tray that is to be used on the 8200 AutoSampler when this Method is run. End Time GC Cycle Time (SPME mode) 0 to 640 minutes Prep Ahead When checked, the 8200 AutoSampler will begin preparing the sample for the next injection before the instrument goes to ready.
Item Description Volatile Sample Used with samples in a high vapor pressure solvent. A solvent flush sampling mode with slow plunger speeds and no upper air gap to minimize flashing of the sample during sampling. Neat Sample Used to minimize the solvent that is injected with the sample. In this mode, solvent flush is turned off. The syringe is washed several times with the sample and overfilled with sample.
User Defined Parameters Item Description Solvent Flush Sampling When Yes is selected, the solvent plug size needs to be specified and whether upper and lower air gaps are to be used must be selected. When No is selected, the solvent plug size and upper and lower air gaps are turned off. Syringe Wash Time (sec) 6 to 180 seconds Sets the amount of time that the wash solvent will be flushed through the syringe.
Item Description Pause Time (sec) 1 to 30 seconds Sets the amount of time that the syringe will be held in the vial after the sample is drawn into the syringe. It allows the pressures to equilibrate and the sample flow into the syringe to stop before withdrawing the syringe from the vial. Hot Needle Time (min) 0.00 to 1.00 minute Sets the amount of time that the syringe needle will reside in the injector before the sample is expelled from the syringe. Injection Rate (ul/sec) 0.2 to 10.
Automated MS Report Generation Overview Once you have added Report sections to your Method, automated reports can be generated from System Control after each injection, after recalculations, or by the use of any of the Print actions in the Sequence window. You may choose to disable automated Report printing during the course of an automated sequence of injections or recalculations. You can do this by disabling automated printing from the Automation menu in the Instrument window.
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Automation File Editor Command Reference Menus File Menu Menu Item Description New A sub-menu displays RecalcList, SampleList and Sequence. Selecting one of them displays the Create a New Automation File dialog box to name a new file of the selected type. Open A sub-menu displays RecalcList, SampleList and Sequence. Selecting one of them displays the Open an Automation File dialog box to open an existing automation file of the selected type .
Edit Menu Menu Item Description Cut Deletes a selection and copies it to the Clipboard. Used to remove or move a selected part of a spreadsheet. Copy Copies a selection to the Clipboard. Used to duplicate a selection and place the duplicate in a new place (using Paste). Paste Inserts previously cut or copied information that was stored in the Clipboard into a spreadsheet. Clear Deletes a selection but leaves the Clipboard unchanged. Add Adds a new line in a Sequence, SampleList or RecalcList.
Main Toolbar Item Description A sub-menu displays RecalcList, SampleList and Sequence. Selecting one of them displays the Create a New Automation File dialog box to name a new file of the selected type. A sub-menu displays RecalcList, SampleList and Sequence. Selecting one of them displays the Open an Automation File dialog box to open an existing automation file of the selected type . Saves the currently displayed automation file with the existing name.
Open Automation File Dialog Box This dialog box is used to specify or open an automation file. The Open Automation File dialog box appears with several different titles, depending upon how you access it. In all cases, it contains the fields listed below in forms appropriate for the type of file you are about to open. Item Description Look in Lists the available folders and files. To see how the current folder fits in the hierarchy on your computer, click the down arrow.
Save Automation File As Dialog Box This dialog box is used to name an automation file. The Save Automation File As dialog box appears with several different titles, depending upon how you access it. In all cases, it contains the fields listed below in forms appropriate for the type of file you are about to save. Item Description Save in Lists the available folders and files. To see how the current folder fits in the hierarchy on your computer, click the down arrow.
Print Setup Dialog Box This dialog box is used to specify the printers that will be used by Varian MS Workstation applications both interactively and during automation. Item Description Default Saturn Printer Displays the printer that is used when printing interactively from Varian MS Workstation applications. Click on the Change button to select a different printer. Instrument Printers Displays the printer that is used when printing under automation from System Control.
Edit Notes Dialog Box This dialog box allows you to enter descriptive notes associated with an automation file. These notes can be viewed when selecting the file, and are included in the file's printout. Item Description Notepad Area Shows any notes attached to the file. The notes may describe the contents of the file, its uses, restrictions, etc. The Notepad Area is scrollable if the notes exceed the available space.
RecalcList Window Data Files can be added to a RecalcList by clicking on a cell in the Data File column and typing the file name, or by pressing the Browse... button and selecting the file name. Another way of quickly adding one or more Data Files to a RecalcList is by selecting the files of interest in the Explorer, and dragging them over the RecalcList Window. When you release the mouse button, the Data Files are automatically appended to the RecalcList.
Item Description AutoLink... Two AutoLink commands when Sample Type is Baseline, Analysis, Calibration, or Verification. One AutoLink command when Sample Type is AutoLink. One Activate Method Command when Sample Type is Activate Method. Opens the AutoLink Parameters dialog box to set the options for linking to a remote application during automation through System Control.
Item Description Defaults… Displays the Set Defaults dialog box, allowing you to specify default values for each applicable field in the RecalcList. Begin Opens the Begin RecalcList Dialog Box to specify a method to be used while recalculating or printing all RUN files in this RecalcList, and to then begin recalculating or printing the files. Suspend Suspends execution of this RecalcList after the current file has been completed.
Item Description Detector Channel Indicates the detector channel that is specified by the remaining fields in the row. Channels are indicated by the detector module name, bus address, and channel identifier. The combo box contains entries for all channels having data handling sections in the active method. If the desired channel is not visible in the combo box, make sure that the correct method is active and that it contains data handling sections for the desired channel.
Item Description Amount Standard 2-8 0.000001 to 1,000,000 Sets the amounts of the second through eighth internal standards. Used to calibrate results for Internal Standard and Normalized Percent calculations involving multiple internal standards. If the peak table does not contain multiple internal standards, these fields will be disabled. Add Adds a line to the end of the list. Insert Adds a new row before the highlighted line. Delete Deletes the highlighted row in the list.
Open Data File Dialog Box Item Description Look in Lists the available folders and files. To see how the current folder fits in the hierarchy on your computer, click the down arrow. To see what's inside a folder, click it. The box below shows the folders and files in the selected location. You can also double-click a folder or file in that box to open it. To open the folder one level higher, click the “up arrow” button on the toolbar. File list Lists the folders and files in the selected location.
Item Description Open File Opens the selected data file using the selected channel. Cancel Cancels file selection. SampleList Window The SampleList window contains injection parameters that are specific to the sample introduction device you are using on your instrument. This section describes the generic SampleList fields. Refer to the appropriate Instrument Control help topic in the System Control Reference Help for a description of the device-specific extensions to the SampleList.
Item Description AutoLink Two AutoLink commands when Sample Type is Baseline, Analysis, Calibration, or Verification. One AutoLink command when Sample Type is AutoLink. One Activate Method Command when Sample Type is Activate Method. Opens the AutoLink Parameters dialog box to set the options for linking to a remote application during automation through System Control.
Item Description Data Files… Opens the Data File Generation dialog box to specify the naming scheme being used for Data Files generated from injections. Note that if the method contains both MS and standard GC DH method sections, then both sms and run files will be generated. RecalcList… Opens the RecalcList Generation dialog box to specify the options for generating or updating RecalcLists after injections.
Data File Generation Dialog Box Item Description Directory for Data Files Shows the currently selected directory where Data Files will be generated. New Folder Allows you to create and name a new folder in the currently displayed directory. Drives Allows you to specify the drive where Data Files will be generated. Data File Names Allows you to enter the Data File name specification.
RecalcList Generation Dialog Box Item Description Do not automatically create and update a RecalcList. No RecalcList will be generated or updated when you create Data Files as a result of injections. Create and update a new RecalcList Allows you to enter the name of a new RecalcList that will be created when Data Files are generated as a result of injections.
AutoLink Parameters Dialog Box With AutoLink, you can specify a program to be executed after all injections of a sample have been performed, or two programs to be executed after each injection of that sample. When AutoLink appears as a sample type in a SampleList or RecalcList, the associated program is executed at that point in the SampleList / RecalcList after the previous SampleList / RecalcList line has completely finished.
Sequence Window Item Description Action Shows the action chosen for each line in the Sequence Method Shows the Method chosen for each line in the Sequence Sample/RecalcList Shows the SampleList or RecalcList chosen for each line in the Sequence Add Adds a new line to the end of the Sequence. Insert Adds a new line above the highlighted line. Delete Deletes the highlighted line in the Sequence. Browse...
Automation File Editor Overview The Automation File Editor is used for editing and creation of SampleLists, RecalcLists, and Sequences outside of the Varian MS Workstation’s System Control application. The off-line Automation File Editor allows access to these files without disrupting automated runs that may be occurring in System Control. SampleLists and Sequences that are active and running in System Control can not be accessed simultaneously in the off-line Automation File Editor.
…or by clicking on the New or Open Automation File button on the toolbar. The RecalcList window for the open RecalcList is displayed. It contains most of the same fields contained in the SampleList. Where the SampleList may contain AutoSampler and sample specific data handling information, the RecalcList contains the Data Filename and data file specific data handling information.
Editing or creating a SampleList Choose either a New SampleList or Open an existing SampleList from the File menu.. …or by clicking on the New or Open Automation File button on the toolbar. After choosing the SampleList to open the “Select SampleList Section Type” dialog box is displayed. This dialog box allows you to choose a SampleList that is appropriate for the AutoSampler that will be used, e.g. CP-8400, CP-8410, 8200 Standalone AutoSampler.
Enter notes about the sample. Enter post-run operations to be performed. Enter information about the samples you plan to inject. Select the location and name for the Data Files to be generated by the SampleList. Specify RecalcList generation options. Spreadsheet columns can be sized by dragging their border using the left mouse button. Move columns by dragging them using the right mouse button. Right click on column headers for formatting options.
If you need to add several similar lines to the sample list, click on the Add Lines… button. You can then enter the common information in the dialog box. For sequentially numbered Sample names, enter the starting number and the number of entries to add to the SampleList. The Sample Names will have these numbers appended to them. Specifying the Data File Name and Path Data File names can be up to 255 characters long.
Specifying Per-Sample Data Handling Parameters Most Data Handling parameters are specified in the Method used during the injection. Some parameters may vary on a per-sample basis, and are therefore specified when you perform the injection.
Specifying a RecalcList From the SampleList RecalcList… button, you can choose to create a new RecalcList, append to an existing RecalcList, or not create nor update a RecalcList. Clicking on the RecalcList button displays the RecalcList Generation dialog box. If you choose to create a new RecalcList, this automatically generated RecalcList will not overwrite an existing RecalcList.
Using More Than One Method for Injections The Varian MS Workstation allows you to perform automated injections using more than one Method. There are two ways in which this can be accomplished. The first is by changing the active Method from within the SampleList. The second is by using a Sequence. You may change the Method used during injections by activating a Method in a SampleList row. Select Activate Method from the Sample Type cell. Click on the AutoLink button.
Editing or Creating a Sequence Choose either a New Sequence or Open an existing Sequence from the File menu... …or by clicking on the New or Open Automation File button on the toolbar. The Sequence window for the open Sequence is displayed. Enter the Method and SampleList to use. You may enter any number of Sequence lines. Choose the action to be done in that step of the Sequence from the drop down box. Browse for a Method or SampleList file in the active cell.
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GC Batch Report Overview The Batch Report application allows you to quickly generate reports for a batch of Data Files without using System Control. Reports are automatically printed when you drag and drop Data Files from the Windows Explorer onto the Batch Report window. You can specify the Method to use when formatting the reports, and the post-run application that you wish to invoke. Click on the Batch Reporting icon in the MS Workstation Toolbar. The Batch Report window is displayed.
Method Selection The Batch Report application allows you to generate reports for a set of Data Files using parameters specified in a Method. You determine whether you to use the Method parameters from the most recent report generation for each Data File (the Data File Method), or whether you wish to specify a different Method for all Data Files in the batch. To use the Data File Method for Data File in the batch, click on the Use Data File Method radio button.
Generating Reports To generate reports for Data Files using the report formatting information in the specified Method drag Data Files from the Windows Explorer and drop them on the Batch Report window. When you do, the upper list box will show the selected files. As each file is processed, a status message is added to the lower list box. During the report generation process, you can click on the Pause button to stop processing after the current job.
The Change Application dialog box displays all post-run applications registered in the Star32.ini file in your Windows directory. The actual command line is listed for each: Command Line Application Report32.exe The Standard Report application. Starwr32.exe Star Custom Report Writer Pvwrai32.exe PolyView Starfi32.exe StarFinder Select the application you wish to invoke from Batch Report and click OK.
GC Data Handling Calibration Types of Calibration There are three types of calibration available with the Varian MS Workstation: External Standard, Internal Standard, and Normalized Percent. Refer to the section GC Data Handling Fundamentals for a brief description of each calibration type. Refer to the Regulatory Compliance Manual for a complete description of the algorithms used by each type to calculate results.
Specify the calibration type. Up to 10 separate replicates. Percent of new versus historical data. Refer to the on-line help in Interactive Graphics for a description of all fields in this window. Refer to the Regulatory Compliance Manual for a description of weighting options. Peak Table The Peak Table contains amounts for each level (the number of which is specified in the Calibration Setup), and the internal standard peak designations. Specify internal standard peaks.
Specify internal standard amounts. You can also calibrate your Method using previously collected Data Files, recalculating them as calibration samples. Add the Data Files to the RecalcList. Enter the Data Files to be used as calibration samples. Select the Calibration sample type. Enter the calibration level for this Data File. Inspecting Calibration Curves Calibration Curves can be viewed and edited from System Control. Pull down the Recalculate menu. Select View Calibration Curves.
You may also view Calibration Curves for the active Method in Interactive Graphics. Pull down the Results menu. Select View Calibration Curves. The Calibration Curve window is displayed. You may also view Calibration Curves from the Calibration Setup window in the Data Handling section of the Method.
Select View Curves. Generating Calibration Block Reports As you create calibration information in System Control, you may wish to generate a Calibration Block Report documenting the calibration curves and replicate statistics for each peak. Open the SampleList (shown) or RecalcList window. Enter a Print Calib line after all calibration runs are completed. A Calibration Block Report is printed when the SampleList or RecalcList line is encountered during automation.
Calibration Verification You may wish to periodically check the validity of your calibration data as you perform analytical injections. You do so by injecting a verification sample with known amounts for each compound and comparing them to amounts calculated from the calibration curves. If the amounts deviate more than a given tolerance, a verification failure occurs and a number of failure actions can take place.
GC Data Handling Fundamentals Introduction Even after optimizing your chromatographic conditions to provide the best separation possible, you may still have unresolved peaks or other situations requiring special post-run Data Handling operations. For instance, you may want to exclude solvent peaks from the total area when doing area percent calculations. You may want to ensure that a very small peak in one part of the chromatogram is detected, and not rejected as a noise peak.
Peak Detection The Varian MS Workstation software reduces the raw data collected from the chromatograph into a results report in four steps: Peak detection Peak integration (and final baseline determination) Peak identification (if a Peak Table is present) Results calculations Peak detection is the process in which the peak start, apex, and end points are determined. This is also the step where fused peaks are identified as a mother/tangent peak pair, or as two valley separated main peaks.
programs a new, wider peak width. Although it is rarely necessary, the software is also able to automatically program narrower peak width settings. Instead of letting the software automatically program peak width settings as needed, you can manually program your own peak width setting. The act of manually programming a peak width event disables automatic peak width programming. In the vast majority of cases, automatic peak width determination is all that is needed.
otherwise it is considered a main peak. The rule of thumb is that the higher the programmed Tangent Percentage value, the more peaks are considered tangents. Note that a tangent peak can only be detected following a main peak. Tangent skimming cannot be done on leading tangents. Tangent Skimmed Peak Valley Separated Peaks Fused tangent peaks are a special case of tangent peaks. Once it is determined that more than one peak is tangent to a main peak, the tangents themselves could be valley separated.
Identifying Peaks Peaks are identified with the use of the Peak Table in the Data Handling section of the Method. The main purpose of the Peak Table is to list the names of your compounds and their expected retention times. Since retention times may vary slightly from run to run, you can specify a window of time during which the Workstation will try to identify a particular peak.
Calibration Curve Report File: c:\star\tutorial\ext std.mth Detector: ADC Board, Address: 16, Channel ID: B 2-Octanone External Standard Analysis Curve Type: Linear Origin: Ignore y = +2.060889e+002x +3.777554e+003 Replicates 2 Resp. Fact. RSD: 40.84% Corr. Coef.(R²): 0.
Internal Standard Calibration When you use the Internal Standard calibration type, you calibrate with regular calibration standards but you also add a known amount of another analyte, the internal standard, to each calibration standard and sample. When you make an injection, any variation in the injection volume will be reflected by a detectable variation in the amount of the internal standard. Fluctuations may also be caused by the process used to prepare the samples.
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GC Data Handling Method Command Reference Integration Parameters Peak Detection: Item Description Subtract Blank Baseline checked or not checked If checked, subtracts the blank baseline in the Method from each Data File. Used to account for predictable changes in the baseline for each run, giving a relatively flat baseline. Initial S/N Ratio 1 to 256 Sets the initial signal-to-noise ratio for the Method. Used to set the sensitivity of peak detection.
Item Description Initial Tangent Height % 0 to 100 Sets the percentage of a mother peak's size below which a given peak is considered a tangent peak. Used to assign tangent peak status as a percentage of the mother peak size. Can be used to force a peak to be integrated as a tangent or as a fused peak. This value is overridden if you time program a Tangent Height Percentage event.
Peak Table Item Description Retention Time 0.001 to 1440.0 Sets the expected retention time of a peak. Specify a retention time at which you expect a peak to elute. Peak Name up to 40 characters Assigns a name to a peak. Specify the compound name or some form of identification for the analyte. Ref checked or not checked If checked, identifies a peak as a reference peak. Used to account for shifting retention times. Std checked or not checked If checked, identifies an internal standard peak.
Item Description Define Peak Windows... Opens the Define Peak Windows dialog box to set time windows for reference peaks and other peaks or to set an Unretained Peak Time. Print Prints the contents of the current peak table. Define Peak Windows Dialog Box For both types of peaks, you set an absolute time window and a percentage time window. The actual time window used will be equal to the absolute time plus the percentage time. Item Description Define Reference Peak Windows: Width 0.00 to 200.
Calibration Setup Item Description Calibration Type % (No Calibration), Internal Standard (IS), External Standard (ES), Normalized % (N%) Sets the calculation type for the Method. Determines what calculations are performed for calibrations and analyses. Number of Calibration Levels 1 to 10 levels Default Curve Origin Include, Ignore, Force Sets the number of calibration levels you will be using. Sets the default treatment of the origin in each curve.
Item Description Weighted Regression None, 1/n, 1/nX, 1/X2, or 1/nX2 Sets the weighted regression scheme to be used in determining calibration coefficients. Replicate Treatment Keep Replicates Separate or Average Calibration Replicates Determines whether new replicates are kept separate or whether they are averaged into an existing historical value. When keeping replicates separate, there is a limit of 10 replicates that can be stored.
Item Description Edit/Lock Calibration Data... Opens the Coefficients window to edit calibration coefficients for the Method. Coefficients Table Item Description Retention Time Shows the retention time of each peak. Peak Name Shows the name of each peak. Lock Coeffs. checked or not checked If checked, coefficients will not be updated on calibration runs. Prevents specific calibration coefficients from changing on subsequent calibration runs.
Calibration Curve Window Item Description Curve Type Shows the type of curve fit currently used. Indicates whether the curve fit has been changed since the calibration (edited). Origin Shows the origin treatment currently used. Indicates whether the origin treatment has been changed since the calibration (edited). Equation y = aX3 + b X2 + cX +d Shows the equation of the calibration curve currently displayed. Indicates whether the coefficients have been changed since the calibration (edited).
Item Description Revert Undoes any changes to the curve since it was last saved. Peak Name Any peak in the chromatogram Selects a peak for which to view the calibration curve Origin Include, Ignore, Force Sets the treatment of the origin in the curve for the current peak. Choose to include the origin, ignore it, or force the curve through the origin. Curve Fit Linear, Quadratic, Cubic Sets how the calibration curve for the current peak is fit.
Print All Dialog Box Item Description Curves Per Page 1, 2, 3, or 4 Lets you set how many curves will be printed on each page. Amount Units Up to 10 characters Lets you label the units for the amount field of the calibration curves. Show Outliers checked or not checked If checked, outliers appear on the printed calibration curves. Overlay Window Item Description Origin Include, Ignore, Force Sets the treatment of the origin for an alternate curve for the selected peak.
Item Description Save 2 Saves overlay curve 2 as the curve for the peak. Point Info Dialog Box Item Description Exclude Selected Point from Calculation If checked, marks the selected point as an outlier, excluding it from calibration calculations. Excluded points are never lost, and can always be included again at a later time. Amount Shows the amount of the standard represented by the selected data point. Peak Size Shows the size of the peak represented by the selected data point.
Item Description Overlay Shows what the calibration curve would look like with changes to the coefficients by overlaying the new curve on the current curve. Save Saves the edited coefficients and closes the Coefficients dialog box. Cancel Closes the Coefficients dialog box without saving the edited coefficients. X <-> Y Dialog Box Item Description Amount (X) or Amt/Amt Std (X) - depending on calculation type 0.
Item Description Deviation Tolerance 0.0 to 500 Sets the percentage of deviation from the calibration curve beyond which a result is considered out of tolerance. Out-of-Tolerance Action No Action, Increment Error Count, Terminate Sample List, Halt Automation Sets which action is taken when results for a verification run are out of tolerance.
Item Description Delete Deletes the highlighted Time Events Table entry from the table. Sort Sorts the table in order of increasing start times. Time Events Event Description Peak Width (WI) Changes the data bunching rate to allow for changing peak widths during a run. If no WI events are programmed, Data Handling will automatically adjust the bunch rate as the peak widths increase or decrease. Any time programming of peak widths prevents automatic updating.
Event Description Forced Peak (FP) Forces integration between the start and end times. A resolved baseline is drawn from the amplitude of the chromatogram at the start time and the amplitude of the chromatogram at the end time. Any Inhibit Integrate events that overlap with a Forced Peak event are ignored. The peak apex is the highest point in the forced peak time range. Split Peak (SP) Splits one peak into two peaks.
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GC Interactive Graphics Dialog Boxes Open Multiple Data Files Dialog Box NOTE: to quickly open files (when the file list spreadsheet is empty), select them from the explorer style file list and hit the OK button or the return key. You only need to add files to the file list spreadsheet if you want to select a channel different from the default channel.
Item Description Look in Lists the available folders and files. To see how the current folder fits in the hierarchy on your computer, click the down arrow. To see what's inside a folder, click it. The box below shows the folders and files in the selected location. You can also double-click a folder or file in that box to add it to the list of files to open. To open the folder one level higher, click the “up arrow” button on the toolbar. File list Lists the folders and files in the selected location.
Item Description Up Moves the selected item up one row. If there is already an entry in the row above, the two entries are exchanged with each other. When moving an item in the top row up, it gets moved to the bottom row. Down Moves the selected item down one row. If there is already an entry in the row below, the two entries are exchanged with each other. When moving an item in the bottom row down, it gets moved to the top row. Colored Buttons Selects the corresponding row in the table.
Open Method File Dialog Box Item Description Look in Lists the available folders and files. To see how the current folder fits in the hierarchy on your computer, click the down arrow. To see what's inside a folder, click it. The box below shows the folders and files in the selected location. You can also double-click a folder or file in that box to open it. To open the folder one level higher, click the “up arrow” button on the toolbar. File list Lists the folders and files in the selected location.
Item Description Recent Files Click on this button to display a list of recently selected files. When you select a file from this list, its name is displayed in the File name box. Notes When checked, displays any notes and/or revision log associated with the currently selected file. Open Opens the selected file. Cancel Cancels file selection. Open Original/Recalc Dialog Boxes Item Description Use Check this box for the method you wish to open.
Save Method As Dialog Box Item Description Save in Specifies the folder into which the method is to be saved. To see how the current folder fits in the hierarchy on your computer, click the down arrow. To see what's inside a folder, click it. The box below shows the folders and files in the selected location. You can also double-click a folder or file in that box to overwrite the Method with that name. To open the folder one level higher, click the “up arrow” button on the toolbar.
Saturn Printer Setup Dialog Box This dialog box is used to specify the printers that will be used by Varian MS Workstation applications both interactively and during automation. Item Description Default Saturn Printer Shows the printer used by all Varian MS Workstation applications for interactive printing. Instrument Printers Shows the printers used during automated report printing in System Control (one for each instrument). (Instruments 1-4) Change... Opens the Print Setup dialog box.
Layout Tab Item Description Show X Axis Show or hide the time axis. Show Y Axis Show or hide the amplitude axis. Show Horizontal Scroll Bar Show or hide the horizontal scroll bar. Show Vertical Scroll Bar Show or hide the vertical scroll bar. Show Attenuation Control Show or hide the attenuation control (to the right of the main window). Wide Attenuation Control When displayed, the attenuation control displays a wedge indicating that as you move the slider up, data is zoomed.
Item Description Show Offset Perspective Displays perspective lines when more than one Data File is open in overlay mode and both the time and amplitude offsets are greater than zero. These perspective lines are a visual aid to help you see the amount of the offset, and for lining up points at the same time on different chromatograms. If the time offset is too great or the amplitude offset too small, the perspective lines are automatically removed.
Item Description Show Peak Names When checked, displays peak names in the Main Window for all reported peaks, so even unidentified peak names will be displayed. Show Integration Baselines When checked, displays the peak baselines and lines that drop from valleys to the baseline. If the Data File has never been reintegrated or if results have been deleted, then the Data File doesn’t contain baseline information, and this option will have no effect.
Item Description NOTE: all data points may not be drawn when zoomed to full or large scale. That is because the data is reduced at large scales so that only important data is displayed. This is especially apparent when the data has been oversampled. Also, when the trace goes off the screen, additional points may be drawn at the edge of the window that are not actual data points, but represent an interpolated point between the point in the window and the next one just outside of the window.
Item Description Offset by If more than one chromatogram is open, enter the amount of vertical or horizontal spacing between chromatograms. The offset has no effect when only one chromatogram is open. Note that when entering an offset by amplitude or time value, the offset at one zoom level may be too large or small at another zoom level. Preset Percentage Offsets These buttons allow you to quickly change between a few preset values.
Item Description Save As … Saves the current color selection. This opens a dialog box into which you enter the name of the theme to save. This saves the colors for the seven data files, the window background color, and whether the background color is faded. Delete Deletes the current theme. Reintegration List Dialog Box NOTE: Post-run reporting actions specified in the active Method (such as ASCII File Conversion) are not done when you perform a recalculation from Interactive Graphics.
Item Description Unidentified Peak Factor 0.00001 to 999999 Sets a calibration factor for unidentified peaks. Used to calculate results for unidentified peaks. Multiplier 0.00001 to 999999 Sets a value for the multiplier. Results for the sample are multiplied by the value. Divisor 0.00001 to 999999 Sets a value for the divisor. Results for the sample are divided by the value. Recalc Notes Button which opens the Recalc Notes Dialog.
Item Description Update List or Update Amounts Copies the current list of internal standards and their amounts from the peak table to the table described above. After copying the list, the button changes to Update Amounts. This allows you to recopy just the amounts from the Peak Table after modifying them. Cancel Dismisses the dialog box without saving any changes. Save Changes Dismisses the dialog box and saves any changes made.
Item Description Group Any integer Allows you to assign an arbitrary group number to a peak. A report can be generated organized by number. Amounts (levels 1 to 10) 1e-6 to 1,000,000 Sets the amount of the standard for each of the calibration mixtures, level by level. Add Adds a peak to the peak table as a new entry. Insert Inserts peak in the peak table above the active row. Delete Deletes the highlighted peaks from the peak table. Sort Sorts the rows by retention time.
GC Interactive Graphics Menus File Menu Menu Item Description Add/Remove Chromatogram … Opens the Open Multiple Data Files dialog box to select a list of up to seven data files and view their chromatograms; all currently open chromatograms are replaced with chromatograms selected in the dialog. New Method Opens a new Untitled Method to edit; closes any previously open Method. Open Method … Opens the Open Method dialog box to open an existing Method file to edit; closes any previously open Method.
Menu Item Description Print Setup … Opens the Saturn Printer Setup dialog box to set preferences for printing. You can open the Print Setup dialog box from the Saturn Printer Setup dialog box. Exit Closes Interactive Graphics. Menu Item Description Undo Undo is not available. Cut Cut is not available. Copy Copies the main window as a Picture (Windows enhanced metafile format) to the clipboard. This Picture can be resized and the contents will stretch to fit the new frame.
Menu Item Description Main Toolbar Shows or hides the main application tool bar, which contains buttons such as the Add/Remove Chromatogram button, the Print button, and the reintegration buttons. Status Bar Shows or hides the Status bar at the bottom of the Interactive Graphics window. Visual Method Edit Window Shows or hides the a window beneath the x-axis that you use to interactively edit the peak table and the time events table.
Edit Method Menu Menu Item Description Set Password … Opens the Add Password Dialog Box which allows you to add or change the password for a method file. Method Notes … Opens the Method Notes window to edit notes for the Method Integration Parameters … Opens the Integration Parameters Dialog Box to edit the integration parameters for a Method. Peak Table … Opens the Peak Table Dialog Box to edit the peak table for a Method.
Help Menu Menu Item Description Help Topics Displays the help you are now viewing. Product Support Web Site If you have Internet access and a web browser installed on your computer, this option will automatically open the Varian MS Workstation Product Support Web Site. Here you will find the latest software and documentation updates for the Varian MS Workstation suite of products, along with additional notes, tips, and answers to frequently asked questions.
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GC Interactive Graphics Toolbars Toolbar Overview There are two toolbars on the main window: the Main Toolbar and the Method QuickLink Toolbar. These can each be dragged with the left mouse button to a docked or undocked location. The third toolbar is the Chromatogram Toolbar. It may not be dragged or undocked, however, it can be scrolled out of view by clicking on the green “minimizer” button. Each toolbar can be hidden or closed.
Reintegrate Now/Clear Moved Events: same as Reintegrate Now, except that any user defined peak start and end points are reset before reintegrating. View Preferences: displays the Preferences dialog box to configure settings for how chromatograms are displayed in Interactive Graphics. View Locator Window: shows or hides the locator window. This window displays a full scale version of the active chromatogram. When you select a region in this window, it zooms the main window instead.
Previous Scaling: zooms to the previous time and amplitude range. Each time you scale chromatogram(s), Interactive Graphics adds the new scaling rectangle to the end of a list of scaling rectangles. Previous scaling zooms the display to the value stored in the previous position on the list. This item is disabled when at the start of the list. Next Scaling: zooms to the next time and amplitude range.
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GC Interactive Graphics Window Locator Window Use the Locator Window to view the entire active chromatogram and to select a section of the chromatogram to view in greater detail in the Main Interactive Graphics Window. The active chromatogram is either the top most chromatogram in overlay mode, or the bottom most trace in tile mode. The Locator Window is a window that floats above the main Interactive Graphics window.
Main Window Use the Main Window to view and manipulate between one and seven chromatograms. This is the main window you use when working with Interactive Graphics. The Main Window occupies the center of the Interactive Graphics window.
2. Show a cursor and its associated “info-panel” containing the time and amplitude of the cursor and peak information. 3. Display baselines and droplines. 4. Display peak names and retention times. 5. Show the Time Events that were performed by data handling. 6. Display a blank baseline. 7. Display peak events in the shape of a triangle. 8. Display the run file “info-panel”. 9.
You can scale vertically using the Attenuation Control to the right of the Main Window. This adjusts the amplitude range on a logarithmic scale. When using the attenuation control, the lowest point of the active trace is fixed, and the amplitude range is adjusted to a smaller range as you slide the position indicator up and to a larger range as you slide it down. You can zoom in the amplitude and time axes in the same way as you do in the Main Window.
When a peak event has been moved manually, peaks whose areas are affected by the moved event are marked in the report with a ‘U‘, designating a user defined endpoint. Viewing Options and Mouse Operations You can customize the appearance of the Main Window with many options that you can set using the View Menu Commands and the Preferences dialog box. The following mouse actions are possible for the Main Window: Action Effect of Action Left mouse button click and drag a selection.
Neither the position of an info-panel, nor the configured list of items are retained when the data file is closed and then reopened. These are reset to default values when the data file is reopened. Cursor Info-Panel When the cursor display is enabled, the cursor info-panel is automatically also displayed. The contents of this info-panel varies depending on the location of the cursor. Usually, it displays only the time and amplitude of the cursor location.
Item Description File The full path name of the active chromatogram. Channel To displayed channel of the active chromatogram. Last recalc The date and time the file was last reintegrated. Fill Peak Table Info-Panel This info-panel displays the time range of the selection and the count of peaks when filling a peak table from a selection. NOTE: to show the Fill Peak Table Info-Panel, select the Fill Peak Table item from the Edit Method menu, then and check the Fill table from selection checkbox.
Color Type of Peak Table Entry Blue Reference peak Red Standard peak Green Relative retention time peak Yellow None of the above – a normal peak Types of Time Events There are two types of time events possible. How they are defined, how they are drawn, and the actions you can take depend on whether it is a time range event or a value event: Type of Time Event How Defined Events of this type (color) How Displayed Time range time event. Start time and end time.
Editing Peak Table Entries and Time Events You can later change any aspect of any time event or peak table entry by double clicking on an item in the Visual Method Edit Window. If you double click on a peak table entry, the Peak Table dialog box is displayed with the row containing that peak event selected. If you double click on a time event, the Time Events Table dialog box is displayed with the row containing that time event selected.
Info Window and Mouse Cursor Types Moving the mouse and pausing over a time event in the Visual Method Edit Window brings up a window containing information about the peak table entry or time event in a condensed format. The window is automatically hidden as soon as you move the mouse. Notice that as you move your mouse in the Visual Method Edit Window, the mouse will change from a cross cursor to the arrow cursor when over a time event.
Action Effect of Action Right mouse button click on a peak table entry or time event. Brings up a context sensitive menu with actions to be taken for one or more items. Select from the list of Move to Front, Delete, or Edit menu items as described in Right Mouse Menus above. Right mouse button click in an empty section. Brings up a context sensitive menu allowing you to add a new peak table entry or time event as described in Adding New Peak Table Entries and Time Events.
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GC Interactive Graphics Viewing Chromatograms in Interactive Graphics Interactive Graphics is the Varian MS Workstation application that allows you to review chromatograms, edit Data Handling Method parameters, and recalculate results. Interactive Graphics may be launched from the MS Workstation Toolbar. Click on the Interactive Graphics / Data Handling button. If the Data File you wish to view appears in a QuickLink button, select View/Edit Chromatogram from the menu.
Elements of the Interactive Graphics Window Once you have selected the file or files to view, they are displayed in the Interactive Graphics window. Main Toolbar Chromatogram Display Chromatogram Display Window Visual Method Editing Attenuation Control Locator Window The Locator Window The Locator Window shows the active chromatogram in full scale. Click and drag in this window to view a portion of the chromatogram.
You can size and position the Locator Window anywhere on the screen. The Locator Window can be closed by clicking on the button in the upper right corner, or by toggling the Locator Display button in the main toolbar, or by deselecting the Locator menu item in the View menu. The display state and position of the Locator Window is retained the next time you start Interactive Graphics. The Chromatogram Display Window The Chromatogram Display Window shows any portion of chromatograms that you have opened.
A separate attenuation control appears for each chromatogram. When you right click on a chromatogram trace, either in overlay or tiled mode, you are presented with a popup menu containing options for that chromatogram. Included in these options are report generation and viewing, along with the ability to remove the chromatogram, or bring the chromatogram to the active, or topmost position (in overlay mode only).
The Attenuation Control Located on the right side of the chromatogram display is an attenuation control, similar to a scrollbar which allows you to adjust the scaling of the amplitude of the chromatogram trace. As you move the thumb tab up, the vertical scale is magnified. The Visual Method Editing Window The area beneath the Chromatogram Display Window is the Visual Method Editing Window. Timed integration events and peak table entries are graphically displayed in this panel.
Toggle display of the Locator Window, the Method Quick Link button, the main Toolbar, or the Status Bar (at the bottom of the window). Toggle display of the Visual Method Edit Window, the Chromatogram Toolbar or the Attenuation Control. Display the Preferences dialog box. The Preferences Dialog Box Select Preferences… from the View menu to display the Preferences dialog box. The dialog box contains four tabs at the top, each corresponding to a different category of preferences.
These settings affect what additional information is displayed with the chromatogram. See the explanation of this option below. These settings affect the way the chromatogram traces are drawn. These settings determine whether peak start, end and apex events are drawn on all chromatograms, only the active chromatogram, or no chromatograms. These settings affect the display of peak start, end and apex points.
You may specify the colors for each of the seven possible chromatogram traces that can be displayed simultaneously in Interactive Graphics. You may also specify the background color of the Chromatogram Display Window, and whether the background is a solid color or is a faded gradient. You may save your color settings as a theme, which can be restored later. Click on the color buttons to choose a new color. Select an existing color theme, or save the current settings as a new theme.
If you wish to use Data Handling parameters from a Method file already stored on disk but not automatically opened when you selected the chromatogram, you can choose one from the File menu. Select the Open Method command. The Open Method dialog box is displayed. Select the Method containing the Data Handling section you wish to use. You can select from a list of recently opened methods here.
Select the method section you wish to open. If you wish to open the Method originally used with any chromatogram that is currently opened in Interactive Graphics, you may do so by selecting Original Method… from the File menu. This item allows you to select from the methods used when the chromatograms were originally generated.
When you select Build Method from Data File, you are prompted for the name of the Method file to be created. This new Method then becomes the active Method. Changing the Data Handling Parameters The Edit Method menu provides access to the Data Handling Method section windows for the open Method. Select the Data Handling section window to edit. Edit the Notes associated with the Method. Method notes are printed with the method, and can be viewed when selecting the method.
Peak Table The Peak Table is used to identify peaks so that results may be calculated. Refer to the on-line help in Interactive Graphics for details on all Peak Table fields. Right-click in a column header for formatting option. Refer to page 510 for the procedure for filling a Peak Table. Specify peak identification windows. Select a column then click here to replicate the first entry on all subsequent rows. Sort peaks by retention time.
This field describes acceptable values for the Value / End Time cell. Calibration Setup Calibration Setup parameters determine the type of calibration to be performed, as well as calibration acceptance criteria. Refer to the on-line help in Interactive Graphics for details on all Calibration Setup fields. Parameters in this window only apply when a calibrated calculation type is selected. The number of levels determines the number of amount columns shown in the Peak Table. Displays calibration curves.
Edit calibration coefficients. Locked coefficients are not updated by calibration runs. Verification Setup Verification Setup options affect the behavior of verification runs. Refer to the online help in Interactive Graphics for details on all Verification Setup fields. Filling the Peak Table The fastest way to build a Peak Table is to create one from the detected peaks in the active chromatogram. To do so, pull down the Edit Method menu. Select the Fill Peak Table command.
When you check this, peaks detected in any region that you select in the Chromatogram Display Window are automatically added to the peak table. The Fill Peak Table window is nearly identical to the Peak Table window, except that you may click on any peak displayed in the Chromatogram Display Window to add an entry into the table. A default name and peak parameters are entered with the retention time of the selected peak.
To add a new time event, right-click in the Interactive Time Events window at the time where you wish the event to occur. When you right-click, a menu of events is displayed. Select the desired event type. The event is added at the point where you right-clicked. Drag a time range endpoint to change the range. Drag the center of a time range to move the entire range. When you change the width of a peak table entry (the yellow boxes), all peak table entries are adjusted to reflect the new window size.
Moving Peak Start and End Points Peak start and end points are indicated on the chromatogram as lines or triangles (depending on the options selected in the Preferences dialog box). You may change the position of these points by dragging them with the mouse. Right-click on a point to return it to its original position or view the peak event information. Manually positioned points are drawn as solid triangles. Drag a point to change its position.
The Reintegration List is displayed. Set the run type (analysis, calibration, verification, baseline). If you are calculating results using an Internal Standard, edit the amount for standard peaks here. Indicates channels on which to run Data Handling. An unchecked row indicates that no new results will be calculated for the corresponding chromatogram. If a calibration run is specified, either add calibration points to existing data, or replace existing data with new calibration points.
Viewing Results You may view results for each peak by enabling the Cursor/Peak Information display from the Chromatogram Display Toolbar. Click on this button to enable the display of peak information. The Cursor/Peak Information display can also be enabled from the Trace Settings tab in the Preferences dialog box. The Peak Information window is updated with peak data when you move the cursor over the peak. Other results viewing functions are available by right-clicking on the chromatogram trace.
Viewing Calibration Curves If you are performing calibrated calculations (external standard, internal standard or normalized percent), you may view the calibration curves associated with the active Method. Pull down the Results menu. Select View Calibration Curves. The Calibration Curve window is displayed if calibration data exists in the active Method.
Double-click on a calibration point to see more information. Select the peak whose curve you wish to view. Changes made here only affect the stored calibration data and are documented in the results report and calibration block report. Refer to the on-line help in Interactive Graphics for a complete description of all fields in the Calibration Curve window. Printing and Copying the Chromatogram Display You may wish to print the image displayed in Interactive Graphics, or paste it into another document.
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GC Standard Report Method Command Reference Print Options 519
Single Run Reports: Item Description Title Up to 60 characters Assigns a title to the report. Print Chromatogram When checked, the Workstation prints the chromatogram from System Control during automation. Print Results When checked, the Workstation prints the results report from System Control during automation. Suppress Printout on Injections When checked, only prints automated reports for Recalc and Print Sequence actions.
Results Format Item Description Units Any units, up to 10 characters Assigns a name for the units used in the results report. Number of 0 to 6 Decimal Digits Sets the number of digits in which results are to be expressed. Run Log If checked, includes the method and the Time Events Log at the end of the report. Entries in the Time Events Log correspond to the actual times when the events occurred. Error Log Includes error messages that occurred during the run at the end of the report.
Chromatogram Format Item Description Start Retention Time, mins 0.00 to 1440.00 End Retention Time, mins 0.01 to 1440.00 Initial Attenuation 1 to 4096 Specifies a start time after injection for the chromatogram display and printout. Specifies an end time for the chromatogram display and printout. If the End Retention Time is greater than the actual end time in the data file, the actual end time is used. Sets the initial scaling of the display or printout.
Item Description Length in Pages 0 to 9 Initial Chart Speed, cm/min 0.0 to 30.0 Minutes per Tick 0.0 to 10.0 Auto Scale If checked, adjusts the attenuation and zero offset so that the chromatogram fills the screen or page. Time Events If checked, annotates the right margin of the chromatogram to show when time events occurred. Shows when peak width (WI), inhibit integrate (II), solvent reject (SR), group (GR), valley baseline (VB), chart speed (CS), and attenuation (ATT) changes occurred.
Item Chart Speed Description 0 .1 to 30.0 Sets the program chart speed. Attenuation 1 to 4096 Sets the program attenuation.. Attenuation is relative to the maximum full scale value of the detector. An attenuation of 1 scales the chromatogram so that a signal 1/4096th of the detector's full scale is the largest signal that will be printed. Add Adds the active parameters to the program list. To add a change in chart speed or attenuation to the report time program.
Generating GC Standard Reports The Standard GC Reports Method Section Note that information about using other reporting applications such as the Custom MS Report Writer are documented in the manuals specific to those applications. Report formatting parameters are specified in the Report section of the Method. The Report Method section is a post-run application section and applies to a specific detector channel.
Creates an ASCII file containing the results report. The file is named based on the Data File name and channel label, with the extension “.txt”. Results Format Results format specifies the layout and contents of the results report. Refer to the on-line help in Report for details on the results report fields and format. Uses the group number set in the Peak Table. Contains the Method used during the injection, along with the Module Information specified in System Control.
Fits the high and low amplitudes to the page. Peaks inhibited with II or SR time events are ignored. When not using Auto Scale, you can time program attenuation and chart speed settings. When not using Auto Scale, sets the magnification of the amplitude axis. 4096 displays the maximum detector range, 1 displays the highest magnification. When not using Auto Scale, sets the offset of the baseline as a percentage of the full page. Set the chromatogram printout length in pages or in cm/minute.
Amount units label the X axis of the curve. Refer to the on-line help in Report for details on all fields in the Report Method section. Automated Report Generation Once you have added Report sections to your Method, automated reports can be generated from System Control after each injection, after recalculations, or by the use of the Print action in the Sequence window. You may choose to disable automated Report printing during the course of an automated sequence of injections or recalculations.
Automated Printing to Multiple Printers If you are running automation on more than one instrument, you may wish to designate a separate printer for each instrument to avoid interleaving of reports. Pull down the File menu in System Control (or any Varian MS Workstation application). Select Printer Setup. The Saturn Printer Setup dialog box is displayed. This printer is used when you print documents from any Varian MS Workstation application interactively. Changes the printer and sets printer options.
Batch Report Printing without Recalculating When you perform batch recalculations in System Control, reports are automatically generated using the Report parameters in the active Method. You may wish to print reports for a batch of Data Files without recalculating them. Batch Printing in System Control Create or open a Sequence from the File menu or toolbar. Specify a Print action. Specify a Method containing the Report sections that you wish to apply.
Batch Printing with Batch Report You may print reports for a set of Data Files without using System Control. Click on the GC Batch Reporting icon in the MS Workstation Toolbar. The Batch Report window is displayed. Reports are printed using the formatting options stored in the Method last used to process the Data Files, or from the specified Method. You may specify the post-run application to invoke. Use REPORT32 for standard reports.
Click on the Standard GC Reports icon in the MS Workstation Toolbar. The Open Data File dialog box is displayed. Select the Data File. Select the channel in the Data File whose report you wish to view. The chromatogram and results report are displayed. You can search for a peak name or other text in the results report using the Search menu.
Specify report formatting parameters. The Data File and Method Quick Link buttons provide access to additional operations, such as reintegrating the chromatogram or editing the Method. The chromatogram is shown with the magnification, offset and time range specified in the Report Method section most recently used on this Data File channel. The results report is shown as it will appear when printed.
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Method Builder Dialog Boxes Create/Open Method File Dialog Box Item Description Select a method file action If Create a New Method File is selected, then the Star Assistant is started to guide you through adding any hardware modules or post-run processing to a new Method file. If Open Existing Method File is selected, then the Open Method File dialog box is displayed for selecting the Method file to open.
Open Method File Dialog Box Item Description Look in Lists the available folders and files. To see how the current folder fits in the hierarchy on your computer, click the down arrow. To see what's inside a folder, click it. The box below shows the folders and files in the selected location. You can also double-click a folder or file in that box to open it. To open the folder one level higher, click the “up arrow” button on the toolbar. File list Lists the folders and files in the selected location.
Item Description Notes When checked, displays any notes and/or revision log associated with the currently selected file. Open Opens the selected file. Cancel Cancels file selection. Save Method File As Dialog Box Item Description Save in Lists the available folders and files. To see how the current folder fits in the hierarchy on your computer, click the down arrow. To see what's inside a folder, click it. The box below shows the folders and files in the selected location.
Item Description File name Shows the currently specified file. Save as type Specifies the type of file to save. Recent Files Click on this button to display a list of recently selected files. When you select a file from this list, it’s name is displayed in the File name box. Notes When checked, displays any notes and/or revision log associated with the currently selected file. Save Saves the file with the specified name. Cancel Cancels file saving.
Change Password Dialog Box Item Description Enter Current Password Enter the password currently used to protect the Method. Enter New Password Enter password to be used in this box. Asterisks will appear as you type it. If you leave this box blank, password protection will be removed from the Method. Re-enter New Password Enter password again. This password will be compared to the previously entered one to guard against typing errors.
Print Method Sections Dialog Box Item Description Sections to Print Lists the sections of the Method. Selected sections will be printed. To print only certain Method sections, click on each section to print, then click on Print. Select All Selects all sections in the Method. Print Prints selected sections of the current Method and closes the dialog box. Cancel Closes the dialog box without out printing sections of the current Method.
Star Printer Setup Dialog Box This dialog box is used to specify the printers that will be used by Varian MS Workstation applications both interactively and during automation. Item Description Default Star Printer Displays the printer that is used when printing interactively from Varian MS Workstation applications. Click on the Change button to select a different printer. Instrument Printers Displays the printer that is used when printing under automation from System Control.
Delete Method Sections Dialog Box Item Description Sections to Delete Lists the sections of the Method. Selected sections will be deleted. To delete only certain Method sections, click on each section to delete, then click on Delete. Select All Selects all sections in the Method. Delete Deletes selected sections of the current Method and closes the dialog box. Cancel Closes the dialog box without out deleting sections of the current Method.
Import Method File Sections Dialog Box Item Description Sections to Import Lists the sections of the Method. Selected sections will be imported. To import only certain Method sections, click on each section to import, then click on Import. Select All Selects all sections in the Method. Import Imports selected sections to the Method being edited and closes the dialog box. Cancel Closes the dialog box without out importing sections into the Method.
Select Configuration Item Description Select a Configuration Select Custom in order to add any configuration of hardware modules to the Method file. Select the Instrument button in order to add only the hardware modules for that instrument configuration to the Method file. The Instrument configuration is the configuration of hardware modules and the associated Varian MS Workstation bus address defined by the user in the System Control application.
Configure Modules Item Description Available Modules Lists the hardware modules that can be configured in the Method file. Configured Modules Lists the hardware modules that have been configured in the Method file. The modules are listed in the order they are added. Add Adds the selected hardware module from the Available Modules list to the Configured Modules list. The Varian MS Workstation bus address is automatically assigned.
Item Description Cancel Closes the Star Assistant. Nothing is added to the Method file. Select Detectors for Post-Run Processing Item Description Detector Modules Specifies the detectors for which you want to add post-run processing to the Method file. If the detector is checked, subsequent steps allow you to configure the post-run processing for the detector. Select All When clicked, all of the listed Detector Modules are checked and configured for post-run processing.
Create Sections for Post-Run Processing Item Description For the following module Specifies the detector module and address for which post-run processing is added. This Star Assistant screen is repeated for each detector modules selected in the previous Select Detectors for Post-Run Processing screen. Select the channel(s) to process If checked, the selected channel is configured for postrun processing.
Confirm Configuration Item Description Added Configuration Displays the hardware modules, hardware control methods, and any post-run processing for detector modules that are to be added to the Method file. Any existing hardware control methods and post-run processing are not overwritten and are not listed in the configuration to be added. Back Displays the previous screen for the Star Assistant.
Method Builder Menus File Menu Menu Item Description New Starts the Star Assistant Method Configuration dialog to aid and guide you through creating the Method sections that you need for an instrument connected to Varian MS Workstation. Open... Opens an existing Method file to edit. Opens the Open Method File Dialog Box. Close Closes the currently selected Method. Save Saves the current settings under the name of the current Method file. Save As... Saves a Method under a new name.
Menu Item Description Exit Closes Method Builder. If you have made any changes to the Method, you are prompted to save the changes before closing Method Builder. Edit Menu Menu Item Description Undo Undoes the last edit to an item. If the last edit cannot be undone, this menu item is disabled (grayed). Cut Copies selected items to the clipboard and removes them from the Method. Copy Copies selected items to the clipboard. Paste Pastes the clipboard contents to the selected item.
Menu Item Description Tile Vertically Tiles the open Method Windows vertically (side by side). Tile Horizontally Tiles the open Method Windows horizontally (one above the other). Arrange Icons Arranges iconized Method Windows along the bottom of the Method Builder Window. Next Pane Switches between The Window Toolbar pane and The Method Builder Window pane. Open Window List A list of the currently open Method Builder windows. Provides quick access to windows that are hidden behind other windows.
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Method Builder Toolbars Overview There are three toolbars on the main window: the Main Toolbar, the Directory Toolbar, and the Window Toolbar. The Main Toolbar can be used to open, save, or print Method files; the Directory Toolbar is used to traverse the Method Directory pane; and the Window Toolbar is used to position the Method windows.
Copies selected items to the clipboard. Pastes the clipboard contents to the selected item. Deletes selected items. If a Method section is selected in the Method Directory pane, the Delete Method Sections dialog box is opened.. Replicates the first selected table line to the other selected table lines. Prints one or more sections from the current Method. Displays the help you are now viewing.
Window Toolbar When pressed, the RecalcList Generation Dialog Box pane is displayed. This pane provides a tree-structured view of the Method and allows mouse click selection of Method sections. This toolbar button toggles to show or hide the Method Directory pane. Opens a second window into the same Method. This is useful for setting up side by side comparisons of the same or different Method sections.
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Method Builder Window Overview The Method is displayed in a window that is split into a left and a right pane. The left pane is the Method Directory pane and provides a tree-structured view of the Method. The right pane is the Method Parameters pane and provides the capability to configure various method parameters. The items displayed in the Method Parameters pane correspond to the selected item in the Method Directory pane. The splitter bar that separates the panes is used to size the panes.
window from the Window menu. In addition, if you open another Method file from the File menu of Method Builder, the Method file is displayed in a new window; any previously open Method file is not closed. From the Window menu or using the Window toolbar, the Method file windows can be selected, cascaded, or tiled in order to compare the same sections in different Method files.
module is expanded into the groups of editable parameters for the control method of that module. If a minus (-) sign is displayed to the left of the name in the directory tree, then that branch in the tree can be collapsed by either clicking the minus sign or by pressing the minus key on the keyboard. If a branch is collapsed, then a plus (+) sign is displayed to the left of the name in the directory tree. Clicking the plus sign or pressing the plus key on the keyboard expands that branch of the tree.
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Module Information Editor Module Information Editor Information about the hardware modules composing your instrument(s) can be maintained and included in all data files produced by this instrument. This information can be included in the reports along with the Run Log. The module information editor lets you define and update the information you want or need to save along with your data. Within loose guidelines, what information you save is entirely up to you.
Entry Description PO# = 123456 Item1 = value1 SO# = A12345B Item2 = value2 Current Limitations There is no protection against duplicated section names or entries. Duplicated section names or entries cause no harm other than confusion if their contents differ. There is no built-in mechanism for copying part or all of the information to another module address. If you need to change the address of a module, rename or copy the MODULEXX.MDF accordingly. Creating a Section 1.
Adding an Entry to a Section 1. Using the mouse or the arrow keys, select the line within the section where you want to insert a new entry. To add an entry at the end of a section, select the blank line at the end of the section. 2. Press the Add button. 3. Provide the item and the value for the entry. To define a new entry like 'Date Serviced = January 12, 1998', type 'Date Serviced' in the 'Key' field, then 'January 12, 1998' in the 'Value Field''.
Creating a Default Module Information Template New .MDF files can be created based on a template file. If MODULE00.MDF is found in the Workstation directory, the new file will be a copy of the template. If the template does not exist, the new file will be created based on the program's built-in defaults. Note that the template is only used to create new files. To recreate an existing .MDF file based on the template, delete the old file (MODULEXX.
When you replace a hardware component, zero out (or adequately edit) the associated number of injections. You can also save free-form text by creating entries with empty Value fields. However, you then won't be able to use the programming interface to retrieve information from such free-form lines. NOTE: It is important that you keep this information current, as the copy of the module information stored in the data files cannot be erased or edited.
confirm this deletion before it is done. File Menu The File menu contains the following commands: Item Description Save Save the contents of the listbox into the module information file. Print Prints the contents of the listbox. Exit Aborts the current session. If you have made changes, you will be prompted to save the file before exiting.
When renaming an existing section, the name field is initialized with its current value. Type in the new name for the section. Press OK if you wish to save the new or modified entry, otherwise Cancel. Select To select a line in the list box, single-click on it with the mouse. The line is then highlighted and would be acted upon by the Add, Edit and Delete buttons as appropriate. Double-clicking on a line will access the appropriate edit dialog directly.
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Security Administration Overview The Security Administration window contains three window tabs that can be used to select the categories of security parameters that can be specified for Varian MS Workstation applications.
Item Description Password for this application Allows you to specify a password required to enter the Security Administration application. Note that there is no way to recover this password if it is lost, so it is recommended that you document the password in a secure location. Change Method Passwords Method passwords can be added, changed and removed from the Security Administration application. Click on the Select Method button to browse for and select the desired Method.
Application Locking Item Description Unlocked Applications This list box shows all top level windows currently running and are not locked. You may select any number of them and click on the Lock button. When you do, they are moved to the Locked Applications list box and their windows are disabled (they will not respond to mouse or keyboard input). Note that applications that are locked by the Security Administration application remain locked even after the Security Administration application is closed.
File Revision Settings Item Description Require Revision Log entry when changes to Methods are saved. When checked, the user is prompted for a description of changes when a Method file is altered and saved. This Revision Log appears in the Notes portion of the File Open dialog box, is listed in the Method Builder application window when the Method is open, and is included in the Method printout. Update Revision Log in Data Files with recalculation date, time and Method name.
Item Description Disable creation of new passwords in Method files. When checked, new passwords cannot be added to Methods. Methods already containing passwords will still prompt you for the password before changes are saved.
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Standard GC Reports Command Reference File Menu Menu Item Description Open Displays the Open Data File dialog box. Print Displays the Print dialog box. Convert (ASCII) Converts the text results report into an ASCII file. The name of the ASCII file is based on the data file name, with the channel number appended to it. The ASCII file ends with a ".txt" extension. Printer Setup Displays the Printer Setup dialog box. Exit Quits the Standard Report application.
View Menu This menu is displayed when the chromatogram window is active. Menu Item Description Change Plot Color Displays a dialog box allowing you to select a color for the chromatogram plot. This plot color is used in the display only. Options Menu Menu Item Description Report Title Displays the Report Title dialog box. Chromatogra m Displays the Chromatogram Options dialog box. Results Displays the Results Options dialog box.
Help Menu Menu Item Description Help Topics Displays the help you are now viewing. Product Support Web Site If you have Internet access and a web browser installed on your computer, this option will automatically open the Saturn GC/MS Workstation Product Support Web Site. Here you will find the latest software and documentation updates for the Saturn GC/MS Workstation suite of products, along with additional notes, tips, and answers to frequently asked questions.
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Standard GC Reports Dialog Boxes Open Data File Dialog Box Item Description Look in Lists the available folders and files. To see how the current folder fits in the hierarchy on your computer, click the down arrow. To see what's inside a folder, click it. The box below shows the folders and files in the selected location. You can also double-click a folder or file in that box to open it. To open the folder one level higher, click the “up arrow” button on the toolbar.
Item Description Run Information Shows information about the currently selected file, including a thumbnail view of the chromatogram. If you are looking at several files and you wish to use a fixed attenuation in the thumbnail display, check the Remember Scaling box. Select the channel you wish to open in the Channel selection box. When you do, the chromatogram thumbnail and Run Information is updated.
Printer Setup Dialog Box Item Description Default Saturn Printer Displays the printer that is used when printing interactively from Varian MS Workstation applications. Click on the Change button to select a different printer. Instrument Printers Displays the printer that is used when printing under automation from System Control. A separate printer can be configured for each instrument (up to four). Click on the Change button to select a different printer for each instrument.
Chromatogram Options Dialog Box Item Description Start Retention Time, mins 0.00 to 1440.00 End Retention Time, mins 0.01 to 1440.00 Specifies a start time after injection for the chromatogram display and printout. Specifies an end time for the chromatogram display and printout. If the End Retention Time is greater than the actual end time in the data file, the actual end time is used. Initial Attenuation 1 to 4096 Sets the initial scaling of the display or printout.
Item Description Initial Chart Speed, cm/min 0.0 to 30.0 Minutes per Tick 0.0 to 10.0 Sets the initial chart speed for the printout. This speed does not change unless you time program the chart speed. Set the Length in Pages to 0 to use this option. Sets the interval between time tick marks on the printout. Auto Scale If checked, adjusts the attenuation and zero offset so that the chromatogram fills the screen or page.
Item Description Attenuation 1 to 4096 Sets the program attenuation.. Attenuation is relative to the maximum full scale value of the detector. An attenuation of 1 scales the chromatogram so that a signal 1/4096th of the detector's full scale is the largest signal that will be printed. Add Adds the active parameters to the program list. To add a change in chart speed or attenuation to the report time program. Delete Deletes the highlighted line in the program.
Notes Includes the notes you entered when you made the injection (original notes) and when you recalculated (appended notes) as part of the report.
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Standard GC Reports Format Descriptions Results Report Below is an example of a results report generated from an analysis run.
Title : Title Run File : Data File name Method File : Method File name Sample ID : Sample name Injection Date: Operator Date/Time Calculation Date: Date/Time : Operator Name Detector Type: Detector Type/Range Workstation: Volume Label Bus Address : module bus address Instrument : Instrument Name Sample Rate : Sample Rate (Hz) Channel Run Time : Run Time (min) : Channel ID/Name *********** Star Chromatography Software ********************************************************* Run Mode :
[Module Run Logs] Time Events: [Data Handling Time Events] Error Log: [Module Error Logs] Calibration Report: [Calibration Report Text] Revision Log: [Revision Log] Original Notes: [Original Note Text] Appended Notes: [Recalc Note Text] ******************************************************************************* Item Description Title Set in the Print Options portion of the Report section of the Method. Run File The file name of the Data File containing the results.
Item Description Measurement Method section. Either Area, Height or Square Root of Height. Calculation Type Set in the Integration Parameters window in the Data Handling Method section. Either Percent, Normalized Percent, Internal Standard or External Standard. If results have been normalized (set in the Integration Parameters window in the Data Handling Method section), it is indicated on this line. Peak No. The number of the peak in the results table.
Item Description Group This column is shown when the Show Peak Group Totals checkbox is checked in the Results Format portion of the Report Method section. The group number for each peak is set in the peak table in the Data Handling Method section. Status Codes A code or codes specific to a peak in the results table. Possible status codes are R: Reference Peak (designated in the peak table) *: No result can be calculated, check the calibration curve.
Item Description The noise used by Data Handling depends upon the noise options set in the Integration Parameters Window in the Data Handling section of the Method. The report includes the noise value for this run, and the noise value actually used, if it is different. Manual injection (injection information) Indicates the type of injection device used (for example, manual injection, 8200 AutoSampler, or AI-200 AutoSampler), and the rack, vial and injection volume, if appropriate.
Verification Report Below is an example of a results report generated from a verification run.
9 Peak 5.580 1.0000 1.4435 44.3 5.586 -0.001 297265 --- ------------ ---------- ========== ----- ------- ======= ======== -----Totals: 14.5762 -0.
Standard GC Reports Toolbar Main Toolbar Displays the Open Data File dialog box. Displays the Print dialog box. Converts the text results report into an ASCII file. The name of the ASCII file is based on the data file name, with the channel number appended to it. The ASCII file ends with a ".txt" extension.. Displays the Find dialog box. Displays the Title dialog box. Displays the Chromatogram Options dialog box. Displays the Results Options dialog box.
