version 5 software upgrade notes - united states home | agilent

Varian Analytical Instruments 2700 Mitchell Drive Walnut Creek, CA 94598-1675/usa

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Version 5 Software Upgrade Notes Saturn GC/MS Workstation

Introduction ..............................................................................................................................................................3 Module Configuration Instructions...........................................................................................................................3

Pre-Upgrade Instructions ..................................................................................................................................... 3 Minimum Computer Requirements .................................................................................................................. 3 Power Management software........................................................................................................................... 4 Virus protection software.................................................................................................................................. 4 Windows 98 ...................................................................................................................................................... 4 Windows NT ..................................................................................................................................................... 4 Removing any existing Star Workstation ......................................................................................................... 4 Removing previously created file associations ................................................................................................ 5 Disk Maintenance............................................................................................................................................. 6

3800 with or without GC Detectors ...................................................................................................................... 6 Install the Software........................................................................................................................................... 6 Configure the Software..................................................................................................................................... 6

3400/3600 without GC Detectors......................................................................................................................... 8 Re-configure the Serial I/O Board ................................................................................................................... 9 Add Jumper for Ready In .............................................................................................................................. 10 Add a Start Cable ........................................................................................................................................... 10 Install the Software......................................................................................................................................... 11 Configure the Software................................................................................................................................... 11

3400/3600 with GC Detectors............................................................................................................................ 14 Configure the ADC Board.............................................................................................................................. 14 Install the ADC Board in the Computer ......................................................................................................... 15 Connect the Serial I/O Cable to the Serial I/O Board..................................................................................... 16 Add a Start Cable between the GC and MS ................................................................................................. 19 Connect the Serial I/O Cable to the ADC Board in the Computer ................................................................. 20 Connect the Analog Signal Cables ................................................................................................................ 21 Install the Software......................................................................................................................................... 21 Configure the Software................................................................................................................................... 21

Using the DOS software to control the Mass Spectrometer .............................................................................. 24 Upgrading Star Workstation 4.51 Files For Use With The Saturn GC/MS Workstation.................................... 25

Upgrading Data Files, Methods, SampleLists and Sequences...................................................................... 25 Converting SampleLogs into RecalcLists....................................................................................................... 25 Changes to Method default values................................................................................................................. 26 Changes to the Automation Validation procedure ......................................................................................... 26

Software Platform Differences...............................................................................................................................26 Architectural Differences.................................................................................................................................... 26

Multiple Applications vs. Single Application ................................................................................................... 26 Single, Integrated MS Method vs. Multi-File MS Method.............................................................................. 26 Unified Module Method vs. Independent Module Methods........................................................................... 26 Integrated Data Handling Methods vs. Scattered Data Handling Parameters .............................................. 27 Integrated and Synchronized MS and GC Detector Acquisition ................................................................... 27 Sequence and Sample Lists vs. Analysis List Automation ............................................................................ 27 Quantitation Results Resident in Data Files vs. Separate Quantitation Files .............................................. 27 Automated Calibration/ Quantitation/ Reporting vs. Manual Processing ....................................................... 27 Custom Graphical Reports vs. Limited Textual Reporting ............................................................................. 27

ros

Temp Errata

SOFTWARE UPGRADE NOTES

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Standard Windows-based Software Components............................................................................................. 28 System Control (System Control/Automation) ............................................................................................... 28 Method Builder (View/Edit Methods)............................................................................................................. 29

Mass Spec Data Acquisition Method......................................................................................................... 29 Mass Spec Data Handling Method ............................................................................................................. 30

Automation Editor (Edit Automation Files) .................................................................................................... 30 MS Data Review (Review/Process MS Data) ............................................................................................... 30

Display Chromatograms & Log Information............................................................................................... 30 Select/Enhance/Search Spectra................................................................................................................. 30 Process/Review Results ............................................................................................................................. 30 Build Compound Table ............................................................................................................................... 31

Standard MS Reports..................................................................................................................................... 31 Custom MS Reports ....................................................................................................................................... 31 BatchSMS (SMS/MS File Conversion).......................................................................................................... 31 Quick Start! (Quick Start!) ............................................................................................................................. 31 Security (Security Administration) .................................................................................................................. 31

Optionally-Installed Windows-based Software Components............................................................................. 32 Interactive Graphics (View/Edit GC Chromatograms) ................................................................................... 32 Report (Standard GC Reports) ..................................................................................................................... 32 Batch Report (GC Batch Reporting).............................................................................................................. 32

Analogous Feature Mapping Table.................................................................................................................... 32


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Introduction The Saturn GC/MS Version 5 Software is the first Windows-based software release

to control the Saturn 2000 GC/MS. These notes are provided to ease the transition of the Version 1.X (DOS-based) software user to the new platform. They describe the hardware and software reconfiguration that is necessary as well as general and detailed information on the differences between the two systems.

(There are also computer-based tutorials available. A quick Getting Started tutorial may be executed directly from the Saturn GC/MS Workstation CD. The CD Brochure, available separately, is also useful for learning about the system.)

The first section, the Module Configuration Instructions, describes what you need to do (before and after the software has been installed) to reconfigure your system for proper operation. Some hardware modifications may be necessary prior to installing the software. However, the Windows-based software can be loaded, and the hardware reconfigured, without affecting the ability to use any of the old DOS-based software for MS Data Acquisition.

The second section, the Software Platform Differences, describes the fundamental differences in the approach of the two systems as well as a table that maps the major features of the old system to those in the new system.

Module Configuration Instructions

All users should complete the Pre-Upgrade Instructions. Once complete, the GC-specific instructions that follow should be completed to properly install and reconfigure your system for the new software.

Pre-Upgrade Instructions

Complete the following Pre-Upgrade checks and procedures to ensure a successful installation:

Minimum Computer Requirements

Ensure that your computer meets the Minimum Computer Requirements listed below:

For Windows 95/98: • Pentium processor, at least 90 MHz (166, or better, recommended) • At least 32 MB RAM • One full-sized ISA slot for the IOtech GPIB board to be installed, plus one PCI

slot if PCI Ethernet card is to be installed. • CD-ROM Drive, at least 4X • Video driver and monitor capable of 800x600 resolution with 256 colors

(1024x768 with 16-bit color strongly recommended) • Keyboard and mouse • Windows 95 or Windows 98


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For Windows NT: • Pentium II processor, at least 300 MHz • At least 64 MB RAM • An ISA, PCI, or PCMCIA slot (as appropriate) for the GPIB board to be installed,

plus one PCI slot if a PCI Ethernet card is to be installed. • CD ROM Drive, at least 4X • Video driver and monitor capable of 800x600 resolution with 256 colors

(1024x768 with 16-bit color strongly recommended) • Windows NT Version 4.0, Service Pack 4+, NTFS • Internet Explorer Version 4.01, or later • Administrator privilege for installation

Power Management software

Power Management software should not be used, except, perhaps, for controlling the computer monitor. The power management software may either be incompatible with the Saturn GC/MS Workstation software or may cause loss of data when it shuts down a particular computer component. Disable any Power Management software.

Virus protection software Disable any “memory-resident” virus protection software before installing or using the Saturn GC/MS Workstation software. Instead, use “on-demand” virus protection software that may be run periodically; at system boot-up or at any other time during which the Saturn GC/MS Workstation software is not active.

Windows 98 Windows 98 is qualified for use with the Saturn GC/MS Workstation software. However, upgrading from Windows 95 to Windows 98 can cause severe computer problems unless you are upgrading to Windows 98, Second Edition. When upgrading to the first release of Windows 98, formatting the hard drive first, and then loading Windows 98, will achieve the best results. The Windows 98 upgrade program will require the Windows 95 CD-ROM to be placed in the CD-ROM drive during installation for upgrade verification.

If you are having long-term reliability problems with Windows 98, please refer to the ReadMe.txt file in the Patches subdirectory on the Workstation CD.

Windows NT Windows NT 4.0 (Service Packs 4 and later) has been qualified for use with the Saturn GC/MS Workstation software.

However, when using Windows NT, the following additional caveats apply: 1) You must use a commercial GPIB driver with your IOtech GP488B

Communications adapter. Complete the instructions for installing it on your PC before attempting to install the Saturn Windows Workstation software.

2) The DOS-based Saturn Workstation will not run on Windows NT. Therefore, you cannot opt to use it to control the MS as described later in this document.

Removing any existing Star Workstation

Prior to installing the Saturn GC/MS Workstation Version 5.X on a computer already containing a previous version of the Star Workstation (as would be the case if you currently use the Star Workstation Version 4.51 to control your GCs), it is strongly recommended that you remove it.

You may use the Data Files, Methods, SampleLists, SampleLogs, and Sequences created with the previous version of the Star Workstation with Saturn GC/MS Workstation Version 5.X (see upgrade notes below). To remove the previous version, perform the following steps. In this procedure, it is assumed that the currently installed version of the Star Workstation is located in the directory C:\STAR.


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1. Close all Star Workstation applications that may be running.

2. Copy the Data Files, Methods, SampleLists/SampleLogs, and Sequences that you wish to upgrade to a backup directory (for example, C:\STAR45).

3. Delete the STAR directory using the Windows Explorer.

4. Run the System Configuration Editor by selecting Run… from the Windows Start button and typing SYSEDIT.EXE. The System Configuration Editor allows you to edit AUTOEXEC.BAT and WIN.INI.

5. Edit your AUTOEXEC.BAT file and remove C:\STAR from your path.

6. Edit the file WIN.INI. Find the line starting with "run=" in the file. Remove START.EXE from the line. For example, if the line was run=START.EXE, replace it with run=.

7. Delete the file STAR.INI from your Windows directory.

8. Reboot your computer.

You should also remove the Varian Star 4.5 item from the Windows Start Menu. To do so, use the following procedure:

1. Right-click on the Windows taskbar (where the Start button is located) and select Properties from the popup menu.

2. Select the Start Menu Programs tab in the Taskbar Properties dialog box.

3. Click on the Remove button and select the Varian Star 4.5 item from the Programs folder.

4. Click on the Remove button to remove the item.

Removing previously created file associations

If you have made associations between files that end with .RUN and the Interactive Graphics/Data Handling application in previous versions of the Star Workstation, you will need to remove this association before installing the Saturn GC/MS Workstation. Similarly, associations between files that end with .MTH and the Method Editor application will also need to be removed.

To remove an association between an application and a file type, use the following procedure:

1. In My Computer or Windows Explorer, click the View menu, and then click Options.

2. Click the File Types tab.

3. In the list of file types, click the one you want to remove (for example RUN file or MTH file).

4. The settings for that file type are shown in the File Type Details box.

5. Click Remove.

If you do not remove these associations before installing the Saturn GC/MS Workstation Version 5 you may see inappropriate selections available on Data File or Method Quick Link buttons. If you select one of these inappropriate entries, you may get error messages stating that the file you are attempting to access is corrupt.


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Disk Maintenance The Saturn GC/MS Workstation software, like most programs, doesn't handle the conditions of low disk space and high disk fragmentation very well. Data acquisition failures, among other problems, can result if the hard disk is not properly maintained. Free disk space should be maintained at a minimum of 25 MB (preferably much higher).

The ScanDisk and Disk Defragmenter programs (both found under Start →Programs →Accessories →System Tools) should be used before installing the software and periodically thereafter. The Windows 95 Plus! pack System Agent is a good tool for performing these on a regular basis (not while using the Saturn system, of course). Disk maintenance is an important part of all system administration regardless of the software used.

3800 with or without GC Detectors

Install the Software Follow the instructions included in the Saturn GC/MS Workstation CD booklet to install the software. If you have GC detectors and intend to use them, you should select the following options by clicking on their respective checkboxes when prompted in the Saturn GC/MS Workstation options dialog during installation:

• GC Data Handling • GC Example Data Files and Methods • GC Advanced Applications Reboot the computer.

Configure the Software Click, with the right mouse button, the right side of the Star Toolbar to bring up a context menu.

Select the Enable/Disable Instrument Modules menu item.

This will open the Enable/Disable Instrument Dialog box as shown.


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The modules in the top window are enabled. The modules in the bottom window are disabled.

Highlight the 3400 and 3600 modules in the top window and click the Disable button. If your system has an 8200 AutoSampler, highlight the 8200 AutoSampler module and click the Enable button.

Click OK to close the Enable/Disable window.

Click on the System Control icon to run System Control. The software will ask to configure the 3800.

Click Next until the Setup Ethernet ports dialog box is open.

Then click the Setup button. This will open the IP Manager. Click the check box labeled Manage IP addresses from this Workstation.

As long as the GC has not been turned off, the IP information will be retained in the GC. To retrieve this information, press the MENU button on the front of the GC, and then press ENTER.


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Enter the Ethernet Address shown on the GC display into the workstation box labeled Ethernet (address).

NOTE: The GC displays colons ":" to separate the numbers, but please use a period "." to separate the numbers when entering them into the workstation software.

GC: 00:60:93:00 etc. Workstation: 00.60.93.00 etc.

Enter the IP address from the GC display, into the Workstation field labeled IP (address). Copy the address exactly as it is shown including the periods ".".

Enter the Alias name from the GC display into the Workstation field labeled Host Name.

Click Enter to finish editing.

Click OK.

Click on the button labeled 44.

Highlight the Host name (or Alias) of your GC from the list. Click OK.

Click OK.

Click Next. Click Finish.

Dismiss any Tuning warning messages by clicking on OK.

The Saturn 2000 and GC icons should be visible in the Available modules area at the bottom of the screen. Click and drag each one into the Instrument 1 configuration area of the screen. If you have an 8200, click and drag it into the AutoStart Module box.

Double-click in the Instrument 1 configuration area to see the Module Windows associated with the instrument.

Double-click on the Saturn 2000 icon to view the status of the Mass Spectrometer.

The software is ready to use.

Click Start→Programs→Saturn GCMS Workstation→On-Line Help→Tutorials for more information about how to use the software.

3400/3600 without GC Detectors

WARNING:SHOCK HAZARD

Dangerous voltages may be exposed when the cover is removed.


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Re-configure the Serial I/O Board

Turn off and unplug the GC.

Lift up and remove the detector cover and any AutoSampler from the GC.

Unscrew and remove the screws holding the GC top cover in place and remove the top cover.

Locate the card slot marked S I/O. The card slots are on the GC Motherboard and are identified by yellow labels on the left, inside of the GC just above the Motherboard.

Turn the yellow connector cam clockwise 90 degrees to unlock and open the card connector.

CAUTION

To keep static electricity from damaging the GC Serial I/O Board attach a grounding strap between your wrist and a well-grounded metal surface.

Remove the Serial I/O Board by sliding it up and out of the GC.

Use the figure below to set the switches on the GC Serial I/O Board to the correct positions. Set switches S1 and S2 on the top edge of the Board to position 1 (the far right position). Set switch S3 as shown below (for 9600 baud). The location of the black square indicates the switch setting. Make sure that the switch is slid completely to the position indicated by the black square. Connect the 12-pin Molex jumper plug (SIOID jumper) across J85 and J86. The SIOID jumper allows the workstation software to identify the type of GC it is connected to, either 3400 or 3600.

S eria l I/O B oard

S I/O J85

S3

J86

J87

S1 S2

Do not use a pencil to change switch settings.


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NOTE: Take care when you plug in Molex connectors. They can easily be plugged in upside down. When they are plugged in correctly, the plug locks to the jack.

Correct Orientation of the Plug and Jack for a Molex Connector

Add Jumper for Ready In

If there is not already a Ready In cable from another device connected, locate J16 on the GC motherboard and connect the 4-pin Molex jumper plug. This indicates to the GC that external devices are ready.

Install the GC Serial I/O Board into the S I/O card slot on the 3400 or 3600 GC Motherboard. Carefully lower the GC Serial I/O Board into the edge connector on the left. Do not force the Serial I/O Board into the connector or guide. If the Serial I/O Board does not insert easily, lift the Serial I/O Board slightly, realign the card edges with the guides and try again.

Turn the yellow connector cam counterclockwise 90 degrees to close and lock the GC Serial I/O Board into place.

Add a Start Cable There are two Start cables available. Use the following instructions to determine which one is correct for your Mass Spectrometer.

Instruments using Saturn DOS software version 1.4 or later should already have a Start cable installed and attached to the back of the Mass Spectrometer (at connector J43). If this is the case, reinstall the top covers of the GC, install the AutoSampler, power on the GC, and skip to the Installing the Software section.


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Remove the Mass Spectrometer top cover.

Place the service switch inside the Mass Spectrometer in the Off position.

Remove the right side panel.

Check the Revision level of the SAP board. The SAP board is the first board visible after removing the cover. Check the top left corner for the Revision.

Rev 1- 3: Use cable 03-930341-02 Rev 4: Use cable 03-930341-01

Connect the end of the Start cable (with the 15-pin D-shell connector) to the Remote Option connector (J43) on the outside, rear panel of the Mass Spectrometer.

Route the other end of the Start cable (with the 4-pin Molex connector) through the oblong opening in the back of the GC and through the cut-out between the GC detector area and the front of the card cage.

Locate J23 on the GC motherboard (see figure for Ready In) and connect the Start cable. If J23 already has a Start cable connected to it (e.g., for a non-MS device), remove the cable and install the 3-way splitter board (03-925099-01). Connect all Start cables to the splitter board.

Install the side cover on the Mass Spectrometer and place the service switch in the on position. Install the Mass Spectrometer top cover.

Install the GC top covers, any AutoSampler, plug in, and turn on the GC.

Install the Software Follow the instructions included in the Saturn GC/MS Workstation CD booklet to install the software. Reboot the computer.




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Highlight the 3800 module in the top window and click the Disable button.

8200 AutoSamplers connected to the GC are controlled through the GC module and do not need the 8200 module Enabled. If the 8200 is configured for SPME operation (and, therefore, not controlled through the GC), highlight the 8200 AutoSampler module and click on the Enable button.


Click on the System Control icon to run System Control. The Workstation software should automatically open the COMM port wizard. Click Next until the COMM Port configuration dialog box is open.

There are four COMM ports available. Click the drop down box for COM1. Highlight 3400 or 3600 to match the GC.

If there is a SPME-configured 8200, click on the drop down box for COM2. Highlight 8200. If the SPME-configured 8200 is not in the list, go back to the Star Toolbar and enable the standalone 8200 module.

Click OK. Click Next. Click Finish.


The Saturn 2000 and GC icons should be visible in the Available Modules area at the bottom of the screen. Click and drag each one into the Instrument 1 area of the screen. If you have an 8200 icon, click and drag it into the AutoStart Module box.


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Double-click in the Instrument 1 configuration area to see the Module Windows associated with the instrument.

Double-click on the GC icon to view the status of the GC.

Click on the Temp Limits Button.

3400 3600

Set the Column Temperature Limit to 320 and all of the Injector Limits to 320. If the temperature limit is less than the temperature in the method, the method will not download. The default temperature limit is 250.

Click Save.

Double-click on the Saturn 2000 icon to view the status and operation of the Mass Spectrometer.




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3400/3600 with GC Detectors

Installing and using the Star GC Serial I/O Cable (03-917742-00) in conjunction with an ADC board (purchased separately) will configure the computer to collect GC detector data along with the MS data. The following is an outline of the major steps involved.

1. Configure the ADC Board

2. Install the ADC Board in the Computer

3. Connect the Serial I/O Cable to the Serial I/O Board

4. Add a Start cable between the GC and MS

5. Connect the Serial I/O Cable to the ADC Board in the Computer

6. Connect the Analog Signal Cables

7. Install the Software

8. Configure the Software

Configure the ADC Board

The Star ADC Board’s analog channels can be independently set for full-scale input signals of either 1V or 10V. The settings for Channel A do not have to be the same as those for Channel B. However, each channel must be consistent for either 1V or 10V operation. The Star ADC Board is shipped with both Channel A and Channel B set for 10V operation.

Use the following procedure to change the full-scale analog input range of the Star ADC Board. Use the 10 V range with a 3400 or 3600 GC.

To keep static electricity from damaging the Star ADC Board, attach a grounding strap between your wrist and a well grounded metal surface.

Remove the Star ADC Board from its anti-static envelope and inspect it for shipping damage.

Set the analog input channel that you will be using to 10V.

Configure the Star ADC Board’s analog channels by placing the jumpers as shown on the right side diagrams in the figure below.

NOTE: All jumper settings for Channel A or Channel B must be consistent for either 1V or 10V operation. Do NOT install jumpers at jumper location XW7, or change the jumper XW6.


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Jumper Settings for 1 and 10 Volt Ranges

Install the ADC Board in the Computer

The procedure for installing the Star ADC Board in the computer varies slightly from computer to computer due to differences in card cage design. For specific details, refer to your computer manual.



Turn off the computer power and unplug the power cord before proceeding.

Remove the computer’s cover. Refer to your computer manual for cover removal instructions.

Attach a grounding strap between your wrist and a well-grounded metal surface.

Remove the expansion board retaining screw that is holding one of the ISA-bus expansion slot covers in place. Save this screw for use in securing the ADC Board.

Remove the ISA expansion slot cover and put it away for storage. You will not need it as long as the Star ADC Board is in the computer.

Insert the Star ADC Board in your computer. Make sure that the Board’s edge connector is fully seated in the expansion slot socket.

Re-install the expansion board retaining screw removed above.

Remove the grounding strap and replace the cover on the computer. Refer to your computer manual for instructions.

Reconnect the power cord and turn on the PC.


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Connect the Serial I/O Cable to the Serial I/O Board

The GC Serial I/O Cable, shown in the figure below, has several connections inside of the GC. This table describes the function of each of these connectors:

Connection Function

P16 (4-pin Molex) connects to J16 on the GC Motherboard

Remote Status Input (Ready In and Start In from the Workstation to the GC)

P23 (5-pin Molex) connects to J23 on the GC Motherboard

GC Status Output (Ready Out and Start Out from the GC to the Workstation)

P87 (AMP miniature cable connector) connects to J87 on the Serial I/O board

Serial communication (for method download and GC status upload)

P85/P86 (12-pin Molex jumper) connects to J85/J86 on the Serial I/O board

Serial I/O identification (enables the serial communication in the GC)

P3 (9-pin D-shell connector) connects to the ADC Board Synchronization Jack J2

Carries synchronization and serial communication signals to the Star ADC Board

Start/R eady O ut5-P in M olex

9-P in D C onnector

S tart/R eady In4-P in M olex

Seria l AM PM iniatu re R ibbonC ab le C onnector

To M otherboard (J16)R em ote S tatus Input

12-P in M olex Jum perTo Seria l I/O Board(J85/J86)

To Sync/Seria l Jack (J2)Input of AD C Board

To M otherboard (J23)G C Sta tus O utput

P/N 03-919939-00

To Seria l I/O Board(J87)

GC Serial I/O Cable



Turn off and unplug the GC.

Lift up and remove the detector cover and any AutoSampler from the GC.

Unscrew and remove the screws holding the GC top cover in place and remove the top cover.


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Locate the card slot marked S I/O. The card slots are on the GC Motherboard and are identified by yellow labels on the left, inside of the GC just above the Motherboard.

Turn the yellow connector cam clockwise 90 degrees to unlock and open the card connector.

CAUTION

To keep static electricity from damaging the GC Serial I/O Board attach a grounding strap between your wrist and a well grounded metal surface.

Remove the Serial I/O board by sliding it up and out of the GC.

Locate the J87 connector on the GC Serial I/O Board.

Disconnect the existing Serial cable (03-920140-00). Remove the other end of this cable from the computer and discard.

Plug the AMP miniature cable connector plug on the new GC Serial I/O Cable (03-917742-00) into J87 on the GC Serial I/O Board.

Secure the GC Serial I/O Cable to the GC Serial I/O Board by screwing the captive screws on the AMP plug into the AMP jack on the Serial I/O Board. Tighten securely.

Use the figure below to set the switches on the GC Serial I/O Board to the correct positions. Set switches S1 and S2 on the top edge of the Board to position 1 (the far right position). Set switch S3 as shown below (for 9600 baud). The location of the black square indicates the switch setting. Make sure that the switch is slid completely to the position indicated by the black square. Connect the 12-pin Molex jumper plug (SIOID jumper) across J85 and J86. The SIOID jumper allows the workstation software to identify the type of GC it is connected to, either 3400 or 3600.

S eria l I/O Board

S I/O J85

S3

J86

J87

S1 S2


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NOTE: Take care when you plug in Molex connectors. They can easily be plugged in upside down. When they are plugged in correctly, the plug locks to the jack.

Correct Orientation of the Plug and Jack for a Molex Connector

Find the Remote Status Input jack (J16) on the GC Motherboard. This will be near the top center of the GC Motherboard. See the GC Serial I/O Cable Connection figure below for help locating this jack.

Plug the 4-pin Molex plug (P16) on the GC Serial I/O Cable into the Remote Status Input jack (J16) on the GC Motherboard.

Install the GC Serial I/O Board into the S I/O card slot on the 3400 or 3600 GC Motherboard. Carefully lower the GC Serial I/O Board into the edge connector on the left. Do not force the Serial I/O Board into the connector or guide. If the Serial I/O Board does not insert easily, lift the Serial I/O Board slightly, realign the card edges with the guides and try again.

Turn the yellow connector cam counterclockwise 90 degrees to close and lock the GC Serial I/O Board into place.

GC Serial I/O Cable Connection Locations


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Before you can make the last connection to the 3400 or 3600 GC Motherboard, you will need to remove the Detector A Electrometer Board to make room in the compartment to access the GC Status Output jack (J23).

Locate the Detector A Electrometer Board in the card slot marked DET A. Label and disconnect detector cable(s) leading to the Detector A Electrometer Board.

CAUTION

To keep static electricity from damaging the Detector Electrometer Board, attach a grounding strap between your wrist and a well grounded metal surface.

Turn the yellow connector cam clockwise 90 degrees to release the Detector A Electrometer Board. Carefully lift the Detector A Electrometer Board straight up and out of the plastic guide slots attached to the chassis.

Place the Detector A Electrometer Board in a clean anti-static envelope and set it aside.

Removing the Detector A Electrometer Board from the printed circuit board compartment should give the required access to the 5-pin GC Status Output jack (J23) near the front, bottom of the GC Motherboard. If you need better access, remove the Detector B Electrometer Board in a manner similar to what was done for the Detector A Board.

If there is already a Start cable attached to J23, remove it, install the 3-way splitter board (03-925099-01) onto J23, and reattach the Start cable to one of the splitter board output jacks.

Pass the GC Serial I/O Cable lead with the 5-pin Molex connector down into the printed circuit board compartment and plug it into one of the J23 Status Output jacks.

Add a Start Cable between the GC and MS

There are two Start cables available. Use the following instructions to determine which one is correct for your Mass Spectrometer.

Instruments using Saturn DOS software version 1.4 or later should already have a Start cable installed and attached to the back of the Mass Spectrometer (at connector J43). If this is the case, reinstall the Detector Electrometers, re-connect the Detector cables, reinstall the top covers of the GC, install the AutoSampler, power on the GC, and skip to the Connect the Serial I/O Cable to the ADC Board in the Computer section..



Remove the Mass Spectrometer top cover.

Place the service switch inside the Mass Spectrometer in the Off position.

Remove the right side panel.


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Check the Revision level of the SAP board. The SAP board is the first board visible after removing the cover. Check the top left corner for the Revision.

Rev 1- 3: Use cable 03-930341-02 Rev 4: Use cable 03-930341-01

Connect the end of the Start cable (with the 15-pin D-shell connector) to the Remote Option connector (J43) on the outside, rear panel of the Mass Spectrometer.

Route the other end of the Start cable (with the 4-pin Molex connector) through the oblong opening in the back of the GC and through the cut-out between the GC detector area and the front of the card cage.

Locate J23 on the GC motherboard (see figure for Ready In) and connect the Start cable to one of the unused output jacks on the splitter board (03-925099-01) that is already attached to J23.

Reinstall the Detector A Electrometer Board and Detector B Electrometer Board (if removed). Carefully lower the Detector Electrometer Board into the edge connector on the left. Do not force the Detector Electrometer Board into the connector or guide. If the Detector Electrometer Board does not insert easily, lift it slightly, realign the card edges with the guides and try again.

Turn the yellow connector cam counterclockwise 90 degrees to close and lock the Detector Electrometer Board into place.

Reconnect the detector cable(s) that were removed.

Connect the Serial I/O Cable to the ADC Board in the Computer

Route the 9-pin D-shell connector end of the GC Serial I/O Cable to the outside of the GC through the oblong opening located on the back panel of the GC.

S tar AD C BoardBack Panel

J2S ynchron izationand S eria lC om m unication Jack

J1A nalogInput Jack

Identification Label Placement on Star ADC Board

Connect the 9-pin D-shell to J2 on the ADC Board installed in the computer.

Install the side cover on the Mass Spectrometer and place the service switch in the On position. Install the Mass Spectrometer top cover.

Install the GC top covers, any AutoSampler, plug in, and turn on the GC.


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Connect the Analog Signal Cables

Install the Analog signal cables (03-907884-01 purchased separately), to transfer the signal from the GC to the ADC Board.

The signal cables connect from the J1 Analog input jack on the ADC Board to the Computer output connectors on the side of the GC. There is an extra spade lug, which connects to the screw below the output connectors. The Computer output is a 0-10V signal. The ADC Board should have been configured for 10 V operation previously.

Install the Software Follow the instructions included in the Saturn GC/MS Workstation CD booklet to install the software. You should select the following options by clicking on their respective checkboxes when prompted in the Saturn GC/MS Workstation options dialog during installation:

• GC Data Handling • GC Example Data Files and Methods • GC Advanced Applications Reboot the computer.





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Highlight the 3800 module in the top window and click the Disable button.

8200 AutoSamplers connected to the GC are controlled through the GC module and do not need the 8200 module Enabled. If the 8200 is configured for SPME operation (and, therefore, not controlled through the GC), highlight the 8200 AutoSampler module and click on the Enable button.


Click on the System Control icon to run System Control. The Workstation software should automatically open the COMM port wizard. If there is a SPME-configured 8200, click Next until the COMM Port configuration dialog is open. All other users should click Cancel and skip (the next two steps) to the dismissal of any Tuning warning messages below.

Click on the drop down box for COM2. Highlight 8200. If 8200 is not in the list, go back to the Star Toolbar and enable the standalone 8200 AutoSampler module.


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Click OK. Click Next. Click Finish.


Within a minute, the Saturn 2000, ADC Board, and GC icons should be visible in the Available Modules area at the bottom of the screen. Click and drag each one into the Instrument 1 area of the screen. If you have an 8200 icon, click and drag it into the AutoStart Module box.

Double-click in the Instrument 1 configuration area to see the Module Windows associated with the Instrument.

Double-click on the GC icon to view the status of the GC.

Click on the Temp Limits Button.

3400 3600

Set the Column Temperature Limit to 320 and all of the Injector Limits to 320. If the temperature limit is less than the temperature in the method, the method will not download. The default temperature limit is 250.

Click Save.

Double-click on the Saturn 2000 icon to view the status and operation of the Mass Spectrometer.




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Using the DOS software to control the Mass Spectrometer

Some users may want to continue to use the DOS Saturn software to collect the MS data while using the Windows software to control the GC. This section will show how to configure the Windows software to collect data with Saturn DOS software versions 1.4 and later. Versions prior to 1.4 will not support this feature.

Complete the instructions to load the Windows-based Saturn GC/MS Workstation software with your GC model.

Invoke the Star Toolbar and then click, with the right mouse button, the right side of the Star Toolbar to bring up a context menu.


This will open the Enable/Disable Instrument Dialog box.

Highlight the 2000 Mass Spectrometer module and click the Disable button.


Click on the System Control icon to open System Control.


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Click on the Instrument 1 Parameters Button.

In the box labeled Ready File, enter the disk drive and directory in which the Saturn DOS software is loaded and append the text “Saturn.rdy”. For example, "C:\saturn\saturn.rdy" would be correct for most users. This instructs the Windows-based Workstation software to wait for the DOS software to create a “ready file” before injecting.

To again use the Windows software to collect data, Enable the Saturn 2000 module and delete the text ("C:\saturn\saturn.rdy") from the box labeled Ready File.

Upgrading Star Workstation 4.51 Files For Use With The Saturn GC/MS Workstation

Upgrading Data Files, Methods, SampleLists and Sequences

Data Files, Methods, SampleLists, and Sequences are automatically upgraded from previous versions as soon as they are accessed by the Saturn GC/MS Workstation Version 5.X. A message box will prompt you to upgrade the file. Note that if you cancel the upgrade operation, you may be prompted several times with this message box—once for each section of the file requiring the upgrade. To preserve the contents of the file in the previous version's format, it is important that each message box is canceled.

If you wish to automatically upgrade all files you access without being prompted, use the following procedure:

1. Edit the STAR32.INI file in your Windows directory using a text editor such as Notepad.

2. Find the line starting with "AutoUpgrade=" in the file. Change the line so that it reads AutoUpgrade=1.

3. Save the file.

Converting SampleLogs into RecalcLists

In the Saturn GC/MS Workstation, SampleLogs have been replaced by RecalcLists. RecalcLists serve the same function as SampleLogs, but they are stored in a separate file from the SampleList that was used to create them. RecalcList files have the extension ".RCL". To convert a SampleLog to a RecalcList, copy the ".SMP" file to the same filename with the extension ".RCL". For example, if you wish to convert the SampleLog in the file MYRECALC.SMP, copy it to MYRECALC.RCL. The first time you access the RecalcList in the Saturn GC/MS Workstation, the file will be


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upgraded in the same manner as Data Files, Methods, SampleLists, and Sequences.

Changes to Method default values

The default number of calibration levels, specified in the Calibration Setup portion of the GC Data Handling Method section, has changed to 1. If you calibrate your Methods against injections of known standards and you use multiple concentrations, you will need to change the number of calibration levels to see the appropriate number of columns in the Peak Table to enter the different amounts.

Changes to the Automation Validation procedure

The Validate command in the Automation menu of System Control has been removed. Validation is performed as each Method is activated for use. If you are going to perform unattended automation that involves the use of multiple Methods, activate each Method to verify that it is valid before starting the automation sequence.

Software Platform Differences

Architectural Differences

The Windows-based Saturn GC/MS Workstation integrates the proven capabilities of the DOS-based Saturn GC/MS Workstation with the flexibility and reliability of the second-generation Star Chromatography Workstation platform. As such, the experienced user will notice a number of architectural differences from the DOS-based software.

In addition to adding new Saturn capabilities, the Windows-based software uses the graphical and multi-tasking features of the standard Windows environment to make it easier for you to set up analyses and to specify qualitative and quantitative reports. It provides you with powerful tools to build and optimize methods and to view and analyze the results.

Multiple Applications vs. Single Application

The Windows-based software is implemented through a suite of interrelated applications while the DOS-based software relied primarily upon a single, monolithic, application. The individual Windows-based applications may be invoked through several means:

• The usual Windows Start menu hierarchy may be used to launch applications. • The Star Toolbar application (which is somewhat analogous to the Exec Page)

may be used to launch applications. • “Shell buttons” in most Workstation applications may be used to launch other

Workstation applications; opening the specified Workstation file (data file, automation file, method, etc.) in the process.

• From the Windows Explorer, right clicking on a Workstation file will display a context menu that allows the file to be opened with the specified Workstation application.

Single, Integrated MS Method vs. Multi-File MS Method

The Windows-based software integrates all of the parameters necessary to control an MS Data Acquisition into a single “section” within a single method file (.MTH). The DOS-based software required the creation of a separate Data Acquisition Method (.IDA), one or more Ion Preparation Methods (.IPM), and one or more Tune Parameter files (.ITN). In the Windows software, the parameters previously found in the three separate file types are roughly partitioned along three separate “tabbed dialogs” within the single MS Data Acquisition Method section.

Unified Module Method The Windows-based software integrates the methods for all of the modules that


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vs. Independent Module Methods

make up an instrument into multiple “sections” within a single method file (.MTH). The DOS-based software maintained separate method files for each of the MS (.IDA/.IPM/.ITN), GC (.IGC), and AutoSampler (.IAS) devices. In the Windows software, an easy-to-use, hierarchical Method Directory list is used to select from the different module method “sections” stored within the single file.

Integrated Data Handling Methods vs. Scattered Data Handling Parameters

The Windows-based software integrates the Data Handling specifications (or method) for each detector into the same file (.MTH) that contains the Data Acquisition methods. The DOS-based software maintained some Data Handling specifications in files (.QCI/.QCE) separate from the Data Acquisition method parameters, and others as Quantitation screen options that were not stored in any method or file.

Integrated and Synchronized MS and GC Detector Acquisition

The Windows-based software allows for synchronized and simultaneous MS and GC detector data acquisition. The DOS-based software had no provision for acquiring data from GC detectors. In the Windows software, the MS Data Review application may be used to qualitatively evaluate both types of files and overlay their chromatograms. While both MS and GC data may be quantitated, they utilize different facilities to do so.

Sequence and Sample Lists vs. Analysis List Automation

The Windows-based software allows for the creation and execution of sophisticated automated data acquisition and data handling processes. In the DOS-based software, a single Analysis List structure was used to individually specify sample names, dilution factors, and the methods with which to acquire each sample.

In the Windows software, a SampleList is used to specify the sample names and dilution factors with which to acquire each sample. However, it is usually the case that a single (unified) method file is associated with a SampleList; eliminating the need to replicate the method specification unless it needs to be changed in the middle.

The Windows software also provides an optionally used structure called a SequenceList. It allows a series of SampleLists to be executed in order. By using Sequence and Sample Lists together, work may be partitioned according to application, client, or other differentiator but linked together to execute in sequence.

Quantitation Results Resident in Data Files vs. Separate Quantitation Files

The Windows-based software stores quantitation results, and a copy of the method used to generate them, in the acquired data file (.SMS) along with the raw data. In the DOS-based software, quantitation results were stored in a separate file (.QD). Having the raw data, method logs, and quantitation results in a single file prevents their separation, making reporting and archival more straightforward.

Automated Calibration/ Quantitation/ Reporting vs. Manual Processing

The Windows-based software integrates auto calibration, quantitation, and reporting into the execution of the SampleList during data acquisition. These same processes may also be redone (if a change needs to be made to the data handling method, for example) after acquisition via the execution of the automatically generated RecalcList. In the DOS-based software, these processes were often performed manually post-run or through custom Procedure Language-based programs.

Custom Graphical Reports vs. Limited Textual Reporting

The Windows-based software provides the capability to define custom report templates based on a set of six basic report types, including Calibration Summary, Sample, Unknowns, Compound, Library Search, and Tune Verification. The reports may include chromatograms, spectra, and custom bitmaps in addition to the usual textual information. In the DOS-based software, a limited number of interactive, and text-based, reports were available.


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Standard Windows-based Software Components

The Windows-based software implements the Workstation System through a suite of separate, but interrelated, application programs. Together they are used to accomplish the tasks performed in the single DOS-based application program. These components may all be invoked via the Star Toolbar.

The following describes the new components, their use, how they relate to other components, and some discussion of the portion of the DOS-based software that they replace.

System Control (System Control/Automation)

The System Control application is used to perform all instrument control activities. It (nominally) replaces all of the functionality as accessed from the upper right portion of the Exec Page in the DOS-based software.

Upon entry to System Control, individual modules (GC, AS, MS) are configured for communications and are then configured to create a single logical instrument. This logical instrument contains a “Module Window” for each configured and communicating module. Each Module Window provides control and status of the respective module.

System Control provides automation and synchronization features that allow the individual modules to work together to complete an acquisition and subsequent data processing. These “automations” are specified via Sequence and Sample Lists.

While all of the other modules (AS and GC) have only a single “Acquisition” mode, the Saturn 2000 Module Window provides six different modes for the different types of operation required. These include Manual Control, Auto Tune, Temperature Control, Diagnostics, Shutdown, and Acquisition.

Manual Control Mode may be used to interactively control the scanning of the Mass Spectrometer. From it, different methods may be activated and different method segments selected to activate different sets of conditions in the trap. There is a SetPoints tab from which the desired filament and Axial Modulation Voltage may be specified. The Adjustments tab is where all of the manual adjustments (Cal. Gas, CI Gas, and RF Adjust) are made. There is a new automated CI Gas adjustment function for the most-commonly-used CI reagents.

Auto Tune Mode is used to perform the auto tuning functions of Electron Multiplier Set (including Electrometer Zero), Mass Calibration (including RF Full Scale Adjust and the Electron Multiplier “boost” portion of the AGC Target function), and Trap Function Calibration. These functions may be optionally preceded by an Air/Water check. The AGC Target and Emission Current set functions that were in the DOS-based software have been eliminated, as these parameters should usually be set to fixed values unless a particular application requires a different set of fixed values.

System Control uses the file STARTUP.INS to store module configuration and tuning information for all of the modules. If the file does not exist, it will create it. When this occurs, it will look in the C:\SATURN directory for tuning information from the Saturn DOS-based system. If it exists, it will load these values into STARTUP.INS and use them. Otherwise, it will load default values. This capability may be used to force the Windows-based software to use the same tuning information as that used by the DOS-based software.

However, despite the fact that a potentially valid tune has been loaded and may be used to acquire data, the Auto Tune page will accurately indicate that a tune has not yet been completed in the Windows software. In Acquisition Mode, the Saturn 2000 Module will “fault” when tuning has not yet been completed. However, after


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clicking on Reset, an acquisition may be performed on the incompletely tuned system.

Temperatures Mode may be used to set the Trap, Manifold, and Transferline temperatures used during acquisition as well as to perform automated bakeouts of the Trap.

Diagnostics Mode may be used to monitor the operating conditions of the Saturn 2000 as well as to diagnose problems with it. There is also a suite of extended Heater tests. The diagnostics in the Windows-based system have been significantly improved and expanded from those available in the DOS-based software.

Shutdown Mode may be used to prepare the system for venting and performing maintenance. If the system is already down upon entry to System Control, the system will enter Shutdown Mode and remain there until the user selects a different mode after the vacuum system has become ready.

Acquisition Mode may be used to acquire data to a data file. The user must manually-select this mode before performing any automation as System Control will not recognize the Saturn 2000 Module as “Ready” until it is both in Acquisition Mode and in the Ready state.

Method Builder (View/Edit Methods)

The Method Builder application is used to display, edit, and print all methods in the system. This includes all GC, AS, and MS data acquisition methods as well as data handling methods for those modules that are detectors. Report methods for GC detectors are defined within the Method Builder application while Report methods for MS detectors are presently defined within the Custom MS Reports application.

All of the method information associated with an acquisition is contained in a single, unified, method file (.MTH) organized into method sections. Method Builder presents a hierarchical Method Directory list of all of the different method sections in a narrow pane on the left side of the window, while the right side displays the currently selected method section.

Mass Spec Data Acquisition Method

The specification of Data Acquisition for the Mass Spec Module has improved substantially over the DOS-based software. Editing information on a single screen (and a few sub-dialogs) is all that is necessary to define a data acquisition method. In the DOS-based software, depending on the sophistication of the method, five or more screens (and sub-dialogs) might need to be accessed to completely define the method.

The Mass Spec data acquisition method screen is divided into an MS Method Segment table at the top and a three-tabbed-dialog on the bottom that allows editing of Setpoints, Ion Mode-specific parameters, and Ion Preparation Mode-specific parameters, respectively.

The MS Method Segment table provides the usual Windows table editing features of cut, copy, paste, and fill down. The table also enables easy navigation between the segments; simply click on the desired row to display its associated parameters for editing.

There have been a few method parameter changes from the DOS-based system. A few have been eliminated and a few have been added. Some changes of note are the ability to specify the Emission Current and a Multiplier Offset on an MS Segment basis, an increase in the number of available Scan Segments from 4 to 6, and the ability to specify the acquisition of Profile Data.


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The Windows-based software includes a form of Chemical Ionization that has been altered slightly from that implemented in the DOS-based system. As such, the defaults for the CI Reagent parameters have been changed to values that give the best performance for this new form of CI. Please carefully consider any changes that you make to these values.

Mass Spec Data Handling Method

The specification of Data Handling also has improved substantially over the DOS-based software. Data Handling parameters are contained in a single method, the compound-specific information is maintained via a true table, and the availability of relevant graphical information and automated building tools greatly simplify method creation and optimization. In the DOS-based software, Data Handling parameters were specified in several screens in both Chro and Quantitation, and were awkward to specify and maintain. Many parameters weren’t stored in a method at all, since the only way to do processing was manually or via a Procedure Language program.

The Data Handling parameters are edited on 3 main screens. The Calculations Setup screen specifies calculations parameters that are global to all Target compounds, and how to process and report Unknown peaks. The Results Treatment screen specifies how to store the calculated data points, and also separate tolerances and out-of-tolerance actions for Calibration, Analysis, and Verification samples. The Compound Table screen displays the compound information and manages a 6-tabbed dialog that allows editing of Compound Attributes, Quan Ions, Calculations, Integration, Identification, and Reference Spectrum parameters, respectively.

Automation Editor (Edit Automation Files)

The Automation Editor application provides the capability to edit the Automation Files (Sequence List, Sample List, and Recalc List) “off-line”, or separate, from System Control. In this way, one set of Automation Files may be defined at the same time that System Control is executing another. In the DOS-based software, Analysis Lists could only be edited when acquisitions were not in-progress.

MS Data Review (Review/Process MS Data)

The MS Data Review (aka SaturnView) application is used to review and/or process MS data files. Its primary role is as an interactive qualitative analysis tool. Facilities to compare chromatograms (from both MS and GC detectors) and spectra, perform library searches, and to easily build Data Handling Method Compound Tables are among its capabilities. MS Data Review (nominally) replaces all of the functionality as accessed from the upper left portion of the Exec Page in the DOS-based software (with the exception of some quantitation functions, the File Manager, Key Sequences, and Run Procedure). Some features of note are described below.

Display Chromatograms & Log Information

Up to 7 chromatograms may be displayed at a time from different data files and with different Quan Ion & Scan Channel specifications. Chromatogram displays may be manipulated in numerous ways, including overlaid, stacked, offset, scaled, zoomed, and annotated. MS Data Review will display data from .SMS, .MS, and .RUN file types.

Select/Enhance/Search Spectra

Up to 2 spectra may be selected from the active chromatogram. A spectrum may be background-corrected, averaged, edited, or added to a spectrum list. A single spectrum or a spectrum list may be added to a user library or library searched. Either Saturn INCOS or NIST library searching may be done. In addition, Reverse Chromatogram searches may be done.

Process/Review Results Results for the active data file or Recalc List may be reviewed, the method may be modified based on the results, and new results may be generated. The optimized method may be used in System Control to process new samples, or to regenerate automated reporting from an existing Recalc List.

The existing summary results for the active data file or for any data file in a Recalc


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List may be reviewed. Detailed results for any compound or unknown peak may be accessed via the summary results. Detailed results show the appropriate portion of the chromatogram, the spectrum from the data point closest to the retention time, and text results that include the values specified in the method, actual values, and any appropriate Pass/Fail information. Manual Integration may be performed from here as well. The Compound Calibration Curves and Calibration Block Report may be viewed or printed.

Build Compound Table The active chromatogram may be used to create a new Compound Table, or to add peaks to a table that already exists in a method. Peaks may be added to a table from different mass chromatograms and different data files. You may automatically add all of the integrated peaks in the chromatogram, or manually add one peak at a time, whether it is integrated or not. Peaks may be optionally library searched, and the desired hit may be selected. The following parameters are automatically set when a compound is added to the table: Retention time, Reference Spectrum from RT scan, Quan Ion = Reference Spectrum Base Peak, Scan Function Channel from RT scan, and Compound Name and CAS# (if library searched).

Standard MS Reports Standard MS Reports are defined via a section in the Unified Method File. The Reports available include a Sample Report, Target and Unidentified Compound Reports, Calibration Reports, and Summary Reports. All reports may be generated under automation when executing a Sample or RecaclList. The Sample and Compound Reports may be generated, and tailored, interactively using the MS Reports application. These same report definitions are used when viewing result reports in the MS Data Review application. The Standard MS Reports facility can also be used to export result data via the generation of ASCII output files.

Custom MS Reports Custom MS Reports (aka SaturnWriter) is a Microsoft Access-based application which allows users to create customized report templates for any of 6 basic report types: Calibration Block Summary, Sample, Target Compound, Unknowns, Library Search, and Tune Verification. These templates may include chromatograms, spectra, and custom bitmaps in addition to text results and documentation. Users who purchase the retail version of MS Access can further extend or significantly modify the basic templates according to their particular needs. Reports can be generated automatically during automation after each run, or they can be batch-processed after a series of runs have been completed.

BatchSMS (SMS/MS File Conversion)

The BatchSMS application allows groups of files to be converted interactively. Files may be selected in the Windows Explorer and dragged into the BatchSMS window for processing. Data files may be converted from .MS to .SMS and vice versa. (Individual files may also be converted during automation using the MAKEMS and MAKESMS programs. See the AutoLink documentation for more information.) When displaying native .MS files, or .SMS files converted from the .MS format while in the Saturn Windows Workstation, the Acquired Mass Range fields display, instead, the Actual Mass Range of each spectrum. The DOS versions of the Saturn GC/MS Workstation did not store the Acquired Mass Range for each spectrum, and it is therefore, unavailable (thought it might be determined by inspection of the Run Log).

Quick Start! (Quick Start!)

The Quick Start application provides a minimal user interface for the System Control application that simplifies data acquisition for simple analyses. It is only installed if the “GC Advanced Applications” option is selected during installation.

Security (Security Administration)

The Security application allows methods and applications to be locked and password-protected to prevent unauthorized access. The DOS-based software had no such provision.


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Optionally-Installed Windows-based Software Components

The following components are primarily of benefit to those users who are using a GC detector along with the Mass Spectrometer. They are not normally installed by the software installation program unless the option is explicitly selected as described below.

Interactive Graphics (View/Edit GC Chromatograms)

The Interactive Graphics application is the analog to MS Data Review for GC detector data (.RUN) files. It allows you to review GC chromatograms, edit GC Data Handling Method parameters, and recalculate results. It is only installed if the “GC Data Handling” option is selected during installation.

Report (Standard GC Reports)

The Report application creates a standard quantitation report for the specified GC detector data (.RUN) file. The Report application is only installed if the “GC Data Handling” option is selected during installation.

Batch Report (GC Batch Reporting)

The Batch Report application creates and prints a series of quantitation reports for the specified set of GC detector data (.RUN) files. The Batch Report application is only installed if the “GC Data Handling” option is selected during installation.

Analogous Feature Mapping Table

The Windows-based software has a number of architectural differences from the DOS-based software. These were necessary due to Windows application conventions, existing Star Workstation paradigms, and general usability improvements. As such, the way in which a particular software capability is invoked has changed.

The following table provides a mapping of the major features of the DOS-based software to its analogous component in the Windows-based software.

DOS Software Feature Windows Software Feature

Chromatogram MS Data Review Chromatogram Plot Specification File�Load Files…, Chromatogram�Data Parameters…, or

Toolbar buttons Chromatogram Display Manipulation Use Chromatogram� <relevant option> command,

Chromatogram Window context menu, Toolbar buttons, or direct graphical manipulation

Chromatogram Annotations Use Chromatogram� <relevant option> command, or Chromatogram Window context menu

Chromatogram Acqu Status Obsolete; access MS Data Review from System Control during acquisition for real-time display

Isometric Plots Obsolete Integrate Peaks Use Quantitation� <relevant option> commands to process &

view results, and Multichro Window to view entire chromatogram; or access Method Builder application to integrate individual compounds

Build/Edit Cali Files Quantitation�Build Compound Table…, or access Method Builder application

Extract Data File Obsolete Spectrum Enhancement Spectra� <relevant option> command, Background� <relevant

option> command, or Toolbar buttons Scan Box Manipulation Spectra� <relevant option> command, Spectrum Window context

menu, Toolbar buttons, or direct graphical manipulation


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DOS Software Feature Windows Software Feature Scan List Manipulation Spectra�List <n>…, and Spectra�Auto Add menu commands.

Use Quantitation�Build Compound Table… to automatically library search integrated peaks and add to DH Method Compound Table.

Access Spectrum Plots With Selected Spectrum

Click on scan in MS Data Review Chromatogram Window

Access Mass/Int Lists With Selected Spectrum

Spectra�Edit Spectra…

Access Library Search With Selected Spectrum

Search� <relevant option> command, or Toolbar buttons

Access Chro Analysis With Selected Spectrum & Range

Use MS Data Review MultiChro Window

Access Log File File�View Log…, or click on the Chromatogram Window Acquisition Segment Bar

Library Editor MS Data Review Read from input Library Search�Saturn or NIST Library Manager…�Edit

Libraries�Import Write to output Library Search�Saturn or NIST Library Manager…�Edit

Libraries�Export Inactivate entry (output library) Search�Saturn or NIST Library Manager…�Edit

Libraries�Inactivate or Activate Get spectrum Search�Saturn or NIST Library Manager…�Edit

Libraries�Import Edit entry Search�Saturn or NIST Library Manager…�Edit Libraries�Edit Spool library spectra File�Use Spooler File; any “Print” command goes to Spool File

while it is selected File Manager Use the Windows Explorer “right click” context menu of

File�Open... option in each application. Key Sequence Use a commercially available program like WinBatch. Library Search MS Data Review Search specifications Search�Library Search�Saturn Target Search Search results Search�Library Search�Saturn Target Search Scan List search Search�List Search Mass/Int Lists Use MS Data Review Spectra�Edit Spectra… window Chro Analysis Use MS Data Review MultiChro Window Log File MS Data Review View contents File�View Log…, or click on the Chromatogram Window

Acquisition Segment Bar Plot Spooler MS Data Review Create, view, edit, print File�<relevant Spooler File option> and File�Preview Report

commands; any “Print” command goes to Spooler File while Use Spooler File is selected


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DOS Software Feature Windows Software Feature Quantitation QA - Update Cali File Method Builder MS Data Handling�Results Treatment dialog (all

compounds, during auto calibrations), or MS Data Handling�Compound Table�Reference Spectrum dialog (manually)

QA - Auto Quan Options Method Builder MS Data Handling� Calculations Setup or Results Treatment dialogs

QC - Compound Editing Functions Method Builder MS Data Handling� Compound Table dialog or via the Compound/Chromatogram Integration Screen within MS Data Review.

QQ - Dilution Factors Automation File Editor Sample List or Recalc List QQ - Quantitation Options Method Builder MS Data Handling� Compound

Table�Calculations dialog QA - Auto Integration QA - Auto Calibration

Use the System Control or MS Data Review Automation features to process/reprocess Sequences, Sample and Recalc Lists to complete Auto Integration or Auto Calibration functions.

QA – AutoInt One Cmpd QA – AutoCal One Cmpd

Use the MS Data Review Quantitation�Review Results of Active File to view the current results for each peak. From the Review Results screen, individual peaks may be selected for closer inspection, method optimization, and/or Manual Integration.

Reporting Functions QC - Calib Reports QC - Calib Plots QC – Compound Report QC - Spool Compound Report QQ - Integration Report QQ - Quan Report (calc) QQ - Quan Report QQ - Edit Quan Report QQ - Print Quan Report QQ - ASCII Conversion

Use the Standard MS Reports facility to generate Sample, Compound, Calibration, or Summary Reports. An MS Reports method section may be defined within a method and used, either under System Control Automation, or interactively with the MSReport Application, to generate reports. With the exception of the Summary Reports, the reports available via the Standard MS Reports facility can also be generated within MS Data Review. Use the System Control Process Sample List or Recalc List commands to generate and print any specified customized reports from Custom MS Reports templates, in addition to the reports listed above.

Run Procedure The Saturn Data File Applications Programming Interface (API) may be used to extract data for custom processing. See the Data File API Documentation optionally installed with the software for more information. Alternatively, one may use the “retail” version of Microsoft Access and the Saturn Data File Server to build custom applications. See the Custom MS Reports API documentation available from Tech Support.

Spectrum Plots Use MS Data Review MultiChro Window Analysis Analysis List Editing Use Automation File Editor (for off-line editing of Automation

files) System Control (for editing and/or execution of Automation Files while connected to an instrument)

Edit (Method) Use Method Builder (many invocation alternatives) Edit (Tune Files/IPM Files) Obsolete: Parameters from Tune and IPM Files have been

incorporated into the Data Acquisition Method.


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DOS Software Feature Windows Software Feature Select (Method) System Control File�Open SequenceList...(select Method cell)

�Browse button Clear (Method) System Control File�Open SequenceList...(select Method

cell)...<backspace> Acqu Crnt Entry System Control Inject... Start AS Run System Control File�Open SampleList�Begin button Cont Acqu Run Obsolete: Acquisitions continue automatically Select DP Mode Obsolete: Data Handling occurs sequentially. Check Current Entry Occurs as part of: System Control File�Activate Method. Check All Entries Obsolete: Not supported. Regenerate Current Entry Occurs as part of: System Control File�Activate Method. Regenerate All Entries Obsolete: Not supported. Change Entry Paths System Control File�Open SampleList...�Data Files... button Diagnostics System Control, Saturn 2000 Module Window, Diagnostics Mode Instr Control System Control, Saturn 2000 Module Window, Manual Control

Mode System Control, Saturn 2000 Module Window, Auto Tune Mode System Control, Saturn 2000 Module Window, Temperatures Mode

Acqu Status System Control, Instrument Status Window

System Control, Saturn 2000 Module Window, Acquisition Mode Shutdown System Control, Saturn 2000 Module Window, Shutdown Mode Reset Saturn System Control, Saturn 2000 Module Window - All Modes (Reset

button becomes enabled when faulted) Turbo Standby Obsolete List Revisions See the Help�About... menu item in each Application Add Comments Use the MS Data Review Chromatogram� <relevant option>

command, or Chromatogram Window context menu Hardcopy Screen Use the MS Data Review File�Use Spooler File to toggle option

off; “Print” command goes to printer while it is selected Spool Screen Use the MS Data Review File�Use Spooler File to toggle option

on; any “Print” command goes to Spool File while it is selected Exit Saturn Click on the “X” button in the upper right corner of each

Application’s window Procedure Editor Obsolete: Use the Data File API or the retail Microsoft Access

development environment Help Page See the Help�Help Topics... menu item in each Application

version 5 software upgrade notes - united states home | agilent

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