PMSL
Last updated: March 3, 2009
By: Puneet Souda
Installing System Software (Mac OS 7.5.3) on Mac Quadras.
Every one in a while Mac Qudras' that run SCIEX mass spectrometers in lab will loose its system files or the files get corrupted. The only solution at that point is to load the System Software and the mass spec software from the CDs. Following are the instructions for doing so:
1. Find the external CD drive that is usually placed on top of the Quadra's or in a secure cabinet. This CD drive is SCSI and should also have a set of SCSI cables that could be used to connect to the computer. The SCSI port on the Quadra will look like a parallel port of a windows computer.
2. Now connect the CD drive to the Quadra using the SCSI cable. Please keep in mind that this SCSI drive might not be recognized the first time (the drive is a bit quirky) so you must be willing to do a few restart attempts on the Quadra. Also keep in mind that there are two SCSI cables available for use. As you will notice, the connecter ends are somewhat rusted; so you must try both cables. This will be a process of trial and error to recognize the drive on Quadra.
3. Find the System Software CD for Mac OS 7.5.3. Its a black CD with red logos on it. Insert the CD into the drive. This CD is safely in the cabinet above Pete's desk. Please ask him if you are unable to find the CD.
4. When loading the System Software (OS) on the Quadra, please connect the drive when the computer is off. Then restart the computer and hold down the "c" key on keyboard. This will make the CD drive as startup drive.
5. You will see the Mac OS load up from the CD and a round CD icon will show up on the screen. A window showing the System Software Install will show up.
6. Go ahead an double click the "System Software Installers" folder. Then double-click "Install System Software" to start installing the System Software. You can also spend some time looking at Readme and Installation text file to see the installation instructions, but this is not necessary.
7. Follow the instructions on the screen and point to the Quadra's hard drive to install the System Software. You might want to rename the hard drive as SCIEX II or something similar so its recognized as such on the appletalk network.
8. The OS install will now proceed and will ask you to "Continue" or "Quit" when its completed. Press "Quit" at this point. You don't want to install Powertalk, OpenDoc, QuickDraw or other such components because this Quadra is meant for collecting mass spec data.
9. Now go to Apple Menu on top left of screen and select the "Startup" drive. Make sure to select the hard drive as the startup drive.
10. Shutdown the Quadra now by going to Special --> Shutdown.
11. Now restart the Quadra and let the system boot from the hard drive. Make sure it boots from the hard drive and not the CD.
12. The system is now ready to install the mass spec software.
13. You can attempt to install the mass spec software using the PE SCIEX "API standard software" 3.5 floppys. However you might also find that the Quadra would like to “initialize” the floppy drive. If you do so, the entire floppy will be wiped out. So at this point using the floppy is not an option and you must install the software from another CD.
14. A SCIEX software CD Backup versions 2.5 and 2.6 (golden color) is also present in the same case of CDs as the Mac OS 7.5.3 CD and is in the cabinet above Pete’s desk. Please use that CD to install the mass spec software.
15. Keep in mind that Quadra’s take only FPU software. The SCIEX software CD contains both FPU and non–FPU software. Use only the FPU software for Quadra.
16. Since the CD drive is still connected. Please use insert the SCIEX software CD into the drive and let it recognize the CD (takes few minutes sometimes).
17. If the Quadra does not recognize the CD, insert the CD in one of G4s in the lab and use appletalk (chooser) to connect to the CD and copy the software onto the Quadra hard drive.
18. You will now copy API2.6-FPU.sea file from the API 2.6 FPU Disk folder. The self extracting archive (.sea) contains all the software that are required to run SCIEX.
19. Open the API2.6-FPU.sea file on the Quadra computer. This will install the mass spec software (MacSpec, Tune, RAD and other files).
20. Please follow the API Software Release Notes Version 2.6 Instructions below for more details.
21. Now copy the NI-DMA file to the System→Extensions folder . This file is also on the CD.
22. Shutdown the Quadra now and connect it to the SCIEX via the cables.
23. Start the computer and see if it scans.
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API Software Release Notes Revision: Dec. 21 1994
API Software Release Notes Version 2.6
General
• The API Software Release Version 2.6 (two disks) contains the following programs and versions of these programs:
Program Version
MS Configure 2.1*
LibEd 1.00b2*
Tune 2.5
RAD 2.6
MacSpec 3.3
MacQuan 1.3*
FileTranslator 1.4
* No changes have been made to these programs for this release.
If you are upgrading your software, do not replace your 'Configuration2' file.
Installation Instructions
1. Select the disk containing the software for your particular Data System. If you have a Power Mac, you should use the nonFPU version of the software. The FPU version will not work on a Power Mac, unless Software FPU is installed. If you have other Macs, you should use the FPU version of the software. The nonFPU version of the software will be very slow on a 68K Mac.
2. Insert the corresponding API Software Version 2.6 Disk to your computer, copy the self extracting archive called "API2.6-FPU.sea" or "API2.6-nonFPU.sea" to your hard disk.
3. To extract the archived files to your hard disk, double click on the archive icon. The decompressed files will be saved in a folder called "API Software 2.6 (FPU)" for the FPU version, or "API Software 2.6 (nonFPU)" for the nonFPU version.
4. Move the file named "NI-DMA/DSP" (version 1.10) to the Extensions folder inside the System Folder.
Please Note: The Tune and RAD programs in this release require the extension "NI-DMA/DSP" from National Instruments. If you boot your computer with the Shift key down (a clean startup), Tune and RAD will not work. If you want to turn off other extensions, you should use the Extension Manager or simply put them into a folder called Disabled Extensions Folder.
5. Make sure that the computer is running in 32 bit mode. The Quadra 840av and Power Macs always run in 32-bit mode. For other Macs, you can check the memory mode by selecting Memory from the Control Panels in the Apple menu. Make sure that 32-bit Addressing is turned on. If you have a IIx for data acquisition, you should contact PE SCIEX technical support at 1-800-762-8288 for further instruction.
6. If you have a Power Mac for data acquisition, it is recommended that the Modern Memory Manager in the Memory Control Panel be turned off.
7. Do not replace your 'Configuration2' file (located in the System Folder).
8. Move the program files from the API Applications folder to the corresponding folders on your hard disk.
9. Restart your computer.
10. MacSpec 3.3 requires a new Default Proc file, which should be stored in the same folder as MacSpec. The Default Proc file in this release is incompatible with the old version. You should delete the old "Default Proc" file on your system and copy the new one.
11. In some cases, when you start Tune or RAD you may be prompted to create a new Default State file. This new file is created using Tune and should be placed in the System Folder. Refer to Page B.2 of the API III Operator's Manual, 009658-H.
12. In some cases, you will be prompted to remove the existing Preferences files from the Preferences Folder inside the System Folder The software will create new Preferences files.
IMPORTANT NOTICE
If a spark is generated from the Corona Discharge Needle while high levels of organic solvents are being sprayed through the Heated Nebulizer, an explosion can occur in the Ion Source if air is used as make-up or nebulizer gas. The reported occurrences of this event appear to have been initiated by accidental selection of the ISV parameter in Tune or RAD while operating in constant current (DI) mode. This leads to a spark from the needle tip when the power supply switched from constant current to constant voltage mode. In a very few cases, this, in combination with a high level of methanol in the Ion Source, was sufficient to initiate an explosion, leading to violent expulsion of the Heated Nebulizer probe from the source. New versions of Tune and RAD provided in this release (and in the previous API Releases 2.3, 2.4, 2.5 and 2.5.1), as well as a hardware fix (see Heated Nebulizer Safety Warning dated February 26, 1993), will prevent this situation from occurring. PE SCIEX highly recommends the use of these new versions.
System Requirements
• The API Software requires a Macintosh with 8 MB of RAM, 160 MB of internal hard disk storage, and a floating point processor (except Power Macs). PE SCIEX recommends a Macintosh with 16 MB of RAM and 230 MB of internal hard disk storage. The API Software requires a Macintosh with System 7.1 or higher. The Macintosh used for API data acquisition requires three available NuBus slots. As of date, the API data acquisition software has been tested on the following computers: Quadra 950, Quadra 900, Quadra 800, Mac IIfx, Mac IIci, Centris 650, Quadra 840av, Power Mac 8100 and Power Mac 7100. The Mac IIcx, Centris 610, Centris 660av, Quadra 630 or Power Mac 6100 cannot be used to acquire data.
• The current versions of Tune, RAD, MacQuan and FileTranslator all require System 7.1 or higher to work properly. If a Power Mac is used, the nonFPU version software should be used. For other Macintosh computers, the FPU version should be used and a data system with a floating point processor is required.
• In order to use a Power Mac for data acquisition, the National Instrument boards must be:
• NB-DMA-2800 revision D2 or higher
• NB-DIO-32F revision D4 or higher
• NB-MIO-16 revision F2 or higher
The NB-DMA-8g board cannot be used in the Power Mac.
Version 2.6 New Features
RAD 2.6
1. Clear list
Two menu items are added to the Edit menu:
• Clear Rules
• Clear Samples
Note, these operations will remove all the rules or samples from the Batch window, except the first rule or sample respectively. RAD requires as a minimum one rule and one sample in a batch. If a rule to be deleted is being used by a sample in the list, an alert dialog will be displayed.
2. Save changes to state files
Previous versions of RAD allowed the user to change the value of state parameters, but the user cannot save these changes in RAD. In RAD 2.6,
• Two new menu items named "Load State File..." and "Save State File As..." have been added into the File menu. A state file can be loaded into the state window and the parameters can be edited. The modified state file can then be saved by selecting the "Save State File As..." menu item.
• A new menu item named "State File Edit..." has been added to the Option menu. Selecting this menu item will prompt a dialog. If the check box named "Allow Changes" is checked, the State window will be editable during data acquisition. Otherwise the State window will be locked from editing.
There are three ways to save the parameter changes during data acquisition.
If "Auto Save" is selected, the parameter changes will automatically be saved back into the State file before RAD loads a new state file.
If "Prompt" is selected, a Save Change dialog will prompt if the user has modified the parameters without saving the state file.
If "Manual" is selected, the user can save the parameter changes by selecting the "Save State File As..." menu item before RAD loads another state file, otherwise the changes made will be discarded when RAD loads a new state file.
Please note:
• Editing state parameters during data acquisition is not GLP since the state parameter values are only written to the data file at the end of each period.
3. Print a specific method
A new Menu item named "Print Current Method" is added to the File menu to print information for a single method.
4. Add last modification time information to API data files
RAD 2.6 will write the last modification time for the state files, Q1 calibration file, Q3 calibration file, RAD method files, and the configuration file, into the API data files. This way, the files can be traced backwards.
5. MRM cross talk suppression
Under some circumstances (with a new Collision Cell, i.e. RX is in the state file) ions can be trapped in Q2 leading to ghost signals. This is most acute in MRM mode when two precursor ions with a common product ion are monitored since the product of one parent may be trapped and detected for the other parent. This phenomenon is called 'cross talk'.
This version includes a new mode of MRM operation that greatly suppresses cross-talk by reducing the RF level between measurements in order to empty the trap. The function is enabled by selecting "Q2 Settling..." in the Options menu.
The Q2 Settling Time is 10% of the Dwell Time. The Q1 Park Mass will be the same as the parent mass.
Please note: the trapping phenomenon also requires that there be a 'fill-time' before ions are detected. This is part of the normal dwell time. As a result, emptying the trap may result in reduced intensities for a given dwell time but will eliminate incorrect signals.
Tune 2.5
1. Add last modification time information to API data files
In version 2.5, Tune will write the last modification time for the state file, Q1 calibration file, Q3 calibration file, and configuration file, into the API data files. In this way, the files can be traced backwards.
2. MRM cross talk problem
Under some circumstances (with a new Collision Cell i.e. RX is in the state file) ions can be trapped in Q2 leading to ghost signals. This is most acute in MRM mode when two precursor ions with a common product ion are monitored since the product of one parent may be trapped and detected for the other parent. This phenomenon is called 'cross talk'.
This version includes a new mode of MRM operation that greatly suppresses cross-talk by reducing the RF level between measurements in order to empty the trap. The function is enabled by selecting "Q2 Settling" in the MRM scan dialog.
The Q2 Settling Time is 10% of the Dwell Time. The Q1 Park Mass will be the same as the parent mass.
Please note: the trapping phenomenon also requires that there be a 'fill-time' before ions are detected. This is part of the normal dwell time. As a result, emptying the trap may result in reduced intensities for a given dwell time but will eliminate incorrect signals.
MacSpec 3.3
1. Base Peak TIC
Base Peak TIC is a chromatogram built with the highest peak(s) in each spectrum. Each point in the chromatogram consists of the sum of the peak heights of the specified number of highest peaks in each spectrum. If fewer peaks are found than specified, then the value of the base peak TIC at that point will be the sum of all peaks found.
A new operation for the production of a base peak TIC was added to MacSpec 3.3. A new menu item named "Base Peak TIC..." is added to the Chromatogram sub menu. Selecting this item will display a dialog for setting the following parameters:
• mass range over which to search for peaks.
• number of peaks (This parameter represents the maximum number of peaks to be included in the Base Peak TIC).
• Min. intensity (Any peak below this intensity will not be used.)
If the "OK" button is clicked in the dialog, MacSpec will produce a new window containing a base peak TIC calculated from the data in the currently active chromatogram window.
2. Threshold-Based Data Selection
A threshold-based data selection operation has been added to the MacSpec 3.3. A new menu item named "Threshold..." was added to the Chromatogram sub menu. Selecting this item will display a dialog for setting the following parameters:
• start mass
• stop mass
• Threshold Values.
Up to 3 sets of the parameters can be entered in the "Set Threshold Value" dialog.
If the "OK" button is clicked in the dialog, MacSpec will create a new data file using the data in the currently active chromatogram window. The new file will contain the same data as the old file but with all mass/intensity data points having intensities below a user-specified threshold being removed from the file ( within the specified mass range(s) ).
FileTranslator 1.4
The FileTranslator has been updated to convert the new API data files (version 2.6).
Version 2.6 Bug Fixes
Tune 2.5
• In previous versions of Tune, if the Default State file is missing or invalid, Tune would give an error message and initialize a set of values in the state window. If you tried to edit the values in the state window, Tune would lock the computer. This problem has been fixed.
• In previous versions of Tune, aliases of the state file, Q1 and Q3 calibration files and the settings file were written to Tune itself. In this version, Tune will save the aliases in a preferences file named "APITunePrefs" in the Preference folder inside the system folder. The window positions and the printer setup will also be saved in this preferences file.
• If a state file is opened that does not match the Configuration Table, Tune will display an error message, "State File does not match Configuration Table. Default State file will be loaded." and load the Default State file instead. In such a case, the invalid state file should be deleted.
• In previous versions of Tune, if a Q1 MI scan was used and TIC displayed, selecting "List Spectrum" in the Utilities menu crashed the computer. This also happened for Q3 MI or MRM scans. This problem has been fixed. The List Spectrum item will only be enabled when a spectrum is displayed in the Display window.
• In previous versions of Tune, if MRM data is saved with MCA option, the TIC in the data file will be corrupted. This problem has been fixed. The MCA mode will have no effect on MRM and zero width MI data.
• In previous versions of Tune, the pause time is not displayed in the Display window. In this version of Tune, the pause time will be displayed in the Display window.
• In previous versions of Tune, if the user entered a long Title( e.g. 150 characters), Tune couldn't display it. If the data was saved, Tune would give error messages -194 and -192. This problem has been fixed. The title can be up to 255 characters.
• In previous versions of Tune, the pause time in the scan dialogs was displayed as 0.0, if the user didn't enter a pause time. In this version of Tune, the pause time will be displayed as the minimum value if the user doesn't specify a pause time.
• In previous versions of Tune, if a data file is centroided or a mass defect value applied, the masses in the data file had more than 2 decimal places. Tune 2.5 will round up the masses to 2 decimal places.
• In previous versions of Tune, if acquiring to disk was aborted before the first scan, Tune would give a file busy error (-47) when data was acquired to the same file next time. This problem has been fixed.
Please note:
• When acquiring a Neutral loss scan, the start mass minus the Neutral loss mass should be larger than 10. When acquiring a Neutral gain scan (with negative Neutral loss mass), the stop mass plus the Neutral gain should be less than 2400.
• If you want to scan in MCA mode, you should select the MCA flag before acquiring data. Changing to MCA mode after the acquisition and before saving the data to disk may corrupt the data file.
• When you are printing out the display window, the time is printed on the printout. This is the time printed, not the time acquired. If you make any changes to the state file parameters after acquisition, these changes will also be printed.
RAD 2.6
• In previous versions of RAD, if a new method was created but not saved, the data files acquired with this method would not have 'STAT' resources for each period (id 1001 and up). This problem has been fixed. RAD 2.6 will save the correct state file information to the data file.
• In previous versions of RAD, when loading a Quant Text file, if an error occurred, the user couldn't abort the operation. The error alert only had a Continue button. This problem has been fixed. An "Abort" button has been added to the error alert.
• In previous versions of RAD, selecting the Set Threshold menu item in the Options menu displayed the R3Auto setting dialog on an API 1. This problem has been fixed.
• In previous versions of RAD, Print Methods did not work properly on an API 1. The printout didn't have correct information on scan type, Q1 calibration filename and state filename. This problem has been fixed. The printout will have correct information about the methods.
• RAD 2.5 had a problem loading a Simple Text file with a new line "\n" as the end of line mark. An extra sample was added at the end of the sample list. This problem has been fixed. RAD treats both a carriage return "\r" and a new line "\n" as the end of line mark. You may use either a carriage return or a new line at the end of each line, but a carriage return and a new line ("\r\n" ) should not be used together.
• In previous versions of RAD, the folder specified in a Simple Text file or a Quant Text file was ignored when the text file was loaded. This problem has been fixed. The full path of the folder should be put in the text file, e.g. "Macintosh HD:testdata folder" indicates that the destination folder is the "testdata folder". If the specified folder is not found, the folder specified in the Rule will be used.
• In previous versions of RAD, for a multi-period method, data acquisition took longer than the duration specified in the method. This problem has been fixed. Data acquisition is controlled by timing. At the end of a scan, RAD will check if the duration specified in the method has elapsed. If so, data acquisition in this period will be ended and RAD will switch to the next period or the next sample accordingly.
• If a method is created and saved on quitting RAD, previous versions of RAD had a problem finding the state file when this method was used next time. This problem has been fixed. The method saved on quitting will work normally.
• In previous versions of RAD, during the acquisition of a batch, RAD could give "Can't allocate DAC buffer" error. This problem has been fixed. RAD 2.6 will allocate the DAC and results buffers on start up and reuse the buffers in the data acquisition as long as they are large enough.
• In previous versions of RAD, the pause time is not displayed in the Display window. In this version of RAD, the pause time will be displayed in the Display window.
• In previous versions of RAD, the Mac user name was printed on the batch sample printout and method list printout. In RAD 2.6, the "Operator" entered in the Batch Info dialog will be printed.
• In previous versions of RAD, the "Acquire" field in the Method Editor was printed as Duration. This problem has been fixed. RAD 2.6 will print the field as "Acquire".
• In previous versions of RAD, the file name and methods fields accepted up to 32 characters, which is over the limit of a Mac file name (31 characters). This problem has been fixed. RAD 2.6 allows up to 31 characters in file name. It allows up to 28 characters in the "Root" of file name. The max. length of alpha or numerical suffix is 3 characters. In case of global suffix or date suffix is used, RAD 2.6 will truncate the Root to ensure that the final file name is less than 32 characters.
• In previous versions of RAD, if all the methods in the Method Editor were removed, selecting the "Print Methods..." menu command would cause a crash. In RAD 2.6, if no method listed in the Method Editor, the "Print Methods..." and "Print Current Method..." menu commands will be disabled.
• In previous versions of RAD, if a data file is centroided or a mass defect value applied, the masses in the data file had more than 2 decimal places. RAD 2.6 will round up the masses to 2 decimal places.
• RAD 2.6 will limit the range of mass defect to -500.0 to 500.0.
Please note:
• If a Quant Text file is loaded into RAD and saved with the "Save Batch As..." command, it will be saved as a binary batch file. All the quantitative information will be lost in the saved binary batch file. If that batch must be run again, please reload the Quant Text file not the binary batch file.
• If a folder used in a rule in RAD was renamed or deleted, the rule with the old folder name should be updated before acquiring data with RAD.
• Be careful when naming rules, methods and other files that interact with the RAD program (such as State and Calibration files). Do not use parentheses, slashes (/), backslashes (\), colons, leading spaces or leading hyphens because the menu handler interprets them as control characters. Use a hyphen (-) if separators are required.
• RAD requires that a Simple Text file and a Quant Text file follow the following rules:
1. Each field is separated by one of the delimiters: the comma “,”, the colon “:”, the semi-colon “;” or the tab key. You should not use any of these characters as part of any of the fields.
2. Each record (each line) is ended by either a carriage return "\r" or a new line "\n".
3. A comment line begins with ">" symbol.
4. The end of data is marked by "//".
MacSpec 3.3
• In MacSpec 3.2.1, if you opened a mass spectrum, turned off the background subtract, set the label defaults to height and then labeled the spectrum, the displayed and printed peak height values were different. This problem has been fixed.
• In MacSpec 3.2.1, when a background spectrum and a sample spectrum were displayed, and "Subtract File" option selected, the net spectrum generated was incorrect. This problem has been fixed.
• The previous versions of MacSpec might quit when doing compare chromatograms. This problem has been fixed.
• The previous versions of MacSpec had a problem saving spectra. This problem has been fixed.
• The previous versions of MacSpec had a problem with Auto HyperMass which could lead to different results compared with those from manual HyperMass. This problem has been fixed.
• The previous versions of MacSpec had a problem printing compared chromatograms. This problem has been fixed.
• MacSpec 3.2.2 gave an extracted ion chrom. which had wrong intensities for some data files. This problem has been fixed.
• MacSpec 3.2.2 gave an incorrect average spectrum from a centroid data file.
